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Sample records for cellulose-specific molecular probes

  1. Microscopic Analysis of Corn Fiber Using Corn Starch- and Cellulose-Specific Molecular Probes

    SciTech Connect

    Porter, S. E.; Donohoe, B. S.; Beery, K. E.; Xu, Q.; Ding, S.-Y.; Vinzant, T. B.; Abbas, C. A.; Himmel, M. E.

    2007-09-01

    Ethanol is the primary liquid transportation fuel produced from renewable feedstocks in the United States today. The majority of corn grain, the primary feedstock for ethanol production, has been historically processed in wet mills yielding products such as gluten feed, gluten meal, starch, and germ. Starch extracted from the grain is used to produce ethanol in saccharification and fermentation steps; however the extraction of starch is not 100% efficient. To better understand starch extraction during the wet milling process, we have developed fluorescent probes that can be used to visually localize starch and cellulose in samples using confocal microscopy. These probes are based on the binding specificities of two types of carbohydrate binding modules (CBMs), which are small substrate-specific protein domains derived from carbohydrate degrading enzymes. CBMs were fused, using molecular cloning techniques, to a green fluorescent protein (GFP) or to the red fluorescent protein DsRed (RFP). Using these engineered probes, we found that the binding of the starch-specific probe correlates with starch content in corn fiber samples. We also demonstrate that there is starch internally localized in the endosperm that may contribute to the high starch content in corn fiber. We also surprisingly found that the cellulose-specific probe did not bind to most corn fiber samples, but only to corn fiber that had been hydrolyzed using a thermochemical process that removes the residual starch and much of the hemicellulose. Our findings should be of interest to those working to increase the efficiency of the corn grain to ethanol process.

  2. Molecular inversion probe assay.

    PubMed

    Absalan, Farnaz; Ronaghi, Mostafa

    2007-01-01

    We have described molecular inversion probe technologies for large-scale genetic analyses. This technique provides a comprehensive and powerful tool for the analysis of genetic variation and enables affordable, large-scale studies that will help uncover the genetic basis of complex disease and explain the individual variation in response to therapeutics. Major applications of the molecular inversion probes (MIP) technologies include targeted genotyping from focused regions to whole-genome studies, and allele quantification of genomic rearrangements. The MIP technology (used in the HapMap project) provides an efficient, scalable, and affordable way to score polymorphisms in case/control populations for genetic studies. The MIP technology provides the highest commercially available multiplexing levels and assay conversion rates for targeted genotyping. This enables more informative, genome-wide studies with either the functional (direct detection) approach or the indirect detection approach. PMID:18025701

  3. Molecular probes for cardiovascular imaging.

    PubMed

    Liang, Grace; Nguyen, Patricia K

    2016-08-01

    Molecular probes provide imaging signal and contrast for the visualization, characterization, and measurement of biological processes at the molecular level. These probes can be designed to target the cell or tissue of interest and must be retained at the imaging site until they can be detected by the appropriate imaging modality. In this article, we will discuss the basic design of molecular probes, differences among the various types of probes, and general strategies for their evaluation of cardiovascular disease. PMID:27189171

  4. Fabrication of molecular tension probes.

    PubMed

    Kim, Sung Bae; Fujii, Rika

    2016-01-01

    A unique bioluminescent imaging probe is introduced for illuminating molecular tension appended by protein-protein interactions (PPIs) of interest. A full-length luciferase is sandwiched between two proteins of interest via minimal flexible linkers. The ligand-activated PPIs append intramolecular tension to the sandwiched luciferase, boosting or dropping the enzymatic activity in a quantitative manner. This method guides construction of a new lineage of bioassays for determining molecular tension appended by ligand-activated PPIs. The summary of the method is: •Molecular tension appended by protein-protein interactions (PPI) is visualized with a luciferase.•Estrogen activities are quantitatively illuminated with the molecular tension probes.•Full-length Renilla luciferase enhances the optical intensities after bending by PPI. PMID:27222821

  5. Fabrication of molecular tension probes

    PubMed Central

    Kim, Sung Bae; Fujii, Rika

    2016-01-01

    A unique bioluminescent imaging probe is introduced for illuminating molecular tension appended by protein–protein interactions (PPIs) of interest. A full-length luciferase is sandwiched between two proteins of interest via minimal flexible linkers. The ligand-activated PPIs append intramolecular tension to the sandwiched luciferase, boosting or dropping the enzymatic activity in a quantitative manner. This method guides construction of a new lineage of bioassays for determining molecular tension appended by ligand-activated PPIs. The summary of the method is: • Molecular tension appended by protein–protein interactions (PPI) is visualized with a luciferase. • Estrogen activities are quantitatively illuminated with the molecular tension probes. • Full-length Renilla luciferase enhances the optical intensities after bending by PPI. PMID:27222821

  6. Design and Development of Molecular Imaging Probes

    PubMed Central

    Chen, Kai; Chen, Xiaoyuan

    2013-01-01

    Molecular imaging, the visualization, characterization and measurement of biological processes at the cellular, subcellular level, or even molecular level in living subjects, has rapidly gained importance in the dawning era of personalized medicine. Molecular imaging takes advantage of the traditional diagnostic imaging techniques and introduces molecular imaging probes to determine the expression of indicative molecular markers at different stages of diseases and disorders. As a key component of molecular imaging, molecular imaging probe must be able to specifically reach the target of interest in vivo while retaining long enough to be detected. A desirable molecular imaging probe with clinical translation potential is expected to have unique characteristics. Therefore, design and development of molecular imaging probe is frequently a challenging endeavor for medicinal chemists. This review summarizes the general principles of molecular imaging probe design and some fundamental strategies of molecular imaging probe development with a number of illustrative examples. PMID:20388106

  7. Developing MR probes for molecular imaging.

    PubMed

    McMahon, Michael T; Chan, Kannie W Y

    2014-01-01

    Molecular imaging plays an important role in the era of personalized medicine, especially with recent advances in magnetic resonance (MR) probes. While the first generation of these probes focused on maximizing contrast enhancement, a second generation of probes has been developed to improve the accumulation within specific tissues or pathologies, and the newest generation of agents is also designed to report on changes in physiological status and has been termed "smart" agents. This represents a paradigm switch from the previously commercialized gadolinium and iron oxide probes to probes with new capabilities, and leads to new challenges as scanner hardware needs to be adapted for detecting these probes. In this chapter, we highlight the unique features for all five different categories of MR probes, including the emerging chemical exchange saturation transfer, (19)F, and hyperpolarized probes, and describe the key physical properties and features motivating their design. As part of this comparison, the strengths and weaknesses of each category are discussed. PMID:25287693

  8. Molecular Imaging Probe Development using Microfluidics

    PubMed Central

    Liu, Kan; Wang, Ming-Wei; Lin, Wei-Yu; Phung, Duy Linh; Girgis, Mark D.; Wu, Anna M.; Tomlinson, James S.; Shen, Clifton K.-F.

    2012-01-01

    In this manuscript, we review the latest advancement of microfluidics in molecular imaging probe development. Due to increasing needs for medical imaging, high demand for many types of molecular imaging probes will have to be met by exploiting novel chemistry/radiochemistry and engineering technologies to improve the production and development of suitable probes. The microfluidic-based probe synthesis is currently attracting a great deal of interest because of their potential to deliver many advantages over conventional systems. Numerous chemical reactions have been successfully performed in micro-reactors and the results convincingly demonstrate with great benefits to aid synthetic procedures, such as purer products, higher yields, shorter reaction times compared to the corresponding batch/macroscale reactions, and more benign reaction conditions. Several ‘proof-of-principle’ examples of molecular imaging probe syntheses using microfluidics, along with basics of device architecture and operation, and their potential limitations are discussed here. PMID:22977436

  9. Activatable Molecular Probes for Cancer Imaging

    PubMed Central

    Lee, Seulki; Xie, Jin; Chen, Xiaoyuan

    2013-01-01

    The development of highly sensitive and specific molecular probes for cancer imaging still remains a daunting challenge. Recently, interdisciplinary research at the interface of imaging sciences and bionanoconjugation chemistry has generated novel activatable imaging probes that can provide high-resolution imaging with ultra-low background signals. Activatable imaging probes are designed to amplify output imaging signals in response to specific biomolecular recognition or environmental changes in real time. This review introduces and highlights the unique design strategies and applications of various activatable imaging probes in cancer imaging. PMID:20388112

  10. New molecular probes of vascular inflammation.

    PubMed

    Vrachimis, Alexis; Honold, Lisa; Faust, Andreas; Hermann, Sven; Schäfers, Michael

    2016-09-01

    New molecular imaging approaches featuring the assessment of inflammatory processes in the vascular wall on top of existing anatomic and functional vessel imaging procedures could emerge as decisive tools for the understanding and prevention of cardiovascular events. In this respect imaging approaches addressing specific molecular and cellular targets in atherosclerosis are of high interest. This review summarizes the rationale and current status of nuclear imaging probes which possess high translational potential. PMID:27280733

  11. Molecular probes for malignant melanoma imaging.

    PubMed

    Ren, Gang; Pan, Ying; Cheng, Zhen

    2010-09-01

    Malignant melanoma represents a serious public health problem and is a deadly disease when it is diagnosed at late stage. Though (18)F-fluorodeoxyglucose ((18)F-FDG) positron emission tomography (PET) has been widely used clinically for melanoma imaging, other approaches to specifically identify, characterize, monitor and guide therapeutics for malignant melanoma are still needed. Consequently, many probes targeting general molecular events including metabolism, angiogenesis, hypoxia and apoptosis in melanoma have been successfully developed. Furthermore, probes targeting melanoma associated targets such as melanocortin receptor 1 (MC1R), melanin, etc. have undergone active investigation and have demonstrated high melanoma specificity. In this review, these molecular probes targeting diverse melanoma biomarkers have been summarized. Some of them may eventually contribute to the improvement of personalized management of malignant melanoma. PMID:20497118

  12. Protein-based tumor molecular imaging probes

    PubMed Central

    Lin, Xin; Xie, Jin

    2013-01-01

    Molecular imaging is an emerging discipline which plays critical roles in diagnosis and therapeutics. It visualizes and quantifies markers that are aberrantly expressed during the disease origin and development. Protein molecules remain to be one major class of imaging probes, and the option has been widely diversified due to the recent advances in protein engineering techniques. Antibodies are part of the immunosystem which interact with target antigens with high specificity and affinity. They have long been investigated as imaging probes and were coupled with imaging motifs such as radioisotopes for that purpose. However, the relatively large size of antibodies leads to a half-life that is too long for common imaging purposes. Besides, it may also cause a poor tissue penetration rate and thus compromise some medical applications. It is under this context that various engineered protein probes, essentially antibody fragments, protein scaffolds, and natural ligands have been developed. Compared to intact antibodies, they possess more compact size, shorter clearance time, and better tumor penetration. One major challenge of using protein probes in molecular imaging is the affected biological activity resulted from random labeling. Site-specific modification, however, allows conjugation happening in a stoichiometric fashion with little perturbation of protein activity. The present review will discuss protein-based probes with focus on their application and related site-specific conjugation strategies in tumor imaging. PMID:20232092

  13. Molecular imaging probe development: a chemistry perspective

    PubMed Central

    Nolting, Donald D; Nickels, Michael L; Guo, Ning; Pham, Wellington

    2012-01-01

    Molecular imaging is an attractive modality that has been widely employed in many aspects of biomedical research; especially those aimed at the early detection of diseases such as cancer, inflammation and neurodegenerative disorders. The field emerged in response to a new research paradigm in healthcare that seeks to integrate detection capabilities for the prediction and prevention of diseases. This approach made a distinct impact in biomedical research as it enabled researchers to leverage the capabilities of molecular imaging probes to visualize a targeted molecular event non-invasively, repeatedly and continuously in a living system. In addition, since such probes are inherently compact, robust, and amenable to high-throughput production, these probes could potentially facilitate screening of preclinical drug discovery, therapeutic assessment and validation of disease biomarkers. They could also be useful in drug discovery and safety evaluations. In this review, major trends in the chemical synthesis and development of positron emission tomography (PET), optical and magnetic resonance imaging (MRI) probes are discussed. PMID:22943038

  14. Mechanisms and Molecular Probes of Sirtuins

    PubMed Central

    Smith, Brian C.; Hallows, William C.; Denu, John M.

    2008-01-01

    Summary Sirtuins are critical regulators of many cellular processes including insulin secretion, the cell cycle, and apoptosis. Sirtuins are associated with a variety of age-associated diseases such as type II diabetes, obesity, and Alzheimer’s disease. A thorough understanding of sirtuin chemical mechanisms will aid toward developing novel therapeutics that regulate metabolic disorders and combat associated diseases. In this review, we discuss the unique deacetylase mechanism of sirtuins and how this information might be employed to develop inhibitors and other molecular probes for therapeutic and basic research applications. We also cover physiological regulation of sirtuin activity and how these modes of regulation may be exploited to manipulate sirtuin activity in live cells. Development of molecular probes and drugs that specifically target sirtuins will further understanding of sirtuin biology and potentially afford new treatments of several human diseases. PMID:18940661

  15. Molecular Probes for Fluorescence Lifetime Imaging

    PubMed Central

    Sarder, Pinaki; Maji, Dolonchampa; Achilefu, Samuel

    2015-01-01

    Visualization of biological processes and pathologic conditions at the cellular and tissue levels largely rely on the use of fluorescence intensity signals from fluorophores or their bioconjugates. To overcome the concentration dependency of intensity measurements, evaluate subtle molecular interactions, and determine biochemical status of intracellular or extracellular microenvironments, fluorescence lifetime (FLT) imaging has emerged as a reliable imaging method complementary to intensity measurements. Driven by a wide variety of dyes exhibiting stable or environment-responsive FLTs, information multiplexing can be readily accomplished without the need for ratiometric spectral imaging. With knowledge of the fluorescent states of the molecules, it is entirely possible to predict the functional status of biomolecules or microevironment of cells. Whereas the use of FLT spectroscopy and microscopy in biological studies is now well established, in vivo imaging of biological processes based on FLT imaging techniques is still evolving. This review summarizes recent advances in the application of the FLT of molecular probes for imaging cells and small animal models of human diseases. It also highlights some challenges that continue to limit the full realization of the potential of using FLT molecular probes to address diverse biological problems, and outlines areas of potential high impact in the future. PMID:25961514

  16. Molecular diagnostics: future probe-based strategies.

    PubMed

    Marsh, Peter; Cardy, Donald L N

    2004-01-01

    Nucleic acid amplification technologies (NAATs) represent powerful tools in clinical microbiology, particularly in areas where traditional culture-based methods alone prove insufficient. A notable advantage is in reducing the time from taking samples to reporting results. This, and the specificity and sensitivity imparted by NAATs, can help to improve patient care. Both thermal and isothermal NAATs have been adapted to aid diagnosis in clinical laboratories. Current molecular diagnostic assays are generally high-tech, and are expensive to buy and perform. Easy-to-use NAATs are beginning to appear, not only facilitating acceptable throughput in clinical laboratories, but also allowing tests to move out of the laboratory, closer to the point of care. Demand for simpler, miniaturized equipment and assays, and the trend toward personalized medicine, is leading towards the development of fully integrated automation and home-use kits. The integration of diverse disciplines, such as genomics, molecular biology, microelectromechanical systems, microfluidics, microfabrication, and organic chemistry, is behind the emerging DNA microarray technology. Development of DNA microchips allows the simultaneous detection of potentially thousands of target sequences, not only favoring high throughput, but also the potential for genotyping patient subsets with respect to their response to particular drug types (pharmakogenomics). It is envisaged that the future of probe-based technologies will see the development of fully integrated assays and devices suitable for nonskilled users. PMID:15148419

  17. Probing adhesion forces at the molecular scale

    SciTech Connect

    Thomas, R.C.; Houston, J.E.; Michalske, T.A.

    1996-12-31

    Measurements of adhesion forces at the molecular scale, such as those discussed here, are necessary to understand macroscopic boundary-layer behavior such as adhesion, friction, wear, lubrication, and many other important phenomena. The authors` recent interfacial force microscopy (IFM) studies have provided detailed information about the mechanical response of both self-assembled monolayer (SAM) films and the underlying substrates. In addition, they recently demonstrated that the IFM is useful for studying the chemical nature of such films. In this talk, the authors discuss a new method for studying surface interactions and chemical reactions using the IFM. To quantitatively measure the work of adhesion and bond energies between two organic thin films, they modify both a Au substrate and a Au probe with self-assembling organomercaptan molecules having either the same or different end groups (-CH{sub 3}, -NH{sub 2}, and -COOH), and then analyze the force-versus-displacement curves (force profiles) that result from the approach to contact of the two surfaces. Their results show that the magnitude of the adhesive forces measured between methyl-methyl interactions are in excellent agreement with van der Waals calculations using Lifshitz theory and previous experimentally determined values. Moreover, the measured peak adhesive forces scale as expected for van der Waals, hydrogen-bonding, and acid-base interactions.

  18. Molecular Crowding Effects on Microgel-Tethered Oligonucleotide Probes.

    PubMed

    Ma, Youlong; Libera, Matthew

    2016-06-28

    Microgel tethering is a nontraditional method with which to bind oligonucleotide hybridization probes to a solid surface. Microgel-tethering physically positions the probes away from the underlying hard substrate and maintains them in a highly waterlike environment. This paper addresses the question of whether molecular crowding affects the performance of microgel-tethered molecular beacon probes. The density of probe-tethering sites is controlled experimentally using thin-film blends of biotin-terminated [PEG-B] and hydroxyl-terminated [PEG-OH] poly(ethylene glycol) from which microgels are synthesized and patterned by electron beam lithography. Fluorescence measurements indicate that the number of streptavidins, linear DNA probes, hairpin probes, and molecular beacon probes bound to the microgels increases linearly with increasing PEG-B/PEG-OH ratio. For a given tethering-site concentration, more linear probes can bind than structured probes. Crowding effects emerge during the hybridization of microgel-tethered molecular beacons but not during the hybridization of linear probes, as the tethering density increases. Crowding during hybridization is associated with conformational constraints imposed by the close proximity of closed and hybridized structured probes. The signal-to-background ratio (SBR) of hybridized beacons is highest and roughly constant for low tethering densities and decreases at the highest tethering densities. Despite differences between microgel tethering and traditional oligonucleotide surface-immobilization approaches, these results show that crowding defines an optimum tethering density for molecular beacon probes that is less than the maximum possible, which is consistent with previous studies involving various linear and structured oligonucleotide probes. PMID:27253904

  19. Molecular beacons: Probes that fluoresce upon hybridization

    SciTech Connect

    Tyagi, S.; Kramer, F.R.

    1996-03-01

    We have developed novel nucleic acid probes that recognize and report the presence of specific nucleic acids in homogeneous solutions. These probes undergo a spontaneous fluorogenic conformational change when they hybridize to their targets. Only perfectly complementary targets elicit this response, as hybridization does not occur when the target contains a mismatched nucleotide or a deletion. The probes are particularly suited for monitoring the synthesis of specific nucleic acids in real time. When used in nucleic acid amplification assays, gene detection is homogeneous and sensitive, and can be carried out in a sealed tube. When introduced into living cells, these probes should enable the origin, movement, and fate of specific mRNAs to be traced. 23 refs., 6 figs.

  20. Magnetomotive molecular probes for targeted contrast enhancement and therapy

    NASA Astrophysics Data System (ADS)

    Boppart, Stephen A.

    2011-03-01

    The diagnostic, interrogational, and therapeutic potential of molecular probes is rapidly being investigated and exploited across virtually every biomedical imaging modality. While many types of probes enhance contrast or delivery therapy by static localization to targeted sites, significant potential exists for utilizing dynamic molecular probes. Recent examples include molecular beacons, photoactivatable probes, or controlled switchable drug-releasing particles, to name a few. In this review, we describe a novel class of dynamic molecular probes that rely on the application and control of localized external magnetic fields. These magnetomotive molecular probes can provide optical image contrast through a modulated scattering signal, can interrogate the biomechanical properties of their viscoelastic microenvironment by tracking their underdamped oscillatory step-response to applied fields, and can potentially delivery therapy through nanometer-to-micrometer mechanical displacement or local hyperthermia. This class of magnetomotive agents includes not only magnetic iron-oxide nanoparticles, but also new magnetomotive microspheres or nanostructures with embedded iron-oxide agents. In vitro three-dimensional cell assays and in vivo targeting studies in animal tumor models have demonstrated the potential for multimodal detection and imaging, using magnetic resonance imaging for whole-body localization, and magnetomotive optical coherence tomography for high-resolution localization and imaging.

  1. Image-guided surgery using multimodality strategy and molecular probes.

    PubMed

    Xi, Lei; Jiang, Hubei

    2016-01-01

    The ultimate goal of cancer surgery is to maximize the excision of tumorous tissue with minimal damage to the collateral normal tissues, reduce the postoperative recurrence, and improve the survival rate of patients. In order to locate tumor lesions, highlight tumor margins, visualize residual disease in the surgical wound, and map potential lymph node metastasis, various imaging techniques and molecular probes have been investigated to assist surgeons to perform more complete tumor resection. Combining imaging techniques with molecular probes is particularly promising as a new approach for image-guided surgery. Considering inherent limitations of different imaging techniques and insufficient sensitivity of nonspecific molecular probes, image-guided surgery with multimodality strategy and specific molecular probes appears to be an optimal choice. In this article, we briefly describe typical imaging techniques and molecular probes followed by a focused review on the current progress of multimodal image-guided surgery with specific molecular navigation. We also discuss optimal strategy that covers all stages of image-guided surgery including preoperative scanning of tumors, intraoperative inspection of surgical bed and postoperative care of patients. PMID:26053199

  2. Silicon cantilever functionalization for cellulose-specific chemical force imaging of switchgrass

    DOE PAGESBeta

    Lee, Ida; Evans, Barbara R.; Foston, Marcus B.; Ragauskas, Arthur J.

    2015-05-08

    A method for direct functionalization of silicon and silicon nitride cantilevers with bifunctional silanes was tested with model surfaces to determine adhesive forces for different hydrogen-bonding chemistries. Application for biomass surface characterization was tested by mapping switchgrass and isolated switchgrass cellulose in topographic and force-volume mode using a cellulose-specific cantilever.

  3. Silicon cantilever functionalization for cellulose-specific chemical force imaging of switchgrass

    SciTech Connect

    Lee, Ida; Evans, Barbara R; Foston, Marcus B; Ragauskas, Arthur J

    2015-01-01

    A method for direct functionalization of silicon and silicon nitride cantilevers with bifunctional silanes was tested with model surfaces to determine adhesive forces for different hydrogen-bonding chemistries. Application for biomass surface characterization was tested by mapping switchgrass and isolated switchgrass cellulose in topographic and force-volume mode using a cellulose-specific cantilever.

  4. Molecular Probe Fluorescence Monitoring of Polymerization

    NASA Technical Reports Server (NTRS)

    Bunton, Patrick

    2002-01-01

    This project investigated the feasibility of using fluorescence spectroscopy to determine viscosity of polymer/monomer in support of Transient Interfacial Phenomena in Miscible Polymer Systems (TIPMPS). This project will attempt to measure gradient induced flow at a miscible interface during and / or after in-flight polymerization of dodecyl acrylate (lauryl acrylate). Concentration and temperature gradients will be intentionally introduced during polymerization and the resultant fluid flow determined by Particle Imaging Velocimetry (PIV). This report describes an investigation of the feasibility of using fluorescence of a probe molecule to monitor viscosity and/or concentration during and after polymerization. The probe used was pyrene which has been shown to be sensitive to its local environment in methyl methacrylate.

  5. Ionization probes of molecular structure and chemistry

    SciTech Connect

    Johnson, P.M.

    1993-12-01

    Various photoionization processes provide very sensitive probes for the detection and understanding of the spectra of molecules relevant to combustion processes. The detection of ionization can be selective by using resonant multiphoton ionization or by exploiting the fact that different molecules have different sets of ionization potentials. Therefore, the structure and dynamics of individual molecules can be studied even in a mixed sample. The authors are continuing to develop methods for the selective spectroscopic detection of molecules by ionization, and to use these methods for the study of some molecules of combustion interest.

  6. Nanoparticle Probes for Structural and Functional Photoacoustic Molecular Tomography

    PubMed Central

    Chen, Haobin; Yuan, Zhen; Wu, Changfeng

    2015-01-01

    Nowadays, nanoparticle probes have received extensive attention largely due to its potential biomedical applications in structural, functional, and molecular imaging. In addition, photoacoustic tomography (PAT), a method based on the photoacoustic effect, is widely recognized as a robust modality to evaluate the structure and function of biological tissues with high optical contrast and high acoustic resolution. The combination of PAT with nanoparticle probes holds promises for detecting and imaging diseased tissues or monitoring their treatments with high sensitivity. This review will introduce the recent advances in the emerging field of nanoparticle probes and their preclinical applications in PAT, as well as relevant perspectives on future development. PMID:26609534

  7. Optically Probed Laser-Induced Field-Free Molecular Alignment

    NASA Astrophysics Data System (ADS)

    Faucher, O.; Lavorel, B.; Hertz, E.; Chaussard, F.

    Molecular alignment induced by laser fields has been investigated in research laboratories for over two decades. It led to a better understanding of the fundamental processes at play in the interaction of strong laser fields with molecules, and also provided significant contributions to the fields of high harmonic generation, laser spectroscopy, and laser filamentation. In this chapter, we discuss molecular alignment produced under field-free conditions, as resulting from the interaction of a laser pulse of duration shorter than the rotational period of the molecule. The experimental results presented will be confined to the optically probed alignment of linear as well as asymmetric top molecules. Special care will be taken to describe and compare various optical methods that can be employed to characterize laser-induced molecular alignment. Promising applications of optically probed molecular alignment will be also demonstrated.

  8. Probing Radiation Damage at the Molecular Level

    NASA Astrophysics Data System (ADS)

    Mason, N. J.; Smialek, M. A.; Moore, S. A.; Folkard, M.; Hoffmann, S. V.

    2006-12-01

    Radiation damage of DNA and other cellular components has traditionally been attributed to ionisation via direct impact of high-energy quanta or by complex radical chemistry. However recent research has shown that strand breaks in DNA may be initiated by secondary electrons and is strongly dependent upon the target DNA base identity. Such research provides the fascinating perspective that it is possible that radiation damage may be described and understood at an individual molecular level introducing new possibilites for therapy and perhaps providing an insight into the origins of life.

  9. An Elegant Biosensor Molecular Beacon Probe: Challenges and Recent Solutions

    PubMed Central

    Kolpashchikov, Dmitry M.

    2012-01-01

    Molecular beacon (MB) probes are fluorophore- and quencher-labeled short synthetic DNAs folded in a stem-loop shape. Since the first report by Tyagi and Kramer, it has become a widely accepted tool for nucleic acid analysis and triggered a cascade of related developments in the field of molecular sensing. The unprecedented success of MB probes stems from their ability to detect specific DNA or RNA sequences immediately after hybridization with no need to wash out the unbound probe (instantaneous format). Importantly, the hairpin structure of the probe is responsible for both the low fluorescent background and improved selectivity. Furthermore, the signal is generated in a reversible manner; thus, if the analyte is removed, the signal is reduced to the background. This paper highlights the advantages of MB probes and discusses the approaches that address the challenges in MB probe design. Variations of MB-based assays tackle the problem of stem invasion, improve SNP genotyping and signal-to-noise ratio, as well as address the challenges of detecting folded RNA and DNA. PMID:24278758

  10. Molecular Probe Data Base: a database on synthetic oligonucleotides.

    PubMed Central

    Romano, P; Aresu, O; Parodi, B; Manniello, A; Campi, G; Angelini, G; Romani, M; Iannotta, B; Rondanina, G; Ruzzon, T

    1993-01-01

    The Molecular Probe Data Base (MPDB) was designed to collect and make information on synthetic oligonucleotides available on-line. This paper briefly describes its purpose, contents and structure, forms and mode of data distribution. Particular emphasis is given to recent data extension and system enhancements that have been carried out in order to simplify access to MPDB for unskilled users. PMID:8332523

  11. Molecular Probe Database: a database on synthetic oligonucleotides

    PubMed Central

    Aresu, Ottavia; Parodi, Barbara; Romano, Paolo; Romani, Massimo; Angelini, Giovanna; Manniello, Assunta; Ianotta, Beatrice; Rondanina, Gabriella; Ruzzon, Tiziana; Santi, Leonardo

    1992-01-01

    The Molecular Probe Data Base (MPDB) is designed to collect and make available on-line information on synthetic oligonucleotides. This paper briefly describes the purpose of MPDB, its content and structure, forms and mode of data distribution, and a series of additional services available to scientists using MPDB. PMID:1598231

  12. Molecular imaging probes derived from natural peptides.

    PubMed

    Charron, C L; Hickey, J L; Nsiama, T K; Cruickshank, D R; Turnbull, W L; Luyt, L G

    2016-06-01

    Covering: up to the end of 2015.Peptides are naturally occurring compounds that play an important role in all living systems and are responsible for a range of essential functions. Peptide receptors have been implicated in disease states such as oncology, metabolic disorders and cardiovascular disease. Therefore, natural peptides have been exploited as diagnostic and therapeutic agents due to the unique target specificity for their endogenous receptors. This review discusses a variety of natural peptides highlighting their discovery, endogenous receptors, as well as their derivatization to create molecular imaging agents, with an emphasis on the design of radiolabelled peptides. This review also highlights methods for discovering new and novel peptides when knowledge of specific targets and endogenous ligands are not available. PMID:26911790

  13. Probing ultrafast thermalization with field-free molecular alignment

    NASA Astrophysics Data System (ADS)

    Houzet, J.; Gateau, J.; Hertz, E.; Billard, F.; Lavorel, B.; Hartmann, J.-M.; Boulet, C.; Faucher, O.

    2012-09-01

    The rotation-translation thermalization of CO2 gas is investigated 500 ps after its preheating by a nonresonant short and intense laser pulse. The temperature of thermalization is optically determined with two additional short laser pulses enabling a field-free molecular alignment process and its probing, respectively. The measurements are performed for various intensities of the preheat pulse, leading to the observation of different temperatures which are in very good agreement with classical molecular dynamics simulations. The results can be regarded as a step towards real-time tracking of ultrafast relaxation pathways in molecular motion.

  14. The Imaging Probe Development Center and the Production of Molecular Imaging Probes

    PubMed Central

    Griffiths, Gary L

    2008-01-01

    The Imaging Probe Development Center (IPDC), part of the NIH Roadmap for Medical Research Initiative (http://nihroadmap.nih.gov/) recently became fully operational at its newly refurbished laboratories in Rockville, MD. The IPDC (http://nihroadmap.nih.gov/molecularlibraries/ipdc/) is dedicated to the production of known and novel molecular imaging probes, with its services currently being used by the NIH intramural community, although in the future it is intended that the extramural community will also benefit from the IPDC’s resources. The Center has been set up with the belief that molecular imaging, and the probe chemistry that underpins it, will constitute key technologies going forward. As part of the larger molecular libraries and imaging initiative, it is planned that the IPDC will work closely with scientists from the molecular libraries effort. Probes produced at the IPDC include optical, radionuclide and magnetic resonance agents and may encompass any type of contrast agent. As IPDC is a trans-NIH resource it can serve each of the 27 Institutes and Centers that comprise NIH so its influence can be expected to impact widely different subjects and disease conditions spanning biological research. IPDC is expected to play a key part in interdisciplinary collaborative imaging projects and to support translational R&D from basic research through clinical development, for all of the imaging modalities. Examples of probes already prepared or under preparation are outlined to illustrate the breadth of the chemistries undertaken together with a reference outline of the diverse biological applications for which the various probes are intended. PMID:20161829

  15. Characterizing molecular probes for diffusion measurements in the brain

    PubMed Central

    Kaur, Gurjinder; Hrabetova, Sabina; Guilfoyle, David N.; Nicholson, Charles; Hrabe, Jan

    2008-01-01

    Brain diffusion properties are at present most commonly evaluated by magnetic resonance (MR) diffusion imaging. MR cannot easily distinguish between the extracellular and intracellular signal components, but the older technique of Real-Time Iontophoresis (RTI) detects exclusively extracellular diffusion. Interpretation of the MR results would therefore benefit from auxiliary RTI measurements. This requires a molecular probe detectable by both techniques. Our aim was to specify a minimum set of requirements that such a diffusion probe should fulfill and apply it to two candidate probes: the cation tetramethylammonium (TMA+), used routinely in the RTI experiments, and the anion hexafluoroantimonate (SbF6−). Desirable characteristics of a molecular diffusion probe include predictable diffusion properties, stability, minimum interaction with cellular physiology, very slow penetration into the cells, and sufficiently strong and selective MR and RTI signals. These properties were evaluated using preparations of rat neocortical slices under normal and ischemic conditions, as well as solutions and agarose gel. While both molecules can be detected by MR and RTI, neither proved an ideal candidate. TMA+ was very stable but it penetrated into the cells and accumulated there within tens of minutes. SbF6− did not enter the cells as readily but it was not stable, particularly in ischemic tissue and at higher temperatures. Its presence also resulted in a decreased extracellular volume. These probe properties help to interpret previously published MR data on TMA+ diffusion and might play a role in other diffusion experiments obtained with them. PMID:18466980

  16. Investigation of the hybrid molecular probe for intracellular studies

    PubMed Central

    Martinez, Karen; Medley, Colin D.; Yang, Chaoyong James; Tan, Weihong

    2009-01-01

    Monitoring gene expression in vivo is essential to the advancement of biological studies, medical diagnostics, and drug discovery. Adding to major efforts in developing molecular probes for mRNA monitoring, we have recently developed an alternative tool, the hybrid molecular probe (HMP). To optimize the probe, a series of experiments were performed to study the properties of HMP hybridization kinetics and stability. The results demonstrated the potential of the HMP as a prospective tool for use in both hybridization studies and in vitro and in vivo analyses. The HMP has shown no tendency to produce false positive signals, which is a major concern for living cell studies. Moreover, HMP has shown the ability to detect the mRNA expression of different genes inside single cells from both basal and stimulated genes. As an effective alternative to conventional molecular probes, the proven sensitivity, simplicity, and stability of HMPs show promise for their use in monitoring mRNA expression in living cells. PMID:18421445

  17. Multiplexed genotyping with sequence-tagged molecular inversion probes.

    PubMed

    Hardenbol, Paul; Banér, Johan; Jain, Maneesh; Nilsson, Mats; Namsaraev, Eugeni A; Karlin-Neumann, George A; Fakhrai-Rad, Hossein; Ronaghi, Mostafa; Willis, Thomas D; Landegren, Ulf; Davis, Ronald W

    2003-06-01

    We report on the development of molecular inversion probe (MIP) genotyping, an efficient technology for large-scale single nucleotide polymorphism (SNP) analysis. This technique uses MIPs to produce inverted sequences, which undergo a unimolecular rearrangement and are then amplified by PCR using common primers and analyzed using universal sequence tag DNA microarrays, resulting in highly specific genotyping. With this technology, multiplex analysis of more than 1,000 probes in a single tube can be done using standard laboratory equipment. Genotypes are generated with a high call rate (95%) and high accuracy (>99%) as determined by independent sequencing. PMID:12730666

  18. Detection of toxoplasma gondii with a DNA molecular beacon probe

    NASA Astrophysics Data System (ADS)

    Xu, Shichao; Yao, Cuicui; Wei, Shuoming; Zhang, Jimei; Sun, Bo; Zheng, Guo; Han, Qing; Hu, Fei; Zhou, Hongming

    2008-12-01

    Toxoplasma gondii is a microscopic parasite that may infect humans, so there is an increasing concern on the early detection of latent Toxoplasma gondii infection in recent years. We currently report a rapid and sensitive method for Toxoplasma gondii based on molecular beacon (MB) probe. The probe based on fluorescence resonance energy transfer (FRET) with a stem-loop DNA oligonucleotide was labeled with CdTe/ZnS quantum dots (energy donor) at 5' end and BHQ-2 (energy acceptor) at 3' end, respectively. The probe was synthesized in PBS buffer at pH 8.2, room temperature for 24 h. Then target DNA was injected under the condition of 37°C, hybridization for 2 h, in Tris-HCl buffer. The data from fluorescence spectrum (FS) showed that ca 65% of emitted fluorescence was quenched, and about 50% recovery of fluorescence intensity was observed after adding target DNA, which indicated that the target DNA was successfully detected by MB probe. The detecting limitation was determined as ca 5 nM. Moreover, specificity of the probe was investigated by adding target DNA with one-base-pair mismatch, the low fluorescence recovery indicated the high specificity. The results showed that the current sensing probe will be a useful and convenient tool in Toxoplasma gondii early detection.

  19. Electrical Probing and Tuning of Molecular Physisorption on Graphene.

    PubMed

    Kulkarni, Girish S; Reddy, Karthik; Zang, Wenzhe; Lee, Kyunghoon; Fan, Xudong; Zhong, Zhaohui

    2016-01-13

    The ability to tune the molecular interaction electronically can have profound impact on wide-ranging scientific frontiers in catalysis, chemical and biological sensor development, and the understanding of key biological processes. Despite that electrochemistry is routinely used to probe redox reactions involving loss or gain of electrons, electrical probing and tuning of the weaker noncovalent interactions, such as molecular physisorption, have been challenging, primarily due to the inability to change the work function of conventional metal electrodes. To this end, we report electrical probing and tuning of the noncovalent physisorption of polar molecules on graphene surface by using graphene nanoelectronic heterodyne sensors. Temperature-dependent molecular desorptions for six different polar molecules were measured in real-time to study the desorption kinetics and extract the binding affinities. More importantly, we demonstrate electrical tuning of molecule-graphene binding kinetics through electrostatic gating of graphene; the molecular desorption can be slowed down nearly three times within a gate voltage range of 15 V. Our results provide insight into small molecule-nanomaterial interaction dynamics and signify the ability to electrically tailor interactions, which can lead to rational designs of complex chemical processes for catalysis and drug discovery. PMID:26709716

  20. Nanoscale probing of dynamics in local molecular environments.

    PubMed

    Atkin, Joanna M; Sass, Paul M; Teichen, Paul E; Eaves, Joel D; Raschke, Markus B

    2015-11-19

    Vibrational spectroscopy can provide information about structure, coupling, and dynamics underlying the properties of complex molecular systems. While measurements of spectral line broadening can probe local chemical environments, the spatial averaging in conventional spectroscopies limits insight into underlying heterogeneity, in particular in disordered molecular solids. Here, using femtosecond infrared scattering scanning near-field optical microscopy (IR s-SNOM), we resolve in vibrational free-induction decay (FID) measurements a high degree of spatial heterogeneity in polytetrafluoroethylene (PTFE) as a dense molecular model system. In nanoscopic probe volumes as small as 10(3) vibrational oscillators, we approach the homogeneous response limit, with extended vibrational dephasing times of several picoseconds, that is, up to 10 times the inhomogeneous lifetime, and spatial average converging to the bulk ensemble response. We simulate the dynamics of relaxation with a finite set of local vibrational transitions subject to random modulations in frequency. The combined results suggest that the observed heterogeneity arises due to static and dynamic variations in the local molecular environment. This approach thus provides real-space and real-time visualization of the subensemble dynamics that define the properties of many functional materials. PMID:26528865

  1. Aptamers: versatile molecular recognition probes for cancer detection

    PubMed Central

    Sun, Hongguang; Tan, Weihong; Zu, Youli

    2015-01-01

    In the past two decades, aptamers have emerged as a novel class of molecular recognition probes comprising uniquely-folded short RNA or single-stranded DNA oligonucleotides that bind to their cognate targets with high specificity and affinity. Aptamers, often referred to as “chemical antibodies”, possess several highly desirable features for clinical use. They can be chemically synthesized and are easily conjugated to a wide range of reporters for different applications, and are able to rapidly penetrate tissues. These advantages significantly enhance their clinical applicability, and render them excellent alternatives to antibody-based probes in cancer diagnostics and therapeutics. Aptamer probes based on fluorescence, colorimetry, magnetism, electrochemistry, and in conjunction with nanomaterials (e.g., nanoparticles, quantum dots, single-walled carbon nanotubes, and magnetic nanoparticles) have provided novel ultrasensitive cancer diagnostic strategies and assays. Furthermore, promising aptamer targeted-multimodal tumor imaging probes have been recently developed in conjunction with fluorescence, positron emission tomography (PET), single-photon emission computed tomography (SPECT), and magnetic resonance imaging (MRI). The capabilities of the aptamer-based platforms described herein underscore the great potential they hold for the future of cancer detection. In this review, we highlight the most prominent recent developments in this rapidly advancing field. PMID:26618445

  2. Probing ultrafast molecular dynamics in O2 using XUV/IR pump-probe studies

    NASA Astrophysics Data System (ADS)

    Ray, D.; Sturm, F. P.; Wright, T. W.; Ranitovic, P.; Shivaram, N. H.; Bocharova, I.; Belkacem, A.; Weber, Th.

    2015-05-01

    We investigate the molecular dynamics via different dissociative and autoionizing pathways in molecular oxygen using a pump-probe scheme with ultrashort extreme ultraviolet (XUV) laser pulses. Our primary focus is to study the molecular dynamics in the superexcited Rydberg states in a time-resolved manner. The O2 molecules are pumped by 20.2 eV and 23.1 eV XUV pulses (13th and 15th harmonics). Probing the relaxation dynamics with an infrared (IR) pulse at very long delays (100s of fs) enables us to measure the lifetimes of these Rydberg states. We also observe an enhancement and suppression of vibrational levels of the O2+ion due to the presence of IR. The high flux XUV pulses used for this experiment are generated in an Ar gas by IR pulses from our state-of-the-art 30 mJ, 50 Hz laser system. The pulses are overlapped with the supersonic jet in our Momentum Imaging for TimE Resolved Studies (MISTERS) setup. The cold target in our setup, combined with a very tight focussing geometry and a 3D momentum detection capability gives a high kinetic energy resolution. Molecular dynamics in other polyatomic molecules are also under investigation. Chemical Sciences Division, Lawrence Berkeley National Laboratory.

  3. A Pan-GTPase Inhibitor as a Molecular Probe

    PubMed Central

    Hong, Lin; Guo, Yuna; BasuRay, Soumik; Agola, Jacob O.; Romero, Elsa; Simpson, Denise S.; Schroeder, Chad E.; Simons, Peter; Waller, Anna; Garcia, Matthew; Carter, Mark; Ursu, Oleg; Gouveia, Kristine; Golden, Jennifer E.; Aubé, Jeffrey; Wandinger-Ness, Angela; Sklar, Larry A.

    2015-01-01

    Overactive GTPases have often been linked to human diseases. The available inhibitors are limited and have not progressed far in clinical trials. We report here a first-in-class small molecule pan-GTPase inhibitor discovered from a high throughput screening campaign. The compound CID1067700 inhibits multiple GTPases in biochemical, cellular protein and protein interaction, as well as cellular functional assays. In the biochemical and protein interaction assays, representative GTPases from Rho, Ras, and Rab, the three most generic subfamilies of the GTPases, were probed, while in the functional assays, physiological processes regulated by each of the three subfamilies of the GTPases were examined. The chemical functionalities essential for the activity of the compound were identified through structural derivatization. The compound is validated as a useful molecular probe upon which GTPase-targeting inhibitors with drug potentials might be developed. PMID:26247207

  4. Probing molecular chirality by coherent optical absorption spectra

    SciTech Connect

    Jia, W. Z.; Wei, L. F.

    2011-11-15

    We propose an approach to sensitively probe the chirality of molecules by measuring their coherent optical-absorption spectra. It is shown that quantum dynamics of the cyclic three-level chiral molecules driven by appropriately designed external fields is total-phase dependent. This will result in chirality-dependent absorption spectra for the probe field. As a consequence, the charality-dependent information in the spectra (such as the locations and relative heights of the characteristic absorption peaks) can be utilized to identify molecular chirality and determinate enantiomer excess (i.e., the percentages of different enantiomers). The feasibility of the proposal with chiral molecules confined in hollow-core photonic crystal fiber is also discussed.

  5. Detection of Toxoplasma gondii with a DNA molecular beacon probe

    NASA Astrophysics Data System (ADS)

    Zhou, Cun; Xu, Shichao; Yang, Juan; Zhang, Jimei; Dai, Zhao; Zheng, Guo; Sun, Bo; Sun, Shuqing; Feng, Teilin; Zi, Yan; Liang, Chu; Luo, Hao

    2009-07-01

    Toxoplasma gondii is a kind of microscopic parasite that may infect humans, and there are increasing concerns on the early detection of latent Toxoplasma gondii infection in recent years. This research highlights a new type of molecular beacon (MB) fluorescent probe for Toxoplasma DNA testing. We combined high-efficiency fluorescent inorganic core-shell quantum dots-CdTe/ZnS (as fluorescent energy donor) and BHQ-2 (energy acceptor) to the single-strand DNA of Toxoplasma gondii, and a molecular beacon sensing system based on fluorescence resonance energy transfer (FRET) was achieved. Core-shell quantum dots CdTe/ZnS was firstly prepared in aqueous solution, and the influencing factor of its fluorescent properties, including CdTe/Na2S/Zn(CH3COO)2 (v/v), dependence of reaction time, temperature, and pH, is investigated systematically. The synthesized quantum dots and molecular beacon were characterized by transmission electron microscopy (TEM), ultraviolet-visible spectrophotometer (UV-vis), fluorescent spectrophotometer (FS), respectively. The TEM results showed that CdTe/ZnS core-shell quantum dots is ~11nm in size, and the quantum dots is water-soluble well. The sensing ability of target DNA of assembled MB was investigated, and results showed that the target Toxoplasma gonddi DNA can be successfully detected by measuring the change of fluorescence intensity. The results showed that the current sensing probe will be a useful and convenient tool in Toxoplasma gondii early detection.

  6. Frequency Domain Fluorescent Molecular Tomography and Molecular Probes for Small Animal Imaging

    NASA Astrophysics Data System (ADS)

    Kujala, Naresh Gandhi

    Fluorescent molecular tomography (FMT) is a noninvasive biomedical optical imaging that enables 3-dimensional quantitative determination of fluorochromes distributed in biological tissues. There are three methods for imaging large volume tissues based on different light sources: (a) using a light source of constant intensity, through a continuous or constant wave, (b) using a light source that is intensity modulated with a radio frequency (RF), and (c) using ultrafast pulses in the femtosecond range. In this study, we have developed a frequency domain fluorescent molecular tomographic system based on the heterodyne technique, using a single source and detector pair that can be used for small animal imaging. In our system, the intensity of the laser source is modulated with a RF frequency to produce a diffuse photon density wave in the tissue. The phase of the diffuse photon density wave is measured by comparing the reference signal with the signal from the tissue using a phasemeter. The data acquisition was performed by using a Labview program. The results suggest that we can measure the phase change from the heterogeneous inside tissue. Combined with fiber optics and filter sets, the system can be used to sensitively image the targeted fluorescent molecular probes, allowing the detection of cancer at an early stage. We used the system to detect the tumor-targeting molecular probe Alexa Fluor 680 and Alexa Fluor 750 bombesin peptide conjugates in phantoms as well as mouse tissues. We also developed and evaluated fluorescent Bombesin (BBN) probes to target gastrin-releasing peptide (GRP) receptors for optical molecular imaging. GRP receptors are over-expressed in several types of human cancer cells, including breast, prostate, small cell lung, and pancreatic cancers. BBN is a 14 amino acid peptide that is an analogue to human gastrin-releasing peptide that binds specifically to GRPr receptors. BBN conjugates are significant in cancer detection and therapy. The

  7. Plant sentinels and molecular probes that monitor environmental munitions contaminants

    SciTech Connect

    Jackson, P.J.; DeWitt, J.G.; Hill, K.K.; Kuske, C.R.; Kim, D.Y.

    1994-08-01

    Plants accumulate TNT and similar compounds from soil. Their sessile nature requires that plants adapt to environmental changes by biochemical and molecular means. In principle, it is possible to develop a monitoring capability based on expression of any gene that is activated by specific environmental conditions. The authors have identified plant genes activated upon exposure to TNT. Partial gene sequences allow design of DNA probes that measure TNT-induced gene activity. These will be used to develop sensitive assays that monitor gene expression in plants growing in environments possibly contaminated with explosives.

  8. Spatially Resolved Analysis of Amines Using a Fluorescence Molecular Probe: Molecular Analysis of IDPs

    NASA Technical Reports Server (NTRS)

    Clemett, S. J.; Messenger, S.; Thomas-Keprta, K. L.; Wentworth, S. J.; Robinson, G. A.; McKay, D. S.

    2002-01-01

    Some Interplanetary Dust Particles (IDPs) have large isotope anomalies in H and N. To address the nature of the carrier phase, we are developing a procedure to spatially resolve the distribution of organic species on IDP thin sections utilizing fluorescent molecular probes. Additional information is contained in the original extended abstract.

  9. E × B probe measurements in molecular and electronegative plasmas

    NASA Astrophysics Data System (ADS)

    Renaud, D.; Gerst, D.; Mazouffre, S.; Aanesland, A.

    2015-12-01

    This paper reports on the design, the building, the calibration, and the use of a compact E × B probe that acts as a velocity filter or a mass filter for ion species. A series of measurements has been performed in the discharge and in the beam of the PEGASES (Plasma Propulsion with Electronegative GASES) ion source. PEGASES is a unique inductively coupled radio-frequency source able to generate a beam of positive and negative ions when operated with an electronegative gas. In this study, experiments have been carried out with SF6. Calibrated E × B probe spectra indicate that the diagnostic tool can be used to determine the ion velocity and the plasma composition even when many molecular fragments are present. In addition, the probe is able to detect both positive and negative ions. Measurements show a large variety of positively charged ions coming from SF6. Conversely, the beam is solely composed of F- and SF 6- negative ions in compliance with computer simulations.

  10. Tailored molecular glass resists for scanning probe lithography

    NASA Astrophysics Data System (ADS)

    Neuber, Christian; Schmidt, Hans-Werner; Strohriegl, Peter; Ringk, Andreas; Kolb, Tristan; Schedl, Andreas; Fokkema, Vincent; van Veghel, Marijn G. A.; Cooke, Mike; Rawlings, Colin; Dürig, Urs; Knoll, Armin; de Marneffe, Jean-François; el Otell, Ziad; Kaestner, Marcus; Krivoshapkina, Yana; Budden, Matthias; Rangelow, Ivo W.

    2015-03-01

    In the presented work solvent-free film preparation from tailored molecular glass resists, their thermal analysis, the characterization of etch resistance for plasma etching transfer processes, and the evaluation of the patterning performance using scanning probe lithography (SPL) tools, in particular electric field and thermal based SPL, are demonstrated. Therefore a series of fully aromatic spiro-based and tris-substituted twisted resist materials were systematically investigated. The materials feature very high glass transition temperatures of up to 173 °C, which allows solvent-free thin film preparation by physical vapor deposition (PVD) due to their high thermal stability. The PVD prepared films offer distinct advantages compared to spin coated films such as no pinholes, defects, or residual solvent domains, which can locally affect the film properties. In addition, PVD prepared films do not need a post apply bake (PAB) and can be precisely prepared in the nanometer range layer thickness. An observed sufficient plasma etching resistance is promising for an efficient pattern transfer even by utilizing only 10 nm thin resist films. Their lithographic resolution potential is demonstrated by a positive and a negative tone patterning using electric field, current controlled scanning probe lithography (EF-CC-SPL) at the Technical University of Ilmenau or thermal scanning probe lithography (tSPL) investigations at the IBM Research - Zurich. High resolution tSPL prepared patterns of 11 nm half pitch and at 4 nm patterning depth are demonstrated.

  11. E × B probe measurements in molecular and electronegative plasmas.

    PubMed

    Renaud, D; Gerst, D; Mazouffre, S; Aanesland, A

    2015-12-01

    This paper reports on the design, the building, the calibration, and the use of a compact E × B probe that acts as a velocity filter or a mass filter for ion species. A series of measurements has been performed in the discharge and in the beam of the PEGASES (Plasma Propulsion with Electronegative GASES) ion source. PEGASES is a unique inductively coupled radio-frequency source able to generate a beam of positive and negative ions when operated with an electronegative gas. In this study, experiments have been carried out with SF6. Calibrated E × B probe spectra indicate that the diagnostic tool can be used to determine the ion velocity and the plasma composition even when many molecular fragments are present. In addition, the probe is able to detect both positive and negative ions. Measurements show a large variety of positively charged ions coming from SF6. Conversely, the beam is solely composed of F(-) and SF6(-) negative ions in compliance with computer simulations. PMID:26724027

  12. Near-infrared dyes for molecular probes and imaging

    NASA Astrophysics Data System (ADS)

    Patonay, Gabor; Beckford, Garfield; Strekowski, Lucjan; Henary, Maged; Kim, Jun Seok; Crow, Sidney

    2009-02-01

    Near-Infrared (NIR) fluorescence has been used both as an analytical tool as molecular probes and in in vitro or in vivo imaging of individual cells and organs. The NIR region (700-1100 nm) is ideal with regard to these applications due to the inherently lower background interference and the high molar absorptivities of NIR chromophores. NIR dyes are also useful in studying binding characteristics of large biomolecules, such as proteins. Throughout these studies, different NIR dyes have been evaluated to determine factors that control binding to biomolecules, including serum albumins. Hydrophobic character of NIR dyes were increased by introducing alkyl and aryl groups, and hydrophilic moieties e.g., polyethylene glycols (PEG) were used to increase aqueous solubility. Recently, our research group introduced bis-cyanines as innovative NIR probes. Depending on their microenvironment, bis-cyanines can exist as an intramolecular dimer with the two cyanines either in a stacked form, or in a linear conformation in which the two subunits do not interact with each other. In this intramolecular H-aggregate, the chromophore has a low extinction coefficient and low fluorescence quantum yield. Upon addition of biomolecules, the H-and D- bands are decreased and the monomeric band is increased, with concomitant increase in fluorescence intensity. Introduction of specific moieties into the NIR dye molecules allows for the development of physiological molecular probes to detect pH, metal ions and other parameters. Examples of these applications include imaging and biomolecule characterizations. Water soluble dyes are expected to be excellent candidates for both in vitro and in vivo imaging of cells and organs.

  13. Interfacial nanorheology: Probing molecular mobility in mesoscopic polymeric systems

    NASA Astrophysics Data System (ADS)

    Sills, Scott E.

    Investigating the finite size limited structural relaxations in mesoscopic polymer systems is central to nanotechnological applications involving thin films, complex structures, and nanoscale phase-separated systems; for example, polymer electrolyte membranes, optoelectronic devices, and ultrahigh-density thermomechanical data storage (terabit recording). In such systems, bulk statistical averaging and continuum models are jeopardized. Interfacial constraints lead to bulk-deviating molecular dynamics and dictate material and transport properties. The objective of this dissertation is to provide insight to the exotic mesoscopic behaviors in thin films by developing novel rheological and tribological analytical methods based on scanning probe microscopy (SPM). Activation energies are deduced for the molecular motions associated with internal friction dissipation, and the temperature resolved length scale for cooperative motion during the glass transition is directly obtained for polystyrene. These results confirm the dynamical heterogeneity of the glass transition and reveal a crossover from intra- to inter-molecular relaxation in the transition regime. The impact of dimensional constraints on molecular mobility in ultrathin polymer films is explored through interfacial glass-transition profiles. With these profiles, a structural model of the rheological changes near interfacial boundaries is constructed as function of molecular weight and crosslinking density. The manifestation of interfacial constraints in nanotechnological applications is illustrated for thermomechanical recording, where rheological gradients near the substrate dictate the contact pressure and strain shielding at the substrate compromises film stability. A foundation for the critical aspects of interfacial stability is developed, and mechanically graded interfaces and modulus-matching techniques are explored as a means of improving the stability, durability, and stress transmission characteristics

  14. X-ray diffraction topography image materials by molecular probe

    NASA Astrophysics Data System (ADS)

    Hentschel, Manfred P.; Lange, Axel; Schors, Joerg; Wald, Oliver

    2005-05-01

    Crystallinity, composition, homogeneity and anisotropy determine the mechanical properties of materials significantly, but the performance of most non-destructive techniques is too poor for measuring these micro structures as they are optimized for finding individual flaws/defects. X-ray (wide angle) Diffraction Topography by single beam scanning images molecular information at a spatial resolution of several ten micrometers even in three dimensions. Especially for the non-destructive characterization of composite materials, they provide additional capabilities by crystallographic contrast by the molecular/atomic probe. The different material phases of compounds and their molecular orientation can be imaged e.g. fibers or polymer chain orientation in composites: A sample is scanned or rotated, while only part of the scattering pattern is pointing at an X-ray detector area. Three different methods have been developed: i) planar X-ray Scanning Topography at one or more pre-selected scattering angles provides high contrast of different phases of components. ii) X-Ray Rotation Topography reveals the texture angle of composite fibers and chain polymers. iii) X-ray Diffraction Microscopy images the texture and phase distribution of transversal sections of the material. The principles of Wide Angle X-Ray Diffraction Topography are explained and examples of investigations will be presented. They combine the advantages of radiographic imaging and crystal structure information. The applied X-ray energies are much lower than in NDT radiography, which recommends preferably the application to light weight materials.

  15. Luminescent chiral lanthanide(III) complexes as potential molecular probes

    PubMed Central

    Muller, Gilles

    2009-01-01

    This perspective gives an introduction into the design of luminescent lanthanide(III)-containing complexes possessing chiral properties and used to probe biological materials. The first part briefly describes general principles, focusing on the optical aspect (i.e. lanthanide luminescence, sensitization processes) of the most emissive trivalent lanthanide ions, europium and terbium, incorporated into molecular luminescent edifices. This is followed by a short discussion on the importance of chirality in the biological and pharmaceutical fields. The second part is devoted to the assessment of the chiroptical spectroscopic tools available (typically circular dichroism and circularly polarized luminescence) and the strategies used to introduce a chiral feature into luminescent lanthanide(III) complexes (chiral structure resulting from a chiral arrangement of the ligand molecules surrounding the luminescent center or presence of chiral centers in the ligand molecules). Finally, the last part illustrates these fundamental principles with recent selected examples of such chiral luminescent lanthanide-based compounds used as potential probes of biomolecular substrates. PMID:19885510

  16. Nitrile and thiocyanate IR probes: Molecular dynamics simulation studies

    NASA Astrophysics Data System (ADS)

    Oh, Kwang-Im; Choi, Jun-Ho; Lee, Joo-Hyun; Han, Jae-Beom; Lee, Hochan; Cho, Minhaeng

    2008-04-01

    Nitrile- and thiocyanate-derivatized amino acids have been found to be useful IR probes for investigating their local electrostatic environments in proteins. To shed light on the CN stretch frequency shift and spectral lineshape change induced by interactions with hydrogen-bonding solvent molecules, we carried out both classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations for MeCN and MeSCN in water. These QM/MM and conventional force field MD simulation results were found to be inconsistent with the experimental results as well as with the high-level ab initio calculation results of MeCN-water and MeSCN-water potential energies. Thus, a new set of atomic partial charges of MeCN and MeSCN is obtained. By using the MD simulation trajectories and the electrostatic potential model recently developed, the CN and SCN stretching mode frequency trajectories were obtained and used to simulate the IR spectra. The C N frequency blueshifts of MeCN and MeSCN in water are estimated to be 9.0 and 1.9cm-1, respectively, in comparison with those of gas phase values. These values are found to be in reasonable agreement with the experimentally measured IR spectra of MeCN, MeSCN, β-cyano-L-alanine, and cyanylated cysteine in water and other polar solvents.

  17. Toxoplasma gondii DNA detection with a magnetic molecular beacon probe

    NASA Astrophysics Data System (ADS)

    Xu, Shichao; Yao, Cuicui; Wei, Shuoming; Zhang, Jimei; Dai, Zhao; Zheng, Guo; Sun, Bo; Han, Qing; Hu, Fei; Zhou, Hongming

    2008-12-01

    Toxoplasma Gondii infection is widespread in humans worldwide and reported infection rates range from 3%-70%, depending on the populations or geographic areas, and it has been recognized as a potential food safety hazard in our daily life. A magnetic molecular beacon probe (mMBP), based on theory of fluorescence resonance energy transfer (FRET), was currently reported to detect Toxoplasma Gondii DNA. Nano-sized Fe3O4 were primarily prepared by coprecipitation method in aqueous phase with NaOH as precipitator, and was used as magnetic core. The qualified coreshell magnetic quantum dots (mQDs), i.e. CdTe(symbol)Fe3O4, were then achieved by layer-by-layer method when mol ratio of Fe3O4/CdTe is 1/3, pH at 6.0, 30 °C, and reactant solution was refluxed for 30 min, the size of mQDs were determined to be 12-15 nm via transmission electron microscopy (TEM). Over 70% overlap between emission spectrum of mQDs and absorbance spectrum of BHQ-2 was observed, this result suggests the synthesized mQDs and BHQ-2 can be utilized as energy donor and energy acceptor, respectively. The sensing probe was fabricated and a stem-loop Toxoplasma Gondii DNA oligonucleotide was labeled with mQDs at the 5' end and BHQ-2 at 3' end, respectively. Target Toxoplasma gondii DNA was detected under conditions of 37 °C, hybridization for 2h, at pH8.0 in Tris-HCl buffer. About 30% recovery of fluorescence intensity was observed via fluorescence spectrum (FS) after the Toxoplasma gondii DNA was added, which suggested that the Toxoplasma Gondii DNA was successfully detected. Specificity investigation of the mMBP indicated that relative low recovery of fluorescence intensity was obtained when the target DNA with one-base pair mismatch was added, this result indicated the high specificity of the sensing probe. Our research simultaneously indicated that mMBP can be conveniently separated from the unhybridized stem-loop DNA and target DNA, which will be meaningful in DNA sensing and purification process.

  18. PVD prepared molecular glass resists for scanning probe lithography

    NASA Astrophysics Data System (ADS)

    Neuber, Christian; Schmidt, Hans-Werner; Strohriegl, Peter; Wagner, Daniel; Krohn, Felix; Schedl, Andreas; Bonanni, Simon; Holzner, Felix; Rawlings, Colin; Dürig, Urs; Knoll, Armin W.

    2016-03-01

    In the presented work solvent-free film preparation from molecular glass resists, the evaluation of the patterning performance using thermal scanning probe lithography (tSPL) and an efficient etch transfer process are demonstrated. As the presented materials have a high tendency to crystallize and thus form crystalline films of bad quality when processed by solution casting, two component mixtures prepared by coevaporation were investigated. Stable amorphous films were obtained by selecting compatible material pairs for the coevaporation. One optimized material pair is based on trissubstituted, twisted resist materials with a distinct difference in molecular design. Here a high resolution tSPL prepared pattern of 18 nm half pitch in a 10 nm thick film is demonstrated. A further optimization is reported for "small" cubic silsequioxane molecules. Again single component films show independent to applied film preparation techniques bad film forming properties due to the high crystallinity of the symmetric cubic silsequioxane molecules. But coevaporation of the phenyl substituted octaphenylsilsequioxane combined with the fully aromatic 2,2',7,7'-tetraphenyl-9,9'-spirobi[fluorene] results in stable amorphous thin films. tSPL investigations demonstrate the patternability by writing high resolution line features of 20 nm half pitch. An important advantage of such a silicon rich resist material is that it can be directly converted to SiO2, yielding to a patterned hardmask of SiO2. This proof of principle is demonstrated and an efficient pattern transfer of 60 nm half pitch line into the underlying HM8006 is reported.

  19. Stability Mechanisms of a Thermophilic Laccase Probed by Molecular Dynamics

    PubMed Central

    Christensen, Niels J.; Kepp, Kasper P.

    2013-01-01

    Laccases are highly stable, industrially important enzymes capable of oxidizing a large range of substrates. Causes for their stability are, as for other proteins, poorly understood. In this work, multiple-seed molecular dynamics (MD) was applied to a Trametes versicolor laccase in response to variable ionic strengths, temperatures, and glycosylation status. Near-physiological conditions provided excellent agreement with the crystal structure (average RMSD ∼0.92 Å) and residual agreement with experimental B-factors. The persistence of backbone hydrogen bonds was identified as a key descriptor of structural response to environment, whereas solvent-accessibility, radius of gyration, and fluctuations were only locally relevant. Backbone hydrogen bonds decreased systematically with temperature in all simulations (∼9 per 50 K), probing structural changes associated with enthalpy-entropy compensation. Approaching Topt (∼350 K) from 300 K, this change correlated with a beginning “unzipping” of critical β-sheets. 0 M ionic strength triggered partial denucleation of the C-terminal (known experimentally to be sensitive) at 400 K, suggesting a general salt stabilization effect. In contrast, F− (but not Cl−) specifically impaired secondary structure by formation of strong hydrogen bonds with backbone NH, providing a mechanism for experimentally observed small anion destabilization, potentially remedied by site-directed mutagenesis at critical intrusion sites. N-glycosylation was found to support structural integrity by increasing persistent backbone hydrogen bonds by ∼4 across simulations, mainly via prevention of F− intrusion. Hydrogen-bond loss in distinct loop regions and ends of critical β-sheets suggest potential strategies for laboratory optimization of these industrially important enzymes. PMID:23658618

  20. Molecular dynamics as observed with probes of different dimensions in thin polymer films

    NASA Astrophysics Data System (ADS)

    Zhao, Jiang; Zhang, Hao; Yang, Jingfa; Wang, Fuyi; Liu, Di

    Rotational motion of individual fluorescence molecules doped in thin films of poly vinylacetate (PVAc) was monitored by single molecule fluorescence de-focus microscopy. Perylendiimide and its derivatives of different dimension were chosen as probes for local dynamics. The results demonstrate that the local vibration mode detected by different molecules probe depends on dimension of the probes - the larger probes the lower frequency. The population of rotating probes is found to increase with temperature elevation, depending on the molecular dimension as well. The comparison of the results with thermo-dynamic measurements helps to shed new light on the physical picture of glass transition. Supported by MoST of China.

  1. Optical probes of atomic and molecular decay processes.

    SciTech Connect

    Pratt, S. T.

    2008-01-01

    characterize both the photoexcitation and subsequent decay processes. These techniques include mass spectrometry, dispersive and threshold photoelectron spectroscopy, laser-induced fluorescence, fluorescence-dip spectroscopy, and laser-induced grating spectroscopy. While the instrumentation is currently available for each of these techniques, two instruments deserve special mention. First, a high-resolution magnetic-bottle electron spectrometer has been developed that is equipped with a pulsed, skimmed molecular beam source. This instrument is capable of {approx}3-4 meV resolution in the electron kinetic energy while providing a collection efficiency of {approx}50%. Second, a time-of-flight mass spectrometer has been constructed with a similar molecular beam source. This instrument is currently being adapted to allow both ion- and electron-imaging studies. A typical experimental study is performed in three steps. First, resonant one-color multiphoton ionization is used to map out the transition between the ground state of the molecule of interest and the low-lying excited state to be used as an intermediate in the double-resonance process. The lasers used in these studies are Nd:YAG-pumped dye lasers with {approx}5 ns pulse durations. In general, this pump transition corresponds to a one- or two-photon process, and the laser output is frequency doubled, tripled, or mixed to generate light in the region of interest. In molecules such as ammonia and aniline, the pump transitions of interest are well characterized, allowing the unambiguous choice of pump transitions that access levels with the rovibronic character of interest. In other cases, the spectroscopy of the pump transition must be analyzed before it can be useful for the double-resonance experiments. In the second step, the pump laser is fixed on the pump transition of interest and a second laser is used to probe transitions from the upper state of the pump transition to the autoionizing or predissociating resonances in

  2. An ALuc-Based Molecular Tension Probe for Sensing Intramolecular Protein-Protein Interactions.

    PubMed

    Kim, Sung-Bae; Nishihara, Ryo; Suzuki, Koji

    2016-01-01

    Optical imaging of protein-protein interactions (PPIs) facilitates comprehensive elucidation of intracellular molecular events. The present protocol demonstrates an optical measure for visualizing molecular tension triggered by any PPI in mammalian cells. A unique design of single-chain probes was fabricated, in which a full-length artificial luciferase (ALuc(®)) was sandwiched between two model proteins of interest, e.g., FKBP and FRB. A molecular tension probe comprising ALuc23 greatly enhances the bioluminescence in response to varying concentrations of rapamycin, and named "tension probe (TP)." The basic probe design can be further modified towards eliminating the C-terminal end of ALuc and was found to improve signal-to-background ratios, named "combinational probe." TPs may become an important addition to the tool box of bioassays in the determination of protein dynamics of interest in mammalian cells. PMID:27424905

  3. Pump-Probe Noise Spectroscopy of Molecular Junctions.

    PubMed

    Ochoa, Maicol A; Selzer, Yoram; Peskin, Uri; Galperin, Michael

    2015-02-01

    The slow response of electronic components in junctions limits the direct applicability of pump-probe type spectroscopy in assessing the intramolecular dynamics. Recently the possibility of getting information on a sub-picosecond time scale from dc current measurements was proposed. We revisit the idea of picosecond resolution by pump-probe spectroscopy from dc measurements and show that any intramolecular dynamics not directly related to charge transfer in the current direction is missed by current measurements. We propose a pump-probe dc shot noise spectroscopy as a suitable alternative. Numerical examples of time-dependent and average responses of junctions are presented for generic models. PMID:26261965

  4. Probing flexible conformations in molecular junctions by inelastic electron tunneling spectroscopy

    SciTech Connect

    Deng, Mingsen; Ye, Gui; Jiang, Jun; Cai, Shaohong; Sun, Guangyu

    2015-01-15

    The probe of flexible molecular conformation is crucial for the electric application of molecular systems. We have developed a theoretical procedure to analyze the couplings of molecular local vibrations with the electron transportation process, which enables us to evaluate the structural fingerprints of some vibrational modes in the inelastic electron tunneling spectroscopy (IETS). Based on a model molecule of Bis-(4-mercaptophenyl)-ether with a flexible center angle, we have revealed and validated a simple mathematical relationship between IETS signals and molecular angles. Our results might open a route to quantitatively measure key geometrical parameters of molecular junctions, which helps to achieve precise control of molecular devices.

  5. A Molecular Imaging Approach to Mercury Sensing Based on Hyperpolarized (129)Xe Molecular Clamp Probe.

    PubMed

    Guo, Qianni; Zeng, Qingbin; Jiang, Weiping; Zhang, Xiaoxiao; Luo, Qing; Zhang, Xu; Bouchard, Louis-S; Liu, Maili; Zhou, Xin

    2016-03-14

    Mercury pollution, in the form of mercury ions (Hg(2+)), is a major health and environmental hazard. Commonly used sensors are invasive and limited to point measurements. Fluorescence-based sensors do not provide depth resolution needed to image spatial distributions. Herein we report a novel sensor capable of yielding spatial distributions by MRI using hyperpolarized (129)Xe. A molecular clamp probe was developed consisting of dipyrrolylquinoxaline (DPQ) derivatives and twocryptophane-A cages. The DPQ derivatives act as cation receptors whereas cryptophane-A acts as a suitable host molecule for xenon. When the DPQ moiety interacts with mercury ions, the molecular clamp closes on the ion. Due to overlap of the electron clouds of the two cryptophane-A cages, the shielding effect on the encapsulated Xe becomes important. This leads to an upfield change of the chemical shift of the encapsulated Xe. This sensor exhibits good selectivity and sensitivity toward the mercury ion. This mercury-activated hyperpolarized (129)Xe-based chemosensor is a new concept method for monitoring Hg(2+) ion distributions by MRI. PMID:26792102

  6. Targeted and Highly Multiplexed Detection of Microorganisms by Employing an Ensemble of Molecular Probes

    PubMed Central

    Xu, Weihong; Krishnakumar, Sujatha; Miranda, Molly; Jensen, Michael A.; Fukushima, Marilyn; Palm, Curtis; Fung, Eula; Davis, Ronald W.; St.Onge, Robert P.

    2014-01-01

    The vast majority of microscopic life on earth consists of microbes that do not grow in laboratory culture. To profile the microbial diversity in environmental and clinical samples, we have devised and employed molecular probe technology, which detects and identifies bacteria that do and do not grow in culture. The only requirement is a short sequence of contiguous bases (currently 60 bases) unique to the genome of the organism of interest. The procedure is relatively fast, inexpensive, customizable, robust, and culture independent and uses commercially available reagents and instruments. In this communication, we report improving the specificity of the molecular probes substantially and increasing the complexity of the molecular probe set by over an order of magnitude (>1,200 probes) and introduce a new final readout method based upon Illumina sequencing. In addition, we employed molecular probes to identify the bacteria from vaginal swabs and demonstrate how a deliberate selection of molecular probes can identify less abundant bacteria even in the presence of much more abundant species. PMID:24795371

  7. Laser-cooled atomic ions as probes of molecular ions

    SciTech Connect

    Brown, Kenneth R.; Viteri, C. Ricardo; Clark, Craig R.; Goeders, James E.; Khanyile, Ncamiso B.; Vittorini, Grahame D.

    2015-01-22

    Trapped laser-cooled atomic ions are a new tool for understanding cold molecular ions. The atomic ions not only sympathetically cool the molecular ions to millikelvin temperatures, but the bright atomic ion fluorescence can also serve as a detector of both molecular reactions and molecular spectra. We are working towards the detection of single molecular ion spectra by sympathetic heating spectroscopy. Sympathetic heating spectroscopy uses the coupled motion of two trapped ions to measure the spectra of one ion by observing changes in the fluorescence of the other ion. Sympathetic heating spectroscopy is a generalization of quantum logic spectroscopy, but does not require ions in the motional ground state or coherent control of the ion internal states. We have recently demonstrated this technique using two isotopes of Ca{sup +} [Phys. Rev. A, 81, 043428 (2010)]. Limits of the method and potential applications for molecular spectroscopy are discussed.

  8. Semiconducting Polymer Nanoparticles as Photoacoustic Molecular Imaging Probes in Living Mice

    PubMed Central

    Pu, Kanyi; Shuhendler, Adam J.; Jokerst, Jesse V.; Mei, Jianguo; Gambhir, Sanjiv S.; Bao, Zhenan; Rao, Jianghong

    2014-01-01

    Photoacoustic (PA) imaging holds great promise for the visualization of physiology and pathology at the molecular level with deep tissue penetration and fine spatial resolution. To fully utilize this potential, PA molecular imaging probes have to be developed. Herein we introduce near infrared (NIR) light absorbing semiconducting polymer nanoparticles (SPNs) as a new class of contrast agents for PA molecular imaging. SPNs can produce stronger signal than commonly used single-wall carbon nanotubes and gold nanorods on a per mass basis, permitting whole-body lymph node PA mapping in living mice at a low systematic injection mass. Furthermore, SPNs possess high structural flexibility, narrow PA spectral profiles, and strong resistance to photodegradation and oxidation, which enables development of the first NIR ratiometric PA probe for in vivo real-time imaging of reactive oxygen species—vital chemical mediators of many diseases. These results demonstrate SPNs an ideal nanoplatform for developing PA molecular probes. PMID:24463363

  9. Molecular modeling of lipid probes and their influence on the membrane.

    PubMed

    Faller, Roland

    2016-10-01

    In this review a number of Molecular Dynamics simulation studies are discussed which focus on the understanding of the behavior of lipid probes in biomembranes. Experiments often use specialized probe moieties or molecules to report on the behavior of a membrane and try to gain information on the membrane as a whole from the probe lipids as these probes are the only things an experiment sees. Probes can be used to make NMR, EPR and fluorescence accessible to the membrane and use fluorescent or spin-active moieties for this purpose. Clearly membranes with and without probes are not identical which makes it worthwhile to elucidate the differences between them with detailed atomistic simulations. In almost all cases these differences are confined to the local neighborhood of the probe molecules which are sparsely used and generally present as single molecules. In general, the behavior of the bulk membrane lipids can be qualitatively understood from the probes but in most cases their properties cannot be directly quantitatively deduced from the probe behavior. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. PMID:26891817

  10. Molecular probes for nonlinear optical imaging of biological membranes

    NASA Astrophysics Data System (ADS)

    Blanchard-Desce, Mireille H.; Ventelon, Lionel; Charier, Sandrine; Moreaux, Laurent; Mertz, Jerome

    2001-12-01

    Second-harmonic generation (SHG) and two-photon excited fluorescence (TPEF) are nonlinear optical (NLO) phenomena that scale with excitation intensity squared, and hence give rise to an intrinsic 3-dimensional resolution when used in microscopic imaging. TPEF microscopy has gained widespread popularity in the biology community whereas SHG microscopy promises to be a powerful tool because of its sensitivity to local asymmetry. We have implemented an approach toward the design of NLO-probes specifically adapted for SHG and/or TPEF imaging of biological membranes. Our strategy is based on the design of nanoscale amphiphilic NLO-phores. We have prepared symmetrical bolaamphiphilic fluorophores combining very high two-photon absorption (TPA) cross-sections in the visible red region and affinity for cellular membranes. Their incorporation and orientation in lipid membranes can be monitored via TPEF anisotropy. We have also prepared amphiphilic push-pull chromophores exhibiting both large TPA cross-sections and very large first hyperpolarizabilities in the near-IR region. These NLO-probes have proved to be particularly useful for imaging of biological membranes by simultaneous SHG and TPEF microscopy and offer attractive prospects for real-time imaging of fundamental biological processes such as adhesion, fusion or reporting of membrane potentials.

  11. Molecular magnetic resonance probe targeting VEGF165: preparation and in vitro and in vivo evaluation.

    PubMed

    You, Xiao-Guang; Tu, Rong; Peng, Ming-Li; Bai, Yu-Jie; Tan, Mingqian; Li, Han-Jian; Guan, Jing; Wen, Li-Jun

    2014-01-01

    A new method for imaging the tumor human vascular endothelial growth factor 165 (VEGF 165) is presented. A magnetic resonance imaging (MRI) probe was prepared by crosslinking ultrasmall superparamagnetic iron oxide (USPIO) nanoparticles to the aptamer for tumor vascular endothelial growth factor 165 (VEGF165-aptamer). The molecular probe was evaluated for its in vitro and in vivo activities toward VEGF165. Enzyme-linked immunosorbent assay showed that the VEGF165-aptamer-USPIO nanoparticles conjugate specifically binds to VEGF165 in vitro. A cell proliferation test showed that VEGF165-aptamer-USPIO seems to block the proliferation of human umbilical vein endothelial cells induced by free VEGF165, suggesting that VEGF165 is an effective target of this molecular probe. In xenograft mice carrying liver cancer that expresses VEGF165, T2-weighted imaging of the tumor displayed marked negative enhancement 3 h after the intravenous administration of VEGF165-aptamer-USPIO. The enhancement disappeared 6 h after administration of the probe. These results suggest the targeted imaging effect of VEGF165-aptamer-USPIO probe in vivo for VEGF165-expressing tumors. This is the first report of a targeted MRI molecular probe based on USPIO and VEGF165-aptamer. PMID:24729581

  12. Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT.

    PubMed

    Kirmizialtin, Serdal; Hennelly, Scott P; Schug, Alexander; Onuchic, Jose N; Sanbonmatsu, Karissa Y

    2015-01-01

    Integration and calibration of molecular dynamics simulations with experimental data remain a challenging endeavor. We have developed a novel method to integrate chemical probing experiments with molecular simulations of RNA molecules by using a native structure-based model. Selective 2'-hydroxyl acylation by primer extension (SHAPE) characterizes the mobility of each residue in the RNA. Our method, SHAPE-FIT, automatically optimizes the potential parameters of the force field according to measured reactivities from SHAPE. The optimized parameter set allows simulations of dynamics highly consistent with SHAPE probing experiments. Such atomistic simulations, thoroughly grounded in experiment, can open a new window on RNA structure-function relations. PMID:25726467

  13. Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT

    PubMed Central

    Kirmizialtin, Serdal; Hennelly, Scott P.; Schug, Alexander; Onuchic, Jose N.; Sanbonmatsu, Karissa Y.

    2016-01-01

    Integration and calibration of molecular dynamics simulations with experimental data remains a challenging endeavor. We have developed a novel method to integrate chemical probing experiments with molecular simulations of RNA molecules by using a native structure-based model. Selective 2’-hydroxyl acylation by primer extension (SHAPE) characterizes the mobility of each residue in the RNA. Our method, SHAPE-FIT, automatically optimizes the potential parameters of the forcefield according to measured reactivities from SHAPE. The optimized parameter set allows simulations of dynamics highly consistent with SHAPE probing experiments. Such atomistic simulations, thoroughly grounded in experiment, can open a new window on RNA structure-function relations. PMID:25726467

  14. Probing Molecular Dynamics at Attosecond Resolution with Femtosecond Laser Pulses

    NASA Astrophysics Data System (ADS)

    Tong, X. M.; Zhao, Z. X.; Lin, C. D.

    2003-12-01

    The kinetic energy distribution of D+ ions resulting from the interaction of a femtosecond laser pulse with D2 molecules is calculated based on the rescattering model. From analyzing the molecular dynamics, it is shown that the recollision time between the ionized electron and the D+2 ion can be read from the D+ kinetic energy peaks to attosecond accuracy. We further suggest that a more precise reading of the clock can be achieved by using shorter fs laser pulses (about 15fs).

  15. Pre-Assembly of Near-Infrared Fluorescent Multivalent Molecular Probes for Biological Imaging.

    PubMed

    Peck, Evan M; Battles, Paul M; Rice, Douglas R; Roland, Felicia M; Norquest, Kathryn A; Smith, Bradley D

    2016-05-18

    A programmable pre-assembly method is described and shown to produce near-infrared fluorescent molecular probes with tunable multivalent binding properties. The modular assembly process threads one or two copies of a tetralactam macrocycle onto a fluorescent PEGylated squaraine scaffold containing a complementary number of docking stations. Appended to the macrocycle periphery are multiple copies of a ligand that is known to target a biomarker. The structure and high purity of each threaded complex was determined by independent spectrometric methods and also by gel electrophoresis. Especially helpful were diagnostic red-shift and energy transfer features in the absorption and fluorescence spectra. The threaded complexes were found to be effective multivalent molecular probes for fluorescence microscopy and in vivo fluorescence imaging of living subjects. Two multivalent probes were prepared and tested for targeting of bone in mice. A pre-assembled probe with 12 bone-targeting iminodiacetate ligands produced more bone accumulation than an analogous pre-assembled probe with six iminodiacetate ligands. Notably, there was no loss in probe fluorescence at the bone target site after 24 h in the living animal, indicating that the pre-assembled fluorescent probe maintained very high mechanical and chemical stability on the skeletal surface. The study shows how this versatile pre-assembly method can be used in a parallel combinatorial manner to produce libraries of near-infrared fluorescent multivalent molecular probes for different types of imaging and diagnostic applications, with incremental structural changes in the number of targeting groups, linker lengths, linker flexibility, and degree of PEGylation. PMID:27088305

  16. Genetically Encoded Molecular Tension Probe for Tracing Protein-Protein Interactions in Mammalian Cells.

    PubMed

    Kim, Sung Bae; Nishihara, Ryo; Citterio, Daniel; Suzuki, Koji

    2016-02-17

    Optical imaging of protein-protein interactions (PPIs) facilitates comprehensive elucidation of intracellular molecular events. We demonstrate an optical measure for visualizing molecular tension triggered by any PPI in mammalian cells. Twenty-three kinds of candidate designs were fabricated, in which a full-length artificial luciferase (ALuc) was sandwiched between two model proteins of interest, e.g., FKBP and FRB. One of the designs greatly enhanced the bioluminescence in response to varying concentrations of rapamycin. It is confirmed with negative controls that the elevated bioluminescence is solely motivated from the molecular tension. The probe design was further modified toward eliminating the C-terminal end of ALuc and was found to improve signal-to-background ratios, named "a combinational probe". The utilities were elucidated with detailed substrate selectivity, bioluminescence imaging of live cells, and different PPI models. This study expands capabilities of luciferases as a tool for analyses of molecular dynamics and cell signaling in living subjects. PMID:26322739

  17. Quantitative analysis of localized surface plasmons based on molecular probing.

    PubMed

    Deeb, Claire; Bachelot, Renaud; Plain, Jérôme; Baudrion, Anne-Laure; Jradi, Safi; Bouhelier, Alexandre; Soppera, Olivier; Jain, Prashant K; Huang, Libai; Ecoffet, Carole; Balan, Lavinia; Royer, Pascal

    2010-08-24

    We report on the quantitative characterization of the plasmonic optical near-field of a single silver nanoparticle. Our approach relies on nanoscale molecular molding of the confined electromagnetic field by photoactivated molecules. We were able to directly image the dipolar profile of the near-field distribution with a resolution better than 10 nm and to quantify the near-field depth and its enhancement factor. A single nanoparticle spectral signature was also assessed. This quantitative characterization constitutes a prerequisite for developing nanophotonic applications. PMID:20687536

  18. Field-free molecular alignment for probing collisional relaxation dynamics

    NASA Astrophysics Data System (ADS)

    Vieillard, Th.; Chaussard, F.; Billard, F.; Sugny, D.; Faucher, O.; Ivanov, S.; Hartmann, J.-M.; Boulet, C.; Lavorel, B.

    2013-02-01

    We report the experimental study of field-free molecular alignment in CO2 gas mixtures induced by intense femtosecond laser pulses in the presence of collisional processes. We demonstrate that the alignment signals exhibit specific features due to nontrivial collisional propensity rules that tend to preserve the orientation of the rotational angular momentum of the molecules. The analysis is performed with a quantum approach based on the modeling of rotational J- and M-dependent state-to-state transfer rates. The present work paves the way for strong-field spectroscopy of collisional dynamics.

  19. Probing Molecular Dynamics by Laser-Induced Backscattering Holography.

    PubMed

    Haertelt, Marko; Bian, Xue-Bin; Spanner, Michael; Staudte, André; Corkum, Paul B

    2016-04-01

    We use differential holography to overcome the forward scattering problem in strong-field photoelectron holography. Our differential holograms of H_{2} and D_{2} molecules exhibit a fishbonelike structure, which arises from the backscattered part of the recolliding photoelectron wave packet. We demonstrate that the backscattering hologram can resolve the different nuclear dynamics between H_{2} and D_{2} with subangstrom spatial and subcycle temporal resolution. In addition, we show that attosecond electron dynamics can be resolved. These results open a new avenue for ultrafast studies of molecular dynamics in small molecules. PMID:27081975

  20. Probing Molecular Dynamics by Laser-Induced Backscattering Holography

    NASA Astrophysics Data System (ADS)

    Haertelt, Marko; Bian, Xue-Bin; Spanner, Michael; Staudte, André; Corkum, Paul B.

    2016-04-01

    We use differential holography to overcome the forward scattering problem in strong-field photoelectron holography. Our differential holograms of H2 and D2 molecules exhibit a fishbonelike structure, which arises from the backscattered part of the recolliding photoelectron wave packet. We demonstrate that the backscattering hologram can resolve the different nuclear dynamics between H2 and D2 with subangstrom spatial and subcycle temporal resolution. In addition, we show that attosecond electron dynamics can be resolved. These results open a new avenue for ultrafast studies of molecular dynamics in small molecules.

  1. Fiber-optic Raman sensing of cell proliferation probes and molecular vibrations: Brain-imaging perspective

    NASA Astrophysics Data System (ADS)

    Doronina-Amitonova, Lyubov V.; Fedotov, Il'ya V.; Ivashkina, Olga I.; Zots, Marina A.; Fedotov, Andrei B.; Anokhin, Konstantin V.; Zheltikov, Aleksei M.

    2012-09-01

    Optical fibers are employed to sense fingerprint molecular vibrations in ex vivo experiments on the whole brain and detect cell proliferation probes in a model study on a quantitatively controlled solution. A specifically adapted spectral filtering procedure is shown to allow the Raman signal from molecular vibrations of interest to be discriminated against the background from the fiber, allowing a highly sensitive Raman detection of the recently demonstrated EdU (5-ethynyl-2'-deoxyuridine) labels of DNA synthesis in cells.

  2. Photolytic Labeling to Probe Molecular Interactions in Lyophilized Powders

    PubMed Central

    Iyer, Lavanya K.; Moorthy, Balakrishnan S.; Topp, Elizabeth M.

    2014-01-01

    Local side-chain interactions in lyophilized protein formulations were mapped using solid-state photolytic labeling-mass spectrometry (ssPL-MS). Photoactive amino acid analogs (PAAs) were used as probes and either added to the lyophilized matrix or incorporated within the amino acid sequence of a peptide. In the first approach, apomyoglobin was lyophilized with sucrose and varying concentrations of photo-leucine (L-2-amino-4, 4′-azipentanoic acid; pLeu). The lyophilized solid was irradiated at 365 nm to initiate photolabeling. The rate and extent of labeling were measured using ESI-HPLC-MS, with labeling reaching a plateau at ∼ 30 min, forming up to 6 labeled populations. Bottom-up MS/MS analysis was able to provide peptidelevel resolution of the location of pLeu. ssPL-MS was also able to detect differences in side-chain environment between sucrose and guanidine hydrochloride formulations. In the second approach, peptide GCG (1-8)* containing p-benzoyl-L-phenylalanine (pBpA) in the amino acid sequence was lyophilized with various excipients and irradiated. Peptide-peptide and peptide-excipient adducts were detected using MS. Top-down MS/MS on the peptide dimer provided amino acidlevel resolution regarding interactions and the cross-linking partner for pBpA in the solid state. The results show that ssPL-MS can provide high-resolution information about protein interactions in the lyophilized environment. PMID:24125175

  3. Molecular Imaging Probes for Diagnosis and Therapy Evaluation of Breast Cancer

    PubMed Central

    Meng, Qingqing; Li, Zheng

    2013-01-01

    Breast cancer is a major cause of cancer death in women where early detection and accurate assessment of therapy response can improve clinical outcomes. Molecular imaging, which includes PET, SPECT, MRI, and optical modalities, provides noninvasive means of detecting biological processes and molecular events in vivo. Molecular imaging has the potential to enhance our understanding of breast cancer biology and effects of drug action during both preclinical and clinical phases of drug development. This has led to the identification of many molecular imaging probes for key processes in breast cancer. Hormone receptors, growth factor receptor, and angiogenic factors, such as ER, PR, HER2, and VEGFR, have been adopted as imaging targets to detect and stage the breast cancer and to monitor the treatment efficacy. Receptor imaging probes are usually composed of targeting moiety attached to a signaling component such as a radionuclide that can be detected using dedicated instruments. Current molecular imaging probes involved in breast cancer diagnosis and therapy evaluation are reviewed, and future of molecular imaging for the preclinical and clinical is explained. PMID:23533377

  4. Spectroscopic Monitoring of Mechanical Forces during Protein Folding by using Molecular Force Probes.

    PubMed

    Stauch, Tim; Hoffmann, Marvin T; Dreuw, Andreas

    2016-05-18

    Detailed folding pathways of proteins are still largely unknown. Real-time monitoring of mechanical forces acting in proteins during structural transitions would provide deep insights into these highly complex processes. Here, we propose two molecular force probes that can be incorporated into the protein backbone to gain insight into the magnitude and direction of mechanical forces acting in proteins during natural folding and unfolding through their optical spectroscopic response. In fact, changes in the infrared and Raman spectra are proportional to the mechanical force deforming the force probes, and the relevant bands can be intensified and shifted to a transparent window in the protein spectrum by isotopic substitution. As a result, the proposed molecular force probes can act as "force rulers", allowing the spectroscopic observation and measurement of mechanical forces acting within the proteins under natural conditions without external perturbation. PMID:26928925

  5. A Bridge Not Too Far: Linking Disciplines Through Molecular Imaging Probes.

    PubMed

    Valliant, John F

    2016-09-01

    The field of nuclear medicine will rely increasingly on the discovery, proper evaluation, and clinical use of molecular imaging probes and on collaborations. Collaborations will include new initiatives among experts already involved in the field and with researchers, technologists, and clinicians from different areas of science and medicine. This article serves to highlight some of the opportunities in which molecular imaging and nuclear medicine in conjunction with probe development, new imaging technologies, and multidisciplinary collaborations can have a significant impact on health care and basic science from the perspective of a person involved in probe development. The article emphasizes breast cancer, but the concepts are readily applied to other areas of medicine and medical research. PMID:27601414

  6. Molecular Dynamic Simulations of Interaction of an AFM Probe with the Surface of an SCN Sample

    NASA Technical Reports Server (NTRS)

    Bune, Adris; Kaukler, William; Rose, M. Franklin (Technical Monitor)

    2001-01-01

    Molecular dynamic (MD) simulations is conducted in order to estimate forces of probe-substrate interaction in the Atomic Force Microscope (AFM). First a review of available molecular dynamic techniques is given. Implementation of MD simulation is based on an object-oriented code developed at the University of Delft. Modeling of the sample material - succinonitrile (SCN) - is based on the Lennard-Jones potentials. For the polystyrene probe an atomic interaction potential is used. Due to object-oriented structure of the code modification of an atomic interaction potential is straight forward. Calculation of melting temperature is used for validation of the code and of the interaction potentials. Various fitting parameters of the probe-substrate interaction potentials are considered, as potentials fitted to certain properties and temperature ranges may not be reliable for the others. This research provides theoretical foundation for an interpretation of actual measurements of an interaction forces using AFM.

  7. A Molecularly Targeted Theranostic Probe for Ovarian Cancer

    PubMed Central

    Chen, Wenxue; Bardhan, Rizia; Bartels, Marc; Perez-Torres, Carlos; Pautler, Robia G.; Halas, Naomi J.; Joshi, Amit

    2014-01-01

    Overexpression of the human epidermal growth factor receptor (HER) family has been implicated in ovarian cancer because of its participation in signaling pathway regulating cellular proliferation, differentiation, motility, and survival. Currently, effective diagnostic and therapeutic schemes are lacking for treating ovarian cancer and consequently ovarian cancer has a high mortality rate. While HER2 receptor expression does not usually affect the survival rates of ovarian cancer to the same extent as in breast cancer, it can be employed as a docking site for directed nanotherapies in cases with de novo or acquired chemotherapy resistance. In this study, we have exploited a novel gold nanoshell-based complex (nanocomplex) for targeting, dual modal imaging, and photothermal therapy of HER2 overexpressing and drug resistant ovarian cancer OVCAR3 cells in vitro. The nanocomplexes are engineered to simultaneously provide contrast as fluorescence optical imaging probe and a magnetic resonance imaging (MRI) agent. Both immunofluorescence staining and MRI successfully demonstrate that nanocomplex-anti-HER2 conjugates specifically bind to OVCAR3 cells as opposed to the control, MDA-MB-231 cells, which have low HER2 expression. In addition, nanocomplexes targeted to OVCAR3 cells, when irradiated with near infrared (NIR) laser result in selective destruction of cancer cells through photothermal ablation. We also demonstrate that NIR light therapy and the nanocomplexes by themselves are non-cytotoxic in vitro. To the best of our knowledge, this is the first demonstration of a successful integration of dual modal bioimaging with photothermal cancer therapy for treatment of ovarian cancer. Based on their efficacy in vitro, these nanocomplexes are highly promising for image guided photo-thermal therapy of ovarian cancer as well as other HER2 overexpressing cancers. PMID:20371708

  8. NEAR-INFRARED DYES: Probe Development and Applications in Optical Molecular Imaging

    PubMed Central

    Nolting, Donald D.; Gore, John C.; Pham, Wellington

    2010-01-01

    The recent emergence of optical imaging has brought forth a unique challenge for chemists: development of new biocompatible dyes that fluoresce in the near-infrared (NIR) region for optimal use in biomedical applications. This review describes the synthesis of NIR dyes and the design of probes capable of noninvasively imaging molecular events in small animal models. PMID:21822405

  9. Optical signaling in biofluids: a nondenaturing photostable molecular probe for serum albumins.

    PubMed

    Dey, Gourab; Gaur, Pankaj; Giri, Rajanish; Ghosh, Subrata

    2016-01-31

    The systematic investigation of the interaction of a new class of molecular materials with proteins through structure-optical signaling relationship studies has led to the development of efficient fluorescent probes that can detect and quantify serum albumins in biofluids without causing any denaturation. PMID:26675447

  10. Viroids and Phloem-limited Viruses: Unique Molecular Probes of Phloem Biology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Viroids and phloem-limited viruses are intracellular parasites move systemically in host plant phloem.These features make them unique molecular probes to discover mechanisms of phloem long-distance movement. In this chapter, we describe current knowledge of long-distance movement and proteins facili...

  11. Force probing cell shape changes to molecular resolution.

    PubMed

    Stewart, Martin P; Toyoda, Yusuke; Hyman, Anthony A; Muller, Daniel J

    2011-08-01

    Atomic force microscopy (AFM) is a force sensing nanoscopic tool that can be used to undertake a multiscale approach to understand the mechanisms that underlie cell shape change, ranging from the cellular to molecular scale. In this review paper, we discuss the use of AFM to characterize the dramatic shape changes of mitotic cells. AFM-based mechanical assays can be applied to measure the considerable rounding force and hydrostatic pressure generated by mitotic cells. A complementary AFM technique, single-molecule force spectroscopy, is able to quantify the interactions and mechanisms that functionally regulate individual proteins. Future developments of these nanomechanical methods, together with advances in light microscopy imaging and cell biological and genetic tools, should provide further insight into the biochemical, cellular and mechanical processes that govern mitosis and other cell shape change phenomena. PMID:21646023

  12. Probing the chemistry of molecular heterojunctions using thermoelectricity.

    PubMed

    Baheti, Kanhayalal; Malen, Jonathan A; Doak, Peter; Reddy, Pramod; Jang, Sung-Yeon; Tilley, T Don; Majumdar, Arun; Segalman, Rachel A

    2008-02-01

    Thermopower measurements offer an alternative transport measurement that can characterize the dominant transport orbital and is independent of the number of molecules in the junction. This method is now used to explore the effect of chemical structure on the electronic structure and charge transport. We interrogate junctions, using a modified scanning tunneling microscope break junction technique, where: (i) the 1,4-benzenedithiol (BDT) molecule has been modified by the addition of electron-withdrawing or -donating groups such as fluorine, chlorine, and methyl on the benzene ring; and (ii) the thiol end groups on BDT have been replaced by the cyanide end groups. Cyanide end groups were found to radically change transport relative to BDT such that transport is dominated by the lowest unoccupied molecular orbital in 1,4-benzenedicyanide, while substituents on BDT generated small and predictable changes in transmission. PMID:18269258

  13. Molecular modeling of enzyme attachment on AFM probes.

    PubMed

    Oliveira, Guedmiller S; Leite, Fabio L; Amarante, Adriano M; Franca, Eduardo F; Cunha, Richard A; Briggs, James M; Freitas, Luiz C G

    2013-09-01

    The immobilization of enzymes on atomic force microscope tip (AFM tip) surface is a crucial step in the development of nanobiosensors to be used in detection process. In this work, an atomistic modeling of the attachment of the acetyl coenzyme A carboxylase (ACC enzyme) on a functionalized AFM tip surface is proposed. Using electrostatic considerations, suitable enzyme-surface orientations with the active sites of the ACC enzyme available for interactions with bulk molecules were found. A 50 ns molecular dynamics trajectory in aqueous solution was obtained and surface contact area, hydrogen bonding and protein stability were analyzed. The enzyme-surface model proposed here with minor adjustment can be applied to study antigen-antibody interactions as well as enzyme immobilization on silica for chromatography applications. PMID:24029365

  14. Molecular Surface Sampling and Chemical Imaging using Proximal Probe Thermal Desorption/Secondary Ionization Mass Spectrometry

    SciTech Connect

    Ovchinnikova, Olga S; Kertesz, Vilmos; Van Berkel, Gary J

    2011-01-01

    Proximal probe thermal desorption/secondary ionization mass spectrometry was studied and applied to molecular surface sampling and chemical imaging using printed patterns on photopaper as test substrates. With the use of a circular cross section proximal probe with a tip diameter of 50 m and fixed temperature (350 C), the influence of probe-to-surface distance, lane scan spacing, and surface scan speed on signal quality and spatial resolution were studied and optimized. As a compromise between signal amplitude, signal reproducibility, and data acquisition time, a surface scan speed of 100 m/s, probe-to-paper surface distance of 5 m, and lane spacing of 10 m were used for imaging. Under those conditions the proximal probe thermal desorption/secondary ionization mass spectrometry method was able to achieve a spatial resolution of about 50 m as determined by the ability to distinguish surface patterns of known dimensions that were printed on the paper substrate. It is expected that spatial resolution and chemical image quality could be further improved by using probes of smaller cross section size and by incorporating a means to maintain a fixed optimal probe-to-surface distance real time, continuously adapting to the changing topography of the surface during a lane scan.

  15. Target-protecting dumbbell molecular probe against exonucleases digestion for sensitive detection of ATP and streptavidin.

    PubMed

    Chen, Jinyang; Liu, Yucheng; Ji, Xinghu; He, Zhike

    2016-09-15

    In this work, a versatile dumbbell molecular (DM) probe was designed and employed in the sensitively homogeneous bioassay. In the presence of target molecule, the DM probe was protected from the digestion of exonucleases. Subsequently, the protected DM probe specifically bound to the intercalation dye and resulted in obvious fluorescence signal which was used to determine the target molecule in return. This design allows specific and versatile detection of diverse targets with easy operation and no sophisticated fluorescence labeling. Integrating the idea of target-protecting DM probe with adenosine triphosphate (ATP) involved ligation reaction, the DM probe with 5'-end phosphorylation was successfully constructed for ATP detection, and the limitation of detection was found to be 4.8 pM. Thanks to its excellent selectivity and sensitivity, this sensing strategy was used to detect ATP spiked in human serum as well as cellular ATP. Moreover, the proposed strategy was also applied in the visual detection of ATP in droplet-based microfluidic platform with satisfactory results. Similarly, combining the principle of target-protecting DM probe with streptavidin (SA)-biotin interaction, the DM probe with 3'-end biotinylation was developed for selective and sensitive SA determination, which demonstrated the robustness and versatility of this design. PMID:27131994

  16. Probing voltage induced bond rupture in a molecular junction

    NASA Astrophysics Data System (ADS)

    Li, Haixing; Su, Timothy; Kim, Nathaniel; Darancet, Pierre; Leighton, James; Steigerwald, Michael; Nuckolls, Colin; Venkataraman, Latha

    We use scanning tunneling microscope break junction to study electric field breakdown at the single molecule level. We investigate breakdown phenomena in atomic chains composed of Si--Si, Si--O, Si--C, Ge--Ge and C--C bonds that are commonly found in the low- κ dielectric material. We see different bond rupture behaviors in a range of molecular backbones, and use the results from a statistically large number of measurements to determine which bond breaks. We find that Si--Si and Ge--Ge bonds rupture above a 1V bias. We also find that the Si--C bond is more robust than Si--O or Si--Si bond at above 1V. Finally, we illustrate how an additional conductance pathway in parallel to the Si--Si bond changes bond rupture behavior under an electric field. We carry out ab initio calculations on these systems and demonstrate that the mechanism for bond rupture under electric field involves ``heating'' of the molecule through electron-vibrational mode coupling. Haixing Li is supported by Semiconductor Research Corporation and New York CAIST program. We thank the NSF for the support of these studies under Grant No. CHE-1404922.

  17. A targeted molecular probe for colorectal cancer imaging

    NASA Astrophysics Data System (ADS)

    Attramadal, T.; Bjerke, R.; Indrevoll, B.; Moestue, S.; Rogstad, A.; Bendiksen, R.; Healey, A.; Johannesen, E.

    2008-02-01

    Colorectal cancer is a major cause of cancer death. Morbidity, mortality and healthcare costs can be reduced if the disease can be detected at an early stage. Screening is a viable approach as there is a clear link to risk factors such as age. We have developed a fluorescent contrast agent for use during colonoscopy. The agent is administered intravenously and is targeted to an early stage molecular marker for colorectal cancer. The agent consists of a targeting section comprising a peptide, and a fluorescent reporter molecule. Clinical imaging of the agent is to be performed with a far red fluorescence imaging channel (635 nm excitation/660-700 nm emission) as an adjunct to white light colonoscopy. Preclinical proof of mechanism results are presented. The compound has a K d of ~3nM. Two human xenograft tumour models were used. Tumour cells were implanted and grown subcutaneously in nude mice. Imaging using a fluorescence reflectance imaging system and quantitative biodistribution studies were performed. Substances tested include the targeted agent, and a scrambled sequence of the peptide (no binding) used as a negative control. Competition studies were also performed by co-administration of 180 times excess unlabelled peptide. Positive imaging contrast was shown in the tumours, with a clear relationship to expression levels (confirmed with quantitative biodistribution data). There was a significant difference between the positive and negative control substances, and a significant reduction in contrast in the competition experiment.

  18. Molecular Imaging Probes for Positron Emission Tomography and Optical Imaging of Sentinel Lymph Node and Tumor

    NASA Astrophysics Data System (ADS)

    Qin, Zhengtao

    Molecular imaging is visualizations and measurements of in vivo biological processes at the molecular or cellular level using specific imaging probes. As an emerging technology, biocompatible macromolecular or nanoparticle based targeted imaging probes have gained increasing popularities. Those complexes consist of a carrier, an imaging reporter, and a targeting ligand. The active targeting ability dramatically increases the specificity. And the multivalency effect may further reduce the dose while providing a decent signal. In this thesis, sentinel lymph node (SLN) mapping and cancer imaging are two research topics. The focus is to develop molecular imaging probes with high specificity and sensitivity, for Positron Emission Tomography (PET) and optical imaging. The objective of this thesis is to explore dextran radiopharmaceuticals and porous silicon nanoparticles based molecular imaging agents. Dextran polymers are excellent carriers to deliver imaging reporters or therapeutic agents due to its well established safety profile and oligosaccharide conjugation chemistry. There is also a wide selection of dextran polymers with different lengths. On the other hand, Silicon nanoparticles represent another class of biodegradable materials for imaging and drug delivery. The success in fluorescence lifetime imaging and enhancements of the immune activation potency was briefly discussed. Chapter 1 begins with an overview on current molecular imaging techniques and imaging probes. Chapter 2 presents a near-IR dye conjugated probe, IRDye 800CW-tilmanocept. Fluorophore density was optimized to generate the maximum brightness. It was labeled with 68Ga and 99mTc and in vivo SLN mapping was successfully performed in different animals, such as mice, rabbits, dogs and pigs. With 99mTc labeled IRDye 800CW-tilmanocept, chapter 3 introduces a two-day imaging protocol with a hand-held imager. Chapter 4 proposed a method to dual radiolabel the IRDye 800CW-tilmanocept with both 68Ga and

  19. Charge transport in molecular junctions: From tunneling to hopping with the probe technique

    SciTech Connect

    Kilgour, Michael; Segal, Dvira

    2015-07-14

    We demonstrate that a simple phenomenological approach can be used to simulate electronic conduction in molecular wires under thermal effects induced by the surrounding environment. This “Landauer-Büttiker’s probe technique” can properly replicate different transport mechanisms, phase coherent nonresonant tunneling, ballistic behavior, and hopping conduction. Specifically, our simulations with the probe method recover the following central characteristics of charge transfer in molecular wires: (i) the electrical conductance of short wires falls off exponentially with molecular length, a manifestation of the tunneling (superexchange) mechanism. Hopping dynamics overtakes superexchange in long wires demonstrating an ohmic-like behavior. (ii) In off-resonance situations, weak dephasing effects facilitate charge transfer, but under large dephasing, the electrical conductance is suppressed. (iii) At high enough temperatures, k{sub B}T/ϵ{sub B} > 1/25, with ϵ{sub B} as the molecular-barrier height, the current is enhanced by a thermal activation (Arrhenius) factor. However, this enhancement takes place for both coherent and incoherent electrons and it does not readily indicate on the underlying mechanism. (iv) At finite-bias, dephasing effects may impede conduction in resonant situations. We further show that memory (non-Markovian) effects can be implemented within the Landauer-Büttiker’s probe technique to model the interaction of electrons with a structured environment. Finally, we examine experimental results of electron transfer in conjugated molecular wires and show that our computational approach can reasonably reproduce reported values to provide mechanistic information.

  20. Charge transport in molecular junctions: From tunneling to hopping with the probe technique

    NASA Astrophysics Data System (ADS)

    Kilgour, Michael; Segal, Dvira

    2015-07-01

    We demonstrate that a simple phenomenological approach can be used to simulate electronic conduction in molecular wires under thermal effects induced by the surrounding environment. This "Landauer-Büttiker's probe technique" can properly replicate different transport mechanisms, phase coherent nonresonant tunneling, ballistic behavior, and hopping conduction. Specifically, our simulations with the probe method recover the following central characteristics of charge transfer in molecular wires: (i) the electrical conductance of short wires falls off exponentially with molecular length, a manifestation of the tunneling (superexchange) mechanism. Hopping dynamics overtakes superexchange in long wires demonstrating an ohmic-like behavior. (ii) In off-resonance situations, weak dephasing effects facilitate charge transfer, but under large dephasing, the electrical conductance is suppressed. (iii) At high enough temperatures, kBT/ɛB > 1/25, with ɛB as the molecular-barrier height, the current is enhanced by a thermal activation (Arrhenius) factor. However, this enhancement takes place for both coherent and incoherent electrons and it does not readily indicate on the underlying mechanism. (iv) At finite-bias, dephasing effects may impede conduction in resonant situations. We further show that memory (non-Markovian) effects can be implemented within the Landauer-Büttiker's probe technique to model the interaction of electrons with a structured environment. Finally, we examine experimental results of electron transfer in conjugated molecular wires and show that our computational approach can reasonably reproduce reported values to provide mechanistic information.

  1. Exogenous Molecular Probes for Targeted Imaging in Cancer: Focus on Multi-modal Imaging

    PubMed Central

    Joshi, Bishnu P.; Wang, Thomas D.

    2010-01-01

    Cancer is one of the major causes of mortality and morbidity in our healthcare system. Molecular imaging is an emerging methodology for the early detection of cancer, guidance of therapy, and monitoring of response. The development of new instruments and exogenous molecular probes that can be labeled for multi-modality imaging is critical to this process. Today, molecular imaging is at a crossroad, and new targeted imaging agents are expected to broadly expand our ability to detect and manage cancer. This integrated imaging strategy will permit clinicians to not only localize lesions within the body but also to manage their therapy by visualizing the expression and activity of specific molecules. This information is expected to have a major impact on drug development and understanding of basic cancer biology. At this time, a number of molecular probes have been developed by conjugating various labels to affinity ligands for targeting in different imaging modalities. This review will describe the current status of exogenous molecular probes for optical, scintigraphic, MRI and ultrasound imaging platforms. Furthermore, we will also shed light on how these techniques can be used synergistically in multi-modal platforms and how these techniques are being employed in current research. PMID:22180839

  2. Molecularly resolved label-free sensing of single nucleobase mismatches by interfacial LNA probes.

    PubMed

    Mishra, Sourav; Lahiri, Hiya; Banerjee, Siddhartha; Mukhopadhyay, Rupa

    2016-05-01

    So far, there has been no report on molecularly resolved discrimination of single nucleobase mismatches using surface-confined single stranded locked nucleic acid (ssLNA) probes. Herein, it is exemplified using a label-independent force-sensing approach that an optimal coverage of 12-mer ssLNA sensor probes formed onto gold(111) surface allows recognition of ssDNA targets with twice stronger force sensitivity than 12-mer ssDNA sensor probes. The force distributions are reproducible and the molecule-by-molecule force measurements are largely in agreement with ensemble on-surface melting temperature data. Importantly, the molecularly resolved detection is responsive to the presence of single nucleobase mismatches in target sequences. Since the labelling steps can be eliminated from protocol, and each force-based detection event occurs within milliseconds' time scale, the force-sensing assay is potentially capable of rapid detection. The LNA probe performance is indicative of versatility in terms of substrate choice - be it gold (for basic research and array-based applications) or silicon (for 'lab-on-a-chip' type devices). The nucleic acid microarray technologies could therefore be generally benefited by adopting the LNA films, in place of DNA. Since LNA is nuclease-resistant, unlike DNA, and the LNA-based assay is sensitive to single nucleobase mismatches, the possibilities for label-free in vitro rapid diagnostics based on the LNA probes may be explored. PMID:27025649

  3. Molecularly resolved label-free sensing of single nucleobase mismatches by interfacial LNA probes

    PubMed Central

    Mishra, Sourav; Lahiri, Hiya; Banerjee, Siddhartha; Mukhopadhyay, Rupa

    2016-01-01

    So far, there has been no report on molecularly resolved discrimination of single nucleobase mismatches using surface-confined single stranded locked nucleic acid (ssLNA) probes. Herein, it is exemplified using a label-independent force-sensing approach that an optimal coverage of 12-mer ssLNA sensor probes formed onto gold(111) surface allows recognition of ssDNA targets with twice stronger force sensitivity than 12-mer ssDNA sensor probes. The force distributions are reproducible and the molecule-by-molecule force measurements are largely in agreement with ensemble on-surface melting temperature data. Importantly, the molecularly resolved detection is responsive to the presence of single nucleobase mismatches in target sequences. Since the labelling steps can be eliminated from protocol, and each force-based detection event occurs within milliseconds' time scale, the force-sensing assay is potentially capable of rapid detection. The LNA probe performance is indicative of versatility in terms of substrate choice - be it gold (for basic research and array-based applications) or silicon (for ‘lab-on-a-chip’ type devices). The nucleic acid microarray technologies could therefore be generally benefited by adopting the LNA films, in place of DNA. Since LNA is nuclease-resistant, unlike DNA, and the LNA-based assay is sensitive to single nucleobase mismatches, the possibilities for label-free in vitro rapid diagnostics based on the LNA probes may be explored. PMID:27025649

  4. Laser Probing of Molecular Beam Epitaxy on SILICON(100) Surface.

    NASA Astrophysics Data System (ADS)

    Smilgys, Russell Victor

    The work presented here investigates the desorption kinetics of Ga and In from films of Ga, In, GaAs, and InAs on Si(100). Films a few monolayers (ML) thick are deposited from molecular beams under ultrahigh vacuum conditions. Laser induced fluorescence (LIF) is used to detect Ga and In in the gas phase. Using the techniques of temperature programmed desorption and isothermal desorption the desorption kinetics of each species are measured. The variation in the kinetic order and rate constant with temperature and coverage reflect the morphology and energetics of the film growth. Individually, Ga, In, and As each interact strongly with Si(100) at low coverages to form a two dimensional film. Above 1 ML for Ga and {1over2 } ML for In three dimensional islands form. For temperatures above 550 K, As coverage saturates at 1 ML. When As is codeposited with either Ga or In, As occupies the interfacial sites bound to Si. Ga and In atoms form three dimensional islands on top of the two dimensional As film. When the As coverage is below 1 ML, Ga and As strongly interact, probably to form a GaAs structure. Under the same conditions no comparable InAs structure is evident. The much larger lattice mismatch between InAs and Si(100) is proposed to explain this difference. The desorption kinetics and dynamics of the interfacial As film are also investigated. To measure As_2 desorption rates and vibrational populations, LIF detection of As_2 is developed. A result is that As_4 dissociates on Si(100) to yield chemisorbed As atoms. During desorption As atoms recombine to yield As_2. The vibrational populations of desorbed As_2 suggest a direct desorption mechanism in which the directionality of the covalent bonding to the substrate strongly influences the dynamics. To expand the detection capabilities to species not readily detected by LIF, a time-of-flight mass spectrometer is built. In the first studies nonresonant multiphoton ionization is used. As_4 is detected using 266 nm

  5. Picosecond Transient Photoconductivity in Functionalized Pentacene Molecular Crystals Probed by Terahertz Pulse Spectroscopy

    NASA Astrophysics Data System (ADS)

    Hegmann, F. A.; Tykwinski, R. R.; Lui, K. P.; Bullock, J. E.; Anthony, J. E.

    2002-11-01

    We have measured transient photoconductivity in functionalized pentacene molecular crystals using ultrafast optical pump-terahertz probe techniques. The single crystal samples were excited using 800nm, 100fs pulses, and the change in transmission of time-delayed, subpicosecond terahertz pulses was used to probe the photoconducting state over a temperature range from 10 to 300K. A subpicosecond rise in photoconductivity is observed, suggesting that mobile carriers are a primary photoexcitation. At times longer than 4ps, a power-law decay is observed consistent with dispersive transport.

  6. Boronate Affinity-Molecularly Imprinted Biocompatible Probe: An Alternative for Specific Glucose Monitoring.

    PubMed

    Chen, Guosheng; Qiu, Junlang; Fang, Xu'an; Xu, Jianqiao; Cai, Siying; Chen, Qing; Liu, Yan; Zhu, Fang; Ouyang, Gangfeng

    2016-08-19

    A biocompatible probe for specific glucose recognition is based on photoinitiated boronate affinity-molecular imprinted polymers (BA-MIPs). The unique pre-self-assembly between glucose and boronic acids creates glucose-specific memory cavities in the BA-MIPs coating. As a result, the binding constant toward glucose was enhanced by three orders of magnitude. The BA-MIPs probe was applied to glucose determination in serum and urine and implanted into plant tissues for low-destructive and long-term in vivo continuous glucose monitoring. PMID:27411946

  7. Probing the structure of metal-substituted molecular sieves by solid-state NMR

    SciTech Connect

    Labouriau, A.; Crawford, S.N.; Ott, K.; Earl, W.L.

    1998-08-01

    Paramagnetic metal ions exert large influences on the NMR spectra of neighboring nuclei. The authors are using these effects to probe metal sites in zeolites and AlPO{sub 4} molecular sieves. In particular, they are studying [Co]-AlPO{sub 4}-5 because similar cobalt substituted AlPO{sub 4} sieves are reported in the literature. They have extended that work to probe the titanium zeolite TS-1 by comparing spectra of normal TS-1 to samples where the titanium has been reduced to the paramagnetic Ti{sup 3+}. This promises to be a useful technique for determining framework substitution in many zeolite systems.

  8. New hairpin-structured DNA probes: alternatives to classical molecular beacons

    NASA Astrophysics Data System (ADS)

    Friedrich, Achim; Habl, Gregor; Sauer, Markus; Wolfrum, Jürgen; Hoheisel, Jörg; Marmé, Nicole; Knemeyer, Jens-Peter

    2007-02-01

    In this article we report on two different classes of self-quenching hairpin-structured DNA probes that can be used as alternatives to Molecular Beacons. Compared to other hairpin-structured DNA probes, the so-called smart probes are labeled with only one extrinsic dye. The fluorescence of this dye is efficiently quenched by intrinsic guanine bases via a photo-induced electron transfer reaction in the closed hairpin. After hybridization to a target DNA, the distance between dye and the guanines is enlarged and the fluorescence is restored. The working mechanism of the second class of hairpin DNA probes is similar, but the probe oligonucleotide is labeled at both ends with an identical chromophore and thus the fluorescence of the closed hairpin is reduced due to formation of non-fluorescent dye dimers. Both types of probes are appropriate for the identification of single nucleotide polymorphisms and in combination with confocal single-molecule spectroscopy sensitivities in the picomolar range can be achieved.

  9. Semiconducting polymer nanoparticles as photoacoustic molecular imaging probes in living mice

    NASA Astrophysics Data System (ADS)

    Pu, Kanyi; Shuhendler, Adam J.; Jokerst, Jesse V.; Mei, Jianguo; Gambhir, Sanjiv S.; Bao, Zhenan; Rao, Jianghong

    2014-03-01

    Photoacoustic imaging holds great promise for the visualization of physiology and pathology at the molecular level with deep tissue penetration and fine spatial resolution. To fully utilize this potential, photoacoustic molecular imaging probes have to be developed. Here, we introduce near-infrared light absorbing semiconducting polymer nanoparticles as a new class of contrast agents for photoacoustic molecular imaging. These nanoparticles can produce a stronger signal than the commonly used single-walled carbon nanotubes and gold nanorods on a per mass basis, permitting whole-body lymph-node photoacoustic mapping in living mice at a low systemic injection mass. Furthermore, the semiconducting polymer nanoparticles possess high structural flexibility, narrow photoacoustic spectral profiles and strong resistance to photodegradation and oxidation, enabling the development of the first near-infrared ratiometric photoacoustic probe for in vivo real-time imaging of reactive oxygen species--vital chemical mediators of many diseases. These results demonstrate semiconducting polymer nanoparticles to be an ideal nanoplatform for developing photoacoustic molecular probes.

  10. Semiconducting polymer nanoparticles as photoacoustic molecular imaging probes in living mice.

    PubMed

    Pu, Kanyi; Shuhendler, Adam J; Jokerst, Jesse V; Mei, Jianguo; Gambhir, Sanjiv S; Bao, Zhenan; Rao, Jianghong

    2014-03-01

    Photoacoustic imaging holds great promise for the visualization of physiology and pathology at the molecular level with deep tissue penetration and fine spatial resolution. To fully utilize this potential, photoacoustic molecular imaging probes have to be developed. Here, we introduce near-infrared light absorbing semiconducting polymer nanoparticles as a new class of contrast agents for photoacoustic molecular imaging. These nanoparticles can produce a stronger signal than the commonly used single-walled carbon nanotubes and gold nanorods on a per mass basis, permitting whole-body lymph-node photoacoustic mapping in living mice at a low systemic injection mass. Furthermore, the semiconducting polymer nanoparticles possess high structural flexibility, narrow photoacoustic spectral profiles and strong resistance to photodegradation and oxidation, enabling the development of the first near-infrared ratiometric photoacoustic probe for in vivo real-time imaging of reactive oxygen species--vital chemical mediators of many diseases. These results demonstrate semiconducting polymer nanoparticles to be an ideal nanoplatform for developing photoacoustic molecular probes. PMID:24463363

  11. Bioengineered Probes for Molecular Magnetic Resonance Imaging in the Nervous System

    PubMed Central

    2012-01-01

    The development of molecular imaging probes has changed the nature of neurobiological research. Some of the most notable successes have involved the use of biological engineering techniques for the creation of fluorescent protein derivatives for optical imaging, but recent work has also led to a number of bioengineered probes for magnetic resonance imaging (MRI), the preeminent technique for noninvasive investigation of brain structure and function. Molecular MRI agents are beginning to be applied for experiments in the nervous system, where they have the potential to bridge from molecular to systems or organismic levels of analysis. Compared with canonical synthetic small molecule agents, biomolecular or semibiosynthetic MRI contrast agents offer special advantages due to their amenability to molecular engineering approaches, their properties in some cases as catalysts, and their specificity in targeting and ligand binding. Here, we discuss an expanding list of instances where biological engineering techniques have aided in the design of MRI contrast agents and reporter systems, examining both advantages and limitations of these types of probes for studies in the central nervous system. PMID:22896803

  12. Strained cyclooctyne as a molecular platform for construction of multimodal imaging probes.

    PubMed

    Sun, Yao; Ma, Xiaowei; Cheng, Kai; Wu, Biying; Duan, Jianli; Chen, Hao; Bu, Lihong; Zhang, Ruiping; Hu, Xianming; Deng, Zixin; Xing, Lei; Hong, Xuechuan; Cheng, Zhen

    2015-05-11

    Small-molecule-based multimodal and multifunctional imaging probes play prominent roles in biomedical research and have high clinical translation ability. A novel multimodal imaging platform using base-catalyzed double addition of thiols to a strained internal alkyne such as bicyclo[6.1.0]nonyne has been established in this study, thus allowing highly selective assembly of various functional units in a protecting-group-free manner. Using this molecular platform, novel dual-modality (PET and NIRF) uPAR-targeted imaging probe: (64)Cu-CHS1 was prepared and evaluated in U87MG cells and tumor-bearing mice models. The excellent PET/NIRF imaging characteristics such as good tumor uptake (3.69%ID/g at 2 h post-injection), high tumor contrast, and specificity were achieved in the small-animal models. These attractive imaging properties make (64)Cu-CHS1 a promising probe for clinical use. PMID:25800807

  13. Protein rotational dynamics investigated with a dual EPR/optical molecular probe. Spin-labeled eosin.

    PubMed Central

    Cobb, C E; Hustedt, E J; Beechem, J M; Beth, A H

    1993-01-01

    An acyl spin-label derivative of 5-aminoeosin (5-SLE) was chemically synthesized and employed in studies of rotational dynamics of the free probe and of the probe when bound noncovalently to bovine serum albumin using the spectroscopic techniques of fluorescence anisotropy decay and electron paramagnetic resonance (EPR) and their long-lifetime counterparts phosphorescence anisotropy decay and saturation transfer EPR. Previous work (Beth, A. H., Cobb, C. E., and J. M. Beechem, 1992. Synthesis and characterization of a combined fluorescence, phosphorescence, and electron paramagnetic resonance probe. Society of Photo-Optical Instrumentation Engineers. Time-Resolved Laser Spectroscopy III. 504-512) has shown that the spin-label moiety only slightly altered the fluorescence and phosphorescence lifetimes and quantum yields of 5-SLE when compared with 5-SLE whose nitroxide had been reduced with ascorbate and with the diamagnetic homolog 5-acetyleosin. In the present work, we have utilized time-resolved fluorescence anisotropy decay and linear EPR spectroscopies to observe and quantitate the psec motions of 5-SLE in solution and the nsec motions of the 5-SLE-bovine serum albumin complex. Time-resolved phosphorescence anisotropy decay and saturation transfer EPR studies have been carried out to observe and quantitate the microseconds motions of the 5-SLE-albumin complex in glycerol/buffer solutions of varying viscosity. These latter studies have enabled a rigorous comparison of rotational correlation times obtained from these complementary techniques to be made with a single probe. The studies described demonstrate that it is possible to employ a single molecular probe to carry out the full range of fluorescence, phosphorescence, EPR, and saturation transfer EPR studies. It is anticipated that "dual" molecular probes of this general type will significantly enhance capabilities for extracting dynamics and structural information from macromolecules and their functional

  14. Advances of molecular imaging probes for the diagnosis of Alzheimer's disease.

    PubMed

    Zhou, Ming; Wang, Xiaobo; Liu, Zhiguo; Yu, Lun; Hu, Shuo; Chen, Lizhang; Zeng, Wenbin

    2014-03-01

    Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive decline in multiple cognitive domains and it becomes the most common cause of dementia in the elderly. There is an urgent need for the early diagnosis and treatment of AD to ease caregiver burden and medical costs, as well as improve patients' living activities associated with the dramatic increasing number of affected individuals. Molecular imaging with target-specific probes is contributing to identify the underlying biology in AD, which benefits to the early diagnosis of AD and the evaluation of anti-AD therapy. Molecular imaging probes, such as (11)C-PIB, (11)C-MP4A, (18)F-AV-45, and (11)F-FDG, can selectively bind to special bimolecular of AD or accurately accumulate at the location of damage areas, thus become an edge tool for a better management of the diseases in the clinical practice and new drug development. In the past decades, a large variety of probes is being developed and tested to be useful for the early and accurate diagnosis of Alzheimer's disease, patient selection for disease-modifying therapeutic trials and monitoring the effect of anti-amyloid therapy. Since imaging probes may also help to guide physicians to identify those patients that could best benefit from a given therapeutic regimen, dose, or duration of drug, this paper is to present a perspective of the available imaging probes for AD, classified on different modalities. Meanwhile, recent advances of those probes that have been selected for clinical trials and are at the different stages of the US Food and Drugs Administration (FDA) approval are outlined. Additionally, future directions and specific application of imaging strategies designed for both diagnosis and treatment for AD are discussed. PMID:24484277

  15. DNA hybridization in nanostructural molecular assemblies enables detection of gene mutations without a fluorescent probe.

    PubMed

    Maruyama, Tatsuo; Park, Lian-Chun; Shinohara, Toshimitsu; Goto, Masahiro

    2004-01-01

    We have developed a simple single nucleotide polymorphisms (SNPs) analysis utilizing DNA hybridization in nanostructural molecular assemblies. The novel technique enables the detection of a single-base mismatch in a DNA sequence without a fluorescent probe. This report describes for the first time that DNA hybridization occurs in the nanostructural molecular assemblies (termed reverse micelles) formed in an organic medium. The restricted nanospace in the reverse micelles amplifies the differences in the hybridization rate between mismatched and perfectly matched DNA probes. For a model system, we hybridized a 20-mer based on the p53 gene sequence to 20-mer complementary oligonucleotides with various types of mismatches. Without any DNA labeling or electrochemical apparatus, we successfully detected the various oligonucleotide mismatches by simply measuring the UV absorbance at 260 nm. PMID:14715007

  16. A robust molecular probe for Ångstrom-scale analytics in liquids

    PubMed Central

    Nirmalraj, Peter; Thompson, Damien; Dimitrakopoulos, Christos; Gotsmann, Bernd; Dumcenco, Dumitru; Kis, Andras; Riel, Heike

    2016-01-01

    Traditionally, nanomaterial profiling using a single-molecule-terminated scanning probe is performed at the vacuum–solid interface often at a few Kelvin, but is not a notion immediately associated with liquid–solid interface at room temperature. Here, using a scanning tunnelling probe functionalized with a single C60 molecule stabilized in a high-density liquid, we resolve low-dimensional surface defects, atomic interfaces and capture Ångstrom-level bond-length variations in single-layer graphene and MoS2. Atom-by-atom controllable imaging contrast is demonstrated at room temperature and the electronic structure of the C60–metal probe complex within the encompassing liquid molecules is clarified using density functional theory. Our findings demonstrates that operating a robust single-molecular probe is not restricted to ultra-high vacuum and cryogenic settings. Hence the scope of high-precision analytics can be extended towards resolving sub-molecular features of organic elements and gauging ambient compatibility of emerging layered materials with atomic-scale sensitivity under experimentally less stringent conditions. PMID:27516157

  17. Advanced electric-field scanning probe lithography on molecular resist using active cantilever

    NASA Astrophysics Data System (ADS)

    Kaestner, Marcus; Aydogan, Cemal; Lipowicz, Hubert-Seweryn; Ivanov, Tzvetan; Lenk, Steve; Ahmad, Ahmad; Angelov, Tihomir; Reum, Alexander; Ishchuk, Valentyn; Atanasov, Ivaylo; Krivoshapkina, Yana; Hofer, Manuel; Holz, Mathias; Rangelow, Ivo W.

    2015-03-01

    The routine "on demand" fabrication of features smaller than 10 nm opens up new possibilities for the realization of many novel nanoelectronic, NEMS, optical and bio-nanotechnology-based devices. Based on the thermally actuated, piezoresistive cantilever technology we have developed a first prototype of a scanning probe lithography (SPL) platform able to image, inspect, align and pattern features down to single digit nano regime. The direct, mask-less patterning of molecular resists using active scanning probes represents a promising path circumventing the problems in today's radiation-based lithography. Here, we present examples of practical applications of the previously published electric field based, current-controlled scanning probe lithography on molecular glass resist calixarene by using the developed tabletop SPL system. We demonstrate the application of a step-and-repeat scanning probe lithography scheme including optical as well as AFM based alignment and navigation. In addition, sequential read-write cycle patterning combining positive and negative tone lithography is shown. We are presenting patterning over larger areas (80 x 80 μm) and feature the practical applicability of the lithographic processes.

  18. A robust molecular probe for Ångstrom-scale analytics in liquids.

    PubMed

    Nirmalraj, Peter; Thompson, Damien; Dimitrakopoulos, Christos; Gotsmann, Bernd; Dumcenco, Dumitru; Kis, Andras; Riel, Heike

    2016-01-01

    Traditionally, nanomaterial profiling using a single-molecule-terminated scanning probe is performed at the vacuum-solid interface often at a few Kelvin, but is not a notion immediately associated with liquid-solid interface at room temperature. Here, using a scanning tunnelling probe functionalized with a single C60 molecule stabilized in a high-density liquid, we resolve low-dimensional surface defects, atomic interfaces and capture Ångstrom-level bond-length variations in single-layer graphene and MoS2. Atom-by-atom controllable imaging contrast is demonstrated at room temperature and the electronic structure of the C60-metal probe complex within the encompassing liquid molecules is clarified using density functional theory. Our findings demonstrates that operating a robust single-molecular probe is not restricted to ultra-high vacuum and cryogenic settings. Hence the scope of high-precision analytics can be extended towards resolving sub-molecular features of organic elements and gauging ambient compatibility of emerging layered materials with atomic-scale sensitivity under experimentally less stringent conditions. PMID:27516157

  19. Synthesis of Optical Molecular Probes for electric potential across a cell membrane

    NASA Astrophysics Data System (ADS)

    Lamichhane, Roshan

    Optical Imaging of neuronal activities is an attractive method, but the two widely used optical imaging methods based on Fluorescence Resonance Transfer (FRET) and electrochromism have some deficiencies that Photo Induced Electron Transfer (PeT) method has eliminated. In the paper we talk about the synthesis of optical molecular probes that rely on PeT mechanism, and which could possibly be used to measure the transmembrane potential across the neuronal cell membranes.

  20. Fabrication of Molecular Strain Probes for Illuminating Protein-Protein Interactions.

    PubMed

    Kim, Sung-Bae; Fujii, Rika

    2016-01-01

    A unique bioluminescent imaging probe is introduced for illuminating molecular tension appended by protein-protein interactions (PPIs) of interest. A full-length luciferase is sandwiched between two proteins of interest via minimal flexible linkers. The ligand-activated PPIs append intramolecular tension to the sandwiched luciferase, boosting or dropping the enzymatic activity in a quantitative manner. This method guides construction of a new lineage of bioassays for ligand-activated PPIs. PMID:27424904

  1. Performance of Molecular Inversion Probes (MIP) in Allele CopyNumber Determination

    SciTech Connect

    Wang, Yuker; Moorhead, Martin; Karlin-Neumann, George; Wang,Nicolas J.; Ireland, James; Lin, Steven; Chen, Chunnuan; Heiser, LauraM.; Chin, Koei; Esserman, Laura; Gray, Joe W.; Spellman, Paul T.; Faham,Malek

    2007-05-14

    We have developed a new protocol for using MolecularInversion Probes (MIP) to accurately and specifically measure allele copynumber (ACN). The new protocol provides for significant improvementsincluding the reduction of input DNA (from 2?g) by more than 25 fold (to75ng total genomic DNA), higher overall precision resulting in one orderof magnitude lower false positive rate, and greater dynamic range withaccurate absolute copy number up to 60 copies.

  2. Monitoring drug-lipid membrane interactions via a molecular rotor probe.

    PubMed

    Xu, Qinqin; Zhao, Tao; Sun, Zhihua

    2016-08-01

    Molecular rotors are fluorescent molecules with a viscosity-sensitive fluorescence quantum yield that are often used to measure viscosity changes in biological membranes. Herein, we report the use of a lipophilic molecular rotor probe to monitor the interactions between the local anesthetic tetracaine (TTC) and small unilamellar vesicles (SUVs) in a label-free manner. The probe was developed by modifying the fluorescent molecular rotor CCVJ with an amphiphilic anchor group that enables adequate integration of the rotor group into the hydrophobic core of lipid bilayers. The temperature-dependent profile of the quantum yield of the probe clearly exhibited the subtransition, pretransition and main phase transition of the lipid bilayers as drastic changes in the activation energies. The temperature-TTC phase diagrams were determined based on an Arrhenius fitting. The results show that TTC has a significant chain ordering effect on liquid-crystalline phase lipids compared to solid-gel phase lipids, especially subgel phase lipids. A TTC-induced interdigitated gel (LβI) phase appeared at the pretransition temperature. The LβI phase spread both its ends in a TTC-dependent fashion, and the low-temperature end merged to the subtransition at a TTC concentration of 25 mM. Adding cholesterol (CHOL) to the SUVs stabilizes the LβI phase and reduces the insertion of TTC into the bilayers. The paper demonstrates that our method is highly sensitive to the microenvironment of the lipid membrane, providing a facile and efficient new tool to study drug-membrane interactions. Also, molecular rotors may potentially be exploited as screen probes for drug development and analysis. PMID:27243370

  3. Probing ultrafast electronic and molecular dynamics with free-electron lasers

    NASA Astrophysics Data System (ADS)

    Fang, L.; Osipov, T.; Murphy, B. F.; Rudenko, A.; Rolles, D.; Petrovic, V. S.; Bostedt, C.; Bozek, J. D.; Bucksbaum, P. H.; Berrah, N.

    2014-06-01

    Molecular dynamics is an active area of research, focusing on revealing fundamental information on molecular structures and photon-molecule interaction and with broad impacts in chemical and biological sciences. Experimental investigation of molecular dynamics has been advanced by the development of new light sources and techniques, deepening our understanding of natural processes and enabling possible control and modification of chemical and biomolecular processes. Free-electron lasers (FELs) deliver unprecedented intense and short photon pulses in the vacuum ultraviolet and x-ray spectral ranges, opening a new era for the study of electronic and nuclear dynamics in molecules. This review focuses on recent molecular dynamics investigations using FELs. We present recent work concerning dynamics of molecular interaction with FELs using an intrinsic clock within a single x-ray pulse as well as using an external clock in a pump-probe scheme. We review the latest developments on correlated and coincident spectroscopy in FEL-based research and recent results revealing photo-induced interaction dynamics using these techniques. We also describe new instrumentations to conduct x-ray pump-x-ray probe experiments with spectroscopy and imaging detectors.

  4. Effective rates from thermodynamically consistent coarse-graining of models for molecular motors with probe particles

    NASA Astrophysics Data System (ADS)

    Zimmermann, Eva; Seifert, Udo

    2015-02-01

    Many single-molecule experiments for molecular motors comprise not only the motor but also large probe particles coupled to it. The theoretical analysis of these assays, however, often takes into account only the degrees of freedom representing the motor. We present a coarse-graining method that maps a model comprising two coupled degrees of freedom which represent motor and probe particle to such an effective one-particle model by eliminating the dynamics of the probe particle in a thermodynamically and dynamically consistent way. The coarse-grained rates obey a local detailed balance condition and reproduce the net currents. Moreover, the average entropy production as well as the thermodynamic efficiency is invariant under this coarse-graining procedure. Our analysis reveals that only by assuming unrealistically fast probe particles, the coarse-grained transition rates coincide with the transition rates of the traditionally used one-particle motor models. Additionally, we find that for multicyclic motors the stall force can depend on the probe size. We apply this coarse-graining method to specific case studies of the F1-ATPase and the kinesin motor.

  5. Probing vacuum-induced coherence via magneto-optical rotation in molecular systems

    NASA Astrophysics Data System (ADS)

    Kumar, Pardeep; Deb, Bimalendu; Dasgupta, Shubhrangshu

    2016-05-01

    Vacuum-induced coherence (VIC) arises due to the quantum interference between the spontaneous emission pathways from the degenerate excited states to a common ground state. The stringent requirement for the VIC to occur is the nonorthogonality of the transition dipole matrix elements. Unlike atoms, molecules are the promising systems for exploration of VIC, as it is possible to identify the non-orthogonal transitions due to the coupling of the rotation of molecular axis with molecular electronic angular momentum. Usually, the possible signatures of VIC are obtained by manipulating the absorption of the probe field. In this paper, we show how the dispersion of the probe field can be manipulated to obtain a measurable signature of VIC. Precisely speaking, we explore a way to probe VIC in molecules by observing its influence on magneto-optical rotation (MOR). We show that VIC in the presence of a control laser and a magnetic field can lead to large enhancement in the rotation of the plane of polarization of a linearly polarized weak laser with vanishing circular dichroism. This effect can be realized in cold molecular gases. Such a large MOR angle may be used as a tool for optical magnetometry to detect weak magnetic field with large measurement sensitivity.

  6. Constitutional Dynamic Chemistry-based New Concept of Molecular Beacons for High Efficient Development of Fluorescent Probes.

    PubMed

    Chang, Xingmao; Yu, Chunmeng; Wang, Gang; Fan, Jiayun; Zhang, Jianyun; Qi, Yanyu; Liu, Kaiqiang; Fang, Yu

    2015-06-01

    Inspired by the concept of constitutional dynamic chemistry, we propose a new and well-adaptable strategy for developing molecular beacon (MB)-like fluorescent probes. To demonstrate the strategy, we synthesized and used an amino group containing pyrenyl derivative of cholesterol (CP) for the construction of new fluorescent probes with EDTA and sulfuric acid. The probes as created were successfully used for n-hexane purity checking and Ba(2+)and Pb(2+)sensing, respectively. PMID:25985384

  7. [The Ion Identification and Molecular Logic Gate of a Thiacalix[4]arene Fluorescent Probe].

    PubMed

    Wu, Fu-yong; Yu, Mei; Mu, Lan; Zeng, Xi; Wang, Rui-xiao; Takehiko Yamato

    2016-01-01

    A disubstituted phthalimide-based thiacalix[4] arene derivative (probe s1) was synthesized from cone 1, 3-thiacalix[4] arene and hydroxyethyl phthalimide, with benzyl appended the lower edge of thiacalix[4]-arene by triazole ring in the 2,4 position. The relative fluorescence quantum yield of probe s1 is 0.43 in CH3CN solvent. The strong fluorescence emission of probe s1 at 390 nm wavelength can be selectively quenched by Fe3+ in DMF/H2O solution. Similarly, the presence of I- also induced a significant fluorescence quenching of probe s1 at 310 nm wavelength in CH3CN solution. Spectral titration and isothermal titration calorimetry were showed that probe s1 with Fe3+ or I- both form 1 : 1 complexes, the binding constants up to 10(5) and coordinate process were spontaneous. The linear ranges of fluorescence detect Fe3+ or I- were 1.0 x 10(-7) - 1.6 x 10(-4) mol x L(-1) and 1.0 x 10(-7) - 8.5 x 10(-5) mol x L(-1), detection limits were up to 2.30 x 10(-8) mol x L(-1) and 1.17 x 10(-8) mol x L(-1), respectively. Meanwhile, take advantage of identification and coordination action, a logic circuit constructed at the molecular level by controlling two input signals of Fe3+ and F-, which causing probe s1 cycling of fluorescence emission or quenching. IR spectrum speculated that the nitrogen atoms of triazole groups are involved in the complexation with Fe3+, while the hydrogen atoms of triazole groups were complexed with I- by hydrogen bonding. PMID:27228760

  8. Probing electron-phonon excitations in molecular junctions by quantum interference

    PubMed Central

    Bessis, C.; Della Rocca, M. L.; Barraud, C.; Martin, P.; Lacroix, J. C.; Markussen, T.; Lafarge, P.

    2016-01-01

    Electron-phonon coupling is a fundamental inelastic interaction in condensed matter and in molecules. Here we probe phonon excitations using quantum interference in electron transport occurring in short chains of anthraquinone based molecular junctions. By studying the dependence of molecular junction’s conductance as a function of bias voltage and temperature, we show that inelastic scattering of electrons by phonons can be detected as features in conductance resulting from quenching of quantum interference. Our results are in agreement with density functional theory calculations and are well described by a generic two-site model in the framework of non-equilibrium Green’s functions formalism. The importance of the observed inelastic contribution to the current opens up new ways for exploring coherent electron transport through molecular devices. PMID:26864735

  9. Probing electron-phonon excitations in molecular junctions by quantum interference.

    PubMed

    Bessis, C; Della Rocca, M L; Barraud, C; Martin, P; Lacroix, J C; Markussen, T; Lafarge, P

    2016-01-01

    Electron-phonon coupling is a fundamental inelastic interaction in condensed matter and in molecules. Here we probe phonon excitations using quantum interference in electron transport occurring in short chains of anthraquinone based molecular junctions. By studying the dependence of molecular junction's conductance as a function of bias voltage and temperature, we show that inelastic scattering of electrons by phonons can be detected as features in conductance resulting from quenching of quantum interference. Our results are in agreement with density functional theory calculations and are well described by a generic two-site model in the framework of non-equilibrium Green's functions formalism. The importance of the observed inelastic contribution to the current opens up new ways for exploring coherent electron transport through molecular devices. PMID:26864735

  10. Functional second harmonic generation microscopy probes molecular dynamics with high temporal resolution

    PubMed Central

    Förderer, Moritz; Georgiev, Tihomir; Mosqueira, Matias; Fink, Rainer H. A.; Vogel, Martin

    2016-01-01

    Second harmonic generation (SHG) microscopy is a powerful tool for label free ex vivo or in vivo imaging, widely used to investigate structure and organization of endogenous SHG emitting proteins such as myosin or collagen. Polarization resolved SHG microscopy renders supplementary information and is used to probe different molecular states. This development towards functional SHG microscopy is calling for new methods for high speed functional imaging of dynamic processes. In this work we present two approaches with linear polarized light and demonstrate high speed line scan measurements of the molecular dynamics of the motor protein myosin with a time resolution of 1 ms in mammalian muscle cells. Such a high speed functional SHG microscopy has high potential to deliver new insights into structural and temporal molecular dynamics under ex vivo or in vivo conditions. PMID:26977360

  11. Functional second harmonic generation microscopy probes molecular dynamics with high temporal resolution.

    PubMed

    Förderer, Moritz; Georgiev, Tihomir; Mosqueira, Matias; Fink, Rainer H A; Vogel, Martin

    2016-02-01

    Second harmonic generation (SHG) microscopy is a powerful tool for label free ex vivo or in vivo imaging, widely used to investigate structure and organization of endogenous SHG emitting proteins such as myosin or collagen. Polarization resolved SHG microscopy renders supplementary information and is used to probe different molecular states. This development towards functional SHG microscopy is calling for new methods for high speed functional imaging of dynamic processes. In this work we present two approaches with linear polarized light and demonstrate high speed line scan measurements of the molecular dynamics of the motor protein myosin with a time resolution of 1 ms in mammalian muscle cells. Such a high speed functional SHG microscopy has high potential to deliver new insights into structural and temporal molecular dynamics under ex vivo or in vivo conditions. PMID:26977360

  12. Probing the Physical Conditions of Dense Molecular Gas in ULIRGs with LVG modelling

    NASA Astrophysics Data System (ADS)

    Leonidaki, Ioanna; Zhang, Zhi-Yu; Greve, Thomas; Xilouris, Manolis

    2015-08-01

    The gas-rich content of Ultra Luminous Infrared Galaxies (ULIRGs) constitutes a great laboratory in characterising the physical processes occuring in molecular gas and hence probing star formation properties. In particular, molecules with large dipole moments such as CS, HCN, HCO+, which are the fuel of star formation, can reveal the physical/excitation conditions of molecular gas phases in galaxies. For that reason, we compiled the aforementioned dense gas tracers in a sample of local (U)LIRGs in order to investigate the physical properties of the gas while at the same time put constrains on their excitation conditions. The sample in use consists of 26 galaxies all observed within the framework of the Herschel Comprehensive (U)LIRG Emission Survey (HerCULES). For all galaxies, we compiled our ground-based spectral line observations as well as all available data from the literature. Using Large Velocity Gradient (LVG) radiative transfer models in these spectral lines and in a wide parameter space [n(H2), Tkin, Nmol], and combining multiple molecules and multiple excitation components, it is possible to break the degeneracy between different parameters and to probe molecular gas physical conditions ranging from the cold and low-density average states in giant molecular clouds all the way up to the state of the gas found only near their star-forming regions. We then analyse the best LVG solution ranges to match the observed SLEDs (using more than one excitation components where necessary) in order to disentangle different molecular gas phases and possibly different molecular gas heating mechanisms.

  13. Molecular recognition of α-cyclodextrin (CD) to choral amino acids based on methyl orange as a molecular probe

    NASA Astrophysics Data System (ADS)

    Yuexian, Fan; Yu, Yang; Shaomin, Shuang; Chuan, Dong

    2005-03-01

    The molecular recognition interaction of α-CD to chiral amino acids was investigated by using spectrophotometry based on methyl orange as a molecular probe. The molecular recognition ability depended on the inclusion formation constants. The molecular recognition of α-CD to aromatic amino acids was the order: DL-tryptophan > L-tryptophan > L-phenylalanine > L-tyrosine ≈ DL-β-3,4-dihydroxy-phenylalanine; whereas for aliphatic amino acids, the order was: L- iso-leucine > L-leucine ≈ L-methionine ≈ DL-mehtionine > D-leucine. The effect of temperature on the inclusion interaction was examined and the thermodynamic parameters of inclusion process, Δ G, Δ H, Δ S, were determined. The experimental results indicated that the inclusion process was an exothermic and enthalpy-driven process accompanied with a negative or minor positive entropic contribution. The inclusion interaction between α-CD and amino acids satisfied the law of enthalpy-entropy compensation. The compensation temperature was 291 K.

  14. Molecular recognition of alpha-cyclodextrin (CD) to choral amino acids based on methyl orange as a molecular probe.

    PubMed

    Yuexian, Fan; Yu, Yang; Shaomin, Shuang; Chuan, Dong

    2005-03-01

    The molecular recognition interaction of alpha-CD to chiral amino acids was investigated by using spectrophotometry based on methyl orange as a molecular probe. The molecular recognition ability depended on the inclusion formation constants. The molecular recognition of alpha-CD to aromatic amino acids was the order: DL-tryptophan > L-tryptophan > L-phenylalanine > L-tyrosine approximately DL-beta-3,4-dihydroxy-phenylalanine; whereas for aliphatic amino acids, the order was: L-iso-leucine > L-leucine approximately L-methionine approximately DL-mehtionine > D-leucine. The effect of temperature on the inclusion interaction was examined and the thermodynamic parameters of inclusion process, delta G, delta H, delta S, were determined. The experimental results indicated that the inclusion process was an exothermic and enthalpy-driven process accompanied with a negative or minor positive entropic contribution. The inclusion interaction between alpha-CD and amino acids satisfied the law of enthalpy-entropy compensation. The compensation temperature was 291 K. PMID:15683802

  15. Molecular and ionic diffusion in aqueous - deep eutectic solvent mixtures: probing inter-molecular interactions using PFG NMR.

    PubMed

    D'Agostino, Carmine; Gladden, Lynn F; Mantle, Mick D; Abbott, Andrew P; Ahmed, Essa I; Al-Murshedi, Azhar Y M; Harris, Robert C

    2015-06-21

    Pulsed field gradient (PFG) NMR has been used to probe self-diffusion of molecular and ionic species in aqueous mixtures of choline chloride (ChCl) based deep eutectic solvents (DESs), in order to elucidate the effect of water on motion and inter-molecular interactions between the different species in the mixtures, namely the Ch(+) cation and hydrogen bond donor (HBD). The results reveal an interesting and complex behaviour of such mixtures at a molecular level. In general, it is observed that the hydroxyl protons ((1)H) of Ch(+) and the hydrogen bond donor have diffusion coefficients significantly different from those measured for their parent molecules when water is added. This indicates a clear and significant change in inter-molecular interactions. In aqueous Ethaline, the hydroxyl species of Ch(+) and HBD show a stronger interaction with water as water is added to the system. In the case of Glyceline, water has little effect on both hydroxyl proton diffusion of Ch(+) and HBD. In Reline, it is likely that water allows the formation of small amounts of ammonium hydroxide. The most surprising observation is from the self-diffusion of water, which is considerably higher that expected from a homogeneous liquid. This leads to the conclusion that Reline and Glyceline form mixtures that are inhomogeneous at a microscopic level despite the hydrophilicity of the salt and HBD. This work shows that PFG NMR is a powerful tool to elucidate both molecular dynamics and inter-molecular interactions in complex liquid mixtures, such as the aqueous DES mixtures. PMID:25994171

  16. Probing vacuum-induced coherence via magneto-optical rotation in molecular systems

    NASA Astrophysics Data System (ADS)

    Kumar, Pardeep; Deb, Bimalendu; Dasgupta, Shubhrangshu

    2016-06-01

    We investigate theoretically the effects of vacuum-induced coherence (VIC) on magneto-optical rotation (MOR). We carry out a model study to show that VIC in the presence of a control laser and a magnetic field can lead to large enhancement in the rotation of the plane of polarization of a linearly polarized weak laser with vanishing circular dichroism. This effect can be realized in cold molecular gases and may be used as a sensitive probe for VIC. Such a large MOR angle can also be used to detect weak magnetic field with large measurement sensitivity.

  17. Spectral Properties of the Anionic Form of the Molecular Probe Fet

    NASA Astrophysics Data System (ADS)

    Tomin, V. I.; Jaworski, R.

    2014-07-01

    The relationship of the fluorescence spectral characteristics of the anionic form of the molecular probe 4'-(diethylamino)-3-hydroxyflavone (FET) to intramolecular proton transfer in a weakly polar solvent (CH2Cl2) was studied. The fluorescence spectrum of this form had a broad featureless band in the area between the shortwavelength and long-wavelength fluorescence bands of FET. Its excitation spectrum had strong UV maxima (350 and 305 nm). This fluorescence disappeared completely if the solution was cooled to 1 °C. The deprotonation mechanism of neutral FET molecules was discussed.

  18. Exploring Ultrafast Molecular Dynamics using Photoelectron Spectra from UV/XUV Pump-Probe Experiments

    NASA Astrophysics Data System (ADS)

    Champenois, Elio; Cryan, James; Shivaram, Niranjan; Wright, Travis; Belkacem, Ali

    2015-05-01

    The motion of atoms in molecules can drive electron dynamics via non-adiabatic couplings. In small molecules such as Ethylene, Carbon Dioxide, and Nitrophenol, this can lead to isomerization, electronic relaxation, or other time-dependent effects following excitation from a bonding to an anti-bonding molecular orbital. To study these mechanisms, we use ultraviolet photons of various energies from a bright High Harmonic Generation source to first initiate dynamics and subsequently probe the system through ionization. We record the kinetic energy and angular distribution of the resultant photoelectrons using a Velocity Map Imaging spectrometer, allowing us to track the evolution of the electronic state.

  19. Probing the Inelastic Interactions in Molecular Junctions by Scanning Tunneling Microscope

    NASA Astrophysics Data System (ADS)

    Xu, Chen

    With a sub-Kelvin scanning tunneling microscope, the energy resolution of spectroscopy is improved dramatically. Detailed studies of finer features of spectrum become possible. The asymmetry in the line shape of carbon monoxide vibrational spectra is observed to correlate with the couplings of the molecule to the tip and substrates. The spin-vibronic coupling in the molecular junctions is revisited with two metal phthalocyanine molecules, unveiling sharp spin-vibronic peaks. Finally, thanks to the improved spectrum resolution, the bonding structure of the acyclic compounds molecules is surveyed with STM inelastic tunneling probe, expanding the capability of the innovative high resolution imaging technique.

  20. Molecular Frame Photoemission: Probe of the Photoionization Dynamics for Molecules in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Dowek, D.; Picard, Y. J.; Billaud, P.; Elkharrat, C.; Houver, J. C.

    2009-04-01

    Molecular frame photoemission is a very sensitive probe of the photoionization (PI) dynamics of molecules. This paper reports a comparative study of non-resonant and resonant photoionization of D2 induced by VUV circularly polarized synchrotron radiation at SOLEIL at the level of the molecular frame photoelectron angular distributions (MFPADs). We use the vector correlation method which combines imaging and time-of-flight resolved electron-ion coincidence techniques, and a generalized formalism for the expression of the I(χ, θe, varphie) MFPADs, where χ is the orientation of the molecular axis with respect to the light quantization axis and (θe, varphie) the electron emission direction in the molecular frame. Selected MFPADs for a molecule aligned parallel or perpendicular to linearly polarized light, or perpendicular to the propagation axis of circularly polarized light, are presented for dissociative photoionization (DPI) of D2 at two photon excitation energies, hν = 19 eV, where direct PI is the only channel opened, and hν = 32.5 eV, i.e. in the region involving resonant excitation of Q1 and Q2 doubly excited state series. We discuss in particular the properties of the circular dichroism characterizing photoemission in the molecular frame for direct and resonant PI. In the latter case, a remarkable behavior is observed which may be attributed to the interference occurring between undistinguishable autoionization decay channels.

  1. Spatial decomposition of molecular ions within 3D atom probe reconstructions.

    PubMed

    Breen, Andrew; Moody, Michael P; Gault, Baptiste; Ceguerra, Anna V; Xie, Kelvin Y; Du, Sichao; Ringer, Simon P

    2013-09-01

    Two methods for separating the constituent atoms of molecular ions within atom probe tomography reconstructions are presented. The Gaussian Separation Method efficiently deconvolutes molecular ions containing two constituent atoms and is tested on simulated data before being applied to an experimental HSLA steel dataset containing NbN. The Delaunay Separation Method extends separation to larger complex ions and is also tested on simulated data before being applied to an experimental GaAs dataset containing many large (>3 atoms) complex ions. First nearest neighbour (1NN) distributions and images of the reconstruction before and after the separations are used to show the effect of the algorithms and their validity and practicality are also discussed. PMID:23522847

  2. Quantitative degenerate four-wave mixing spectroscopy: Probes for molecular species

    SciTech Connect

    Farrow, R.; Rakestraw, D.; Paul, P.; Lucht, R.; Danehy, P.; Friedman-Hill, E.; Germann, G.

    1993-12-01

    Resonant degenerate four-wave mixing (DFWM) is currently the subject of intensive investigation as a sensitive diagnostic tool for molecular species. DFWM has the advantage of generating a coherent (beam-like) signal which results in null-background detection and provides excellent immunity to background-light interference. Since multiple one-photon resonances are involved in the signal generation process, the DFWM technique can allow sensitive detection of molecules via electronic, vibrational or rotational transitions. These properties combine to make DFWM a widely applicable diagnostic technique for the probing of molecular species. The authors are conducting fundamental and applied investigations of DFWM for quantitative measurements of trace species in reacting gases. During the past year, efforts have been focussed in two areas: (1) understanding the effects of collisional processes on the DFWM signal generation process, and (2) exploring the applicability of infrared DFWM to detect polyatomic molecules via rovibrational transitions.

  3. C3H2 observations as a diagnostic probe for molecular clouds

    NASA Technical Reports Server (NTRS)

    Avery, L. W.

    1986-01-01

    Recently the three-membered ring molecule, cyclopropenylidene, C3H2, has been identified in the laboratory and detected in molecular clouds by Thaddeus, Vrtilek and Gottlieb (1985). This molecule is wide-spread throughout the Galaxy and has been detected in 25 separate sources including cold dust clouds, circumstellar envelopes, HII regions, and the spiral arms observed against the Cas supernova remnant. In order to evaluate the potential of C3H2 as a diagnostic probe for molecular clouds, and to attempt to identify the most useful transitions, statistical equilibrium calculations were carried out for the lowest 24 levels of the ortho species and the lowest 10 levels of the para species. Many of the sources observed by Matthews and Irvine (1985) show evidence of being optically thick in the 1(10)-1(01) line. Consequently, the effects of radiative trapping should be incorporated into the equilibrium calculations. This was done using the Large Velocity Gradient approximation for a spherical cloud of uniform density. Some results of the calculations for T(K)=10K are given. Figures are presented which show contours of the logarithm of the ratio of peak line brightness temperatures for ortho-para pairs of lines at similar frequencies. It appears that the widespread nature of C3H2, the relatively large strength of its spectral lines, and their sensitivity to density and molecular abundance combine to make this a useful molecule for probing physical conditions in molecular clouds. The 1(10)-1(01) and 2(20)-2(11) K-band lines may be especially useful in this regard because of the ease with which they are observed and their unusual density-dependent emission/absorption properties.

  4. Microfluidic means of achieving attomolar detection limits with molecular beacon probes.

    PubMed

    Puleo, Christopher M; Wang, Tza-Huei

    2009-04-21

    We used inline, micro-evaporators to concentrate and transport DNA targets to a nanoliter single molecule fluorescence detection chamber for subsequent molecular beacon probe hybridization and analysis. This use of solvent removal as a unique means of target transport in a microanalytical platform led to a greater than 5000-fold concentration enhancement and detection limits that pushed below the femtomolar barrier commonly reported using confocal fluorescence detection. This simple microliter-to-nanoliter interconnect for single molecule counting analysis resolved several common limitations, including the need for excessive fluorescent probe concentrations at low target levels and inefficiencies in direct handling of highly dilute biological samples. In this report, the hundreds of bacteria-specific DNA molecules contained in approximately 25 microliters of a 50 aM sample were shuttled to a four nanoliter detection chamber through micro-evaporation. Here, the previously undetectable targets were enhanced to the pM regime and underwent probe hybridization and highly-efficient fluorescent event analysis via microfluidic recirculation through the confocal detection volume. This use of microfluidics in a single molecule detection (SMD) platform delivered unmatched sensitivity and introduced compliment technologies that may serve to bring SMD to more widespread use in replacing conventional methodologies for detecting rare target biomolecules in both research and clinical labs. PMID:19350088

  5. Upconversion particles coated with molecularly imprinted polymers as fluorescence probe for detection of clenbuterol.

    PubMed

    Tang, Yiwei; Gao, Ziyuan; Wang, Shuo; Gao, Xue; Gao, Jingwen; Ma, Yong; Liu, Xiuying; Li, Jianrong

    2015-09-15

    A novel fluorescence probe based on upconversion particles, YF3:Yb(3+), Er(3+), coating with molecularly imprinted polymers (MIPs@UCPs) has been synthesized for selective recognition of the analyte clenbuterol (CLB), which was characterized by scan electron microscope and X-ray powder diffraction. The fluorescence of the MIPs@UCPs probe is quenched specifically by CLB, and the effect is much stronger than the NIPs@UCPs (non-imprinting polymers, NIPs). Good linear correlation was obtained for CLB over the concentration range of 5.0-100.0 μg L(-1) with a detection limit of 0.12 μg L(-1) (S/N=3). The developed method was also used in the determination of CLB in water and pork samples, and the recoveries ranged from 81.66% to 102.46% were obtained with relative standard deviation of 2.96-4.98% (n=3). The present study provides a new and general tactics to synthesize MIPs@UCPs fluorescence probe with highly selective recognition ability to the CLB and is desirable for application widely in the near future. PMID:25884733

  6. Site-selective Characterization of Src Homology 3 Domain Molecular Recognition with Cyanophenylalanine Infrared Probes

    PubMed Central

    Horness, Rachel E.; Basom, Edward J.; Thielges, Megan C.

    2015-01-01

    Local heterogeneity of microenvironments in proteins is important in biological function, but difficult to characterize experimentally. One approach is the combination of infrared (IR) spectroscopy and site-selective incorporation of probe moieties with spectrally resolved IR absorptions that enable characterization within inherently congested protein IR spectra. We employed this method to study molecular recognition of a Src homology 3 (SH3) domain from the yeast protein Sho1 for a peptide containing the proline-rich recognition sequence of its physiological binding partner Pbs2. Nitrile IR probes were introduced at four distinct sites in the protein by selective incorporation of p-cyanophenylalanine via the amber codon suppressor method and characterized by IR spectroscopy. Variation among the IR absorption bands reports on heterogeneity in local residue environments dictated by the protein structure, as well as on residue-dependent changes upon peptide binding. The study informs on the molecular recognition of SH3Sho1 and illustrates the speed and simplicity of this approach for characterization of select microenvironments within proteins. PMID:26491469

  7. NIR fluorescence lifetime sensing through a multimode fiber for intravascular molecular probing

    NASA Astrophysics Data System (ADS)

    Ingelberts, H.; Hernot, S.; Debie, P.; Lahoutte, T.; Kuijk, M.

    2016-04-01

    Coronary artery disease (CAD) contributes to millions of deaths each year. The identification of vulnerable plaques is essential to the diagnosis of CAD but is challenging. Molecular probes can improve the detection of these plaques using intravascular imaging methods. Fluorescence lifetime sensing is a safe and robust method to image these molecular probes. We present two variations of an optical system for intravascular near-infrared (NIR) fluorescence lifetime sensing through a multimode fiber. Both systems are built around a recently developed fast and efficient CMOS detector, the current-assisted photonic sampler (CAPS) that is optimized for sub-nanosecond NIR fluorescence lifetime sensing. One system mimics the optical setup of an epifluorescence microscope while the other uses a practical fiber optic coupler to separate fluorescence excitation and emission. We test both systems by measuring the lifetime of several NIR dyes in DMSO solutions and we show that these systems are capable of detecting lifetimes of solutions with concentrations down to 370 nM and this with short acquisition times. These results are compared with time-correlated single photon counting (TCSPC) measurements for reference.

  8. Real-time observation of DNA repair: 2-aminopurine as a molecular probe

    NASA Astrophysics Data System (ADS)

    Krishnan, Rajagopal; Butcher, Christina E.; Oh, Dennis H.

    2008-02-01

    Triplex forming oligos (TFOs) that target psoralen photoadducts to specific DNA sequences have generated interest as a potential agent in gene therapy. TFOs also offer an opportunity to study the mechanism of DNA repair in detail. In an effort to understand the mechanism of DNA repair at a specific DNA sequence in real-time, we have designed a plasmid containing a psoralen reaction site adjacent to a TFO binding site corresponding to a sequence within the human interstitial collagenase gene. Two 2-aminopurine residues incorporated into the purine-rich strand of the TFO binding site and located within six nucleotides of the psoralen reaction site serve as molecular probes for excision repair events involving the psoralen photoadducts on that DNA strand. In duplex DNA, the 2-aminopurine fluorescence is quenched. However, upon thermal or formamide-induced denaturation of duplex DNA to single stranded DNA, the 2-aminopurine fluorescence increases by eight fold. These results suggest that monitoring 2-aminopurine fluorescence from plasmids damaged by psoralen TFOs may be a method for measuring excision of single-stranded damaged DNA from the plasmid in cells. A fluorescence-based molecular probe to the plasmid may significantly simplify the real-time observation of DNA repair in both populations of cells as well as single cells.

  9. Noninvasive imaging of multiple myeloma using near infrared fluorescent molecular probe

    NASA Astrophysics Data System (ADS)

    Hathi, Deep; Zhou, Haiying; Bollerman-Nowlis, Alex; Shokeen, Monica; Akers, Walter J.

    2016-03-01

    Multiple myeloma is a plasma cell malignancy characterized by monoclonal gammopathy and osteolytic bone lesions. Multiple myeloma is most commonly diagnosed in late disease stages, presenting with pathologic fracture. Early diagnosis and monitoring of disease status may improve quality of life and long-term survival for multiple myeloma patients from what is now a devastating and fatal disease. We have developed a near-infrared targeted fluorescent molecular probe with high affinity to the α4β1 integrin receptor (VLA-4)overexpressed by a majority of multiple myeloma cells as a non-radioactive analog to PET/CT tracer currently being developed for human diagnostics. A near-infrared dye that emits about 700 nm was conjugated to a high affinity peptidomimmetic. Binding affinity and specificity for multiple myeloma cells was investigated in vitro by tissue staining and flow cytometry. After demonstration of sensitivity and specificity, preclinical optical imaging studies were performed to evaluate tumor specificity in murine subcutaneous and metastatic multiple myeloma models. The VLA-4-targeted molecular probe showed high affinity for subcutaneous MM tumor xenografts. Importantly, tumor cells specific accumulation in the bone marrow of metastatic multiple myeloma correlated with GFP signal from transfected cells. Ex vivo flow cytometry of tumor tissue and bone marrow further corroborated in vivo imaging data, demonstrating the specificity of the novel agent and potential for quantitative imaging of multiple myeloma burden in these models.

  10. A low molecular weight artificial RNA of unique size with multiple probe target regions

    NASA Technical Reports Server (NTRS)

    Pitulle, C.; Dsouza, L.; Fox, G. E.

    1997-01-01

    Artificial RNAs (aRNAs) containing novel sequence segments embedded in a deletion mutant of Vibrio proteolyticus 5S rRNA have previously been shown to be expressed from a plasmid borne growth rate regulated promoter in E. coli. These aRNAs accumulate to high levels and their detection is a promising tool for studies in molecular microbial ecology and in environmental monitoring. Herein a new construct is described which illustrates the versatility of detection that is possible with aRNAs. This 3xPen aRNA construct carries a 72 nucleotide insert with three copies of a unique 17 base probe target sequence. This aRNA is 160 nucleotides in length and again accumulates to high levels in the E. coli cytoplasm without incorporating into ribosomes. The 3xPen aRNA illustrates two improvements in detection. First, by appropriate selection of insert size, we obtained an aRNA which provides a unique and hence, easily quantifiable peak, on a high resolution gel profile of low molecular weight RNAs. Second, the existence of multiple probe targets results in a nearly commensurate increase in signal when detection is by hybridization. These aRNAs are naturally amplified and carry sequence segments that are not found in known rRNA sequences. It thus may be possible to detect them directly. An experimental step involving RT-PCR or PCR amplification of the gene could therefore be avoided.

  11. Detection of early primary colorectal cancer with upconversion luminescent NP-based molecular probes.

    PubMed

    Liu, Chunyan; Qi, Yifei; Qiao, Ruirui; Hou, Yi; Chan, Kaying; Li, Ziqian; Huang, Jiayi; Jing, Lihong; Du, Jun; Gao, Mingyuan

    2016-07-01

    Early detection and diagnosis of cancers is extremely beneficial for improving the survival rate of cancer patients and molecular imaging techniques are believed to be relevant for offering clinical solutions. Towards early cancer detection, we developed a primary animal colorectal cancer model and constructed a tumor-specific imaging probe by using biocompatible NaGdF4:Yb,Er@NaGdF4 upconversion luminescent NPs for establishing a sensitive early tumor imaging method. The primary animal tumor model, which can better mimic the human colorectal cancer, was built upon continual administration of 1,2-dimethylhydrazine in Kunming mice and the tumor development was carefully monitored through histopathological and immunohistochemical analyses to reveal the pathophysiological processes and molecular features of the cancer microenvironment. The upconversion imaging probe was constructed through covalent coupling of PEGylated core-shell NPs with folic acid whose receptor is highly expressed in the primary tumors. Upon 980 nm laser excitation, the primary colorectal tumors in the complex abdominal environment were sensitively imaged owing to the ultralow background of the upconversion luminescence and the high tumor-targeting specificity of the nanoprobe. We believe that the current studies provide a highly effective and potential approach for early colorectal cancer diagnosis and tumor surgical navigation. PMID:26662173

  12. 08-ERD-071 Final Report: New Molecular Probes and Catalysts for Bioenergy Research

    SciTech Connect

    Thelen, M P; Rowe, A A; Siebers, A K; Jiao, Y

    2011-03-07

    A major thrust in bioenergy research is to develop innovative methods for deconstructing plant cell wall polymers, such as cellulose and lignin, into simple monomers that can be biologically converted to ethanol and other fuels. Current techniques for monitoring a broad array of cell wall materials and specific degradation products are expensive and time consuming. To monitor various polymers and assay their breakdown products, molecular probes for detecting specific carbohydrates and lignins are urgently needed. These new probes would extend the limited biochemical techniques available, and enable realtime imaging of ultrastructural changes in plant cells. Furthermore, degradation of plant biomass could be greatly accelerated by the development of catalysts that can hydrolyze key cell wall polysaccharides and lignin. The objective of this project was to develop cheap and efficient DNA reagents (aptamers) used to detect and quantify polysaccharides, lignin, and relevant products of their breakdown. A practical goal of the research was to develop electrochemical aptamer biosensors, which could be integrated into microfluidic devices and used for high-throughput screening of enzymes or biological systems that degrade biomass. Several important model plant cell wall polymers and compounds were targeted for specific binding and purification of aptamers, which were then tested by microscopic imaging, circular dichroism, surface plasmon resonance, fluorescence anisotropy, and electrochemical biosensors. Using this approach, it was anticiated that we could provide a basis for more efficient and economically viable biofuels, and the technologies established could be used to design molecular tools that recognize targets sought in medicine or chemical and biological defense projects.

  13. Single cell molecular recognition of migrating and invading tumor cells using a targeted fluorescent probe to receptor PTPmu.

    PubMed

    Burden-Gulley, Susan M; Qutaish, Mohammed Q; Sullivant, Kristin E; Tan, Mingqian; Craig, Sonya E L; Basilion, James P; Lu, Zheng-Rong; Wilson, David L; Brady-Kalnay, Susann M

    2013-04-01

    Detection of an extracellular cleaved fragment of a cell-cell adhesion molecule represents a new paradigm in molecular recognition and imaging of tumors. We previously demonstrated that probes that recognize the cleaved extracellular domain of receptor protein tyrosine phosphatase mu (PTPmu) label human glioblastoma brain tumor sections and the main tumor mass of intracranial xenograft gliomas. In this article, we examine whether one of these probes, SBK2, can label dispersed glioma cells that are no longer connected to the main tumor mass. Live mice with highly dispersive glioma tumors were injected intravenously with the fluorescent PTPmu probe to test the ability of the probe to label the dispersive glioma cells in vivo. Analysis was performed using a unique three-dimensional (3D) cryo-imaging technique to reveal highly migratory and invasive glioma cell dispersal within the brain and the extent of colabeling by the PTPmu probe. The PTPmu probe labeled the main tumor site and dispersed cells up to 3.5 mm away. The cryo-images of tumors labeled with the PTPmu probe provide a novel, high-resolution view of molecular tumor recognition, with excellent 3D detail regarding the pathways of tumor cell migration. Our data demonstrate that the PTPmu probe recognizes distant tumor cells even in parts of the brain where the blood-brain barrier is likely intact. The PTPmu probe has potential translational significance for recognizing tumor cells to facilitate molecular imaging, a more complete tumor resection and to serve as a molecular targeting agent to deliver chemotherapeutics to the main tumor mass and distant dispersive tumor cells. PMID:22987116

  14. Detection of early primary colorectal cancer with upconversion luminescent NP-based molecular probes

    NASA Astrophysics Data System (ADS)

    Liu, Chunyan; Qi, Yifei; Qiao, Ruirui; Hou, Yi; Chan, Kaying; Li, Ziqian; Huang, Jiayi; Jing, Lihong; Du, Jun; Gao, Mingyuan

    2016-06-01

    Early detection and diagnosis of cancers is extremely beneficial for improving the survival rate of cancer patients and molecular imaging techniques are believed to be relevant for offering clinical solutions. Towards early cancer detection, we developed a primary animal colorectal cancer model and constructed a tumor-specific imaging probe by using biocompatible NaGdF4:Yb,Er@NaGdF4 upconversion luminescent NPs for establishing a sensitive early tumor imaging method. The primary animal tumor model, which can better mimic the human colorectal cancer, was built upon continual administration of 1,2-dimethylhydrazine in Kunming mice and the tumor development was carefully monitored through histopathological and immunohistochemical analyses to reveal the pathophysiological processes and molecular features of the cancer microenvironment. The upconversion imaging probe was constructed through covalent coupling of PEGylated core-shell NPs with folic acid whose receptor is highly expressed in the primary tumors. Upon 980 nm laser excitation, the primary colorectal tumors in the complex abdominal environment were sensitively imaged owing to the ultralow background of the upconversion luminescence and the high tumor-targeting specificity of the nanoprobe. We believe that the current studies provide a highly effective and potential approach for early colorectal cancer diagnosis and tumor surgical navigation.Early detection and diagnosis of cancers is extremely beneficial for improving the survival rate of cancer patients and molecular imaging techniques are believed to be relevant for offering clinical solutions. Towards early cancer detection, we developed a primary animal colorectal cancer model and constructed a tumor-specific imaging probe by using biocompatible NaGdF4:Yb,Er@NaGdF4 upconversion luminescent NPs for establishing a sensitive early tumor imaging method. The primary animal tumor model, which can better mimic the human colorectal cancer, was built upon continual

  15. Novel molecular beacon DNA probes for protein-nucleic acid interaction studies

    NASA Astrophysics Data System (ADS)

    Li, Jianwei J.; Perlette, John; Fang, Xiaohong; Kelley, Shannon; Tan, Weihong

    2000-03-01

    We report a novel approach to study protein-nucleic acid interactions by using molecular beacons (MBs). Molecular beacons are hairpin-shaped DNA oligonucleotide probes labeled with a fluorophore and a quencher, and can report the presence of target DNA/RNA sequences. MBs can also report the existence of single-stranded DNA binding proteins (SSB) through non-sequence specific binding. The interaction between SSB and MB has resulted in significant fluorescence restoration of the MB. The fluorescence enhancement brought by SSB and by complementary DNA is very comparable. The molar ratio of the binding between SSB and the molecular beacon is 1:1 with a binding constant of 2 X 107 M-1. Using the MB-SSB binding, we are able to determine SSB at 2 X 10-10 M with a conventional spectrometer. We have also applied MB DNA probes for the analysis of an enzyme lactic dehydrogenase (LDH), and for the investigation of its binding properties with ssDNA. The biding process between MB and different isoenzymes of LDH has been studied. We also show that there are significant differences in MB binding affinity to different proteins, which will enable selective binding studies of a variety of proteins. This new approach is potentially useful for protein-DNA/RNA interaction studies that require high sensitivity, speed and convenience. The results also open the possibility of using easily obtainable, custom designed, modified DNA molecules for studies of drug interactions and targeting. Our results demonstrate that MB can be effectively used for sensitive protein quantitation and for efficient protein-DNA interaction studies. MB has the signal transduction mechanism built within the molecule, and can thus be used for quick protein assay development and for real-time measurements.

  16. Multiscale diffusion of a molecular probe in a crowded environment: a concept

    NASA Astrophysics Data System (ADS)

    Currie, Megan; Thao, Chang; Timerman, Randi; Welty, Robb; Berry, Brenden; Sheets, Erin D.; Heikal, Ahmed A.

    2015-08-01

    Living cells are crowded with macromolecules and organelles. Yet, it is not fully understood how macromolecular crowding affects the myriad of biochemical reactions, transport and the structural stability of biomolecules that are essential to cellular function and survival. These molecular processes, with or without electrostatic interactions, in living cells are therefore expected to be distinct from those carried out in test tube in dilute solutions where excluded volumes are absent. Thus there is an urgent need to understand the macromolecular crowding effects on cellular and molecular biophysics towards quantitative cell biology. In this report, we investigated how biomimetic crowding affects both the rotational and translation diffusion of a small probe (rhodamine green, RhG). For biomimetic crowding agents, we used Ficoll-70 (synthetic polymer), bovine serum albumin and ovalbumin (proteins) at various concentrations in a buffer at room temperature. As a control, we carried out similar measurements on glycerolenriched buffer as an environment with homogeneous viscosity as a function of glycerol concentration. The corresponding bulk viscosity was measured independently to test the validity of the Stokes-Einstein model of a diffusing species undergoing a random walk. For rotational diffusion (ps-ns time scale), we used time-resolved anisotropy measurements to examine potential binding of RhG as a function of the crowding agents (surface structure and size). For translational diffusion (μs-s time scale), we used fluorescence correlation spectroscopy for single-molecule fluctuation analysis. Our results allow us to examine the diffusion model of a molecular probe in crowded environments as a function of concentration, length scale, homogeneous versus heterogeneous viscosity, size and surface structures. These biomimetic crowding studies, using non-invasive fluorescence spectroscopy methods, represent an important step towards understanding cellular biophysics and

  17. Intraoperative Assessment of Breast Cancer Margins ex vivo using Aqueous Quantum Dot-Functionalized Molecular Probes

    NASA Astrophysics Data System (ADS)

    Au, Giang Hoang Thuy

    Breast cancer is increasingly diagnosed at an early stage, allowing the diseased breast to be removed only partially or breast conserving surgery (BCS). Current BCS procedures have no rapid methods during surgery to assess if the surgical margin is clear of cancer, often resulting in re-excision. The current breast cancer re-excision rate is estimated to be 15% to as high as 60%. It would be desirable if there is a rapid and reliable breast cancer margin assessment tool in the operating room to help assess if the surgical margin is clean to minimize unnecessary re-excisions. In this research, we seek to develop an intraoperative, molecular probe-based breast cancer surgical margin assessment tool using aqueous quantum dots (AQDs) coupled with cancer specific biomarkers. Quantum dots (QDs) are photoluminescent semiconductor nanoparticles that do not photobleach and are brighter than organic fluorescent dyes. Aqueous quantum dots (AQDs) such as CdSe and near infrared (NIR) CdPbS developed in Shih's lab emit light longer than 600 nm. We have examined conjugating AQDs with antibodies to cancer specific biomarkers such as Tn antigen, a cancer-associated glycan antigen for epithelial cancers. We showed that AQDs could achieve ~80% antibody conjugation efficiency, i.e., 100 times less antibodies than required by commercial, making such AQD molecular probe surgical margin evaluation economically feasible. By conjugating AQDs with anti-Tn-antigen antibody, the AQDs molecular probe exhibited 94% sensitivity and 92% specificity in identifying breast cancer against normal breast tissues as well as benign breast tumors in 480 tissue blocks from 126 patients. Furthermore, mice model and clinical human studies indicated that AQDs imaging did not interfere with the following pathological staining. More interestingly, we showed that it it possible to directly conjugate one antibody to multiple AQDs, further reduces the required amount of antibodies needed, a feat that could not be

  18. Molecular Cooling as a Probe of Star Formation: Spitzer Looking Forward to Herschel

    NASA Technical Reports Server (NTRS)

    Bergin, Edwin A.; Maret, Sebastien; Yuan, Yuan; Sonnentrucker, Paule; Green, Joel D.; Watson, Dan M.; Harwit, Martin O.; Kristensen, Lars E.; Melnick, Gary J.; Tolls, Volker; Werner, Michael W.; Willacy, Karen

    2009-01-01

    We explore here the question of how cloud physics can be more directly probed when one observes the majority of cooling emissions from molecular gas. For this purpose we use results from a recent Spitzer Space Telescope study of the young cluster of embedded objects in NGC1333. For this study we mapped the emission from eight pure H2 rotational lines, from S(0) to S(7). The H2 emission appears to be associated with the warm gas shocked by the multiple outflows present in the region. The H2 lines are found to contribute to 25 - 50% of the total outflow luminosity, and can be used to more directly ascertain the importance of star formation feedback on the natal cloud. From these lines, we determine the outflow mass loss rate and, indirectly, the stellar infall rate, the outflow momentum and the kinetic energy injected into the cloud over the embedded phase. The latter is found to exceed the binding energy of individual cores, suggesting that outflows could be the main mechanism for cores disruption. Given the recent launch of Herschel and the upcoming operational lifetime of SOFIA we discuss how studies of molecular cooling can take a step beyond understanding thermal balance to exploring the origin, receipt, and transfer of energy in atomic and molecular gas in a wide range of physical situations.

  19. Positron annihilation lifetime spectroscopy (PALS): a probe for molecular organisation in self-assembled biomimetic systems.

    PubMed

    Fong, Celesta; Dong, Aurelia W; Hill, Anita J; Boyd, Ben J; Drummond, Calum J

    2015-07-21

    Positron annihilation lifetime spectroscopy (PALS) has been shown to be highly sensitive to conformational, structural and microenvironmental transformations arising from subtle geometric changes in molecular geometry in self-assembling biomimetic systems. The ortho-positronium (oPs) may be considered an active probe that can provide information on intrinsic packing and mobility within low molecular weight solids, viscous liquids, and soft matter systems. In this perspective we provide a critical overview of the literature in this field, including the evolution of analysis software and experimental protocols with commentary upon the practical utility of PALS. In particular, we discuss how PALS can provide unique insight into the macroscopic transport properties of several porous biomembrane-like nanostructures and suggest how this insight may provide information on the release of drugs from these matrices to aid in developing therapeutic interventions. We discuss the potentially exciting and fruitful application of this technique to membrane dynamics, diffusion and permeability. We propose that PALS can provide novel molecular level information that is complementary to conventional characterisation techniques. PMID:25948334

  20. Proposed experimental probes of chemical reaction molecular dynamics in solution: ICN photodissociation

    NASA Astrophysics Data System (ADS)

    Benjamin, I.; Wilson, Kent R.

    1989-04-01

    Knowledge of how translational and rotational motions are influenced by the solvent during the course of a photodissociation ``half-collision'' reaction in solution is of interest in itself and can also help our understanding of how thermally activated reactions take place in solution by means of fluctuations in translational and rotational motion. With this goal, the molecular dynamics of the photodissociation of the triatomic molecule ICN are compared in the gas phase and in Xe solution. The time evolution of the trajectories (particularly with respect to interfragment distance and CN orientation) and of the energy partitioning (particularly into fragment translational recoil and into rotation of the CN) are displayed. Two types of solution experiments are proposed and simulated, both closely related to recent gas phase studies by Dantus, Rosker, and Zewail. These experiments are designed to probe the detailed dynamics of chemical reactions in solution during the time period the reaction is in progress, in particular to reveal the dramatic effects of the solvent on translational motions and energies. Both are pump-probe experiments in which the first photon dissociates the ICN and the second induces fluorescence in the CN fragment. In the first type of experiment, which is particularly sensitive to fragment translational motion, the fluorescence intensity is measured as a function of photon energy and of time delay. In the second type of experiment, which is particularly sensitive to fragment rotation, in addition the angle between the polarizations of the pump and probe photons is varied. In the calculations presented here, the effect of the absorption of the photodissociation photon is treated using the classical Frank-Condon principle. The coupling between the assumed two upper electronic surfaces is taken into account semiclassically using a generalization to the condensed phase of the classical electron model of Miller and Meyer, which was applied to ICN

  1. PALS: A unique probe for the molecular organisation of biopolymer matrices

    NASA Astrophysics Data System (ADS)

    Roussenova, M.; Alam, M. A.

    2013-06-01

    This short review aims to illustrate the versatility of Positron Annihilation Lifetime Spectroscopy (PALS) when utilized for the characterization of biopolymers (e.g.: starch, fractionated maltooligomers, gelatin and cellulose derivatives) commonly used for the formulation of pharmaceutical encapsulants. By showing examples from a number of recent PALS studies, we illustrate that this technique can be used to probe the changes in thermodynamic state and molecular packing for a wide range of biopolymer matrices as a function of temperature, matrix composition and water content. This provides a basis for establishing composition-structure-property relationships for these materials, which would eventually enable the rational control of their macroscopic properties and the design of optimal encapsulating matrices and intelligent drug delivery systems.

  2. 2-Carbamido-1,3-indandione - a Fluorescent Molecular Probe and Sunscreen Candidate.

    PubMed

    Enchev, Venelin; Angelov, Ivan; Mantareva, Vanya; Markova, Nadezhda

    2015-11-01

    The present work reports theoretical and experimental studies on the photophysical properties of two tautomeric forms of 2-carbamido-1,3-indandione (CAID). By means of UV-vis, steady-state and time-dependent fluorescence spectroscopy it is shown that both enol forms, 2-(hydroxylaminomethylidene)-indan-1,3-dione and 2-carboamide-1-hydroxy-3-oxo-indan, coexist in solution. On the base of spectroscopic studies of CAID interaction with human serum albumin and DNA sequences, it was shown that the compound has potential and it is suitable for use as fluorescent molecular probe for investigation of different biomolecules. CAID shows relatively high photostability within 3 h irradiation period. Such behavior of the investigated compound supposes possibilities for using of the CAID molecule as sunscreen because of strong absorption in UVA, UVB and UVC light spectra. PMID:26342735

  3. Development of Functional Fluorescent Molecular Probes for the Detection of Biological Substances

    PubMed Central

    Suzuki, Yoshio; Yokoyama, Kenji

    2015-01-01

    This review is confined to sensors that use fluorescence to transmit biochemical information. Fluorescence is, by far, the most frequently exploited phenomenon for chemical sensors and biosensors. Parameters that define the application of such sensors include intensity, decay time, anisotropy, quenching efficiency, and luminescence energy transfer. To achieve selective (bio)molecular recognition based on these fluorescence phenomena, various fluorescent elements such as small organic molecules, enzymes, antibodies, and oligonucleotides have been designed and synthesized over the past decades. This review describes the immense variety of fluorescent probes that have been designed for the recognitions of ions, small and large molecules, and their biological applications in terms of intracellular fluorescent imaging techniques. PMID:26095660

  4. Imaging and therapeutic applications of zinc(ii)-dipicolylamine molecular probes for anionic biomembranes.

    PubMed

    Rice, Douglas R; Clear, Kasey J; Smith, Bradley D

    2016-07-01

    This feature article describes the development of synthetic zinc(ii)-dipicolylamine (ZnDPA) receptors as selective targeting agents for anionic membranes in cell culture and living subjects. There is a strong connection between anionic cell surface charge and disease, and ZnDPA probes have been employed extensively for molecular imaging and targeted therapeutics. Fluorescence and nuclear imaging applications include detection of diseases such as cancer, neurodegeneration, arthritis, and microbial infection, and also quantification of cell death caused by therapy. Therapeutic applications include selective targeting of cytotoxic agents and drug delivery systems, photodynamic inactivation, and modulation of the immune system. The article concludes with a summary of expected future directions. PMID:27302091

  5. Motion of Molecular Probes and Viscosity Scaling in Polyelectrolyte Solutions at Physiological Ionic Strength.

    PubMed

    Sozanski, Krzysztof; Wisniewska, Agnieszka; Kalwarczyk, Tomasz; Sznajder, Anna; Holyst, Robert

    2016-01-01

    We investigate transport properties of model polyelectrolyte systems at physiological ionic strength (0.154 M). Covering a broad range of flow length scales-from diffusion of molecular probes to macroscopic viscous flow-we establish a single, continuous function describing the scale dependent viscosity of high-salt polyelectrolyte solutions. The data are consistent with the model developed previously for electrically neutral polymers in a good solvent. The presented approach merges the power-law scaling concepts of de Gennes with the idea of exponential length scale dependence of effective viscosity in complex liquids. The result is a simple and applicable description of transport properties of high-salt polyelectrolyte solutions at all length scales, valid for motion of single molecules as well as macroscopic flow of the complex liquid. PMID:27536866

  6. Motion of Molecular Probes and Viscosity Scaling in Polyelectrolyte Solutions at Physiological Ionic Strength

    PubMed Central

    Sozanski, Krzysztof; Wisniewska, Agnieszka; Kalwarczyk, Tomasz; Sznajder, Anna; Holyst, Robert

    2016-01-01

    We investigate transport properties of model polyelectrolyte systems at physiological ionic strength (0.154 M). Covering a broad range of flow length scales—from diffusion of molecular probes to macroscopic viscous flow—we establish a single, continuous function describing the scale dependent viscosity of high-salt polyelectrolyte solutions. The data are consistent with the model developed previously for electrically neutral polymers in a good solvent. The presented approach merges the power-law scaling concepts of de Gennes with the idea of exponential length scale dependence of effective viscosity in complex liquids. The result is a simple and applicable description of transport properties of high-salt polyelectrolyte solutions at all length scales, valid for motion of single molecules as well as macroscopic flow of the complex liquid. PMID:27536866

  7. In vivo targeting of cell death using a synthetic fluorescent molecular probe

    PubMed Central

    Smith, Bryan A.; Xiao, Shuzhang; Wolter, William; Wheeler, James; Suckow, Mark A.

    2011-01-01

    A synthetic, near-infrared, fluorescent probe, named PSS-794 was assessed for its ability to detect cell death in two animal models. The molecular probe contains a zinc(II)-dipicolylamine (Zn2+-DPA) affinity ligand that selectively targets exposed phosphatidylserine on the surface of dead and dying cells. The first animal model used rats that were treated with dexamethasone to induce thymic atrophy. Ex vivo fluorescence imaging and histological analysis of excised organs showed thymus uptake of PSS-794 was four times higher than a control fluorophore that lacked the Zn2+-DPA affinity ligand. In addition, the presence of PSS-794 produced a delayed and higher build up of dead and dying cells in the rat thymus. The second animal model employed focal beam radiation to induce cell death in tumor-bearing rats. Whole-body and ex vivo imaging showed that the amount of PSS-794 in a radiation-treated tumor was almost twice that in a non-treated tumor. The results indicate that PSS-794 may be useful for pre-clinical optical detection of tumor cell death due to therapy. PMID:21499791

  8. Probing Solvation Dynamics around Aromatic and Biological Molecules at the Single-Molecular Level.

    PubMed

    Dopfer, Otto; Fujii, Masaaki

    2016-05-11

    Solvation processes play a crucial role in chemical reactions and biomolecular recognition phenomena. Although solvation dynamics of interfacial or biological water has been studied extensively in aqueous solution, the results are generally averaged over several solvation layers and the motion of individual solvent molecules is difficult to capture. This review describes the development and application of a new experimental approach, namely, picosecond time-resolved pump-probe infrared spectroscopy of size- and isomer-selected aromatic clusters, in which for the first time the dynamics of a single individual solvent molecule can be followed in real time. The intermolecular isomerization reaction is triggered by resonant photoionization (pump), and infrared photodissociation (probe) at variable delay generates the spectroscopic signature of salient properties of the reaction, including rates, yields, pathways, branching ratios of competing reactions, existence of reaction intermediates, occurrence of back reactions, and time scales of energy relaxation processes. It is shown that this relevant information can reliably be decoded from the experimental spectra by sophisticated molecular dynamics simulations. This review covers a description of the experimental strategies and spectroscopic methods along with all applications to date, which range from aromatic clusters with nonpolar solvent molecules to aromatic monohydrated biomolecules. PMID:27054835

  9. Nanolithography by scanning probes on calixarene molecular glass resist using mix-and-match lithography

    NASA Astrophysics Data System (ADS)

    Kaestner, Marcus; Hofer, Manuel; Rangelow, Ivo W.

    2013-07-01

    Going "beyond the CMOS information-processing era," taking advantage of quantum effects occurring at sub-10-nm level, requires novel device concepts and associated fabrication technologies able to produce promising features at acceptable cost levels. Herein, the challenge affecting the lithographic technologies comprises the marriage of down-scaling the device-relevant feature size towards single-nanometer resolution with a simultaneous increase of the throughput capabilities. Mix-and-match lithographic strategies are one promising path to break through this trade-off. Proof-of-concept combining electron beam lithography (EBL) with the outstanding capabilities of closed-loop electric field current-controlled scanning probe nanolithography (SPL) is demonstrated. This combination, whereby also extreme ultraviolet lithography (EUVL) is possible instead of EBL, enables more: improved patterning resolution and reproducibility in combination with excellent overlay and placement accuracy. Furthermore, the symbiosis between EBL (EUVL) and SPL expands the process window of EBL (EUVL) beyond the state of the art, allowing SPL-based pre- and post-patterning of EBL (EUVL) written features at critical dimension levels with scanning probe microscopy-based pattern overlay alignment capability. Moreover, we are able to modify the EBL (EUVL) pattern even after the development step. The ultra-high resolution mix-and-match lithography experiments are performed on the molecular glass resist calixarene using a Gaussian e-beam lithography system operating at 10 keV and a home-developed SPL setup.

  10. Molecular probes for two-photon excited fluorescence and second harmonic generation imaging of biological membranes

    NASA Astrophysics Data System (ADS)

    Porres, Laurent; Mongin, Olivier; Bhatthula, Bharath K. G.; Blanchard-Desce, Mireille H.; Ventelon, Lionel; Moreaux, Laurent; Pons, T.; Mertz, Jerome

    2002-11-01

    Novel microscopies based on nonlinear optical (NLO) phenomena are attracting increasing interest in the biology community owing to their potentialities in the area of real-time, non-damaging imaging of biological systems. In particular, second-harmonic generation (SHG) and two-photon excited fluorescence (TPEF) are NLO phenomena that scale with excitation intensity squared, and thus give rise to an intrinsic 3-dimensional resolution when used in microscopic imaging. In this perspective, we have implemented a molecular engineering approach toward NLO-probes specifically designed for SHG and/or TPEF imaging of cellular membranes. We have designed nanoscale rod-like fluorophores showing very large TPEF cross-sections in the visible red, outperforming standard fluorophores such as fluorescein by up to two orders of magnitude. Bolaamphiphilic derivatives combining high TPEF cross-sections and affinity for cellular membranes were prepared. Their incorporation into model or cell membranes can be monitored by TPEF microscopy. Amphiphilic push-pull chromophores showing both high TPA and SHG cross-sections in the near-IR region were designed as NLO-probes for imaging of biological membranes by simultaneous SHG and TPEF microscopy. These NLO-phores offer intriguing potentialities for imaging of fundamental biological processes such as adhesion, fusion or for reporting of membrane electrical potentials.

  11. Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design.

    PubMed

    Tan, Yaw Sing; Reeks, Judith; Brown, Christopher J; Thean, Dawn; Ferrer Gago, Fernando Jose; Yuen, Tsz Ying; Goh, Eunice Tze Leng; Lee, Xue Er Cheryl; Jennings, Claire E; Joseph, Thomas L; Lakshminarayanan, Rajamani; Lane, David P; Noble, Martin E M; Verma, Chandra S

    2016-09-01

    Protein flexibility poses a major challenge in binding site identification. Several computational pocket detection methods that utilize small-molecule probes in molecular dynamics (MD) simulations have been developed to address this issue. Although they have proven hugely successful at reproducing experimental structural data, their ability to predict new binding sites that are yet to be identified and characterized has not been demonstrated. Here, we report the use of benzenes as probe molecules in ligand-mapping MD (LMMD) simulations to predict the existence of two novel binding sites on the surface of the oncoprotein MDM2. One of them was serendipitously confirmed by biophysical assays and X-ray crystallography to be important for the binding of a new family of hydrocarbon stapled peptides that were specifically designed to target the other putative site. These results highlight the predictive power of LMMD and suggest that predictions derived from LMMD simulations can serve as a reliable basis for the identification of novel ligand binding sites in structure-based drug design. PMID:27532490

  12. Thioflavin T as a fluorescence probe for monitoring RNA metabolism at molecular and cellular levels.

    PubMed

    Sugimoto, Shinya; Arita-Morioka, Ken-ichi; Mizunoe, Yoshimitsu; Yamanaka, Kunitoshi; Ogura, Teru

    2015-08-18

    The intrinsically stochastic dynamics of mRNA metabolism have important consequences on gene regulation and non-genetic cell-to-cell variability; however, no generally applicable methods exist for studying such stochastic processes quantitatively. Here, we describe the use of the amyloid-binding probe Thioflavin T (ThT) for monitoring RNA metabolism in vitro and in vivo. ThT fluoresced strongly in complex with bacterial total RNA than with genomic DNA. ThT bound purine oligoribonucleotides preferentially over pyrimidine oligoribonucleotides and oligodeoxyribonucleotides. This property enabled quantitative real-time monitoring of poly(A) synthesis and phosphorolysis by polyribonucleotide phosphorylase in vitro. Cellular analyses, in combination with genetic approaches and the transcription-inhibitor rifampicin treatment, demonstrated that ThT mainly stained mRNA in actively dividing Escherichia coli cells. ThT also facilitated mRNA metabolism profiling at the single-cell level in diverse bacteria. Furthermore, ThT can also be used to visualise transitions between non-persister and persister cell states, a phenomenon of isogenic subpopulations of antibiotic-sensitive bacteria that acquire tolerance to multiple antibiotics due to stochastically induced dormant states. Collectively, these results suggest that probing mRNA dynamics with ThT is a broadly applicable approach ranging from the molecular level to the single-cell level. PMID:25883145

  13. Synthesis and characterization of arylamine derivatives of rauwolscine as molecular probes for alpha 2-adrenergic receptors

    SciTech Connect

    Lanier, S.M.; Graham, R.M.; Hess, H.J.; Grodski, A.; Repaske, M.G.; Nunnari, J.M.; Limbird, L.E.; Homcy, C.J.

    1987-06-01

    The selective alpha 2-adrenergic receptor antagonist rauwolscine was structurally modified to yield a series of arylamine carboxamide derivatives, which were investigated as potential molecular probes for the localization and structural characterization of alpha 2-adrenergic receptors. The arylamine carboxamides differ in the number of carbon atoms separating the reactive phenyl moiety from the fused ring structure of the parent compound, rauwolscine carboxylate. Competitive inhibition studies with (/sup 3/H)rauwolscine in rat kidney membranes indicate that the affinity for the carboxamide derivatives is inversely related to the length of the carbon spacer arm with rauwolscine 4-aminophenyl carboxamide exhibiting the highest affinity (Kd = 2.3 +/- 0.2 nM). Radioiodination of rau-AMPC yields a ligand, /sup 125/I-rau-AMPC, which binds to rat kidney alpha 2-adrenergic receptors with high affinity, as determined by both kinetic analysis (Kd = k2/k1 = 0.016 min-1/2.1 X 10(7) M-1 min-1 = 0.76 nM) and equilibrium binding studies (Kd = 0.78 +/- 0.16 nM). /sup 125/I-rau-AMPC was quantitatively converted to the photolabile arylazide derivative 17 alpha-hydroxy-20 alpha-yohimban-16 beta-(N-4-azido-3-(/sup 125/I)iodophenyl) carboxamide (/sup 125/I-rau-AZPC). In a partially purified receptor preparation from porcine brain, this compound photolabels a major (Mr = 62,000) peptide. The labeling of this peptide is inhibited by adrenergic agonists and antagonists with a rank order of potency consistent with an alpha 2-adrenergic receptor binding site. Both /sup 125/I-rau-AMPC and the photolabile arylazide derivative, /sup 125/I-rau-AZPC, should prove useful as molecular probes for the structural and biochemical characterization of alpha 2-adrenergic receptors.

  14. Double-cladding-fiber-based detection system for intravascular mapping of fluorescent molecular probes

    NASA Astrophysics Data System (ADS)

    Razansky, R. Nika; Rozental, Amir; Mueller, Mathias S.; Deliolanis, Nikolaos; Jaffer, Farouc A.; Koch, Alexander W.; Ntziachristos, Vasilis

    2011-03-01

    Early detection of high-risk coronary atherosclerosis remains an unmet clinical challenge. We have previously demonstrated a near-infrared fluorescence catheter system for two-dimensional intravascular detection of fluorescence molecular probes [1]. In this work we improve the system performance by introducing a novel high resolution sensor. The main challenge of the intravascular sensor is to provide a highly focused spot at an application relevant distance on one hand and a highly efficient collection of emitted light on the other. We suggest employing a double cladding optical fiber (DCF) in combination with focusing optics to provide a sensor with both highly focused excitation light and highly efficient fluorescent light collection. The excitation laser is coupled into the single mode core of DCF and guided through a focusing element and a right angle prism. The resulting side-fired beam exhibits a small spot diameter (50 μm) throughout a distance of up to 2 mm from the sensor. This is the distance of interest for intravascular coronary imaging application, determined by an average human coronary artery diameter. At the blood vessel wall, an activatable fluorescence molecular probe is excited in the diseased lesions. Next light of slightly shifted wavelength emits only in the places of the inflammations, associated with dangerous plaques [2]. The emitted light is collected by the cladding of the DCF, with a large collection angle (NA=0.4). The doublecladding acts as multimodal fiber and guides the collected light to the photo detection elements. The sensor automatically rotates and pulled-back, while each scanned point is mapped according to the amount of detected fluorescent emission. The resulting map of fluorescence activity helps to associate the atherosclerotic plaques with the inflammation process. The presented detection system is a valuable tool in the intravascular plaque detection and can help to differentiate the atherosclerotic plaques based on

  15. Molecular fiber sensor probes based on surface enhanced Raman scattering (SERS)

    NASA Astrophysics Data System (ADS)

    Shi, Chao

    Molecular sensors based on surface enhanced Raman scattering (SERS) and optical fibers have been widely used in biological, environmental and chemical detection procedures due to their unique advantages, such as molecular specificity, high sensitivity and flexibility. In this thesis, I review the development and highlight some of the important milestones of SERS fiber sensor development with emphasis on recent work to improve the sensitivity of the fiber sensors. In particular in the area to increase the sensitivity, we've developed various methods of sample preparation as well as different fiber SERS sensors. One way is to strengthen the field enhancement around the surface of the probe tip and the other is to increase the number of the interacting particles during the SERS process. These techniques are known as the double substrate "sandwich" structure (DSSS) and the liquid core photonic crystal fiber (LCPCF) respectively, and in both cases the sensitivities are significantly improved. The combination of these two mechanisms is also proposed as inner wall coated hollow core waveguide (IWCHCW). As the portable Raman spectrometer is developed and commercially available, a portable fiber SERS sensor system is demonstrated as well in order to make it practical in out of laboratory applications. These fiber sensors were tested with Rhodamine 6G, human insulin, tryptophan, prostate specific antigen, and alpha-synuclein and showed excellent performance.

  16. Targeted next-generation sequencing for the detection of ciprofloxacin resistance markers using molecular inversion probes

    PubMed Central

    Stefan, Christopher P.; Koehler, Jeffrey W.; Minogue, Timothy D.

    2016-01-01

    Antibiotic resistance (AR) is an epidemic of increasing magnitude requiring rapid identification and profiling for appropriate and timely therapeutic measures and containment strategies. In this context, ciprofloxacin is part of the first-line of countermeasures against numerous high consequence bacteria. Significant resistance can occur via single nucleotide polymorphisms (SNP) and deletions within ciprofloxacin targeted genes. Ideally, use of ciprofloxacin would be prefaced with AR determination to avoid overuse or misuse of the antibiotic. Here, we describe the development and evaluation of a panel of 44 single-stranded molecular inversion probes (MIPs) coupled to next-generation sequencing (NGS) for the detection of genetic variants known to confer ciprofloxacin resistance in Bacillus anthracis, Yersinia pestis, and Francisella tularensis. Sequencing results demonstrate MIPs capture and amplify targeted regions of interest at significant levels of coverage. Depending on the genetic variant, limits of detection (LOD) for high-throughput pooled sequencing ranged from approximately 300–1800 input genome copies. LODs increased 10-fold in the presence of contaminating human genome DNA. In addition, we show that MIPs can be used as an enrichment step with high resolution melt (HRM) real-time PCR which is a sensitive assay with a rapid time-to-answer. Overall, this technology is a multiplexable upfront enrichment applicable with multiple downstream molecular assays for the detection of targeted genetic regions. PMID:27174456

  17. Molecular Bottlebrushes as Tensile Machines for Probing Specific Bonds under Tension

    NASA Astrophysics Data System (ADS)

    Li, Yuanchao; Nese, Alper; Lebedeva, Natalia; Davis, Tyler; Matyjaszewski, Krzysztof; Sheiko, Sergei

    2012-02-01

    Significant tension on the order of 1 nN is self-generated along the backbone of bottlebrush macromolecules due to steric repulsion between densely grafted side chains. The intrinsic tension is amplified upon adsorption of bottlebrush molecules onto a substrate and increases with grafting density, side chain length, and strength of adhesion of the substrate. This allows us to employ these molecular bottlebrushes as miniature tensile machines to probe the mechanochemistry of specific bonds. For this purpose, bottlebrush macromolecules with a disulfide linker in the middle of the backbone were synthesized by atom transfer radical polymerization (ATRP). Two processes, (i) homolytic cleavage of disulfide and (ii) scission of disulfide due to reduction by dithiothreitol were monitored through molecular imaging by atomic force microscope (AFM). In both cases, the corresponding rate constants increase exponentially with mechanical tension along the disulfide bond. Moreover, the reduction rate at zero force is found to be significantly lower than that in bulk solution, which suggests an acidic composition of the water surface with pH=3.7. This opens a new application of brush-like macromolecules as surface pH sensors.

  18. Probing flexibility in porphyrin-based molecular wires using double electron electron resonance.

    PubMed

    Lovett, Janet E; Hoffmann, Markus; Cnossen, Arjen; Shutter, Alexander T J; Hogben, Hannah J; Warren, John E; Pascu, Sofia I; Kay, Christopher W M; Timmel, Christiane R; Anderson, Harry L

    2009-09-30

    A series of butadiyne-linked zinc porphyrin oligomers, with one, two, three, and four porphyrin units and lengths of up to 75 A, have been spin-labeled at both ends with stable nitroxide TEMPO radicals. The pulsed EPR technique of double electron electron resonance (DEER) was used to probe the distribution of intramolecular end-to-end distances, under a range of conditions. DEER measurements were carried out at 50 K in two types of dilute solution glasses: deutero-toluene (with 10% deutero-pyridine) and deutero-o-terphenyl (with 5% 4-benzyl pyridine). The complexes of the porphyrin oligomers with monodentate ligands (pyridine or 4-benzyl pyridine) principally adopt linear conformations. Nonlinear conformations are less populated in the lower glass-transition temperature solvent. When the oligomers bind star-shaped multidentate ligands, they are forced to bend into nonlinear geometries, and the experimental end-to-end distances for these complexes match those from molecular mechanics calculations. Our results show that porphyrin-based molecular wires are shape-persistent, and yet that their shapes can deformed by binding to multivalent ligands. Self-assembled ladder-shaped 2:2 complexes were also investigated to illustrate the scope of DEER measurements for providing structural information on synthetic noncovalent nanostructures. PMID:19736940

  19. Molecular probes based on microstructured fibers and surface enhanced Raman scattering

    NASA Astrophysics Data System (ADS)

    Zhang, Yi; Shi, Chao; Gu, Claire; Seballos, Leo; Schwartzberg, Adam; Zhang, Jin Z.; Chen, Bin

    2007-09-01

    In recent years, there has been significant interest in using surface enhanced Raman scattering (SERS) and optical fibers for chemical, biological, and environmental detections. The combination of SERS and optical fibers offers the advantages of the molecular specificity of Raman scattering, huge enhancement factor of SERS, and flexibility of optical fibers. In this paper, we report our work on the development of fiber biosensors based on SERS emphasizing on recent progress in the fabrication of photonic crystal fiber (PCF) SERS sensors for highly sensitive molecular detection. To increase the sensitivity, one needs to increase either the excitation laser power or the amount of analyte molecules in the active region of the sensor. The high excitation intensity is not desirable for biosensors due to the low damage threshold of live tissues or bio-molecules. In our investigation of various fiber configurations, hollow core (HC) PCFs show the greatest advantages over all other types of fiber probes because of the large contact area. The hollow core nature allows the analytes and SERS substrate to fill the inner surface of the air channels. In addition, by sealing the cladding holes of the HCPCF, only the central hole will be open and filled with liquid samples. As both the light and the sample are confined in the fiber core, the sensitivity is significantly improved. The newly developed liquid core PCF sensor was tested in the detection of rhodamine 6G (R6G), human insulin, and tryptophan with good sensitivity due to the enhanced interaction volume.

  20. Patterning a hydrogen-bonded molecular monolayer with a hand-controlled scanning probe microscope.

    PubMed

    Green, Matthew F B; Esat, Taner; Wagner, Christian; Leinen, Philipp; Grötsch, Alexander; Tautz, F Stefan; Temirov, Ruslan

    2014-01-01

    One of the paramount goals in nanotechnology is molecular-scale functional design, which includes arranging molecules into complex structures at will. The first steps towards this goal were made through the invention of the scanning probe microscope (SPM), which put single-atom and single-molecule manipulation into practice for the first time. Extending the controlled manipulation to larger molecules is expected to multiply the potential of engineered nanostructures. Here we report an enhancement of the SPM technique that makes the manipulation of large molecular adsorbates much more effective. By using a commercial motion tracking system, we couple the movements of an operator's hand to the sub-angstrom precise positioning of an SPM tip. Literally moving the tip by hand we write a nanoscale structure in a monolayer of large molecules, thereby showing that our method allows for the successful execution of complex manipulation protocols even when the potential energy surface that governs the interaction behaviour of the manipulated nanoscale object(s) is largely unknown. PMID:25383304

  1. Patterning a hydrogen-bonded molecular monolayer with a hand-controlled scanning probe microscope

    PubMed Central

    Green, Matthew F B; Esat, Taner; Wagner, Christian; Leinen, Philipp; Grötsch, Alexander; Tautz, F Stefan

    2014-01-01

    Summary One of the paramount goals in nanotechnology is molecular-scale functional design, which includes arranging molecules into complex structures at will. The first steps towards this goal were made through the invention of the scanning probe microscope (SPM), which put single-atom and single-molecule manipulation into practice for the first time. Extending the controlled manipulation to larger molecules is expected to multiply the potential of engineered nanostructures. Here we report an enhancement of the SPM technique that makes the manipulation of large molecular adsorbates much more effective. By using a commercial motion tracking system, we couple the movements of an operator's hand to the sub-angstrom precise positioning of an SPM tip. Literally moving the tip by hand we write a nanoscale structure in a monolayer of large molecules, thereby showing that our method allows for the successful execution of complex manipulation protocols even when the potential energy surface that governs the interaction behaviour of the manipulated nanoscale object(s) is largely unknown. PMID:25383304

  2. Biomarkers and Molecular Probes for Cell Death Imaging and Targeted Therapeutics

    PubMed Central

    Smith, Bryan A.; Smith, Bradley D.

    2012-01-01

    Cell death is a critically important biological process. Disruption of homeostasis, either by excessive or deficient cell death, is a hallmark of many pathological conditions. Recent research advances have greatly increased our molecular understanding of cell death and its role in a range of diseases and therapeutic treatments. Central to these ongoing research and clinical efforts is the need for imaging technologies that can locate and identify cell death in a wide array of in vitro and in vivo biomedical samples with varied spatiotemporal requirements. This review article summarizes community efforts over the past five years to identify useful biomarkers for dead and dying cells, and to develop molecular probes that target these biomarkers for optical, radionuclear, or magnetic resonance imaging. Apoptosis biomarkers are classified as either intracellular (caspase enzymes, mitochondrial membrane potential, cytosolic proteins) or extracellular (plasma membrane phospholipids, membrane potential, surface exposed histones). Necrosis, autophagy, and senescence biomarkers are described, as well as unexplored cell death biomarkers. The article discusses possible chemotherapeutic and theranostic strategies, and concludes with a summary of current challenges and expected eventual rewards of clinical cell death imaging. PMID:22989049

  3. Targeted next-generation sequencing for the detection of ciprofloxacin resistance markers using molecular inversion probes.

    PubMed

    Stefan, Christopher P; Koehler, Jeffrey W; Minogue, Timothy D

    2016-01-01

    Antibiotic resistance (AR) is an epidemic of increasing magnitude requiring rapid identification and profiling for appropriate and timely therapeutic measures and containment strategies. In this context, ciprofloxacin is part of the first-line of countermeasures against numerous high consequence bacteria. Significant resistance can occur via single nucleotide polymorphisms (SNP) and deletions within ciprofloxacin targeted genes. Ideally, use of ciprofloxacin would be prefaced with AR determination to avoid overuse or misuse of the antibiotic. Here, we describe the development and evaluation of a panel of 44 single-stranded molecular inversion probes (MIPs) coupled to next-generation sequencing (NGS) for the detection of genetic variants known to confer ciprofloxacin resistance in Bacillus anthracis, Yersinia pestis, and Francisella tularensis. Sequencing results demonstrate MIPs capture and amplify targeted regions of interest at significant levels of coverage. Depending on the genetic variant, limits of detection (LOD) for high-throughput pooled sequencing ranged from approximately 300-1800 input genome copies. LODs increased 10-fold in the presence of contaminating human genome DNA. In addition, we show that MIPs can be used as an enrichment step with high resolution melt (HRM) real-time PCR which is a sensitive assay with a rapid time-to-answer. Overall, this technology is a multiplexable upfront enrichment applicable with multiple downstream molecular assays for the detection of targeted genetic regions. PMID:27174456

  4. Probing the molecular design of hyper-branched aryl polyesters towards lubricant applications

    DOE PAGESBeta

    Robinson, Joshua W.; Zhou, Yan; Bhattacharya, Priyanka; Erck, Robert; Qu, Jun; Bays, J. Timothy; Cosimbescu, Lelia

    2016-01-05

    We report novel polymeric materials that may be used as viscosity index improvers (VII) for lubricant applications. Our efforts included probing the comb-burst hyper-branched aryl polyester architecture for beneficial viscosity and friction behavior when utilized as an additive in a group I oil. The monomer was designed as to undergo polymerization via polycondensation within the architectural construct (AB2), typical of hyperbranched polymers. The monomer design was comprised of aliphatic arms (12 or 16 methylenes) to provide the necessary lipophilicity to achieve solubility in a non-polar medium. Once polymerized, via catalyst and heat, the surface alcohols were functionalized with fatty acidsmore » (lauric and palmitic). Controlling the aliphatic nature of the internal arms and peripheral end-groups provided four unique flexible polymer designs. Changing the reaction time and concentration provided opportunities to investigate the influence of molecular weight and branching density on oil-solubility, viscosity, and friction. Oil-solubility was found to decrease with fewer internal carbons, but the number of internal carbons appears to have little influence on the bulk solution viscosity. Increased branching and degree of polymerization, and thus molecular weight, were found to reduce the solubility of these systems in the base oil. At concentrations of 2 wt % in a group I base oil, these polymer additives demonstrated improved viscosity index and reduced friction coefficient, validating the basic approach.« less

  5. Rational chemical design of the next generation of molecular imaging probes based on physics and biology: mixing modalities, colors and signals

    PubMed Central

    Longmire, Michelle R.; Ogawa, Mikako; Choyke, Peter L.

    2012-01-01

    In recent years, numerous in vivo molecular imaging probes have been developed. As a consequence, much has been published on the design and synthesis of molecular imaging probes focusing on each modality, each type of material, or each target disease. More recently, second generation molecular imaging probes with unique, multi-functional, or multiplexed characteristics have been designed. This critical review focuses on (i) molecular imaging using combinations of modalities and signals that employ the full range of the electromagnetic spectra, (ii) optimized chemical design of molecular imaging probes for in vivo kinetics based on biology and physiology across a range of physical sizes, (iii) practical examples of second generation molecular imaging probes designed to extract complementary data from targets using multiple modalities, color, and comprehensive signals (277 references). PMID:21607237

  6. A transient molecular probe for characterizing the surface properties of TiO II nanoparticle in colloidal solution

    NASA Astrophysics Data System (ADS)

    Weng, Yu-Xiang; Du, Lu-Chao; Zhang, Qing-Li

    2006-08-01

    A transient molecular probe for characterization of the surface properties of TiO II nanoparticles in colloidal solution has been developed recently in our laboratory. The probe molecule is all-trans-retinoic acid (ATRA) adsorbed on the TiO2 nanoparticle surface. After photoexcitation, the photoinduced interfacial charge recombination would generate ATRA triplet state (ATRA T) with a substantial quantum yield. While the quantum yield of triplet ATRA generated in the solution phase is substantially low, which renders the interfacial-charge-recombination generated triplet ATRA being a transient probe molecule specific only to the interface. It is found that the triplet-triplet absorption spectrum of ATRA adsorbed molecule is sensitive to its binding form with the surface Ti atom through the carboxylic group, as well as to the polarity of the medium. Especially the apparent lifetime of ATRA T at the TiO II surface changes substantially when the local polarity around the TiO II nanoparticle changes. We found that the ATRAT monolayer adsorbed at the TiO II surface can be used as a transient molecular probe for the surface binding forms, coordination state of the surface Ti atoms and the light-induced wettability change of the TiO II nanoparticle. TiO II nanoparticle, all-trans-retinoic acid, molecular probe, interfacial charge recombination, surface binding form, light-induced wettability change.

  7. A New Probe of the Molecular Gas Content in Galaxies: Application to M101

    NASA Technical Reports Server (NTRS)

    Smith, Denise A.; Allen, Ronald J.; Bohlin, Ralph C.; Nicholson, Natalya; Stecher, Theodore P.

    1999-01-01

    Recent studies of nearby spiral galaxies suggest that photodissoiation regions (PDRS) are capable of producing much of the observed HI in galaxy disks. In that case, measurements of the observed HI column density and the far-ultraviolet (FUV) photon flux responsible for the photodissociation process provide a new probe of the volume density of the local underlying molecular hydrogen. We develop the method and apply it to the giant Scd spiral M101. The HI column density and amount of FUV emission have been measured for a sample of 35 candidate PDRs located throughout the disk of M101 using the Very Large Array and the Ultraviolet Imaging Telescope. We find that, after correction for the known gradient of metallicity in the Interstellar Medium (ISM) of M101 and for the extinction of the ultraviolet emission, molecular gas with a narrow range of density from 30-1000/ cubic cm is found near star-forming regions at all radii in the disk of M101 out to a distance of 12 seconds approximately equals 26 kpc, close to the photometric limit of R(sub 25) approximately equals 13.5 seconds. In this picture, the ISM is virtually all molecular in the inner parts of M101. The strong decrease of the HI column density in the inner disk of the galaxy at R(sub G) < 10 kpc is a consequence of a strong increase in the dust-to-gas ratio there, resulting in an increase of the H(sub 2) formation rate on grains and a corresponding disappearance of hydrogen in its atomic form.

  8. High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays

    SciTech Connect

    Wang, Yuker; Carlton, Victoria E.H.; Karlin-Neumann, George; Sapolsky, Ronald; Zhang, Li; Moorhead, Martin; Wang, Zhigang C.; Richardson, Andrea L.; Warren, Robert; Walther, Axel; Bondy, Melissa; Sahin, Aysegul; Krahe, Ralf; Tuna, Musaffe; Thompson, Patricia A.; Spellman, Paul T.; Gray, Joe W.; Mills, Gordon B.; Faham, Malek

    2009-02-24

    A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small ({approx}40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue. Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE. MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.

  9. Continuous sensing of tumor-targeted molecular probes with a vertical cavity surface emitting laser-based biosensor

    NASA Astrophysics Data System (ADS)

    Parashurama, Natesh; O'Sullivan, Thomas D.; De La Zerda, Adam; El Kalassi, Pascale; Cho, Seongjae; Liu, Hongguang; Teed, Robert; Levy, Hart; Rosenberg, Jarrett; Cheng, Zhen; Levi, Ofer; Harris, James S.; Gambhir, Sanjiv S.

    2012-11-01

    Molecular optical imaging is a widespread technique for interrogating molecular events in living subjects. However, current approaches preclude long-term, continuous measurements in awake, mobile subjects, a strategy crucial in several medical conditions. Consequently, we designed a novel, lightweight miniature biosensor for in vivo continuous optical sensing. The biosensor contains an enclosed vertical-cavity surface-emitting semiconductor laser and an adjacent pair of near-infrared optically filtered detectors. We employed two sensors (dual sensing) to simultaneously interrogate normal and diseased tumor sites. Having established the sensors are precise with phantom and in vivo studies, we performed dual, continuous sensing in tumor (human glioblastoma cells) bearing mice using the targeted molecular probe cRGD-Cy5.5, which targets αVβ3 cell surface integrins in both tumor neovasculature and tumor. The sensors capture the dynamic time-activity curve of the targeted molecular probe. The average tumor to background ratio after signal calibration for cRGD-Cy5.5 injection is approximately 2.43±0.95 at 1 h and 3.64±1.38 at 2 h (N=5 mice), consistent with data obtained with a cooled charge coupled device camera. We conclude that our novel, portable, precise biosensor can be used to evaluate both kinetics and steady state levels of molecular probes in various disease applications.

  10. Continuous sensing of tumor-targeted molecular probes with a vertical cavity surface emitting laser-based biosensor

    PubMed Central

    Parashurama, Natesh; O’Sullivan, Thomas D.; De La Zerda, Adam; El Kalassi, Pascale; Cho, Seongjae; Liu, Hongguang; Teed, Robert; Levy, Hart; Rosenberg, Jarrett; Cheng, Zhen; Levi, Ofer; Harris, James S.

    2012-01-01

    Abstract. Molecular optical imaging is a widespread technique for interrogating molecular events in living subjects. However, current approaches preclude long-term, continuous measurements in awake, mobile subjects, a strategy crucial in several medical conditions. Consequently, we designed a novel, lightweight miniature biosensor for in vivo continuous optical sensing. The biosensor contains an enclosed vertical-cavity surface-emitting semiconductor laser and an adjacent pair of near-infrared optically filtered detectors. We employed two sensors (dual sensing) to simultaneously interrogate normal and diseased tumor sites. Having established the sensors are precise with phantom and in vivo studies, we performed dual, continuous sensing in tumor (human glioblastoma cells) bearing mice using the targeted molecular probe cRGD-Cy5.5, which targets αVβ3 cell surface integrins in both tumor neovasculature and tumor. The sensors capture the dynamic time-activity curve of the targeted molecular probe. The average tumor to background ratio after signal calibration for cRGD-Cy5.5 injection is approximately 2.43±0.95 at 1 h and 3.64±1.38 at 2 h (N=5 mice), consistent with data obtained with a cooled charge coupled device camera. We conclude that our novel, portable, precise biosensor can be used to evaluate both kinetics and steady state levels of molecular probes in various disease applications. PMID:23123976

  11. Molecular probes and microarrays for the detection of toxic algae in the genera Dinophysis and Phalacroma (Dinophyta).

    PubMed

    Edvardsen, Bente; Dittami, Simon M; Groben, René; Brubak, Sissel; Escalera, Laura; Rodríguez, Francisco; Reguera, Beatriz; Chen, Jixin; Medlin, Linda K

    2013-10-01

    Dinophysis and Phalacroma species containing diarrheic shellfish toxins and pectenotoxins occur in coastal temperate waters all year round and prevent the harvesting of mussels during several months each year in regions in Europe, Chile, Japan, and New Zealand. Toxicity varies among morphologically similar species, and a precise identification is needed for early warning systems. Molecular techniques using ribosomal DNA sequences offer a means to identify and detect precisely the potentially toxic species. We designed molecular probes targeting the 18S rDNA at the family and genus levels for Dinophysis and Phalacroma and at the species level for Dinophysis acuminata, Dinophysis acuta, and Dinophysis norvegica, the most commonly occurring, potentially toxic species of these genera in Western European waters. Dot blot hybridizations with polymerase chain reaction (PCR)-amplified rDNA from 17 microalgae were used to demonstrate probe specificity. The probes were modified along with other published fluorescence in situ hybridization and PCR probes and tested for a microarray platform within the MIDTAL project ( http://www.midtal.com ). The microarray was applied to field samples from Norway and Spain and compared to microscopic cell counts. These probes may be useful for early warning systems and monitoring and can also be used in population dynamic studies to distinguish species and life cycle stages, such as cysts, and their distribution in time and space. PMID:23263760

  12. Aromatic units from the macromolecular material in meteorites: Molecular probes of cosmic environments

    NASA Astrophysics Data System (ADS)

    Sephton, Mark A.

    2013-04-01

    Ancient meteorites contain several percent of organic matter that represents a chronicle of chemical evolution in the early solar system. Aromatic hydrocarbon units make up the majority of meteorite organic matter but reading their record of organic evolution is not straightforward and their formation mechanisms have remained elusive. Most aromatic units reside in a macromolecular material and new perceptions of its structure have been provided by a novel on-line hydrogenation approach. When applied to the Orgueil (CI1) and Murchison (CM2) meteorites the technique releases a range of aromatic hydrocarbons along with some oxygen, sulphur and nitrogen-containing aromatic units. When on-line hydrogenation is compared to conventional pyrolysis, more high molecular weight units and a wider range of liberated entities are evident. Comparisons of results from Orgueil and Murchison reveal variations that are most likely related to differing levels of parent body alteration. The enhancement of straight-chain hydrocarbons (n-alkanes) in the hydrogenation products imply a source of these common contaminants from straight-chain carboxylic acid (n-alkanoic acid) precursors, perhaps from bacterial contributions on Earth. The on-line hydrogenation data also highlight a long-standing but unexplained observation related to the relative preference for specific isomers in methyl-substituted benzenes (meta-, ortho- and para-xylenes). The new hydrogenation approach appears to release and transform macromolecular material meta-structures (benzenes with substituents separated by single carbon atoms) into their free hydrocarbon counterparts. Their release characteristics suggest that the meta-structures are bound by oxygen-linkages. The meta-structures may be molecular probes of specific ancient cosmic environments. Parent body processing may have performed a similar function as hydrogenation to produce the most common meta configuration for free substituted benzenes. Notably, this

  13. Detection of enzyme activity in orthotopic murine breast cancer by fluorescence lifetime imaging using a fluorescence resonance energy transfer-based molecular probe

    NASA Astrophysics Data System (ADS)

    Solomon, Metasebya; Guo, Kevin; Sudlow, Gail P.; Berezin, Mikhail Y.; Edwards, W. Barry; Achilefu, Samuel; Akers, Walter J.

    2011-06-01

    Cancer-related enzyme activity can be detected noninvasively using activatable fluorescent molecular probes. In contrast to ``always-on'' fluorescent molecular probes, activatable probes are relatively nonfluorescent at the time of administration due to intramolecular fluorescence resonance energy transfer (FRET). Enzyme-mediated hydrolysis of peptide linkers results in reduced FRET and increase of fluorescence yield. Separation of signal from active and inactive probe can be difficult with conventional intensity-based fluorescence imaging. Fluorescence lifetime (FLT) measurement is an alternative method to detect changes in FRET. Thus, we investigate FLT imaging for in vivo detection of FRET-based molecular probe activation in an orthotopic breast cancer model. Indeed, the measured FLT of the enzyme-activatable molecular probe increases from 0.62 ns just after injection to 0.78 ns in tumor tissue after 4 h. A significant increase in FLT is not observed for an always-on targeted molecular probe with the same fluorescent reporter. These results show that FLT contrast is a powerful addition to preclinical imaging because it can report molecular activity in vivo due to changes in FRET. Fluorescence lifetime imaging exploits unique characteristics of fluorescent molecular probes that can be further translated into clinical applications, including noninvasive detection of cancer-related enzyme activity.

  14. Probing and characterizing the early stages of cavitation in glassy polymers in molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Estevez, R.; Long, D.

    2011-06-01

    This work focuses on a specific aspect of polymer fracture: the onset of cavitation during deformation. Failure in polymers involves plastic deformation by shear yielding and crazing. The competition between these two mechanisms is thought to govern the ductile versus brittle response of the material. The present molecular dynamics (MD) analysis shows that at a small scale, cavitation results from a transition between a homogeneous to a highly heterogeneous deformation field during loading. We characterize here these two regimes thanks to a scalar non-affine displacement probe, which displays a sharp transition at the onset of cavitation. Close scrutiny of cavitation allows for defining a stress-based cavitation criterion, the validity of which is checked for two temperatures in the glassy state. A mapping between the MD results and the corresponding estimates at the continuum scale indicates that the onset of cavitation at high deformation rates corresponds to a noticeably larger stress level as compared with that at low and intermediate loading rates. Since cavitation precedes failure in glassy polymers, this effect could be responsible for the marked increase in toughness reported experimentally under impact conditions.

  15. Molecular Inversion Probes for targeted resequencing in non-model organisms

    PubMed Central

    Niedzicka, M.; Fijarczyk, A.; Dudek, K.; Stuglik, M.; Babik, W.

    2016-01-01

    Applications that require resequencing of hundreds or thousands of predefined genomic regions in numerous samples are common in studies of non-model organisms. However few approaches at the scale intermediate between multiplex PCR and sequence capture methods are available. Here we explored the utility of Molecular Inversion Probes (MIPs) for the medium-scale targeted resequencing in a non-model system. Markers targeting 112 bp of exonic sequence were designed from transcriptome of Lissotriton newts. We assessed performance of 248 MIP markers in a sample of 85 individuals. Among the 234 (94.4%) successfully amplified markers 80% had median coverage within one order of magnitude, indicating relatively uniform performance; coverage uniformity across individuals was also high. In the analysis of polymorphism and segregation within family, 77% of 248 tested MIPs were confirmed as single copy Mendelian markers. Genotyping concordance assessed using replicate samples exceeded 99%. MIP markers for targeted resequencing have a number of advantages: high specificity, high multiplexing level, low sample requirement, straightforward laboratory protocol, no need for preparation of genomic libraries and no ascertainment bias. We conclude that MIP markers provide an effective solution for resequencing targets of tens or hundreds of kb in any organism and in a large number of samples. PMID:27046329

  16. Molecular Inversion Probes for targeted resequencing in non-model organisms.

    PubMed

    Niedzicka, M; Fijarczyk, A; Dudek, K; Stuglik, M; Babik, W

    2016-01-01

    Applications that require resequencing of hundreds or thousands of predefined genomic regions in numerous samples are common in studies of non-model organisms. However few approaches at the scale intermediate between multiplex PCR and sequence capture methods are available. Here we explored the utility of Molecular Inversion Probes (MIPs) for the medium-scale targeted resequencing in a non-model system. Markers targeting 112 bp of exonic sequence were designed from transcriptome of Lissotriton newts. We assessed performance of 248 MIP markers in a sample of 85 individuals. Among the 234 (94.4%) successfully amplified markers 80% had median coverage within one order of magnitude, indicating relatively uniform performance; coverage uniformity across individuals was also high. In the analysis of polymorphism and segregation within family, 77% of 248 tested MIPs were confirmed as single copy Mendelian markers. Genotyping concordance assessed using replicate samples exceeded 99%. MIP markers for targeted resequencing have a number of advantages: high specificity, high multiplexing level, low sample requirement, straightforward laboratory protocol, no need for preparation of genomic libraries and no ascertainment bias. We conclude that MIP markers provide an effective solution for resequencing targets of tens or hundreds of kb in any organism and in a large number of samples. PMID:27046329

  17. Probing the molecular design of hyper-branched aryl polyesters towards lubricant applications

    PubMed Central

    Robinson, Joshua W.; Zhou, Yan; Bhattacharya, Priyanka; Erck, Robert; Qu, Jun; Bays, J. Timothy; Cosimbescu, Lelia

    2016-01-01

    We report novel polymeric materials that may be used as viscosity index improvers (VII) for lubricant applications. Our efforts included probing the comb-burst hyper-branched aryl polyester architecture for beneficial viscosity and friction behavior when utilized as an additive in a group I oil. The monomer was designed as to undergo polymerization via polycondensation within the architectural construct (AB2), typical of hyperbranched polymers. The monomer design was comprised of aliphatic arms (12 or 16 methylenes) to provide the necessary lipophilicity to achieve solubility in a non-polar medium. Once polymerized, via catalyst and heat, the surface alcohols were functionalized with fatty acids (lauric and palmitic). Controlling the aliphatic nature of the internal arms and peripheral end-groups provided four unique flexible polymer designs. Changing the reaction time and concentration provided opportunities to investigate the influence of molecular weight and branching density on oil-solubility, viscosity, and friction. Oil-solubility was found to decrease with fewer internal carbons, but the number of internal carbons appears to have little influence on the bulk solution viscosity. At concentrations of 2 wt % in a group I base oil, these polymer additives demonstrated an improved viscosity index and reduced friction coefficient, validating the basic approach. PMID:26727881

  18. Probing the molecular design of hyper-branched aryl polyesters towards lubricant applications.

    PubMed

    Robinson, Joshua W; Zhou, Yan; Bhattacharya, Priyanka; Erck, Robert; Qu, Jun; Bays, J Timothy; Cosimbescu, Lelia

    2016-01-01

    We report novel polymeric materials that may be used as viscosity index improvers (VII) for lubricant applications. Our efforts included probing the comb-burst hyper-branched aryl polyester architecture for beneficial viscosity and friction behavior when utilized as an additive in a group I oil. The monomer was designed as to undergo polymerization via polycondensation within the architectural construct (AB2), typical of hyperbranched polymers. The monomer design was comprised of aliphatic arms (12 or 16 methylenes) to provide the necessary lipophilicity to achieve solubility in a non-polar medium. Once polymerized, via catalyst and heat, the surface alcohols were functionalized with fatty acids (lauric and palmitic). Controlling the aliphatic nature of the internal arms and peripheral end-groups provided four unique flexible polymer designs. Changing the reaction time and concentration provided opportunities to investigate the influence of molecular weight and branching density on oil-solubility, viscosity, and friction. Oil-solubility was found to decrease with fewer internal carbons, but the number of internal carbons appears to have little influence on the bulk solution viscosity. At concentrations of 2 wt % in a group I base oil, these polymer additives demonstrated an improved viscosity index and reduced friction coefficient, validating the basic approach. PMID:26727881

  19. Molecular Platform for Design and Synthesis of Targeted Dual-Modality Imaging Probes

    PubMed Central

    2015-01-01

    We report a versatile dendritic structure based platform for construction of targeted dual-modality imaging probes. The platform contains multiple copies of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) branching out from a 1,4,7-triazacyclononane-N,N′,N″-triacetic acid (NOTA) core. The specific coordination chemistries of the NOTA and DOTA moieties offer specific loading of 68/67Ga3+ and Gd3+, respectively, into a common molecular scaffold. The platform also contains three amino groups which can potentiate targeted dual-modality imaging of PET/MRI or SPECT/MRI (PET: positron emission tomography; SPECT: single photon emission computed tomography; MRI: magnetic resonance imaging) when further functionalized by targeting vectors of interest. To validate this design concept, a bimetallic complex was synthesized with six peripheral Gd-DOTA units and one Ga-NOTA core at the center, whose ion T1 relaxivity per gadolinium atom was measured to be 15.99 mM–1 s–1 at 20 MHz. Further, the bimetallic agent demonstrated its anticipated in vivo stability, tissue distribution, and pharmacokinetic profile when labeled with 67Ga. When conjugated with a model targeting peptide sequence, the trivalent construct was able to visualize tumors in a mouse xenograft model by both PET and MRI via a single dose injection. PMID:25615011

  20. Preparation and characterization of a magnetic and optical dual-modality molecular probe

    NASA Astrophysics Data System (ADS)

    Bumb, A.; Regino, C. A. S.; Perkins, M. R.; Bernardo, M.; Ogawa, M.; Fugger, L.; Choyke, P. L.; Dobson, P. J.; Brechbiel, M. W.

    2010-04-01

    Multi-modality imaging probes combine the advantages of individual imaging techniques to yield highly detailed anatomic and molecular information in living organisms. Herein, we report the synthesis and characterization of a dual-modality nanoprobe that couples the magnetic properties of ultrasmall superparamagnetic iron oxide nanoparticles (USPIOs) with the near infrared fluorescence of Cy5.5. The fluorophore is encapsulated in a biocompatible shell of silica surrounding the iron oxide core for a final diameter of ~ 17 nm. This silica-coated iron oxide nanoparticle (SCION) has been analyzed by transmission electron microscopy, dynamic light scattering, and superconducting quantum interference device (SQUID). The particle demonstrates a strong negative surface charge and maintains colloidal stability in the physiological pH range. Magnetic hysteresis analysis confirms superparamagnetic properties that could be manipulated for thermotherapy. The viability of primary human monocytes, T cells, and B cells incubated with the particle has been examined in vitro. In vivo analysis of agent leakage into subcutaneous A431 tumors in mice was also conducted. This particle has been designed for diagnostic application with magnetic resonance and fluorescence imaging, and has future potential to serve as a heat-sensitive targeted drug delivery platform.

  1. Probing the molecular design of hyper-branched aryl polyesters towards lubricant applications

    NASA Astrophysics Data System (ADS)

    Robinson, Joshua W.; Zhou, Yan; Bhattacharya, Priyanka; Erck, Robert; Qu, Jun; Bays, J. Timothy; Cosimbescu, Lelia

    2016-01-01

    We report novel polymeric materials that may be used as viscosity index improvers (VII) for lubricant applications. Our efforts included probing the comb-burst hyper-branched aryl polyester architecture for beneficial viscosity and friction behavior when utilized as an additive in a group I oil. The monomer was designed as to undergo polymerization via polycondensation within the architectural construct (AB2), typical of hyperbranched polymers. The monomer design was comprised of aliphatic arms (12 or 16 methylenes) to provide the necessary lipophilicity to achieve solubility in a non-polar medium. Once polymerized, via catalyst and heat, the surface alcohols were functionalized with fatty acids (lauric and palmitic). Controlling the aliphatic nature of the internal arms and peripheral end-groups provided four unique flexible polymer designs. Changing the reaction time and concentration provided opportunities to investigate the influence of molecular weight and branching density on oil-solubility, viscosity, and friction. Oil-solubility was found to decrease with fewer internal carbons, but the number of internal carbons appears to have little influence on the bulk solution viscosity. At concentrations of 2 wt % in a group I base oil, these polymer additives demonstrated an improved viscosity index and reduced friction coefficient, validating the basic approach.

  2. Low-dose laulimalide represents a novel molecular probe for investigating microtubule organization.

    PubMed

    Bennett, Melissa J; Chan, Gordon K; Rattner, J B; Schriemer, David C

    2012-08-15

    Laulimalide is a natural product that has strong taxoid-like properties but binds to a distinct site on β-tubulin in the microtubule (MT) lattice. At elevated concentrations, it generates MTs that are resistant to depolymerization, and it induces a conformational state indistinguishable from taxoid-treated MTs. In this study, we describe the effect of low-dose laulimalide on various stages of the cell cycle and compare these effects to docetaxel as a representative of taxoid stabilizers. No evidence of MT bundling in interphase was observed with laulimalide, in spite of the fact that MTs are stabilized at low dose. Cells treated with laulimalide enter mitosis but arrest at prometaphase by generating multiple asters that coalesce into supernumerary poles and interfere with the integrity of the metaphase plate. Cells with a preformed bipolar spindle exist under heightened tension under laulimalide treatment, and chromosomes rapidly shear from the plate, even though the bipolar spindle is well-preserved. Docetaxel generates a similar phenotype for HeLa cells entering mitosis, but when treated at metaphase, cells undergo chromosomal fragmentation and demonstrate reduced centromere dynamics, as expected for a taxoid. Our results suggest that laulimalide represents a new class of molecular probe for investigating MT-mediated events, such as kinetochore-MT interactions, which may reflect the location of the ligand binding site within the interprotofilament groove. PMID:22871740

  3. Development and field application of a molecular probe for the primary pathogen of the coral disease white plague type II.

    PubMed

    Richardson, Laurie L; Mills, DeEtta K; Remily, Elizabeth R; Voss, Joshua D

    2005-05-01

    One of the current problems in the field of coral disease research is that of tracking coral pathogens in the natural environment. A promising method to do this is by use of pathogen-specific molecular probes. However, this approach has been little used to date. We constructed, and validated in the laboratory, a fluorochrome-labeled molecular probe specific to Aurantimonas coralicida, the bacterial pathogen of the Caribbean coral disease white plague type II (WPIl). We then used the probe to test field samples of diseased coral tissue for the presence of this pathogen. Probe design was based on a unique subset (25 nucleotides) of the complete l6S rRNA gene sequence derived from a pure culture of the pathogen. The pathogen-specific probe was labeled with the fluorochrome GreenStar* FITC (fluorescein isothiocyanate, GeneDetect Ltd, New Zealand). As a control, we used the universal eubacterial probe EUB 338, labeled with a different fluorochrome (TRITC, tetra-methylrhodamine isothiocyanate). Both probes were applied to laboratory samples of pure cultures of bacteria, and field samples collected from the surface of the disease line of corals exhibiting signs of white plague (types I and II), healthy controls, and corals with an uncharacterized disease ("patchy necrosis"). All samples were analyzed using fluorescence in situ hybridization (FISH). We have determined that the probe is specific to our laboratory culture of the coral pathogen, and does not react with other bacterial species (the eubacterial probe does). The WPII pathogen was detected in association with diseased coral samples collected from coral colonies on reefs of the Bahamas (n= 9 samples) exhibiting signs of both WPI and WPII. Diseased (and healthy) tissue samples (n- 4) from corals exhibiting signs of "patchy necrosis" were also assayed. In this case the results were negative, indicating that the same pathogen is not involved in the two diseases. Incorporation and use of pathogen-specific probes can

  4. Complementary optical and nuclear imaging of caspase-3 activity using combined activatable and radio-labeled multimodality molecular probe

    NASA Astrophysics Data System (ADS)

    Lee, Hyeran; Akers, Walter J.; Cheney, Philip P.; Edwards, W. Barry; Liang, Kexian; Culver, Joseph P.; Achilefu, Samuel

    2009-07-01

    Based on the capability of modulating fluorescence intensity by specific molecular events, we report a new multimodal optical-nuclear molecular probe with complementary reporting strategies. The molecular probe (LS498) consists of tetraazacyclododecanetetraacetic acid (DOTA) for chelating a radionuclide, a near-infrared fluorescent dye, and an efficient quencher dye. The two dyes are separated by a cleavable peptide substrate for caspase-3, a diagnostic enzyme that is upregulated in dying cells. LS498 is radiolabeled with 64Cu, a radionuclide used in positron emission tomography. In the native form, LS498 fluorescence is quenched until caspase-3 cleavage of the peptide substrate. Enzyme kinetics assay shows that LS498 is readily cleaved by caspase-3, with excellent enzyme kinetic parameters kcat and KM of 0.55+/-0.01 s-1 and 1.12+/-0.06 μM, respectively. In mice, the initial fluorescence of LS498 is ten-fold less than control. Using radiolabeled 64Cu-LS498 in a controlled and localized in-vivo model of caspase-3 activation, a time-dependent five-fold NIR fluorescence enhancement is observed, but radioactivity remains identical in caspase-3 positive and negative controls. These results demonstrate the feasibility of using radionuclide imaging for localizing and quantifying the distribution of molecular probes and optical imaging for reporting the functional status of diagnostic enzymes.

  5. High resolution single-mode-fiber-based sensor for intravascular detection of fluorescent molecular probes

    NASA Astrophysics Data System (ADS)

    Razansky, R. Nika; Mueller, Mathias S.; Borisov, Alexander; Koch, Alexander W.; Jaffer, Farouc A.; Ntziachristos, Vasilis

    2010-04-01

    Early detection of coronary atherosclerosis is an unmet clinical challenge. The detection system has to be highly sensitive and possess high spacial resolution, in order to provide precise information of the vulnerable plaque location and size. Recently molecular fluorescence probes have been identified as efficient inflammation biomarkers for the inflammation process within vulnerable plaques1 and being used in the proposed application to detect inflamed lesions in the blood vessel wall. The general principle of the proposed solution is based on a sensor whose head is guided by an intravascular catheter to the region of interest (coronary artery). When the sensor illuminates an activated fluorescent probe, located in inflamed areas of vulnerable plaques, the fluorescence is excited and light is emitted with a slightly shifted spectrum. The emitted light is being collected by the same sensor head, guided through the optical fiber and finally detected by photo-detectors. In this way, by detecting emitted fluorescence one can obtain information about the location of vulnerable plaques. The localization resolution is critically depending on the spot size of the illuminating light beam. Moreover, for a high signal to noise ratio in the detection electronics, as much fluorescent light as possible has to be collected from the plaque location. It has been already demonstrated that using single-mode fibers in combination with graded index fibers, a Gaussian beam, with adjustable waist position and diameter can be formed, representing the fundamental limit of achievable spot size2. However, when using single mode fibers in this application, the collection efficiency would be very low due to the small core diameter of this fiber and thus signal to noise ratio would be strongly reduced. In this work, we present a solution to this challenge, combining both principles. A single mode fiber in combination with a graded index fiber is used for illumination purposes, while the

  6. Immobilization of ɛ-polylysine onto the probe surface for molecular adsorption type endotoxin detection system

    NASA Astrophysics Data System (ADS)

    Ooe, Katsutoshi; Tsuji, Akihito; Nishishita, Naoki; Hirano, Yoshiaki

    2007-04-01

    adsorption reaction between ɛ-polylysine and endotoxin. ɛ-polylysine has the structure of straight chain molecule composed by 25-30 residues made by lysine, and it is used as an antimicrobial agent, moreover, cellulose beads with immobilized ɛ-polylysine is used as the barrier filter for endotoxin removal. Therefore, it is expected that the endotoxin be adsorbed to the immobilized ɛ-polylysine onto the probe. As the result of this reaction, the mass of the probe is increased, and endotoxin can be detected by using of Quartz Crystal Microbalance (QCM). In our previous research, we have already acquired the proteins immobilization technique onto Au and Si surface. In this report, the proposal of molecular adsorption type endotoxin detection system, and the immobilization of ɛ-polylysine onto the probe are described. We use X-ray Photoelectron Spectroscopy (XPS) to confirm the ɛ-polylysine immobilization, and the adsorptive activity of immobilized ɛ-polylysine is measured by XPS and AFM. The purpose of this study is to bring about the realization of "Real-time endotoxin detection system".

  7. Perspectives of Deuteron Field-Cycling NMR Relaxometry for Probing Molecular Dynamics in Soft Matter.

    PubMed

    Flämig, M; Becher, M; Hofmann, M; Körber, T; Kresse, B; Privalov, A F; Willner, L; Kruk, D; Fujara, F; Rössler, E A

    2016-08-11

    Due to the single-particle character of the quadrupolar interaction in molecular systems, (2)H NMR poses a unique method for probing reorientational dynamics. Spin-lattice relaxation gives access to the spectral density, and its frequency dependency can be monitored by field-cycling (FC) techniques. However, most FC NMR studies employ (1)H; the use of (2)H is still rare. We report on the application of (2)H FC NMR for investigating the dynamics in molecular liquids and polymers. Commercial as well as home-built relaxometers are employed accessing a frequency range from 30 Hz to 6 MHz. Due to low gyromagnetic ratio, high coupling constants, and finite FC switching times, current (2)H FC NMR does not reach the dispersion region in liquids (toluene and glycerol), yet good agreement with the results from conventional high-field (HF) relaxation studies is demonstrated. The pronounced difference at low frequencies between (2)H and (1)H FC NMR data shows the relevance of intermolecular relaxation in the case of (1)H NMR. In the case of the polymers polybutadiene and poly(ethylene-alt-propylene), very similar relaxation dispersion is observed and attributed to Rouse and entanglement dynamics. Combination with HF (2)H relaxation data via applying frequency-temperature superposition allows the reconstruction of the full spectral density reflecting both polymer as well as glassy dynamics. Transformation into the time domain yields the reorientational correlation function C2(t) extending over nine decades in time with a long-time power law, C2(t) ∝ t(-0.45±0.05), which does not conform to the prediction of the tube-reptation model, for which ∝ t(-0.25) is expected. Entanglement sets in below C2(t = τe) ≅ S(2) = 0.001, where τe is the entanglement time and S the corresponding order parameter. Finally, we discuss the future prospects of the (2)H FC NMR technique. PMID:27420118

  8. A Molecular Probe for the Detection of Polar Lipids in Live Cells.

    PubMed

    Bader, Christie A; Shandala, Tetyana; Carter, Elizabeth A; Ivask, Angela; Guinan, Taryn; Hickey, Shane M; Werrett, Melissa V; Wright, Phillip J; Simpson, Peter V; Stagni, Stefano; Voelcker, Nicolas H; Lay, Peter A; Massi, Massimiliano; Plush, Sally E; Brooks, Douglas A

    2016-01-01

    Lipids have an important role in many aspects of cell biology, including membrane architecture/compartment formation, intracellular traffic, signalling, hormone regulation, inflammation, energy storage and metabolism. Lipid biology is therefore integrally involved in major human diseases, including metabolic disorders, neurodegenerative diseases, obesity, heart disease, immune disorders and cancers, which commonly display altered lipid transport and metabolism. However, the investigation of these important cellular processes has been limited by the availability of specific tools to visualise lipids in live cells. Here we describe the potential for ReZolve-L1™ to localise to intracellular compartments containing polar lipids, such as for example sphingomyelin and phosphatidylethanolamine. In live Drosophila fat body tissue from third instar larvae, ReZolve-L1™ interacted mainly with lipid droplets, including the core region of these organelles. The presence of polar lipids in the core of these lipid droplets was confirmed by Raman mapping and while this was consistent with the distribution of ReZolve-L1™ it did not exclude that the molecular probe might be detecting other lipid species. In response to complete starvation conditions, ReZolve-L1™ was detected mainly in Atg8-GFP autophagic compartments, and showed reduced staining in the lipid droplets of fat body cells. The induction of autophagy by Tor inhibition also increased ReZolve-L1™ detection in autophagic compartments, whereas Atg9 knock down impaired autophagosome formation and altered the distribution of ReZolve-L1™. Finally, during Drosophila metamorphosis fat body tissues showed increased ReZolve-L1™ staining in autophagic compartments at two hours post puparium formation, when compared to earlier developmental time points. We concluded that ReZolve-L1™ is a new live cell imaging tool, which can be used as an imaging reagent for the detection of polar lipids in different intracellular

  9. A Molecular Probe for the Detection of Polar Lipids in Live Cells

    PubMed Central

    Bader, Christie A.; Shandala, Tetyana; Carter, Elizabeth A.; Ivask, Angela; Guinan, Taryn; Hickey, Shane M.; Werrett, Melissa V.; Wright, Phillip J.; Simpson, Peter V.; Stagni, Stefano; Voelcker, Nicolas H.; Lay, Peter A.; Massi, Massimiliano; Brooks, Douglas A.

    2016-01-01

    Lipids have an important role in many aspects of cell biology, including membrane architecture/compartment formation, intracellular traffic, signalling, hormone regulation, inflammation, energy storage and metabolism. Lipid biology is therefore integrally involved in major human diseases, including metabolic disorders, neurodegenerative diseases, obesity, heart disease, immune disorders and cancers, which commonly display altered lipid transport and metabolism. However, the investigation of these important cellular processes has been limited by the availability of specific tools to visualise lipids in live cells. Here we describe the potential for ReZolve-L1™ to localise to intracellular compartments containing polar lipids, such as for example sphingomyelin and phosphatidylethanolamine. In live Drosophila fat body tissue from third instar larvae, ReZolve-L1™ interacted mainly with lipid droplets, including the core region of these organelles. The presence of polar lipids in the core of these lipid droplets was confirmed by Raman mapping and while this was consistent with the distribution of ReZolve-L1™ it did not exclude that the molecular probe might be detecting other lipid species. In response to complete starvation conditions, ReZolve-L1™ was detected mainly in Atg8-GFP autophagic compartments, and showed reduced staining in the lipid droplets of fat body cells. The induction of autophagy by Tor inhibition also increased ReZolve-L1™ detection in autophagic compartments, whereas Atg9 knock down impaired autophagosome formation and altered the distribution of ReZolve-L1™. Finally, during Drosophila metamorphosis fat body tissues showed increased ReZolve-L1™ staining in autophagic compartments at two hours post puparium formation, when compared to earlier developmental time points. We concluded that ReZolve-L1™ is a new live cell imaging tool, which can be used as an imaging reagent for the detection of polar lipids in different intracellular

  10. Atom probe tomography characterisation of a laser diode structure grown by molecular beam epitaxy

    SciTech Connect

    Bennett, Samantha E.; Humphreys, Colin J.; Oliver, Rachel A.; Smeeton, Tim M.; Hooper, Stewart E.; Heffernan, Jonathan; Saxey, David W.; Smith, George D. W.

    2012-03-01

    Atom probe tomography (APT) has been used to achieve three-dimensional characterization of a III-nitride laser diode (LD) structure grown by molecular beam epitaxy (MBE). Four APT data sets have been obtained, with fields of view up to 400 nm in depth and 120 nm in diameter. These data sets contain material from the InGaN quantum well (QW) active region, as well as the surrounding p- and n-doped waveguide and cladding layers, enabling comprehensive study of the structure and composition of the LD structure. Two regions of the same sample, with different average indium contents (18% and 16%) in the QW region, were studied. The APT data are shown to provide easy access to the p-type dopant levels, and the composition of a thin AlGaN barrier layer. Next, the distribution of indium within the InGaN QW was analyzed, to assess any possible inhomogeneity of the distribution of indium (''indium clustering''). No evidence for a statistically significant deviation from a random distribution was found, indicating that these MBE-grown InGaN QWs do not require indium clusters for carrier localization. However, the APT data show steps in the QW interfaces, leading to well-width fluctuations, which may act to localize carriers. Additionally, the unexpected presence of a small amount (x = 0.005) of indium in a layer grown intentionally as GaN was revealed. Finally, the same statistical method applied to the QW was used to show that the indium distribution within a thick InGaN waveguide layer in the n-doped region did not show any deviation from randomness.

  11. Probing the Conformation of FhaC with Small-Angle Neutron Scattering and Molecular Modeling

    PubMed Central

    Gabel, Frank; Lensink, Marc F.; Clantin, Bernard; Jacob-Dubuisson, Françoise; Villeret, Vincent; Ebel, Christine

    2014-01-01

    Probing the solution structure of membrane proteins represents a formidable challenge, particularly when using small-angle scattering. Detergent molecules often present residual scattering contributions even at their match point in small-angle neutron scattering (SANS) measurements. Here, we studied the conformation of FhaC, the outer-membrane, β-barrel transporter of the Bordetella pertussis filamentous hemagglutinin adhesin. SANS measurements were performed on homogeneous solutions of FhaC solubilized in n-octyl-d17-βD-glucoside and on a variant devoid of the α helix H1, which critically obstructs the FhaC pore, in two solvent conditions corresponding to the match points of the protein and the detergent, respectively. Protein-bound detergent amounted to 142 ± 10 mol/mol as determined by analytical ultracentrifugation. By using molecular modeling and starting from three distinct conformations of FhaC and its variant embedded in lipid bilayers, we generated ensembles of protein-detergent arrangement models with 120–160 detergent molecules. The scattered curves were back-calculated for each model and compared with experimental data. Good fits were obtained for relatively compact, connected detergent belts, which occasionally displayed small detergent-free patches on the outer surface of the β barrel. The combination of SANS and modeling clearly enabled us to infer the solution structure of FhaC, with H1 inside the pore as in the crystal structure. We believe that our strategy of combining explicit atomic detergent modeling with SANS measurements has significant potential for structural studies of other detergent-solubilized membrane proteins. PMID:24988353

  12. In search of the cochlear amplifier: New mechanical and molecular tools to probe transduction channel function

    NASA Astrophysics Data System (ADS)

    Karavitaki, K. Domenica; Indzhykulian, Artur A.; Zhang, Duan-Sun; Corey, David P.

    2015-12-01

    The study of mechanotransduction in cochlear hair cells requires stimulus methods that mimic the in-vivo stimulation. We have developed a new mechanical probe to better mimic the physiological stimulus delivered to cochlear hair cells through the overlying tectorial membrane. We combine these new probes with electroporation to study the contribution of different components of the transduction apparatus.

  13. Conditionally fluorescent molecular probes for detecting single base changes in double-stranded DNA

    NASA Astrophysics Data System (ADS)

    Chen, Sherry Xi; Zhang, David Yu; Seelig, Georg

    2013-09-01

    Small variations in nucleic acid sequences can have far-reaching phenotypic consequences. Reliably distinguishing closely related sequences is therefore important for research and clinical applications. Here, we demonstrate that conditionally fluorescent DNA probes are capable of distinguishing variations of a single base in a stretch of target DNA. These probes use a novel programmable mechanism in which each single nucleotide polymorphism generates two thermodynamically destabilizing mismatch bubbles rather than the single mismatch formed during typical hybridization-based assays. Up to a 12,000-fold excess of a target that contains a single nucleotide polymorphism is required to generate the same fluorescence as one equivalent of the intended target, and detection works reliably over a wide range of conditions. Using these probes we detected point mutations in a 198 base-pair subsequence of the Escherichia coli rpoB gene. That our probes are constructed from multiple oligonucleotides circumvents synthesis limitations and enables long continuous DNA sequences to be probed.

  14. Molecular Probes for Diagnosis of Clinically Relevant Bacterial Infections in Blood Cultures▿

    PubMed Central

    Hansen, Wendy L. J.; Beuving, Judith; Bruggeman, Cathrien A.; Wolffs, Petra F. G.

    2010-01-01

    Broad-range real-time PCR and sequencing of the 16S rRNA gene region is a widely known method for the detection and identification of bacteria in clinical samples. However, because of the need for sequencing, such identification of bacteria is time-consuming. The aim of our study was to develop a more rapid 16S real-time PCR-based identification assay using species- or genus-specific probes. The Gram-negative bacteria were divided into Pseudomonas species, Pseudomonas aeruginosa, Escherichia coli, and other Gram-negative species. Within the Gram-positive species, probes were designed for Staphylococcus species, Staphylococcus aureus, Enterococcus species, Streptococcus species, and Streptococcus pneumoniae. The assay also included a universal probe within the 16S rRNA gene region for the detection of all bacterial DNA. The assay was evaluated with a collection of 248 blood cultures. In this study, the universal probe and the probes targeting Pseudomonas spp., P. aeruginosa, E. coli, Streptococcus spp., S. pneumoniae, Enterococcus spp., and Staphylococcus spp. all had a sensitivity and specificity of 100%. The probe specific for S. aureus showed eight discrepancies, resulting in a sensitivity of 100% and a specificity of 93%. These data showed high agreement between conventional testing and our novel real-time PCR assay. Furthermore, this assay significantly reduced the time needed for identification. In conclusion, using pathogen-specific probes offers a faster alternative for pathogen detection and could improve the diagnosis of bloodstream infections. PMID:20962139

  15. Validation of DNA probes for molecular cytogenetics by mapping onto immobilized circular DNA

    SciTech Connect

    Greulich-Bode, Karin; Wang, Mei; Rhein, Andreas; Weier, Jingly; Weier, Heinz-Ulli

    2008-12-16

    Fluorescence in situ hybridization (FISH) is a sensitive and rapid procedure to detect gene rearrangements in tumor cells using non-isotopically labeled DNA probes. Large insert recombinant DNA clones such as bacterial artificial chromosome (BAC) or P1/PAC clones have established themselves in recent years as preferred starting material for probe preparations due to their low rates of chimerism and ease of use. However, when developing probes for the quantitative analysis of rearrangements involving genomic intervals of less than 100kb, careful probe selection and characterization are of paramount importance. We describe a sensitive approach to quality control probe clones suspected of carrying deletions or for measuring clone overlap with near kilobase resolution. The method takes advantage of the fact that P1/PAC/BAC's can be isolated as circular DNA molecules, stretched out on glass slides and fine-mapped by multicolor hybridization with smaller probe molecules. Two examples demonstrate the application of this technique: mapping of a gene-specific {approx}6kb plasmid onto an unusually small, {approx}55kb circular P1 molecule and the determination of the extent of overlap between P1 molecules homologous to the human NF-?B2 locus. The relatively simple method presented here does not require specialized equipment and may thus find widespread applications in DNA probe preparation and characterization, the assembly of physical maps for model organisms or in studies on gene rearrangements.

  16. Validation of DNA probes for molecular cytogenetics by mapping onto immobilized circular DNA

    SciTech Connect

    Greulich-Bode, Karin M.; Wang, Mei; Rhein, Andreas P.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-12-04

    Fluorescence in situ hybridization (FISH) is a sensitive and rapid procedure to detect gene rearrangements in tumor cells using non-isotopically labeled DNA probes. Large insert recombinant DNA clones such as bacterial artificial chromosome (BAC) or P1/PAC clones have established themselves in recent years as preferred starting material for probe preparations due to their low rates of chimerism and ease of use. However, when developing probes for the quantitative analysis of rearrangements involving genomic intervals of less than 100kb, careful probe selection and characterization are of paramount importance. We describe a sensitive approach to quality control probe clones suspected of carrying deletions or for measuring clone overlap with near kilobase resolution. The method takes advantage of the fact that P1/PAC/BAC's can be isolated as circular DNA molecules, stretched out on glass slides and fine-mapped by multicolor hybridization with smaller probe molecules. Two examples demonstrate the application of this technique: mapping of a gene-specific {approx}6kb plasmid onto an unusually small, {approx}55kb circular P1 molecule and the determination of the extent of overlap between P1 molecules homologous to the human NF-{kappa}B2 locus. The relatively simple method presented here does not require specialized equipment and may thus find widespread applications in DNA probe preparation and characterization, the assembly of physical maps for model organisms or in studies on gene rearrangements.

  17. Chemical Probes for Molecular Imaging and Detection of Hydrogen Sulfide and Reactive Sulfur Species in Biological Systems

    PubMed Central

    2014-01-01

    Hydrogen sulfide (H2S), a gaseous species produced by both bacteria and higher eukaryotic organisms, including mammalian vertebrates, has attracted attention in recent years for its contributions to human health and disease. H2S has been proposed as a cytoprotectant and gasotransmitter in many tissue types, including mediating vascular tone in blood vessels as well as neuromodulation in the brain. The molecular mechanisms dictating how H2S affects cellular signaling and other physiological events remain insufficiently understood. Furthermore, the involvement of H2S in metal-binding interactions and formation of related RSS such as sulfane sulfur may contribute to other distinct signaling pathways. Owing to its widespread biological roles and unique chemical properties, H2S is an appealing target for chemical biology approaches to elucidate its production, trafficking, and downstream function. In this context, reaction-based fluorescent probes offer a versatile set of screening tools to visualize H2S pools in living systems. Three main strategies used in molecular probe development for H2S detection include azide and nitro group reduction, nucleophilic attack, and CuS precipitation. Each of these approaches exploit the strong nucleophilicity and reducing potency of H2S to achieve selectivity over other biothiols. In addition, a variety of methods have been developed for the detection of other reactive sulfur species (RSS), including sulfite and bisulfite, as well as sulfane sulfur species and related modifications such as S-nitrosothiols. Access to this growing chemical toolbox of new molecular probes for H2S and related RSS sets the stage for applying these developing technologies to probe reactive sulfur biology in living systems. PMID:25474627

  18. Cell-Penetrating, Guanidinium-Rich Oligophosphoesters: Effective and Versatile Molecular Transporters for Drug and Probe Delivery.

    PubMed

    McKinlay, Colin J; Waymouth, Robert M; Wender, Paul A

    2016-03-16

    The design, synthesis, and biological evaluation of a new family of highly effective cell-penetrating molecular transporters, guanidinium-rich oligophosphoesters, are described. These unique transporters are synthesized in two steps, irrespective of oligomer length, by the organocatalytic ring-opening polymerization (OROP) of 5-membered cyclic phospholane monomers followed by oligomer deprotection. Varying the initiating alcohol results in a wide variety of cargo attachment strategies for releasable or nonreleasable transporter applications. Initiation of oligomerization with a fluorescent probe produces, upon deprotection, a transporter-probe conjugate that is shown to readily enter multiple cell lines in a dose-dependent manner. These new transporters are superior in cell uptake to previously studied guanidinium-rich oligocarbonates and oligoarginines, showing over 2-fold higher uptake than the former and 6-fold higher uptake than the latter. Initiation with a protected thiol gives, upon deprotection, thiol-terminated transporters which can be thiol-click conjugated to a variety of probes, drugs and other cargos as exemplified by the conjugation and delivery of the model probe fluorescein-maleimide and the medicinal agent paclitaxel (PTX) into cells. Of particular significance given that drug resistance is a major cause of chemotherapy failure, the PTX-transporter conjugate, designed to evade Pgp export and release free PTX after cell entry, shows efficacy against PTX-resistant ovarian cancer cells. Collectively this study introduces a new and highly effective class of guanidinium-rich cell-penetrating transporters and methodology for their single-step conjugation to drugs and probes, and demonstrates that the resulting drug/probe-conjugates readily enter cells, outperforming previously reported guanidinium-rich oligocarbonates and peptide transporters. PMID:26900771

  19. Functionalized Congeners of 1,4-Dihydropyridines as Antagonist Molecular Probes for A3 Adenosine Receptors

    PubMed Central

    Li, An-Hu; Chang, Louis; Ji, Xiao-duo; Melman, Neli; Jacobson, Kenneth A.

    2012-01-01

    4-Phenylethynyl-6-phenyl-1,4-dihydropyridine derivatives are selective antagonists at human A3 adenosine receptors, with Ki values in a radioligand binding assay vs [125I]AB-MECA [N6-(4-amino-3-iodobenzyl)-5′-N-methylcarbamoyl-adenosine] in the submicromolar range. In this study, functionalized congeners of 1,4-dihydropyridines were designed as chemically reactive adenosine A3 antagonists, for the purpose of synthesizing molecular probes for this receptor subtype. Selectivity of the new analogues for cloned human A3 adenosine receptors was determined in radioligand binding in comparison to binding at rat brain A1 and A2A receptors. Benzyl ester groups at the 3- and/or 5-positions and phenyl groups at the 2- and/or 6-positions were introduced as potential sites for chain attachment. Structure–activity analysis at A3 adenosine receptors indicated that 3,5-dibenzyl esters, but not 2,6-diphenyl groups, are tolerated in binding. Ring substitution of the 5-benzyl ester with a 4-fluorosulfonyl group provided enhanced A3 receptor affinity resulting in a Ki value of 2.42 nM; however, a long-chain derivative containing terminal amine functionalization at the 4-position of the 5-benzyl ester showed only moderate affinity. This sulfonyl fluoride derivative appeared to bind irreversibly to the human A3 receptor (1 h incubation at 100 nM resulting in the loss of 56% of the specific radioligand binding sites), while the binding of other potent dihydropyridines and other antagonists was generally reversible. At the 3-position of the dihydropyridine ring, an amine-functionalized chain attached at the 4-position of a benzyl ester provided higher A3 receptor affinity than the corresponding 5-position isomer. This amine congener was also used as an intermediate in the synthesis of a biotin conjugate, which bound to A3 receptors with a Ki value of 0.60 μM. PMID:10411465

  20. Specific estrogen sulfotransferase (SULT1E1) substrates and molecular imaging probe candidates

    PubMed Central

    Cole, Graham B.; Keum, Gyochang; Liu, Jie; Small, Gary W.; Satyamurthy, Nagichettiar; Kepe, Vladimir; Barrio, Jorge R.

    2010-01-01

    This work focuses on the development of specific substrates for estrogen sulfotransferase (SULT1E1) to produce molecular imaging probes for this enzyme. SULT1E1 is a key enzyme in estrogen homeostasis, playing a central role in the prevention and development of human disease. In vitro sulfation assays showed alkyl and aryl substitutions to a fused heterocyclic system modeled after β-naphthol (βN), based on compounds that interact with the estrogen receptor, rendered several molecules with enhanced specificity for SULT1E1 over SULT1A1*1, SULT1A1*2, SULT1A3, and SULT2A1. Several 6-hydroxy-2-arylbenzothiazoles tested demonstrated excellent affinity—Vmax/Km ratios—and specificity for SULT1E1. Km values ranged from 0.12–2.36 μM. A strong correlation was observed between polarity of the 4′-sustituent on the 2-aryl moiety (Hammett σp) and the log(Vmax/Km) (r = 0.964). Substrate sensitivity is influenced by the acidity of the 6-phenolic group demonstrated by correlating its 1H NMR chemical shift (δOH) with the log(Vmax/Km) (r = 0.963). Acidity is mediated by the electron withdrawing capacity of the 4′-substituent outlined by the correlation of the C-2 13C NMR chemical shift (δC2) with the log(Vmax/Km) (r = 0.987). 2-[4-(Methylamino)phenyl]-6-hydroxybenzothiazole (2b) was radiolabeled with carbon-11 (11C-(2b)) and used in vivo for microPET scanning and tissue metabolite identification. High PET signal was paralleled with the presence of radiolabeled 11C-(2b)-6-O-sulfate and the SULT1E1 protein detected by western blot. Because this and other members of this family presenting specificity for SULT1E1 can be labeled with carbon-11 or fluorine-18, in vivo assays of SULT1E1 functional activity are now feasible in humans. PMID:20304798

  1. Oligonucleotide primers, probes and molecular methods for the environmental monitoring of methanogenic archaea

    PubMed Central

    Narihiro, Takashi; Sekiguchi, Yuji

    2011-01-01

    Summary For the identification and quantification of methanogenic archaea (methanogens) in environmental samples, various oligonucleotide probes/primers targeting phylogenetic markers of methanogens, such as 16S rRNA, 16S rRNA gene and the gene for the α‐subunit of methyl coenzyme M reductase (mcrA), have been extensively developed and characterized experimentally. These oligonucleotides were designed to resolve different groups of methanogens at different taxonomic levels, and have been widely used as hybridization probes or polymerase chain reaction primers for membrane hybridization, fluorescence in situ hybridization, rRNA cleavage method, gene cloning, DNA microarray and quantitative polymerase chain reaction for studies in environmental and determinative microbiology. In this review, we present a comprehensive list of such oligonucleotide probes/primers, which enable us to determine methanogen populations in an environment quantitatively and hierarchically, with examples of the practical applications of the probes and primers. PMID:21375721

  2. A novel adenosine-based molecular beacon probe for room temperature nucleic acid rapid detection in cotton thread device.

    PubMed

    Du, Ting-E; Wang, Yiyun; Zhang, Yi; Zhang, Tian; Mao, Xun

    2015-02-25

    We used cotton thread as substrate to develop a novel room temperature DNA detection device for low-cost, sensitive and rapid detection of a human genetic disease, hereditary tyrosinemia type I related DNA sequences. A novel adenosine based molecular beacon (ABMB) probe modified on gold nanoparticle was used as reporter probe. In the presence of coralyne, a small molecule which can react with adenosines, the ABMB would form a hairpin structure just like traditional molecular beacon used extensively. In the presence of target DNA sequences, the hairpin structure of ABMB modified on gold nanoparticles will be opened and the biotin group modified at one end of the DNA probes will be released and react with the streptavidin immobilized on the test zone of the cotton thread. The response of the thread based DNA test device is linear over the range of 2.5-100 nM complementary DNA. The ability of our developed device for discriminating the single base mismatched DNA related to a human genetic disease, hereditary tyrosinemia type I, was improved comparing with previous report. It is worth mentioning that the whole assay procedure for DNA test is performed under room temperature which simplified the assay procedures greatly. PMID:25702276

  3. Detection of supercoiled hepatitis B virus DNA and related forms by means of molecular hybridization to an oligonucleotide probe

    SciTech Connect

    Lin, H.J.; Chung, H.T.; Lai, C.L.; Leong, S.; Tam, O.S. )

    1989-12-01

    A novel assay for supercoiled and other fully double-stranded forms of hepatitis B virus (HBV) DNA in blood is presented that utilizes molecular hybridisation to a radiophosphorous-labeled oligonucleotide probe. The probe (5'-d(ACGTGCAGAGGTGAAGCGA)) is complementary to the S(+)-strand sequence furthest downstream, at the end of the gap. We examined blood specimens from 137 healthy HBsAg-positive individuals, applying the probe to dots representing 2-3.5 ml serum or plasma. We found that supercoiled HBV is present in many HBV DNA-positive blood specimens albeit in small quantities. Of the 104 specimens that were positive for HBV DNA of any form, 53 annealed to the probe. Serial specimens from the same subject taken over a period of months showed that the proportion of supercoil to other HBV DNA forms was variable. The presence of supercoil HBV DNA was not closely correlated with the level of serum HBV DNA polymerase. The supercoil is an HBV DNA form that can persist in the liver in the presence or absence of other replicative intermediates. This assay may enable further characterization of the status of HBV infection.

  4. Tracing ultrafast molecular transitions in C2H4 using two­color XUV pump­ XUV probe

    NASA Astrophysics Data System (ADS)

    Ray, D.; Sturm, F. P.; Wright, T. W.; Shivaram, N.; Bocharova, I.; Belkacem, A.; Weber, Th.

    2014-05-01

    We present the study of the ultrafast energy transfer near a conical intersection in C2H4, using an extreme ultraviolet (XUV) pump XUV probe scheme. The high harmonic pulses, which have sufficiently high flux to split into both pump and probe arms, are generated in a noble gas by IR pulses from our state of the art 30 mJ, 50 Hz laser system. The pulses are overlapped with the supersonic jet in our Momentum Imaging for TimE Resolved Studies (MISTERS) setup. The C2H4 is pumped by the 13.5 eV XUV pulses (9th harmonic) to populate the excited valence state (π*)2 orbitals. The double ionization of these molecular cations from this transient state is triggered by the 15th harmonic (22.5 eV) as the probe. The ionic fragments are imaged with the reaction microscope. The MISTERS setup allows us to do an ion-ion coincidence detection in full 3D momentum space. The Kinetic Energy Release (KER) distributions are studied as a function of pump probe delay to trace the evolution of the transient states. Supported by the Director, Office of Science, Office of Basic Energy Sciences, and by the Division of Chemical Sciences, Geosciences, and Biosciences of the U.S. Department of Energy at LBNL under Contract No. DE­AC02­05CH11231.

  5. Molecular-Level Insights into Photocatalysis from Scanning Probe Microscopy Studies on TiO2(110)

    SciTech Connect

    Henderson, Michael A.; Lyubinetsky, Igor

    2013-06-12

    The field of heterogeneous photocatalysis has grown considerably in the decades since Fujishima and Honda's ground-breaking publications of photoelectrochemistry on TiO2. Numerous review articles continue to point to both progress made in the use of heterogeneous materials (such as TiO2) to perform photoconversion processes, and the many opportunities and challenges in heterogeneous photocatalysis research such as solar energy conversion and environmental remediation. The past decade has also seen an increase in the use of molecular-level approaches applied to model single crystal surfaces in an effort to obtain new insights into photocatalytic phenomena. In particular, scanning probe techniques (SPM) have enabled researchers to take a ‘nanoscale’ approach to photocatalysis that includes interrogation of the reactivities of specific sites and adsorbates on a model photocatalyst surface. The rutile TiO2(110) surface has become the prototypical oxide single crystal surface for fundamental studies of many interfacial phenomena. In particular, TiO2(110) has become an excellent model surface for probing photochemical and photocatalytic reactions at the molecular level. A variety of experimental approaches have emerged as being ideally suited for studying photochemical reactions on TiO2(110), including desorption-oriented approaches and electronic spectroscopies, but perhaps the most promising techniques for evaluating site-specific properties are those of SPM. In this review, we highlight the growing use of SPM techniques in providing molecular-level insights into surface photochemistry on the model photocatalyst surface of rutile TiO2(110). Our objective is to both illustrate the unique knowledge that scanning probe techniques have already provided the field of photocatalysis, and also to motivate a new generation of effort into the use of such approaches to obtain new insights into the molecular level details of photochemical events occurring at interfaces

  6. DNA and RNA "traffic lights": synthetic wavelength-shifting fluorescent probes based on nucleic acid base substitutes for molecular imaging.

    PubMed

    Holzhauser, Carolin; Wagenknecht, Hans-Achim

    2013-08-01

    The DNA base substitute approach by the (S)-3-amino-1,2-propanediol linker allows placing two fluorophores in a precise way inside a given DNA framework. The double helical architecture around the fluorophores, especially the DNA-induced twist, is crucial for the desired photophysical interactions. Excitonic, excimer, and energy transfer interactions yield fluorescent DNA and RNA probes with dual emission color readout. Especially, our DNA and RNA "traffic light" that combines the green emission of TO with the red emission of TR represents an important tool for molecular imaging and can be applied as aptasensors and as probes to monitor the siRNA delivery into cells. The concept can be extended to the synthetically easier to access postsynthetic 2'-modifications and the NIR range. Thereby, the pool of tailor-made fluorescent nucleic acid conjugates can be extended. PMID:23796243

  7. Molecular probe dynamics and free volume in organic glass-formers and their relationships to structural relaxation: 1-propanol

    NASA Astrophysics Data System (ADS)

    Bartoš, J.; Švajdlenková, H.; Šauša, O.; Lukešová, M.; Ehlers, D.; Michl, M.; Lunkenheimer, P.; Loidl, A.

    2016-01-01

    A joint study of the rotational dynamics and free volume in amorphous 1-propanol (1-PrOH) as a prototypical monohydroxy alcohol by electron spin resonance (ESR) or positron annihilation lifetime spectroscopy (PALS), respectively, is reported. The dynamic parameters of the molecular spin probe 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) and the annihilation ones of the atomic ortho-positronium (o-Ps) probe as a function of temperature are compared. A number of coincidences between various effects in the ESR and PALS responses at the corresponding characteristic ESR and PALS temperatures were found suggesting a common origin of the underlying dynamic processes that were identified using viscosity (VISC) in terms of the two-order parameter (TOP) model and broadband dielectric spectroscopy (BDS) data.

  8. Improvement in the assessment of direct and facilitated ion transfers by electrochemically induced redox transformations of common molecular probes.

    PubMed

    Zhou, Min; Gan, Shiyu; Zhong, Lijie; Dong, Xiandui; Ulstrup, Jens; Han, Dongxue; Niu, Li

    2012-03-14

    A new strategy based on a thick organic film modified electrode allowed us, for the first time, to explore the voltammetric processes for a series of hydrophilic ions by electrochemically induced redox transformations of common molecular probes. During the limited time available for voltammetry, this thick organic film ensured that the generated product of the molecular probe, which is within a limited diffusion layer, was kept far away from the aqueous-organic solvent interface; therefore, regardless of the degree of hydrophobicity, the generated product never participates in ion exchange across the interface and the charge neutrality of the organic film (containing an extremely hydrophobic electrolyte) can only be maintained by the injection of ions from the aqueous phase. Taking advantage of this fact, common redox probes, such as ferrocene (Fc) and 7,7,8,8-tetracyanoquinodimethane (TCNQ), which are almost useless for both three-phase electrode (TPE) and thin-layer cyclic voltammetry (TLCV) methods, can induce the transfer of numerous highly hydrophilic anions and cations. Consequently, the majority of their Gibbs transfer energies have been accurately determined for the first time to the best of our knowledge. With this in mind, using TCNQ as a redox probe to induce facilitated cation transfer, a stategy that is more advantageous than traditional methods has been developed. The main advantages are that: (i) voltammetric experiments performed on this system were free from the polarized potential window (ppw) in the aqueous phase and, as a result, this allowed the assessment of weakly assisted ion transfers, which appear at the terminal of the ppw at single polarized interfaces; (ii) without introducing the tetraphenylarsonium-tetraphenylborate (TPAs-TPB) thermodynamic assumption, one can conveniently evaluate both the association constant and the stoichiometric parameter between the ion and its ionophore by comparison of their direct and facilitated ion transfer

  9. Probing molecular pathways for DNA orientational trapping, unzipping and translocation in nanopores by using a tunable overhang sensor

    NASA Astrophysics Data System (ADS)

    Wang, Yong; Tian, Kai; Hunter, Lehr L.; Ritzo, Brandon; Gu, Li-Qun

    2014-09-01

    Nanopores provide a unique single-molecule platform for genetic and epigenetic detection. The target nucleic acids can be accurately analyzed by characterizing their specific electric fingerprints or signatures in the nanopore. Here we report a series of novel nanopore signatures generated by target nucleic acids that are hybridized with a probe. A length-tunable overhang appended to the probe functions as a sensor to specifically modulate the nanopore current profile. The resulting signatures can reveal multiple mechanisms for the orientational trapping, unzipping, escaping and translocation of nucleic acids in the nanopore. This universal approach can be used to program various molecular movement pathways, elucidate their kinetics, and enhance the sensitivity and specificity of the nanopore sensor for nucleic acid detection.Nanopores provide a unique single-molecule platform for genetic and epigenetic detection. The target nucleic acids can be accurately analyzed by characterizing their specific electric fingerprints or signatures in the nanopore. Here we report a series of novel nanopore signatures generated by target nucleic acids that are hybridized with a probe. A length-tunable overhang appended to the probe functions as a sensor to specifically modulate the nanopore current profile. The resulting signatures can reveal multiple mechanisms for the orientational trapping, unzipping, escaping and translocation of nucleic acids in the nanopore. This universal approach can be used to program various molecular movement pathways, elucidate their kinetics, and enhance the sensitivity and specificity of the nanopore sensor for nucleic acid detection. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr03195d

  10. A probe molecule composed of seventeen percent of total diffracting matter gives correct solutions in molecular replacement.

    PubMed

    Oh, B H

    1995-03-01

    It is often found in the crystallization of enzyme-inhibitor complexes that an inhibitor causes crystal packing which is different to that of native protein. This is the case for crystals of human non-pancreatic secreted phospholipase A(2) (124 residues) containing six molecules in the asymmetric unit when the protein is complexed with a potential acylamino analogue of a phospholid. The hexameric structure was determined by molecular replacement using the structure of monomeric native protein as a probe. As an extension to the experiment, it was tested whether a backbone polypeptide composed of 17% of a known monomeric structure could find its correct position on a target molecule in molecular replacement. A probe model composed of the backbone atoms of the N-terminal 77 residues of lysine-, arginine-, ornithine-binding protein (LAO, a total of 238 residues) liganded with lysine correctly finds its position on LAO liganded with histidine which crystallizes as a monomer in the asymmetric unit. The results indicate that as little as 17% of total diffracting matter can be used in molecular replacement to solve crystal structures or to obtain phase information which can be combined with phases obtained by the isomorphous-replacement method. PMID:15299314

  11. Dual-Modal Colorimetric/Fluorescence Molecular Probe for Ratiometric Sensing of pH and Its Application.

    PubMed

    Wu, Luling; Li, Xiaolin; Huang, Chusen; Jia, Nengqin

    2016-08-16

    As traditional pH meters cannot work well for minute regions (such as subcellular organelles) and in harsh media, molecular pH-sensitive devices for monitoring pH changes in diverse local heterogeneous environments are urgently needed. Here, we report a new dual-modal colorimetric/fluorescence merocyanine-based molecular probe (CPH) for ratiometric sensing of pH. Compared with previously reported pH probes, CPH bearing the benzyl group at the nitrogen position of the indolium group and the phenol, which is used as the acceptor for proton, could respond to pH changes immediately through both the ratiometric fluorescence signal readout and naked-eye colorimetric observation. The sensing process was highly stable and reversible. Most importantly, the suitable pKa value (6.44) allows CPH to presumably accumulate in lysosomes and become a lysosome-target fluorescent probe. By using CPH, the intralysosomal pH fluctuation stimulated by antimalaria drug chloroquine was successfully tracked in live cells through the ratiometric fluorescence images. Additionally, CPH could be immobilized on test papers, which exhibited a rapid and reversible colorimetric response to acid/base vapor through the naked-eye colorimetric analysis. This proof-of-concept study presents the potential application of CPH as a molecular tool for monitoring intralysosomal pH fluctuation in live cells, as well as paves the way for developing the economic, reusable, and fast-response optical pH meters for colorimetric sensing acid/base vapor with direct naked-eye observation. PMID:27431089

  12. TiO2 Nanoparticles as a Soft X-ray Molecular Probe

    SciTech Connect

    Larabell, Carolyn; Ashcroft, Jared M.; Gu, Weiwei; Zhang, Tierui; Hughes, Steven M.; Hartman, Keith B.; Hofmann, Cristina; Kanaras, Antonios G.; Kilcoyne, David A.; Le Gros, Mark; Yin, Yadong; Alivisatos, A. Paul; Larabell, Carolyn A.

    2007-06-30

    With the emergence of soft x-ray techniques for imaging cells, there is a pressing need to develop protein localization probes that can be unambiguously identified within the region of x-ray spectrum used for imaging. TiO2 nanocrystal colloids, which have a strong absorption cross-section within the "water-window" region of x-rays, areideally suited as soft x-ray microscopy probes. To demonstrate their efficacy, TiO2-streptavidin nanoconjugates were prepared and subsequently labeled microtubules polymerized from biotinylated tubulin. The microtubules were imaged using scanning transmission x-ray microscopy (STXM), and the TiO2 nanoparticle tags were specifically identified using x-ray absorption near edge spectroscopy (XANES). These experiments demonstrate that TiO2 nanoparticles are potential probes for protein localization analyses using soft x-ray microscopy.

  13. Inner-shell photoexcitations as probes of the molecular ions CH+, OH+, and SiH+: Measurements and theory

    NASA Astrophysics Data System (ADS)

    Mosnier, J.-P.; Kennedy, E. T.; van Kampen, P.; Cubaynes, D.; Guilbaud, S.; Sisourat, N.; Puglisi, A.; Carniato, S.; Bizau, J.-M.

    2016-06-01

    Spectral probes for the CH+, OH+, and SiH+ hydride molecular ions that play key roles in astrophysics and plasma processes are presented. The merged-beam technique at the SOLEIL synchrotron was used to record the photoionization (ion yield) spectra of CH+, OH+, and SiH+ and that of their parent atomic ions, in the K -shell and L -shell regions, respectively. Energies and oscillator strengths for the K α (CH+ and OH+) and L α (SiH+) transitions were determined from the spectra. Ab initio calculations interpret the experimental data in terms of contributions from ground and excited valence electronic states.

  14. Molecular Probe Dynamics Reveals Suppression of Ice-Like Regions in Strongly Confined Supercooled Water

    PubMed Central

    Banerjee, Debamalya; Bhat, Shrivalli N.; Bhat, Subray V.; Leporini, Dino

    2012-01-01

    The structure of the hydrogen bond network is a key element for understanding water's thermodynamic and kinetic anomalies. While ambient water is strongly believed to be a uniform, continuous hydrogen-bonded liquid, there is growing consensus that supercooled water is better described in terms of distinct domains with either a low-density ice-like structure or a high-density disordered one. We evidenced two distinct rotational mobilities of probe molecules in interstitial supercooled water of polycrystalline ice [Banerjee D, et al. (2009) ESR evidence for 2 coexisting liquid phases in deeply supercooled bulk water. Proc Natl Acad Sci USA 106: 11448–11453]. Here we show that, by increasing the confinement of interstitial water, the mobility of probe molecules, surprisingly, increases. We argue that loose confinement allows the presence of ice-like regions in supercooled water, whereas a tighter confinement yields the suppression of this ordered fraction and leads to higher fluidity. Compelling evidence of the presence of ice-like regions is provided by the probe orientational entropy barrier which is set, through hydrogen bonding, by the configuration of the surrounding water molecules and yields a direct measure of the configurational entropy of the same. We find that, under loose confinement of supercooled water, the entropy barrier surmounted by the slower probe fraction exceeds that of equilibrium water by the melting entropy of ice, whereas no increase of the barrier is observed under stronger confinement. The lower limit of metastability of supercooled water is discussed. PMID:23049747

  15. Probing the role of the magnetic field in the formation of structure in molecular clouds with Planck

    NASA Astrophysics Data System (ADS)

    Diego Soler, Juan

    2015-08-01

    The Planck observations of intensity and polarization of thermal emission from Galactic dust over the whole sky, and down to scales that probe the interiors of nearby molecular clouds, constitute an unprecedented data set for the study of the morphology of the magnetic field.Within ten nearby (d < 450 pc) Gould Belt molecular clouds we evaluate statistically the relative orientation between the magnetic field projected on the plane of sky, inferred from the polarized thermal emission of Galactic dust observed by Planck at 353 GHz, and the gas column density structures, quantified by the gradient of the column density, NH. The relative orientation is evaluated pixel by pixel and analyzed in bins of column density using the novel statistical tool called "Histogram of Relative Orientations".Within most clouds we find that the relative orientation changes progressively with increasing NH, from preferentially parallel or having no preferred orientation to preferentially perpendicular.In simulations of magnetohydrodynamic turbulence in molecular clouds this trend in relative orientation is a signature of Alfvénic or sub-Alfvénic turbulence, implying that the magnetic field is significant for the gas dynamics at the scales probed by Planck.We compare the deduced plane-of-the-sky magnetic field strength with estimates we obtain from the Davis-Chandrasekhar-Fermi method and with the line-of-sight magnetic field strengths derived from Zeeman splitting observations towards some of the studied regions.Finally, we discuss the implications of the Planck observations for the general picture of molecular cloud formation and evolution.This work is presented on behalf of the Planck Collaboration.

  16. Probing the molecular character of periodic mesoporous organosilicates via photoluminescence of Lewis acid-base adducts.

    PubMed

    Thiel, Indre; Fedorov, Alexey; Verel, Rene; Yakunin, Sergii; Kovalenko, Maksym V; Copéret, Christophe

    2016-05-18

    Photoluminescence decay was used as a structure-sensitive method to compare the distribution of emitting sites in periodic mesoporous organosilicates (PMOs) to their respective molecular analogs. The observed close similarity of PL decays confirms the molecular nature of PMOs and high homogeneity of emitting sites. PMID:27156706

  17. A pectin-methylesterase-inhibitor-based molecular probe for in situ detection of plant pectin methylesterase activity.

    PubMed

    Jolie, Ruben P; Duvetter, Thomas; Vandevenne, Evelien; Van Buggenhout, Sandy; Van Loey, Ann M; Hendrickx, Marc E

    2010-05-12

    In the quest of obtaining a molecular probe for in situ detection of pectin methylesterase (PME), the PME inhibitor (PMEI) was biotinylated and the biotinylated PMEI (bPMEI) was extensively characterized. Reaction conditions for single labeling of the purified PMEI with retention of its inhibitory capacity were identified. High-performance size-exclusion chromatography (HPSEC) analysis revealed that the bPMEI retained its ability to form a complex with plant PME and that it gained the capacity to strongly bind an avidin species. By means of dot-blot binding assays, the ability of the probe to recognize native and high-temperature or high-pressure denatured plant PMEs, coated on an absorptive surface, was investigated and compared to the binding characteristics of recently reported anti-PME monoclonal antibodies. Contrary to the antibodies, bPMEI only detected active PME molecules. Subsequently, both types of probes were used for PME localization in tissue-printing experiments. bPMEI proved its versatility by staining prints of carrot root, broccoli stem, and tomato fruit. Applying the tissue-printing technique on carrot roots after thermal treatment demonstrated the complementarity of bPMEI and anti-PME antibodies, with the former selectively detecting the remaining active PME and the latter staining both native and inactivated PME molecules. PMID:20380375

  18. Probing the Spatial Organization of Molecular Complexes Using Triple-Pair-Correlation

    PubMed Central

    Yin, Yandong; Rothenberg, Eli

    2016-01-01

    Super-resolution microscopy coupled with multiplexing techniques can resolve specific spatial arrangements of different components within molecular complexes. However, reliable quantification and analysis of such specific organization is extremely problematic because it is frequently obstructed by random co-localization incidents between crowded molecular species and the intrinsic heterogeneity of molecular complexes. To address this, we present a Triple-Pair-Correlation (TPC) analysis approach for unbiased interpretation of the spatial organization of molecular assemblies in crowded three-color super-resolution (SR) images. We validate this approach using simulated data, as well as SR images of DNA replication foci in human cells. This demonstrates the applicability of TPC in deciphering the specific spatial organization of molecular complexes hidden in dense multi-color super-resolution images. PMID:27545293

  19. Probing the Spatial Organization of Molecular Complexes Using Triple-Pair-Correlation.

    PubMed

    Yin, Yandong; Rothenberg, Eli

    2016-01-01

    Super-resolution microscopy coupled with multiplexing techniques can resolve specific spatial arrangements of different components within molecular complexes. However, reliable quantification and analysis of such specific organization is extremely problematic because it is frequently obstructed by random co-localization incidents between crowded molecular species and the intrinsic heterogeneity of molecular complexes. To address this, we present a Triple-Pair-Correlation (TPC) analysis approach for unbiased interpretation of the spatial organization of molecular assemblies in crowded three-color super-resolution (SR) images. We validate this approach using simulated data, as well as SR images of DNA replication foci in human cells. This demonstrates the applicability of TPC in deciphering the specific spatial organization of molecular complexes hidden in dense multi-color super-resolution images. PMID:27545293

  20. In vivo quantifying molecular specificity of Cy5.5-labeled cyclic 9-mer peptide probe with dynamic fluorescence imaging.

    PubMed

    Dai, Yunpeng; Yin, Jipeng; Huang, Yu; Chen, Xueli; Wang, Guodong; Liu, Yajun; Zhang, Xianghan; Nie, Yongzhan; Wu, Kaichun; Liang, Jimin

    2016-04-01

    We quantified molecular specificity of Cy5.5-GX1 in vivo with dynamic fluorescence imaging to better understand its kinetic properties. According to whether or not free GX1 was injected and when it was injected, twelve of BGC-823 xenografted mice were randomly divided into three groups and underwent a 60 minute dynamic fluorescence scanning. Combined with a principal-component analysis, the binding potential (Bp) of the probe was determined by both Logan graphical analysis with reference tissue model (GARTM) and Lammertsma simplified reference tissue model (SRTM). The sum of the pharmacokinetic rate constants (SKRC) was quantified by the Gurfinkel exponential model (GEXPM). Cy5.5-GX1 specifically targeted tumor both in vitro and in vivo. We obtained similar quantification results of Bp (GARTM Bp = 0.582 ± 0.2655, SRTM Bp = 0.618 ± 0.2923), and obtained a good linear relation between the Bp value and the SKRC value. Our results indicate that the SKRC value is more suitable for an early-stage kinetic data analysis, and the Bp value depicts kinetic characteristics under the equilibrium state. Dynamic fluorescence imaging in conjunction with various kinetic models are optimal tools to quantify molecular specificity of the Cy5.5-GX1 probe in vivo. PMID:27446643

  1. In vivo quantifying molecular specificity of Cy5.5-labeled cyclic 9-mer peptide probe with dynamic fluorescence imaging

    PubMed Central

    Dai, Yunpeng; Yin, Jipeng; Huang, Yu; Chen, Xueli; Wang, Guodong; Liu, Yajun; Zhang, Xianghan; Nie, Yongzhan; Wu, Kaichun; Liang, Jimin

    2016-01-01

    We quantified molecular specificity of Cy5.5-GX1 in vivo with dynamic fluorescence imaging to better understand its kinetic properties. According to whether or not free GX1 was injected and when it was injected, twelve of BGC-823 xenografted mice were randomly divided into three groups and underwent a 60 minute dynamic fluorescence scanning. Combined with a principal-component analysis, the binding potential (Bp) of the probe was determined by both Logan graphical analysis with reference tissue model (GARTM) and Lammertsma simplified reference tissue model (SRTM). The sum of the pharmacokinetic rate constants (SKRC) was quantified by the Gurfinkel exponential model (GEXPM). Cy5.5-GX1 specifically targeted tumor both in vitro and in vivo. We obtained similar quantification results of Bp (GARTM Bp = 0.582 ± 0.2655, SRTM Bp = 0.618 ± 0.2923), and obtained a good linear relation between the Bp value and the SKRC value. Our results indicate that the SKRC value is more suitable for an early-stage kinetic data analysis, and the Bp value depicts kinetic characteristics under the equilibrium state. Dynamic fluorescence imaging in conjunction with various kinetic models are optimal tools to quantify molecular specificity of the Cy5.5-GX1 probe in vivo. PMID:27446643

  2. How does the molecular linker in dynamic force spectroscopy affect probing molecular interactions at the single-molecule level?

    NASA Astrophysics Data System (ADS)

    Taninaka, Atsushi; Aizawa, Kota; Hanyu, Tatsuya; Hirano, Yuuichi; Takeuchi, Osamu; Shigekawa, Hidemi

    2016-08-01

    Dynamic force spectroscopy (DFS) based on atomic force microscopy, which enables us to obtain information on the interaction potential between molecules such as antigen–antibody complexes at the single-molecule level, is a key technique for advancing molecular science and technology. However, to ensure the reliability of DFS measurement, its basic mechanism must be well understood. We examined the effect of the molecular linker used to fix the target molecule to the atomic force microscope cantilever, i.e., the force direction during measurement, for the first time, which has not been discussed until now despite its importance. The effect on the lifetime and barrier position, which can be obtained by DFS, was found to be ∼10 and ∼50%, respectively, confirming the high potential of DFS.

  3. How does the molecular linker in dynamic force spectroscopy affect probing molecular interactions at the single-molecule level?

    NASA Astrophysics Data System (ADS)

    Taninaka, Atsushi; Aizawa, Kota; Hanyu, Tatsuya; Hirano, Yuuichi; Takeuchi, Osamu; Shigekawa, Hidemi

    2016-08-01

    Dynamic force spectroscopy (DFS) based on atomic force microscopy, which enables us to obtain information on the interaction potential between molecules such as antigen-antibody complexes at the single-molecule level, is a key technique for advancing molecular science and technology. However, to ensure the reliability of DFS measurement, its basic mechanism must be well understood. We examined the effect of the molecular linker used to fix the target molecule to the atomic force microscope cantilever, i.e., the force direction during measurement, for the first time, which has not been discussed until now despite its importance. The effect on the lifetime and barrier position, which can be obtained by DFS, was found to be ˜10 and ˜50%, respectively, confirming the high potential of DFS.

  4. Molecular Probing of the HPV-16 E6 Protein Alpha Helix Binding Groove with Small Molecule Inhibitors

    PubMed Central

    Rietz, Anne; Petrov, Dino P.; Bartolowits, Matthew; DeSmet, Marsha; Davisson, V. Jo; Androphy, Elliot J.

    2016-01-01

    The human papillomavirus (HPV) HPV E6 protein has emerged as a central oncoprotein in HPV-associated cancers in which sustained expression is required for tumor progression. A majority of the E6 protein interactions within the human proteome use an alpha-helix groove interface for binding. The UBE3A/E6AP HECT domain ubiquitin ligase binds E6 at this helix-groove interface. This enables formation of a trimeric complex with p53, resulting in destruction of this tumor suppressor. While recent x-ray crystal structures are useful, examples of small molecule probes that can modulate protein interactions at this interface are limited. To develop insights useful for potential structure-based design of ligands for HPV E6, a series of 2,6-disubstituted benzopyranones were prepared and tested as competitive antagonists of E6-E6AP helix-groove interactions. These small molecule probes were used in both binding and functional assays to evaluate recognition features of the E6 protein. Evidence for an ionic functional group interaction within the helix groove was implicated by the structure-activity among the highest affinity ligands. The molecular topographies of these protein-ligand interactions were evaluated by comparing the binding and activities of single amino acid E6 mutants with the results of molecular dynamic simulations. A group of arginine residues that form a rim-cap over the E6 helix groove offer compensatory roles in binding and recognition of the small molecule probes. The flexibility and impact on the overall helix-groove shape dictated by these residues offer new insights for structure-based targeting of HPV E6. PMID:26915086

  5. Molecular Probing of the HPV-16 E6 Protein Alpha Helix Binding Groove with Small Molecule Inhibitors.

    PubMed

    Rietz, Anne; Petrov, Dino P; Bartolowits, Matthew; DeSmet, Marsha; Davisson, V Jo; Androphy, Elliot J

    2016-01-01

    The human papillomavirus (HPV) HPV E6 protein has emerged as a central oncoprotein in HPV-associated cancers in which sustained expression is required for tumor progression. A majority of the E6 protein interactions within the human proteome use an alpha-helix groove interface for binding. The UBE3A/E6AP HECT domain ubiquitin ligase binds E6 at this helix-groove interface. This enables formation of a trimeric complex with p53, resulting in destruction of this tumor suppressor. While recent x-ray crystal structures are useful, examples of small molecule probes that can modulate protein interactions at this interface are limited. To develop insights useful for potential structure-based design of ligands for HPV E6, a series of 2,6-disubstituted benzopyranones were prepared and tested as competitive antagonists of E6-E6AP helix-groove interactions. These small molecule probes were used in both binding and functional assays to evaluate recognition features of the E6 protein. Evidence for an ionic functional group interaction within the helix groove was implicated by the structure-activity among the highest affinity ligands. The molecular topographies of these protein-ligand interactions were evaluated by comparing the binding and activities of single amino acid E6 mutants with the results of molecular dynamic simulations. A group of arginine residues that form a rim-cap over the E6 helix groove offer compensatory roles in binding and recognition of the small molecule probes. The flexibility and impact on the overall helix-groove shape dictated by these residues offer new insights for structure-based targeting of HPV E6. PMID:26915086

  6. ADAPT, a Novel Scaffold Protein-Based Probe for Radionuclide Imaging of Molecular Targets That Are Expressed in Disseminated Cancers.

    PubMed

    Garousi, Javad; Lindbo, Sarah; Nilvebrant, Johan; Åstrand, Mikael; Buijs, Jos; Sandström, Mattias; Honarvar, Hadis; Orlova, Anna; Tolmachev, Vladimir; Hober, Sophia

    2015-10-15

    Small engineered scaffold proteins have attracted attention as probes for radionuclide-based molecular imaging. One class of these imaging probes, termed ABD-Derived Affinity Proteins (ADAPT), has been created using the albumin-binding domain (ABD) of streptococcal protein G as a stable protein scaffold. In this study, we report the development of a clinical lead probe termed ADAPT6 that binds HER2, an oncoprotein overexpressed in many breast cancers that serves as a theranostic biomarker for several approved targeting therapies. Surface-exposed amino acids of ABD were randomized to create a combinatorial library enabling selection of high-affinity binders to various proteins. Furthermore, ABD was engineered to enable rapid purification, to eradicate its binding to albumin, and to enable rapid blood clearance. Incorporation of a unique cysteine allowed site-specific conjugation to a maleimido derivative of a DOTA chelator, enabling radionuclide labeling, ¹¹¹In for SPECT imaging and ⁶⁸Ga for PET imaging. Pharmacologic studies in mice demonstrated that the fully engineered molecule (111)In/⁶⁸Ga-DOTA-(HE)3-ADAPT6 was specifically bound and taken up by HER2-expressing tumors, with a high tumor-to-normal tissue ratio in xenograft models of human cancer. Unbound tracer underwent rapid renal clearance followed by high renal reabsorption. HER2-expressing xenografts were visualized by gamma-camera or PET at 1 hour after infusion. PET experiments demonstrated feasibility for discrimination of xenografts with high or low HER2 expression. Our results offer a preclinical proof of concept for the use of ADAPT probes for noninvasive in vivo imaging. PMID:26297736

  7. Fluorescence Probe Based on Hybrid Mesoporous Silica/Quantum Dot/Molecularly Imprinted Polymer for Detection of Tetracycline.

    PubMed

    Zhang, Liang; Chen, Ligang

    2016-06-29

    A newly designed fluorescence probe made from a hybrid quantum dot/mesoporous silica/molecularly imprinted polymer (QD/MS/MIP) was successfully created, and the probe was used for the detection of tetracycline (TC) in serum sample. QD/MS/MIP was characterized by transmission electron microscope, Fourier transform infrared spectroscopy, UV spectroscopy, X-ray powder diffraction, nitrogen adsorption-desorption experiment and fluorescence spectroscopy. Tetracycline, which is a type of broad-spectrum antibiotic, was selected as the template. The monomer and the template were combined by covalent bonds. After the template was removed to form a binding site, a hydrogen bonding interaction formed between the hole and the target molecule. Moreover, when rebinding TC, a new complex was produced between the amino group of QD/MS/MIP and the hydroxyl group of TC. After that, the energy of the QDs could transfer to the complex, which explains the fluorescence quenching phenomenon. The fluorescent intensity of QD/MS/MIP decreased in 10 min, and an excellent linearity from 50 to 1000 ng mL(-1) was correspondingly obtained. This composite material has a high selectivity with an imprinting factor of 6.71. In addition, the confirmed probe strategy was successfully applied to serum sample analyses, and the recoveries were 90.2%-97.2% with relative standard deviations of 2.2%-5.7%. This current work offers a novel and suitable method to synthesize QD/MS/MIP with a highly selective recognition ability. This composite material will be valuable for use in fluorescence probe applications. PMID:27280785

  8. Structural Changes of a Doubly Spin-Labeled Chemically Driven Molecular Shuttle Probed by PELDOR Spectroscopy.

    PubMed

    Franchi, Paola; Bleve, Valentina; Mezzina, Elisabetta; Schäfer, Christian; Ragazzon, Giulio; Albertini, Marco; Carbonera, Donatella; Credi, Alberto; Di Valentin, Marilena; Lucarini, Marco

    2016-06-20

    Gaining detailed information on the structural rearrangements associated with stimuli-induced molecular movements is of utmost importance for understanding the operation of molecular machines. Pulsed electron-electron double resonance (PELDOR) was employed to monitor the geometrical changes arising upon chemical switching of a [2]rotaxane that behaves as an acid-base-controlled molecular shuttle. To this aim, the rotaxane was endowed with stable nitroxide radical units in both the ring and axle components. The combination of PELDOR data and molecular dynamic calculations indicates that in the investigated rotaxane, the ring displacement along the axle, caused by the addition of a base, does not alter significantly the distance between the nitroxide labels, but it is accompanied by a profound change in the geometry adopted by the macrocycle. PMID:27123774

  9. Complexation of tetrandrine with calcium ion probed by various spectroscopic methods and molecular modeling

    NASA Astrophysics Data System (ADS)

    Stanculescu, Ioana; Mandravel, Cristina; Landy, David; Woisel, Patrice; Surpateanu, Gheorghe

    2003-07-01

    The formation of the complex between tetrandrine and the calcium ion, in solution, was studied using FTIR, UV-Vis, 1H NMR, 13C NMR and electrospray mass spectroscopy spectroscopic methods and molecular modeling. The calcium salts used were: Ca(ClO 4) 2·4H 2O and Ca(Picrate) 2 in the solvents: acetonitrile (CH 3CN), deuterated acetonitrile (CD 3CN) and tetrahydrofurane (THF). The determined complex stability constant was: 20277±67 dm 3 mol -1 and corresponding free energy Δ G0=-5.820±0.002 kcal mol -1. The molecular simulation of the complex formation with the MM3 Augmented force field integrated in CAChe provided useful data about its energy. Combining the experimental results and molecular modeling we propose a model for the structure of tetrandrine-Ca complex with an eight coordinated geometry.

  10. Molecular imaging of hepatocellular carcinoma xenografts with epidermal growth factor receptor targeted affibody probes.

    PubMed

    Zhao, Ping; Yang, Xiaoyang; Qi, Shibo; Liu, Hongguang; Jiang, Han; Hoppmann, Susan; Cao, Qizhen; Chua, Mei-Sze; So, Samuel K; Cheng, Zhen

    2013-01-01

    Hepatocellular carcinoma (HCC) is a highly aggressive and lethal cancer. It is typically asymptomatic at the early stage, with only 10%-20% of HCC patients being diagnosed early enough for appropriate surgical treatment. The delayed diagnosis of HCC is associated with limited treatment options and much lower survival rates. Therefore, the early and accurate detection of HCC is crucial to improve its currently dismal prognosis. The epidermal growth factor receptor (EGFR) has been reported to be involved in HCC tumorigenesis and to represent an attractive target for HCC imaging and therapy. In this study, an affibody molecule, Ac-Cys-ZEGFR:1907, targeting the extracellular domain of EGFR, was used for the first time to assess its potential to detect HCC xenografts. By evaluating radio- or fluorescent-labeled Ac-Cys-ZEGFR:1907 as a probe for positron emission tomography (PET) or optical imaging of HCC, subcutaneous EGFR-positive HCC xenografts were found to be successfully imaged by the PET probe. Thus, affibody-based PET imaging of EGFR provides a promising approach for detecting HCC in vivo. PMID:23710458

  11. Advanced electric-field scanning probe lithography on molecular resist using active cantilever

    NASA Astrophysics Data System (ADS)

    Kaestner, Marcus; Aydogan, Cemal; Ivanov, Tzvetan; Ahmad, Ahmad; Angelov, Tihomir; Reum, Alexander; Ishchuk, Valentyn; Krivoshapkina, Yana; Hofer, Manuel; Lenk, Steve; Atanasov, Ivaylo; Holz, Mathias; Rangelow, Ivo W.

    2015-07-01

    The routine "on demand" fabrication of features smaller than 10 nm opens up new possibilities for the realization of many devices. Driven by the thermally actuated piezoresistive cantilever technology, we have developed a prototype of a scanning probe lithography (SPL) platform which is able to image, inspect, align, and pattern features down to the single digit nanoregime. Here, we present examples of practical applications of the previously published electric-field based current-controlled scanning probe lithography. In particular, individual patterning tests are carried out on calixarene by using our developed table-top SPL system. We have demonstrated the application of a step-and-repeat SPL method including optical as well as atomic force microscopy-based navigation and alignment. The closed-loop lithography scheme was applied to sequentially write positive and negative tone features. Due to the integrated unique combination of read-write cycling, each single feature is aligned separately with the highest precision and inspected after patterning. This routine was applied to create a pattern step by step. Finally, we have demonstrated the patterning over larger areas, over existing topography, and the practical applicability of the SPL processes for lithography down to 13-nm pitch patterns. To enhance the throughput capability variable beam diameter electric field, current-controlled SPL is briefly discussed.

  12. First-trimester spontaneous pregnancy loss - molecular analysis using multiplex ligation-dependent probe amplification.

    PubMed

    Zimowski, J G; Massalska, D; Pawelec, M; Bijok, J; Michałowska, A; Roszkowski, T

    2016-05-01

    Spontaneous miscarriages are the most frequent complications of pregnancy and, in at least half of cases, are caused by chromosomal abnormalities, mainly aneuploidies. We present the preliminary results of the implementation of multiplex ligation-dependent probe amplification (MLPA) in the detection of chromosomal aberrations in the tissue derived from first-trimester miscarriage and evaluate the limitations and requirements of the method. We studied 181 MLPA analyses with subtelomeric and subcentromeric probe kits for all chromosomes (SALSA P070 and SALSA P181) performed on the first-trimester spontaneous miscarriage products in our Department of Genetics between September 2012 and December 2014. Conclusive MLPA results were obtained in 97.2% of samples. Chromosomal aberrations were detected in 40.3% of samples: 61.8% samples of good quality and 12.6% samples of poor quality (p < 0.001). The normal female karyotype was detected in 14.7% of good quality samples and 84.8% of poor quality samples (p < 0.001). MLPA is a useful tool for the detection of chromosomal aberrations in first-trimester miscarriage products. However, the tissue has to be well prepared before testing and the results 46,XX should be interpreted with caution. PMID:26748861

  13. Which Microbial Communities Are Present? Importance of Selecting Appropriate Primers and Probes for Use in Molecular Microbiological Methods (MMM) in Oilfields

    NASA Astrophysics Data System (ADS)

    Sørensen, Ketil Bernt

    Molecular microbiology techniques play an increasing role in the oil industry. Most of the current applications are based on either Fluorescence in situ Hybridisation (FISH) or polymerase chain reaction (PCR) or some variation thereof. These types of approaches require the use of oligonucleotide primers and probes (i.e. short fragments of DNA that are complementary to the target DNA/RNA of the microorganism of interest). In the case of FISH, the probes are fluorescently labelled in order to identify the target cells. Before undertaking either FISH or PCR approaches, it is important to select the most appropriate primers or probes for targeting the microorganisms of interest in a given environment.

  14. Molecular imaging of a cancer-targeting theragnostics probe using a nucleolin aptamer- and microRNA-221 molecular beacon-conjugated nanoparticle.

    PubMed

    Kim, Jin Kyeoung; Choi, Kyung-Ju; Lee, Minhyung; Jo, Mi-hee; Kim, Soonhag

    2012-01-01

    MicroRNAs (miRNA, miR) have been reported as cancer biomarkers that regulate tumor suppressor genes. Hence, simultaneous detecting and inhibiting of miRNA function will be useful as a cancer theragnostics probe to minimize side effects and invasiveness. In this study, we developed a cancer-targeting therangostics probe in a single system using an AS1411 aptamer - and miRNA-221 molecular beacon (miR-221 MB)-conjugated magnetic fluorescence (MF) nanoparticle (MFAS miR-221 MB) to simultaneously target to cancer tissue, image intracellularly expressed miRNA-221 and treat miRNA-221-involved carcinogenesis. AS1411 aptamer-conjugated MF (MFAS) nanoparticles displayed a great selectivity and delivery into various cancer cell lines. The miR-221 MB detached from the MFAS miR-221 MB in the cytoplasm of C6 cells clearly imaged miRNA-221 biogenesis and simultaneously resulted in antitumor therapeutic effects by inhibiting miRNA function, indicating a successful astrocytoma-targeting theragnostics. MFAS miRNA MB can be easily applied to other cancers by simply changing a targeted miRNA highly expressed in cancers. PMID:21944470

  15. Microfluidic Technology Platforms for Synthesizing, Labeling and Measuring the Kinetics of Transport and Biochemical Reactions for Developing Molecular Imaging Probes

    SciTech Connect

    Phelps, Michael E.

    2009-09-01

    Radiotracer techniques are used in environmental sciences, geology, biology and medicine. Radiotracers with Positron Emission Tomography (PET) provided biological examinations of ~3 million patients 2008. Despite the success of positron labeled tracers in many sciences, there is limited access in an affordable and convenient manner to develop and use new tracers. Integrated microfluidic chips are a new technology well matched to the concentrations of tracers. Our goal is to develop microfluidic chips and new synthesis approaches to enable wide dissemination of diverse types of tracers at low cost, and to produce new generations of radiochemists for which there are many unfilled jobs. The program objectives are to: 1. Develop an integrated microfluidic platform technology for synthesizing and 18F-labeling diverse arrays of different classes of molecules. 2. Incorporate microfluidic chips into small PC controlled devices (“Synthesizer”) with a platform interfaced to PC for electronic and fluid input/out control. 3. Establish a de-centralized model with Synthesizers for discovering and producing molecular imaging probes, only requiring delivery of inexpensive [18F]fluoride ion from commercial PET radiopharmacies vs the centralized approach of cyclotron facilities synthesizing and shipping a few different types of 18F-probes. 4. Develop a position sensitive avalanche photo diode (PSAPD) camera for beta particles embedded in a microfluidic chip for imaging and measuring transport and biochemical reaction rates to valid new 18F-labeled probes in an array of cell cultures. These objectives are met within a research and educational program integrating radio-chemistry, synthetic chemistry, biochemistry, engineering and biology in the Crump Institute for Molecular Imaging. The Radiochemistry Training Program exposes PhD and post doctoral students to molecular imaging in vitro in cells and microorganisms in microfluidic chips and in vivo with PET, from new technologies

  16. Probing the clumping structure of giant molecular clouds through the spectrum, polarisation and morphology of X-ray reflection nebulae

    NASA Astrophysics Data System (ADS)

    Molaro, Margherita; Khatri, Rishi; Sunyaev, Rashid A.

    2016-04-01

    We introduce a new method for probing global properties of clump populations in giant molecular clouds (GMCs) in the case where these act as X-ray reflection nebulae (XRNe), based on the study of the clumping's overall effect on the reflected X-ray signal, in particular on the Fe K-α line's shoulder. We consider the particular case of Sgr B2, one of the brightest and most massive XRN in the Galactic center (GC) region. We parametrise the gas distribution inside the cloud using a simple clumping model with theslope of the clump mass function (α), the minimum clump mass (mmin), the fraction of the cloud's mass contained in clumps (fDGMF), and the mass-size relation of individual clumps as free parameters, and investigate how these affect the reflected X-ray spectrum. In the case of very dense clumps, similar to those presently observed in Sgr B2, these occupy a small volume of the cloud and present a small projected area to the incoming X-ray radiation. We find that these contribute negligibly to the scattered X-rays. Clump populations with volume-filling factors of >10-3 do leave observational signatures, that are sensitive to the clump model parameters, in the reflected spectrum and polarisation. Future high angular resolution X-ray observations could therefore complement the traditional optical and radio observations of these GMCs, and prove to be a powerful probe in the study of their internal structure. Clumps in GMCs should further be visible both as bright spots and regions of heavy absorption in high resolution X-ray observations. We therefore also study the time-evolution of the X-ray morphology, under illumination by a transient source, as a probe of the 3D distribution and column density of individual clumps by future X-ray observatories.

  17. The identification, characterization and optimization of small molecule probes of cysteine proteases: experiences of the Penn Center for Molecular Discovery with cathepsin B and cathepsin L.

    PubMed

    Huryn, Donna M; Smith, Amos B

    2009-01-01

    During the pilot phase of the NIH Molecular Library Screening Network, the Penn Center for Molecular Discovery focused on a series of projects aimed at high throughput screening and the development of probes of a variety of protease targets. This review provides our medicinal chemistry experience with two such targets--cathepsin B and cathepsin L. We describe our approach for hit validation, characterization and triage that led to a critical understanding of the nature of hits from the cathepsin B project. In addition, we detail our experience at hit identification and optimization that led to the development of a novel thiocarbazate probe of cathepsin L. PMID:19807666

  18. Probing surface and interfacial molecular structures of a rubbery adhesion promoter using sum frequency generation vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Fang, Yong; Li, Bolin; Yu, Jincheng; Zhou, Jie; Xu, Xin; Shao, Wei; Lu, Xiaolin

    2013-09-01

    The molecular structures of an adhesion promoter, polybutadiene-modified epoxy (PBME) rubber at surfaces and buried interfaces with gold (Au) were studied using sum frequency generation (SFG) vibrational spectroscopy. The SFG spectra showed that the soft butadiene part of PBME can segregate to the surfaces and buried interfaces in two base formulations. This is consistent with its application as an adhesion promoter. For the first time, the orientation of the segregated vinyl methylene groups of PBME at the surface and buried interface was evaluated. We found that the vinyl methylene groups at the surface were highly tilted and twisted by quantitative analysis; while the vinyl methylene groups at the buried Au interface were highly tilted by qualitative estimation. Furthermore, this study confirms that the sandwiched-face-down experimental setup can be employed to study the buried interfaces. This could be developed into a standard way to probe the buried interfaces between the commercialized resins and metal substrates.

  19. Probing the Nanosecond Dynamics of a Designed Three-Stranded Beta-Sheet with a Massively Parallel Molecular Dynamics Simulation

    PubMed Central

    Voelz, Vincent A.; Luttmann, Edgar; Bowman, Gregory R.; Pande, Vijay S.

    2009-01-01

    Recently a temperature-jump FTIR study of a designed three-stranded sheet showing a fast relaxation time of ~140 ± 20 ns was published. We performed massively parallel molecular dynamics simulations in explicit solvent to probe the structural events involved in this relaxation. While our simulations produce similar relaxation rates, the structural ensemble is broad. We observe the formation of turn structure, but only very weak interaction in the strand regions, which is consistent with the lack of strong backbone-backbone NOEs in previous structural NMR studies. These results suggest that either DPDP-II folds at time scales longer than 240 ns, or that DPDP-II is not a well-defined three-stranded β-sheet. This work also provides an opportunity to compare the performance of several popular forcefield models against one another. PMID:19399235

  20. Influence of freezing and low molecular weight cryoprotectants on microsomal membrane structure: a study by multiparametric fluorescent probe.

    PubMed

    Dyubko, Tatyana S; Onishchenko, Elena V; Pivovarenko, Vasyl G

    2006-11-01

    The influence of low molecular weight cryoprotectants (CPs) such as glycerol (GL), 1,2-propanediol (PD) and dimethylsulfoxide (DMSO) on the structure of rat liver microsomal membranes on the stages of equilibration and upon freezing up to -196 degrees C was studied using a multiparametric fluorescent probe of flavonol nature. It was estimated that the studied CPs have individual concentration ranges defining low amplitude of their action on biomembranes. An exceeding of these ranges strongly increases the violation of membrane native structure already at the stage of incubation with CPs, strengthening it during the freezing procedure. According to the perturbation effect on microsomal membranes the studied CPs can be arranged in a sequence: DMSO>PD>GL. PMID:16977488

  1. 1-Naphthol as an ESPT fluorescent molecular probe for sensing thermotropic microenvironmental changes of pluronic F127 in aqueous media.

    PubMed

    Swain, Jitendriya; Mishra, Ashok Kumar

    2015-07-14

    Thermotropic microenvironmental changes and the level of hydration in different microenvironments of pluronic F127 (PF127), (PEO106 PPO70 PEO106, average molar mass 13 000) in aqueous media have been studied using 1-naphthol, which is an ESPT fluorescent molecular probe. The appearance of 1-naphthol neutral form fluorescence in aqueous PF127 (10% w/v) solution indicates the ability of 1-naphthol to sense hydrophobic domains in micellar aggregations. There is a marked enhancement of the neutral form fluorescence at and above the gelation temperature (20 °C), which shows that the probe can accurately sense the sol-gel transition. In the temperature range of 10-40 °C, with increase in temperature there is a progressive enhancement of the neutral form fluorescence and the blue shift of the neutral and anionic form fluorescence; a decrease in the deprotonation rate constant (kpt) indicates that the water-polymer interfacial region is progressively dehydrated. Because kpt is related to the availability of proton-accepting water in the microenvironment of 1-naphthol, the reduction of kpt indicates progressive dehydration. The thermotropic response of the I1/I3 vibronic band ratio of pyrene-1-butyric acid fluorescence shows a progressive increase in the non-polarity of the interfacial domain with increasing temperature. The increase in non-polarity and the decrease of the hydration level are strongly correlated. PMID:26018747

  2. Molecular imaging of hemoglobin using ground state recovery pump-probe optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Applegate, Brian E.; Izatt, Joseph A.

    2007-02-01

    We have undertaken an effort to further develop ground state recovery Pump-Probe Optical Coherence Tomograpy (gsrPPOCT) to specifically target and measure 3-D images of hemoglobin concentration with the goals of mapping tissue vasculature, total hemoglobin, and hemoglobin oxygen saturation. As a first step toward those goals we have measured the gsrPPOCT signal from the hemoglobin in the filament arteries of a zebra danio fish. We have further processed the resulting signal to extract a qualitative map of the hemoglobin concentration. We have also demonstrated the potential to use ground state recovery times to differentiate between two chromophores which may prove to be an effective tool for differentiating between oxy and deoxy hemoglobin.

  3. Fluorescence molecular probes for sensitive point detection of amyloid fibrils and protofibrils

    NASA Astrophysics Data System (ADS)

    Lindgren, Mikael; Jonsson, Per; Sörgjerd, Karin; Hammarström, Per

    2005-10-01

    Protein based infections such as prion diseases have lately attracted a large amount of interest, primarily due to the Mad Cow Epidemic in Great Britain, and the increase of Alzheimer's disease and related diseases in the ageing Western society. Infective proteins are very stable and almost untraceable prior to infection making them ideal as biological weapons. Particularly if the used agent is of human origin, the immunoresponse can be avoided, leaving no trace of the infectious agent. The transient nature of infectious oligomeric intermediates of misfolded proteins or peptide fragments that later matures into fibrillar aggregates makes them hard to study, and methods to detect and study these species are sparse. There exist a number of fluorescent probes that bind specifically to protein amyloidic structures. Thioflavins (ThT, ThS), Congo and Nile red, 4-(dicyanovinyl)-julolidine (DCVJ), as well as derivatives amino-8-naphtalene sulphonate (ANS, Bis-ANS) which are known to bind to the fibrillar or pre-fibrillar states with dissociation constants of typically 1 - 20 μM. Here, transthyretin (TTR), insulin and lysozyme were used as model proteins to detect different amyloid precursor states for diseases such as senile systemic amyloidosis, familial amyloidotic polyneuropathy (FAP) and iatrogenic amyloidosis. Specifically, the probes were employed in static assays to characterize protofibrillar and mature amyloid fibrillar states using steady state and time-resolved fluorescence techniques. Particularly, we investigate and report on the possibility to detect protofibrillar states at low concentration levels using modern fluorescence array detector systems in conjunction with lasers operating in the blue or ultraviolett wavelengths as excitation source. Results of ANS, ThT and a ThT analogue (abbreviated ThC) are discussed.

  4. Carbon-11 and fluorine-18 chemistry devoted to molecular probes for imaging the brain with positron emission tomography.

    PubMed

    Dollé, Frédéric

    2013-01-01

    Exploration of the living human brain in real-time and in a noninvasive way was for centuries only a dream, made, however, possible today with the remarkable development during the four last decades of powerful molecular imaging techniques, and especially positron emission tomography (PET). Molecular PET imaging relies, from a chemical point of view, on the use and preparation of a positron-emitting radiolabelled probe or radiotracer, notably compounds incorporating one of two short-lived radionuclides fluorine-18 (T1/2 : 109.8 min) and carbon-11 (T1/2 : 20.38 min). The growing availability and interest for the radiohalogen fluorine-18 in radiopharmaceutical chemistry undoubtedly results from its convenient half-life and the successful use in clinical oncology of 2-[(18) F]fluoro-2-deoxy-d-glucose ([(18) F]FDG). The special interest of carbon-11 is not only that carbon is present in virtually all biomolecules and drugs allowing therefore for isotopic labelling of their chemical structures but also that a given molecule could be radiolabelled at different functions or sites, permitting to explore (or to take advantage of) in vivo metabolic pathways. PET chemistry includes production of these short-lived radioactive isotopes via nuclear transmutation reactions using a cyclotron, and is directed towards the development of rapid synthetic methods, at the trace level, for the introduction of these nuclides into a molecule, as well as the use of fast purification, analysis and formulation techniques. PET chemistry is the driving force in molecular PET imaging, and this special issue of the Journal of Labelled Compounds and Radiopharmaceuticals, which is strongly chemistry and radiochemistry-oriented, aims at illustrating, be it in part only, the state-of-the-art arsenal of reactions currently available and its potential for the research and development of specific molecular probes labelled with the positron emitters carbon-11 and fluorine-18, with optimal imaging

  5. Planck intermediate results. XXXV. Probing the role of the magnetic field in the formation of structure in molecular clouds

    NASA Astrophysics Data System (ADS)

    Planck Collaboration; Ade, P. A. R.; Aghanim, N.; Alves, M. I. R.; Arnaud, M.; Arzoumanian, D.; Ashdown, M.; Aumont, J.; Baccigalupi, C.; Banday, A. J.; Barreiro, R. B.; Bartolo, N.; Battaner, E.; Benabed, K.; Benoît, A.; Benoit-Lévy, A.; Bernard, J.-P.; Bersanelli, M.; Bielewicz, P.; Bock, J. J.; Bonavera, L.; Bond, J. R.; Borrill, J.; Bouchet, F. R.; Boulanger, F.; Bracco, A.; Burigana, C.; Calabrese, E.; Cardoso, J.-F.; Catalano, A.; Chiang, H. C.; Christensen, P. R.; Colombo, L. P. L.; Combet, C.; Couchot, F.; Crill, B. P.; Curto, A.; Cuttaia, F.; Danese, L.; Davies, R. D.; Davis, R. J.; de Bernardis, P.; de Rosa, A.; de Zotti, G.; Delabrouille, J.; Dickinson, C.; Diego, J. M.; Dole, H.; Donzelli, S.; Doré, O.; Douspis, M.; Ducout, A.; Dupac, X.; Efstathiou, G.; Elsner, F.; Enßlin, T. A.; Eriksen, H. K.; Falceta-Gonçalves, D.; Falgarone, E.; Ferrière, K.; Finelli, F.; Forni, O.; Frailis, M.; Fraisse, A. A.; Franceschi, E.; Frejsel, A.; Galeotta, S.; Galli, S.; Ganga, K.; Ghosh, T.; Giard, M.; Gjerløw, E.; González-Nuevo, J.; Górski, K. M.; Gregorio, A.; Gruppuso, A.; Gudmundsson, J. E.; Guillet, V.; Harrison, D. L.; Helou, G.; Hennebelle, P.; Henrot-Versillé, S.; Hernández-Monteagudo, C.; Herranz, D.; Hildebrandt, S. R.; Hivon, E.; Holmes, W. A.; Hornstrup, A.; Huffenberger, K. M.; Hurier, G.; Jaffe, A. H.; Jaffe, T. R.; Jones, W. C.; Juvela, M.; Keihänen, E.; Keskitalo, R.; Kisner, T. S.; Knoche, J.; Kunz, M.; Kurki-Suonio, H.; Lagache, G.; Lamarre, J.-M.; Lasenby, A.; Lattanzi, M.; Lawrence, C. R.; Leonardi, R.; Levrier, F.; Liguori, M.; Lilje, P. B.; Linden-Vørnle, M.; López-Caniego, M.; Lubin, P. M.; Macías-Pérez, J. F.; Maino, D.; Mandolesi, N.; Mangilli, A.; Maris, M.; Martin, P. G.; Martínez-González, E.; Masi, S.; Matarrese, S.; Melchiorri, A.; Mendes, L.; Mennella, A.; Migliaccio, M.; Miville-Deschênes, M.-A.; Moneti, A.; Montier, L.; Morgante, G.; Mortlock, D.; Munshi, D.; Murphy, J. A.; Naselsky, P.; Nati, F.; Netterfield, C. B.; Noviello, F.; Novikov, D.; Novikov, I.; Oppermann, N.; Oxborrow, C. A.; Pagano, L.; Pajot, F.; Paladini, R.; Paoletti, D.; Pasian, F.; Perotto, L.; Pettorino, V.; Piacentini, F.; Piat, M.; Pierpaoli, E.; Pietrobon, D.; Plaszczynski, S.; Pointecouteau, E.; Polenta, G.; Ponthieu, N.; Pratt, G. W.; Prunet, S.; Puget, J.-L.; Rachen, J. P.; Reinecke, M.; Remazeilles, M.; Renault, C.; Renzi, A.; Ristorcelli, I.; Rocha, G.; Rossetti, M.; Roudier, G.; Rubiño-Martín, J. A.; Rusholme, B.; Sandri, M.; Santos, D.; Savelainen, M.; Savini, G.; Scott, D.; Soler, J. D.; Stolyarov, V.; Sudiwala, R.; Sutton, D.; Suur-Uski, A.-S.; Sygnet, J.-F.; Tauber, J. A.; Terenzi, L.; Toffolatti, L.; Tomasi, M.; Tristram, M.; Tucci, M.; Umana, G.; Valenziano, L.; Valiviita, J.; Van Tent, B.; Vielva, P.; Villa, F.; Wade, L. A.; Wandelt, B. D.; Wehus, I. K.; Ysard, N.; Yvon, D.; Zonca, A.

    2016-02-01

    Within ten nearby (d < 450 pc) Gould belt molecular clouds we evaluate statistically the relative orientation between the magnetic field projected on the plane of sky, inferred from the polarized thermal emission of Galactic dust observed by Planck at 353 GHz, and the gas column density structures, quantified by the gradient of the column density, NH. The selected regions, covering several degrees in size, are analysed at an effective angular resolution of 10' FWHM, thus sampling physical scales from 0.4 to 40 pc in the nearest cloud. The column densities in the selected regions range from NH≈ 1021 to1023 cm-2, and hence they correspond to the bulk of the molecular clouds. The relative orientation is evaluated pixel by pixel and analysed in bins of column density using the novel statistical tool called "histogram of relative orientations". Throughout this study, we assume that the polarized emission observed by Planck at 353 GHz is representative of the projected morphology of the magnetic field in each region, i.e., we assume a constant dust grain alignment efficiency, independent of the local environment. Within most clouds we find that the relative orientation changes progressively with increasing NH, from mostly parallel or having no preferred orientation to mostly perpendicular. In simulations of magnetohydrodynamic turbulence in molecular clouds this trend in relative orientation is a signature of Alfvénic or sub-Alfvénic turbulence, implying that the magnetic field is significant for the gas dynamics at the scales probed by Planck. We compare the deduced magnetic field strength with estimates we obtain from other methods and discuss the implications of the Planck observations for the general picture of molecular cloud formation and evolution.

  6. Molecular hydrogen physisorption on boron-nitride nanotubes probed by second harmonic generation

    NASA Astrophysics Data System (ADS)

    Salazar-Aparicio, R. V.; Vázquez-Nava, R. A.; Arzate, N.; Mendoza, B. S.

    2014-10-01

    We present ab initio calculations to investigate second harmonic generation (SHG) response of single wall zigzag pristine boron-nitride nanotubes (BNNTs) and BNNTs modified by the molecular hydrogen adsorption. Calculations have been performed using density functional theory (DFT) within the local-density approximation (LDA) together with the GW Green function method to determine the band gap. A length gauge approach has been used to calculate the nonlinear optical response with the scissors correction to obtain the nonlinear susceptibility χzzz(-2ω ;ω,ω) of the zigzag BNNTs. We have found that, contrary to reports in the literature, the (5,0) and (9,0) BNNTs have a nonvanishing SHG response. We have also found that SHG intensity decreases with the increase of the molecular hydrogen coverage.

  7. Molecular mechanisms of ionic liquid cytotoxicity probed by an integrated experimental and computational approach

    DOE PAGESBeta

    Yoo, Brian; Jing, Benxin; Jones, Stuart E.; Lamberti, Gary A.; Zhu, Yingxi; Shah, Jindal K.; Maginn, Edward J.

    2016-02-02

    Ionic liquids (ILs) are salts that remain liquid down to low temperatures, and sometimes well below room temperature. ILs have been called “green solvents” because of their extraordinarily low vapor pressure and excellent solvation power, but ecotoxicology studies have shown that some ILs exhibit greater toxicity than traditional solvents. A fundamental understanding of the molecular mechanisms responsible for IL toxicity remains elusive. Here we show that one mode of IL toxicity on unicellular organisms is driven by swelling of the cell membrane. Cytotoxicity assays, confocal laser scanning microscopy, and molecular simulations reveal that IL cations nucleate morphological defects in themore » microbial cell membrane at concentrations near the half maximal effective concentration (EC50) of several microorganisms. Lastly, cytotoxicity increases with increasing alkyl chain length of the cation due to the ability of the longer alkyl chain to more easily embed in, and ultimately disrupt, the cell membrane.« less

  8. Molecular mechanisms of ionic liquid cytotoxicity probed by an integrated experimental and computational approach

    PubMed Central

    Yoo, Brian; Jing, Benxin; Jones, Stuart E.; Lamberti, Gary A.; Zhu, Yingxi; Shah, Jindal K.; Maginn, Edward J.

    2016-01-01

    Ionic liquids (ILs) are salts that remain liquid down to low temperatures, and sometimes well below room temperature. ILs have been called “green solvents” because of their extraordinarily low vapor pressure and excellent solvation power, but ecotoxicology studies have shown that some ILs exhibit greater toxicity than traditional solvents. A fundamental understanding of the molecular mechanisms responsible for IL toxicity remains elusive. Here we show that one mode of IL toxicity on unicellular organisms is driven by swelling of the cell membrane. Cytotoxicity assays, confocal laser scanning microscopy, and molecular simulations reveal that IL cations nucleate morphological defects in the microbial cell membrane at concentrations near the half maximal effective concentration (EC50) of several microorganisms. Cytotoxicity increases with increasing alkyl chain length of the cation due to the ability of the longer alkyl chain to more easily embed in, and ultimately disrupt, the cell membrane. PMID:26831599

  9. Molecular mechanisms of ionic liquid cytotoxicity probed by an integrated experimental and computational approach.

    PubMed

    Yoo, Brian; Jing, Benxin; Jones, Stuart E; Lamberti, Gary A; Zhu, Yingxi; Shah, Jindal K; Maginn, Edward J

    2016-01-01

    Ionic liquids (ILs) are salts that remain liquid down to low temperatures, and sometimes well below room temperature. ILs have been called "green solvents" because of their extraordinarily low vapor pressure and excellent solvation power, but ecotoxicology studies have shown that some ILs exhibit greater toxicity than traditional solvents. A fundamental understanding of the molecular mechanisms responsible for IL toxicity remains elusive. Here we show that one mode of IL toxicity on unicellular organisms is driven by swelling of the cell membrane. Cytotoxicity assays, confocal laser scanning microscopy, and molecular simulations reveal that IL cations nucleate morphological defects in the microbial cell membrane at concentrations near the half maximal effective concentration (EC50) of several microorganisms. Cytotoxicity increases with increasing alkyl chain length of the cation due to the ability of the longer alkyl chain to more easily embed in, and ultimately disrupt, the cell membrane. PMID:26831599

  10. GAS PHASE MOLECULAR DYNAMICS: HIGH-RESOLUTION SPECTROSCOPIC PROBES OF CHEMICAL DYNAMICS.

    SciTech Connect

    HALL, G.E.

    2006-05-30

    This research is carried out as part of the Gas Phase Molecular Dynamics group program in the Chemistry Department at Brookhaven National Laboratory. High-resolution spectroscopic tools are developed and applied to problems in chemical dynamics. Recent topics have included the state-resolved studies of collision-induced electronic energy transfer, dynamics of barrierless unimolecular reactions, and the kinetics and spectroscopy of transient species.

  11. The `Carina Flare' supershell: probing the atomic and molecular ISM in a Galactic chimney

    NASA Astrophysics Data System (ADS)

    Dawson, J. R.; Mizuno, N.; Onishi, T.; McClure-Griffiths, N. M.; Fukui, Y.

    2008-06-01

    The `Carina Flare' supershell, GSH 287+04-17, is a molecular supershell originally discovered in 12CO(J = 1-0) with the NANTEN 4m telescope. We present the first study of the shell's atomic ISM, using HI 21-cm line data from the Parkes 64-m telescope Southern Galactic Plane Survey. The data reveal a gently expanding, ~230 × 360 pc HI supershell that shows strong evidence of Galactic Plane blowout, with a break in its main body at z ~ 280 pc and a capped high-latitude extension reaching z ~ 450 pc. The molecular clouds form comoving parts of the atomic shell, and the morphology of the two phases reflects the supershell's influence on the structure of the ISM. We also report the first discovery of an ionized component of the supershell, in the form of delicate, streamer-like filaments aligned with the proposed direction of blowout. The distance estimate to the shell is re-examined, and we find strong evidence to support the original suggestion that it is located in the Carina Arm at a distance of 2.6 +/- 0.4 kpc. Associated HI and H2 masses are estimated as MHI ~ 7 +/- 3 × 105Msolar and , and the kinetic energy of the expanding shell as EK ~ 1 × 1051 erg. We examine the results of analytical and numerical models to estimate a required formation energy of several 1051 to ~1052 erg, and an age of ~107 yr. This age is compatible with molecular cloud formation time-scales, and we briefly consider the viability of a supershell-triggered origin for the molecular component.

  12. Probing Molecular Recognition at the Solid-Gas Interface by Sum-Frequency Vibrational Spectroscopy.

    PubMed

    Aprile, Arianna; Ciuchi, Federica; Pinalli, Roberta; Dalcanale, Enrico; Pagliusi, Pasquale

    2016-08-01

    Molecular recognition is among the most important chemical events in living systems and has been emulated in supramolecular chemistry, driven by chemical and biochemical sensing potential. Identifying host-guest association in situ at the interface, between the substrate-bound receptors and the analyte-containing media, is essential to predict complexation performances in term of the receptor conformation, orientation and organization. Herein, we report the first sum-frequency vibrational spectroscopy study of molecular recognition at the solid-gas interface. The binding capability of tetraquinoxaline cavitands toward volatile aromatic and aliphatic compounds, namely benzonitrile and acetonitrile, is investigated as test system. We prove the selective complexation of the receptors, organized in a solid-supported hybrid bilayer, toward aromatic compounds. Quantitative analysis allows to correlate the average orientations of the guest molecules and the host binding pockets, establishing "on-axis" complexation of benzonitrile within the cavitand cavity. The study is readily applicable to other receptors, molecular architectures, interfaces and analytes. PMID:27438350

  13. The Chemistry of Interstellar Argonium and Other Probes of the Molecular Fraction in Diffuse Clouds

    NASA Astrophysics Data System (ADS)

    Neufeld, David A.; Wolfire, Mark G.

    2016-08-01

    We present a general parameter study in which the abundance of interstellar argonium (ArH+) is predicted using a model for the physics and chemistry of diffuse interstellar gas clouds. Results have been obtained as a function of UV radiation field, cosmic-ray ionization rate, and cloud extinction. No single set of cloud parameters provides an acceptable fit to the typical ArH+, OH+, and {{{H}}}2{{{O}}}+ abundances observed in diffuse clouds within the Galactic disk. Instead, the observed abundances suggest that ArH+ resides primarily in a separate population of small clouds of total visual extinction of at most 0.02 mag per cloud, within which the column-averaged molecular fraction is in the range {10}-5{--}{10}-2, while OH+ and {{{H}}}2{{{O}}}+ reside primarily in somewhat larger clouds with a column-averaged molecular fraction ∼0.2. This analysis confirms our previous suggestion that the argonium molecular ion is a unique tracer of almost purely atomic gas.

  14. Transferring biomarker into molecular probe: melanin nanoparticle as a naturally active platform for multimodality imaging.

    PubMed

    Fan, Quli; Cheng, Kai; Hu, Xiang; Ma, Xiaowei; Zhang, Ruiping; Yang, Min; Lu, Xiaomei; Xing, Lei; Huang, Wei; Gambhir, Sanjiv Sam; Cheng, Zhen

    2014-10-29

    Developing multifunctional and easily prepared nanoplatforms with integrated different modalities is highly challenging for molecular imaging. Here, we report the successful transfer of an important molecular target, melanin, into a novel multimodality imaging nanoplatform. Melanin is abundantly expressed in melanotic melanomas and thus has been actively studied as a target for melanoma imaging. In our work, the multifunctional biopolymer nanoplatform based on ultrasmall (<10 nm) water-soluble melanin nanoparticle (MNP) was developed and showed unique photoacoustic property and natural binding ability with metal ions (for example, (64)Cu(2+), Fe(3+)). Therefore, MNP can serve not only as a photoacoustic contrast agent, but also as a nanoplatform for positron emission tomography (PET) and magnetic resonance imaging (MRI). Traditional passive nanoplatforms require complicated and time-consuming processes for prebuilding reporting moieties or chemical modifications using active groups to integrate different contrast properties into one entity. In comparison, utilizing functional biomarker melanin can greatly simplify the building process. We further conjugated αvβ3 integrins, cyclic c(RGDfC) peptide, to MNPs to allow for U87MG tumor accumulation due to its targeting property combined with the enhanced permeability and retention (EPR) effect. The multimodal properties of MNPs demonstrate the high potential of endogenous materials with multifunctions as nanoplatforms for molecular theranostics and clinical translation. PMID:25292385

  15. Transferring Biomarker into Molecular Probe: Melanin Nanoparticle as a Naturally Active Platform for Multimodality Imaging

    PubMed Central

    2015-01-01

    Developing multifunctional and easily prepared nanoplatforms with integrated different modalities is highly challenging for molecular imaging. Here, we report the successful transfer of an important molecular target, melanin, into a novel multimodality imaging nanoplatform. Melanin is abundantly expressed in melanotic melanomas and thus has been actively studied as a target for melanoma imaging. In our work, the multifunctional biopolymer nanoplatform based on ultrasmall (<10 nm) water-soluble melanin nanoparticle (MNP) was developed and showed unique photoacoustic property and natural binding ability with metal ions (for example, 64Cu2+, Fe3+). Therefore, MNP can serve not only as a photoacoustic contrast agent, but also as a nanoplatform for positron emission tomography (PET) and magnetic resonance imaging (MRI). Traditional passive nanoplatforms require complicated and time-consuming processes for prebuilding reporting moieties or chemical modifications using active groups to integrate different contrast properties into one entity. In comparison, utilizing functional biomarker melanin can greatly simplify the building process. We further conjugated αvβ3 integrins, cyclic c(RGDfC) peptide, to MNPs to allow for U87MG tumor accumulation due to its targeting property combined with the enhanced permeability and retention (EPR) effect. The multimodal properties of MNPs demonstrate the high potential of endogenous materials with multifunctions as nanoplatforms for molecular theranostics and clinical translation. PMID:25292385

  16. Molecular adsorbates as probes of the local properties of doped graphene

    PubMed Central

    Pham, Van Dong; Joucken, Frédéric; Repain, Vincent; Chacon, Cyril; Bellec, Amandine; Girard, Yann; Rousset, Sylvie; Sporken, Robert; Santos, Maria Cristina dos; Lagoute, Jérôme

    2016-01-01

    Graphene-based sensors are among the most promising of graphene’s applications. The ability to signal the presence of molecular species adsorbed on this atomically thin substrate has been explored from electric measurements to light scattering. Here we show that the adsorbed molecules can be used to sense graphene properties. The interaction of porphyrin molecules with nitrogen-doped graphene has been investigated using scanning tunneling microscopy and ab initio calculations. Molecular manipulation was used to reveal the surface below the adsorbed molecules allowing to achieve an atomic-scale measure of the interaction of molecules with doped graphene. The adsorbate’s frontier electronic states are downshifted in energy as the molecule approaches the doping site, with largest effect when the molecule sits over the nitrogen dopant. Theoretical calculations showed that, due to graphene’s high polarizability, the adsorption of porphyrin induces a charge rearrangement on the substrate similar to the image charges on a metal. This charge polarization is enhanced around nitrogen site, leading to an increased interaction of molecules with their image charges on graphene. Consequently, the molecular states are stabilized and shift to lower energies. These findings reveal the local variation of polarizability induced by nitrogen dopant opening new routes towards the electronic tuning of graphene. PMID:27097555

  17. The Chemistry of Interstellar Argonium and Other Probes of the Molecular Fraction in Diffuse Clouds

    NASA Astrophysics Data System (ADS)

    Neufeld, David A.; Wolfire, Mark G.

    2016-08-01

    We present a general parameter study in which the abundance of interstellar argonium (ArH+) is predicted using a model for the physics and chemistry of diffuse interstellar gas clouds. Results have been obtained as a function of UV radiation field, cosmic-ray ionization rate, and cloud extinction. No single set of cloud parameters provides an acceptable fit to the typical ArH+, OH+, and {{{H}}}2{{{O}}}+ abundances observed in diffuse clouds within the Galactic disk. Instead, the observed abundances suggest that ArH+ resides primarily in a separate population of small clouds of total visual extinction of at most 0.02 mag per cloud, within which the column-averaged molecular fraction is in the range {10}-5{--}{10}-2, while OH+ and {{{H}}}2{{{O}}}+ reside primarily in somewhat larger clouds with a column-averaged molecular fraction ˜0.2. This analysis confirms our previous suggestion that the argonium molecular ion is a unique tracer of almost purely atomic gas.

  18. Molecular adsorbates as probes of the local properties of doped graphene

    NASA Astrophysics Data System (ADS)

    Pham, Van Dong; Joucken, Frédéric; Repain, Vincent; Chacon, Cyril; Bellec, Amandine; Girard, Yann; Rousset, Sylvie; Sporken, Robert; Santos, Maria Cristina Dos; Lagoute, Jérôme

    2016-04-01

    Graphene-based sensors are among the most promising of graphene’s applications. The ability to signal the presence of molecular species adsorbed on this atomically thin substrate has been explored from electric measurements to light scattering. Here we show that the adsorbed molecules can be used to sense graphene properties. The interaction of porphyrin molecules with nitrogen-doped graphene has been investigated using scanning tunneling microscopy and ab initio calculations. Molecular manipulation was used to reveal the surface below the adsorbed molecules allowing to achieve an atomic-scale measure of the interaction of molecules with doped graphene. The adsorbate’s frontier electronic states are downshifted in energy as the molecule approaches the doping site, with largest effect when the molecule sits over the nitrogen dopant. Theoretical calculations showed that, due to graphene’s high polarizability, the adsorption of porphyrin induces a charge rearrangement on the substrate similar to the image charges on a metal. This charge polarization is enhanced around nitrogen site, leading to an increased interaction of molecules with their image charges on graphene. Consequently, the molecular states are stabilized and shift to lower energies. These findings reveal the local variation of polarizability induced by nitrogen dopant opening new routes towards the electronic tuning of graphene.

  19. Molecular self-assembly of conducting polymer by Conducting Probe Technique in Atomic Force Microscope

    NASA Astrophysics Data System (ADS)

    Yamamoto, Shin-ichi; Ogawa, Kazufumi

    2007-04-01

    A polypyrrole derivative monolayer was investigated for the application as a wire. First, a pyrrole derivative monolayer was prepared by chemically adsorbing (self-assembling) monolayer (CAM) of 6-pyrrolylhexyl-12,12,12-trichloro-12- siladodecanoate (PEN) on a glass substrate. Then, the monolayer was polymerized in the presence of pure water by electrooxidation. The surface characterization of the molecular interaction was investigated by measuring the properties of CAMs attached to the glass substrate in the lateral direction. We formed PEN having polypyrrolyl groups, using Pt-patterned electrodes on glass surfaces and measured the conductance under a small bias voltage, using a conductive cantilever of atomic force microscopy (AFM). The polypyrrole derivative monolayer thus synthesized was covalently bonded to the glass substrate and showed conductivity as high as 3.05..103 S/cm after electro-oxidized. The method of preparing a conductive polymer monolayer by the combining chemical adsorption and electro-oxidation leads to a lot molecular wire to perpendicular to the Pt electrodes, and it is one of the key technologies for molecular devices.

  20. Probing the interface between semiconducting nanocrystals and molecular metal chalcogenide surface ligands: insights from first principles

    NASA Astrophysics Data System (ADS)

    Scalise, Emilio; Wippermann, Stefan; Galli, Giulia; Talapin, Dmitri

    Colloidal nanocrystals (NCs) are emerging as cost-effective materials offering exciting prospects for solar energy conversion, light emission and electronic applications. Recent experimental advances demonstrate the synthesis of fully inorganic nanocrystal solids from chemical solution processing. The properties of the NC-solids are heavily determined by the NCs surface and their interactions with the host matrix. However, information on the atomistic structure of such composites is hard to obtain, due to the complexity of the synthesis conditions and the unavailability of robust experimental techniques to probe nanointerfaces at the microscopic level. Here we present a systematic theoretical study of the interaction between InAs and InP NCs with Sn2S64- ligands. Employing a grand canonical ab initio thermodynamic approach we investigate the relative stability of a multitude of configurations possibly realized at the NC-ligand interface. Our study highlights the importance of different structural details and their strong impact on the resulting composite's properties. We show that to obtain a detailed understanding of experimental data it is necessary to take into account complex interfacial structures beyond simplified NC-ligand model interfaces. S. W. acknowledges BMBF NanoMatFutur Grant No. 13N12972. G.G. acknowledges DOE-BES for funding part of this work.

  1. Lineage-specific molecular probing reveals novel diversity and ecological partitioning of haplosporidians

    PubMed Central

    Hartikainen, Hanna; Ashford, Oliver S; Berney, Cédric; Okamura, Beth; Feist, Stephen W; Baker-Austin, Craig; Stentiford, Grant D; Bass, David

    2014-01-01

    Haplosporidians are rhizarian parasites of mostly marine invertebrates. They include the causative agents of diseases of commercially important molluscs, including MSX disease in oysters. Despite their importance for food security, their diversity and distributions are poorly known. We used a combination of group-specific PCR primers to probe environmental DNA samples from planktonic and benthic environments in Europe, South Africa and Panama. This revealed several highly distinct novel clades, novel lineages within known clades and seasonal (spring vs autumn) and habitat-related (brackish vs littoral) variation in assemblage composition. High frequencies of haplosporidian lineages in the water column provide the first evidence for life cycles involving planktonic hosts, host-free stages or both. The general absence of haplosporidian lineages from all large online sequence data sets emphasises the importance of lineage-specific approaches for studying these highly divergent and diverse lineages. Combined with host-based field surveys, environmental sampling for pathogens will enhance future detection of known and novel pathogens and the assessment of disease risk. PMID:23966100

  2. VUV pump - infrared probe studies of molecular dissociation following state-selective photoexcitation

    NASA Astrophysics Data System (ADS)

    Malakar, Y.; Kaderiya, B.; Pearson, W. L.; Kanaka Raju, P.; Li, Xiang; Cao, Wei; Ben-Itzhak, I.; Rudenko, A.; Trabert, D.; Wilhelm, F.

    2015-05-01

    Time-resolved measurements employing light sources based on high-harmonics generation are typically performed using broad-band pulses aiming at the shortest pulse duration achievable. This inherently results in a population of a superposition of states. In contrast, we employed ~ 100 fs VUV pulses with a narrow bandwidth of ~ 200 meV (filtered by a grating pair), to achieve state-selective excitation. We used 11th harmonic pump (centered at 17.3 eV) - 800 nm probe pulse sequence to trigger the dissociative ionization of O2 and CO2, which was characterized by energy- and angle-resolved photoion and photoelectron detection. While for the case of O2 the data can be understood in terms of the (net) absorption of one and two 800 nm photons from the VUV-excited ionic state, the preliminary CO2 results manifest rich dynamics, which surprisingly resembles the behavior observed in a recent experiment, where a comb of 11th to 17th harmonics was used. Supported by the Chemical Sciences, Geosciences, and Biosciences Division, Office of Basic Energy Science, Office of Science, U.S. Department of Energy. K.R.P. supported by National Science Foundation Award No. IIA-1430493.

  3. Probing the bioactivity-relevant chemical space of robust reactions and common molecular building blocks.

    PubMed

    Hartenfeller, Markus; Eberle, Martin; Meier, Peter; Nieto-Oberhuber, Cristina; Altmann, Karl-Heinz; Schneider, Gisbert; Jacoby, Edgar; Renner, Steffen

    2012-05-25

    In the search for new bioactive compounds, there is a trend toward increasingly complex compound libraries aiming to target the demanding targets of the future. In contrast, medicinal chemistry and traditional library design rely mainly on a small set of highly established and robust reactions. Here, we probe a set of 58 such reactions for their ability to sample the chemical space of known bioactive molecules, and the potential to create new scaffolds. Combined with ~26,000 common available building blocks, the reactions retrieve around 9% of a scaffold-diverse set of compounds active on human target proteins covering all major pharmaceutical target classes. Almost 80% of generated scaffolds from virtual one-step synthesis products are not present in a large set of known bioactive molecules for human targets, indicating potential for new discoveries. The results suggest that established synthesis resources are well suited to cover the known bioactivity-relevant chemical space and that there are plenty of unexplored regions accessible by these reactions, possibly providing valuable "low-hanging fruit" for hit discovery. PMID:22512717

  4. Solution Phase Molecular Dynamics Probed with Synchrotron Hard X-rays

    NASA Astrophysics Data System (ADS)

    March, Anne; Doumy, Gilles; Kanter, Elliot; Southworth, Stephen; Young, Linda; Nemeth, Zoltan; Vankó, Gyorgy; Assefa, Tadesse; Gawelda, Wojciech

    2013-05-01

    The ability to measure short-lived transient states during a chemical reaction is key to understanding many important processes such as oxygen binding in hemeproteins and electron transport in photosynthesis. Time resolved hard x-ray spectroscopies, which are based on laser-pump/x-ray-probe methods, are a unique tool because unlike UV-VIS techniques they are element specific and can provide electronic and structural information with atomic resolution in the vicinity of a particular atom or ion. These characteristics make them particularly powerful for studying molecules in complex environments such as solutions. Using a MHz, picosecond, high average power laser system implemented at Sector 7ID-D of the Advanced Photon Source we have been developing time resolved x-ray emission techniques to track the evolution of photoexcited molecules in solution. We will present recent studies which include the ligand substitution reaction and hydrated electron formation in the coordination complex ferrocyanide Fe(CN)64-. This work was supported by the Chemical Sciences, Geosciences, and Biosciences Division and the Advanced Photon Source by the Office of Basic Energy Sciences, Office of Science, US Dept of Energy, Contract DE-AC02-06CH11357.

  5. Application of steered molecular dynamics (SMD) to study DNA drug complexes and probing helical propensity of amino acids

    NASA Astrophysics Data System (ADS)

    Orzechowski, Marek; Cieplak, Piotr

    2005-05-01

    We present the preliminary results of two computer experiments involving the application of an external force to molecular systems. In the first experiment we simulated the process of pulling out a simple intercalator, the 9-aminoacridine molecule, from its complex with a short DNA oligonucleotide in aqueous solution. Removing a drug from the DNA is assumed to be an opposite process to the complex formation. The force and energy profiles suggest that formation of the DNA-9-aminoacridine complex is preferred when the acridine approaches the DNA from the minor groove rather than the major groove side. For a given mode of pulling the intercalation process is also shown to be nucleotide sequence dependent. In another computer experiment we performed a series of molecular dynamics simulations for stretching short, containing 15 amino acids, helical polypeptides in aqueous solution using an external force. The purpose of these simulations is to check whether this type of approach is sensitive enough to probe the sequence dependent helical propensity of short polypeptides.

  6. Probing the Dynamics of Rydberg and Valence States of Molecular Nitrogen with Attosecond Transient Absorption Spectroscopy.

    PubMed

    Warrick, Erika R; Cao, Wei; Neumark, Daniel M; Leone, Stephen R

    2016-05-19

    An attosecond pulse is used to create a wavepacket in molecular nitrogen composed of multiple bound and autoionizing electronic states of Rydberg and valence character between 12 and 16.7 eV. A time-delayed, few-femtosecond, near-infrared (NIR) laser pulse is used to couple individual states in the wavepacket to multiple neighboring states, resulting in time-dependent modification of the absorption spectrum and revealing both individual quantum beats of the wavepacket and the energy shifts of the excited states in the presence of the strong NIR field. The broad bandwidth of the attosecond pulse and high energy resolution of the extreme ultraviolet spectrometer allow the simultaneous observation of time-dependent dynamics for many individual vibrational levels in each electronic state. Quantum beating with periods from 1.3 to 12 fs and transient line shape changes are observed among vibrational levels of a progression of electronically autoionizing Rydberg states leading to the excited A (2)Πu N2(+) ion core. Vibrational levels in the valence b (1)Πu state exhibit 50 fs oscillation periods, revealing superpositions between individual vibrational levels within this state. Comparisons are made to previous studies of electronic wavepackets in atoms that highlight similarities to atomic behavior yet illustrate unique contributions of the diatomic molecular structure to the wavepacket, including the influence of different electronic potentials and vibrational-level-specific electronic dynamics. PMID:26862883

  7. Microgravity: Molecular Dynamics Simulations at the NCCS Probe the Behavior of Liquids in Low Gravity

    NASA Technical Reports Server (NTRS)

    2002-01-01

    The life of the very small, whether in something as complicated as a human cell or as simple as a drop of water, is of fundamental scientific interest: By knowing how a tiny amount of material reacts to changes in its environment, scientists maybe able to answer questions about how a bulk of material would react to comparable changes. NASA is in the forefront of computational research into a broad range of basic scientific questions about fluid dynamics and the nature of liquid boundary instability. For example, one important issue for the space program is how drops of water and other materials will behave in the low-gravity environment of space and how the low gravity will affect the transport and containment of these materials. Accurate prediction of this behavior is among the aims of a set of molecular dynamics experiments carried out on the NCCSs Cray supercomputers. In conventional computational studies of materials, matter is treated as continuous - a macroscopic whole without regard to its molecular parts - and the behavior patterns of the matter in various physical environments are studied using well-established differential equations and mathematical parameters based on physical properties such as compressibility density, heat capacity, and vapor pressure of the bulk material.

  8. Density functional simulations as a tool to probe molecular interactions in wet supercritical CO2

    SciTech Connect

    Glezakou, Vassiliki Alexandra; McGrail, B. Peter

    2013-06-03

    Recent advances in mixed Gaussian and plane wave algorithms have made possible the effective use of density functional theory (DFT) in ab initio molecular dynamics (AIMD) simulations for large and chemically complex models of condensed phase materials. In this chapter, we are reviewing recent progress on the modeling and characterization of co-sequestration processes and reactivity in wet supercritical CO2 (sc-CO2). We examine the molecular transformations of mineral and metal components of a sequestration system in contact with water-bearing scCO2 media and aim to establish a reliable correspondence between experimental observations and theory models with predictive ability and transferability of results in large scale geomechanical simulators. This work is funded by the Department of Energy, Office of Fossil Energy. A portion of the research was performed using EMSL, a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research located at Pacific Northwest National Laboratory. The Pacific Norhtwest National Laboratory (PNNL) is operated by Battelle for DOE under contract DE-AC06-76RL01830.

  9. Probing confinement resonances by photoionizing Xe inside a C60+ molecular cage

    NASA Astrophysics Data System (ADS)

    Phaneuf, R. A.; Kilcoyne, A. L. D.; Aryal, N. B.; Baral, K. K.; Thomas, C. M.; Esteves-Macaluso, D. A.; Lomsadze, R.; Gorczyca, T. W.; Ballance, C. P.; Manson, S. T.; Hasoglu, M. F.; Hellhund, J.; Schippers, S.; Müller, A.

    2014-05-01

    Double photoionization accompanied by loss of n C atoms (n = 0 , 2 , 4 , 6) was investigated by merging beams of Xe@C60+ ions and synchrotron radiation and measuring the yields of product ions. The giant 4 d dipole resonance of the caged Xe atom has a prominent signature in the cross section for these product channels, which together account for 6 . 2 +/- 1 . 4 of the total Xe 4 d oscillator strength of 10. Compared to that for a free Xe atom, the oscillator strength is redistributed in photon energy due to multipath interference of outgoing Xe 4 d photoelectron waves that may be transmitted or reflected by the spherical C60+ molecular cage, yielding so-called confinement resonances. The data are compared with an earlier measurement and with theoretical predictions for this single-molecule photoelectron interferometer system. Relativistic R-matrix calculations for the Xe atom in a spherical potential shell representing the fullerene cage show the sensitivity of the interference pattern to the molecular geometry.

  10. Probing the Flexibility of Tropomyosin and Its Binding to Filamentous Actin Using Molecular Dynamics Simulations

    PubMed Central

    Zheng, Wenjun; Barua, Bipasha; Hitchcock-DeGregori, Sarah E.

    2013-01-01

    Tropomyosin (Tm) is a coiled-coil protein that binds to filamentous actin (F-actin) and regulates its interactions with actin-binding proteins like myosin by moving between three positions on F-actin (the blocked, closed, and open positions). To elucidate the molecular details of Tm flexibility in relation to its binding to F-actin, we conducted extensive molecular dynamics simulations for both Tm alone and Tm-F-actin complex in the presence of explicit solvent (total simulation time >400 ns). Based on the simulations, we systematically analyzed the local flexibility of the Tm coiled coil using multiple parameters. We found a good correlation between the regions with high local flexibility and a number of destabilizing regions in Tm, including six clusters of core alanines. Despite the stabilization by F-actin binding, the distribution of local flexibility in Tm is largely unchanged in the absence and presence of F-actin. Our simulations showed variable fluctuations of individual Tm periods from the closed position toward the open position. In addition, we performed Tm-F-actin binding calculations based on the simulation trajectories, which support the importance of Tm flexibility to Tm-F-actin binding. We identified key residues of Tm involved in its dynamic interactions with F-actin, many of which have been found in recent mutational studies to be functionally important, and the rest of which will make promising targets for future mutational experiments. PMID:24138864

  11. Near-infrared molecular imaging probes based on chlorin-bacteriochlorin dyads

    NASA Astrophysics Data System (ADS)

    Ptaszek, Marcin; Kee, Hooi Ling; Muthiah, Chinnasamy; Nothdurft, Ralph; Akers, Walter; Achilefu, Samuel; Culver, Joseph P.; Holten, Dewey

    2010-02-01

    Chlorin-bacteriochlorin dyads as a new class of near-infrared fluorophores were synthesized and spectroscopically characterized. Each dyad is comprised of a chlorin macrocycle (free base or zinc chelate) as an energy donor (and absorber) and a free base bacteriochlorin as an energy acceptor (and emitter). Excitation of the chlorin (λ= 650 nm, zinc chelate; 675 nm, free base) results in fast (5 ps) and nearly quantitative (>99%) energy transfer to the adjacent bacteriochlorin moiety, and consequently bacteriochlorin fluorescence (λ= 760 nm). Thus, each chlorinbacteriochlorin dyad behaves as a single chromophore, with a large effective Stokes shift (85 or 110 nm), a significant fluorescence quantum yield (Φf = 0.19), long excited-state lifetime (τ = 5.4 ns), narrow excitation and emission bands (<20 nm), and high chemical stability. Imaging experiments performed using phantoms show that the chlorin-bacteriochlorin dyads exhibit a range of superior properties compare with commercially available imaging dyes. While the latter are six-fold brighter (comparing ɛ•Φf values), the chlorin-bacteriochlorin dyads exhibit narrower excitation and emission bands and larger Stokes shift, therefore allowing more efficient and selective excitation and detection of fluorescence. The high selectivity is further demonstrated with in vivo imaging studies using mice. This selectivity together with the tunability of absorption and emission wavelengths using substituent effects under synthetic control make the chlorin-bacteriochlorin dyads ideal candidates for multicolor imaging applications. In addition, the long fluorescence lifetimes make those probes suitable for lifetime-imaging applications.

  12. Neocarzinostatin as a probe for DNA protection activity--molecular interaction with caffeine.

    PubMed

    Chin, Der-Hang; Li, Huang-Hsien; Kuo, Hsiu-Maan; Chao, Pei-Dawn Lee; Liu, Chia-Wen

    2012-04-01

    Neocarzinostatin (NCS), a potent mutagen and carcinogen, consists of an enediyne prodrug and a protein carrier. It has a unique double role in that it intercalates into DNA and imposes radical-mediated damage after thiol activation. Here we employed NCS as a probe to examine the DNA-protection capability of caffeine, one of common dietary phytochemicals with potential cancer-chemopreventive activity. NCS at the nanomolar concentration range could induce significant single- and double-strand lesions in DNA, but up to 75 ± 5% of such lesions were found to be efficiently inhibited by caffeine. The percentage of inhibition was caffeine-concentration dependent, but was not sensitive to the DNA-lesion types. The well-characterized activation reactions of NCS allowed us to explore the effect of caffeine on the enediyne-generated radicals. Postactivation analyses by chromatographic and mass spectroscopic methods identified a caffeine-quenched enediyne-radical adduct, but the yield was too small to fully account for the large inhibition effect on DNA lesions. The affinity between NCS chromophore and DNA was characterized by a fluorescence-based kinetic method. The drug-DNA intercalation was hampered by caffeine, and the caffeine-induced increases in DNA-drug dissociation constant was caffeine-concentration dependent, suggesting importance of binding affinity in the protection mechanism. Caffeine has been shown to be both an effective free radical scavenger and an intercalation inhibitor. Our results demonstrated that caffeine ingeniously protected DNA against the enediyne-induced damages mainly by inhibiting DNA intercalation beforehand. The direct scavenging of the DNA-bound NCS free radicals by caffeine played only a minor role. PMID:21538576

  13. Engineering Agatoxin, a Cystine-Knot Peptide from Spider Venom, as a Molecular Probe for In Vivo Tumor Imaging

    PubMed Central

    Norton, Heidi K.; Cochran, Jennifer R.

    2013-01-01

    -targeting knottins as probes for in vivo molecular imaging. PMID:23573262

  14. Artemisinin activity-based probes identify multiple molecular targets within the asexual stage of the malaria parasites Plasmodium falciparum 3D7

    PubMed Central

    Ismail, Hanafy M.; Barton, Victoria; Phanchana, Matthew; Charoensutthivarakul, Sitthivut; Wong, Michael H. L.; Hemingway, Janet; Biagini, Giancarlo A.; O’Neill, Paul M.; Ward, Stephen A.

    2016-01-01

    The artemisinin (ART)-based antimalarials have contributed significantly to reducing global malaria deaths over the past decade, but we still do not know how they kill parasites. To gain greater insight into the potential mechanisms of ART drug action, we developed a suite of ART activity-based protein profiling probes to identify parasite protein drug targets in situ. Probes were designed to retain biological activity and alkylate the molecular target(s) of Plasmodium falciparum 3D7 parasites in situ. Proteins tagged with the ART probe can then be isolated using click chemistry before identification by liquid chromatography–MS/MS. Using these probes, we define an ART proteome that shows alkylated targets in the glycolytic, hemoglobin degradation, antioxidant defense, and protein synthesis pathways, processes essential for parasite survival. This work reveals the pleiotropic nature of the biological functions targeted by this important class of antimalarial drugs. PMID:26858419

  15. Artemisinin activity-based probes identify multiple molecular targets within the asexual stage of the malaria parasites Plasmodium falciparum 3D7.

    PubMed

    Ismail, Hanafy M; Barton, Victoria; Phanchana, Matthew; Charoensutthivarakul, Sitthivut; Wong, Michael H L; Hemingway, Janet; Biagini, Giancarlo A; O'Neill, Paul M; Ward, Stephen A

    2016-02-23

    The artemisinin (ART)-based antimalarials have contributed significantly to reducing global malaria deaths over the past decade, but we still do not know how they kill parasites. To gain greater insight into the potential mechanisms of ART drug action, we developed a suite of ART activity-based protein profiling probes to identify parasite protein drug targets in situ. Probes were designed to retain biological activity and alkylate the molecular target(s) of Plasmodium falciparum 3D7 parasites in situ. Proteins tagged with the ART probe can then be isolated using click chemistry before identification by liquid chromatography-MS/MS. Using these probes, we define an ART proteome that shows alkylated targets in the glycolytic, hemoglobin degradation, antioxidant defense, and protein synthesis pathways, processes essential for parasite survival. This work reveals the pleiotropic nature of the biological functions targeted by this important class of antimalarial drugs. PMID:26858419

  16. Probing molecular dynamics at the nanoscale via an individual paramagnetic centre

    PubMed Central

    Staudacher, T.; Raatz, N.; Pezzagna, S.; Meijer, J.; Reinhard, F.; Meriles, C. A.; Wrachtrup, J.

    2015-01-01

    We demonstrate a protocol using individual nitrogen-vacancy centres in diamond to observe the time evolution of proton spins from organic molecules located a few nanometres from the diamond surface. The protocol records temporal correlations among the interacting protons, and thus is sensitive to the local dynamics via its impact on the nuclear spin relaxation and interaction with the nitrogen vacancy. We gather information on the nanoscale rotational and translational diffusion dynamics by analysing the time dependence of the nuclear magnetic resonance signal. Applying this technique to liquid and solid samples, we find evidence that liquid samples form a semi-solid layer of 1.5-nm thickness on the surface of diamond, where translational diffusion is suppressed while rotational diffusion remains present. Extensions of the present technique could be exploited to highlight the chemical composition of molecules tethered to the diamond surface or to investigate thermally or chemically activated dynamical processes such as molecular folding. PMID:26456017

  17. On the dynamic and static manifestation of molecular absorption in thin films probed by a microcantilever

    SciTech Connect

    Finot, Eric; Fabre, Arnaud; Passian, Ali; Thundat, Thomas

    2014-03-01

    Mechanical resonators shaped like microcantilevers have been demonstrated as a platform for very sensitive detection of chemical and biological analytes. However, its use as an analytical tool will require fundamental understanding of the molecular absorption-induced effects in the static and dynamic sensor response. The effect of absorption-induced surface stress on the microcantilever response is here investigated using palladium hydride formation. It is shown that the resonance and deformation states of the cantilever monitored simultaneously exhibit excellent correlation with the phase of the hydride formation. However, the associated frequency shifts and quasistatic bending are observed to be independent during solid solution phase. Importantly, absorption-induced changes in the elastic parameters of the palladium film are found to play a dominant role in the static and dynamic response. The presented results help in discerning the parameters that control the cantilever response as well as the relationships between these parameters.

  18. The rotation of NO3- as a probe of molecular ion - water interactions

    NASA Astrophysics Data System (ADS)

    Thøgersen, J.; Nielsen, J. B.; Knak Jensen, S.; Keiding, S. R.; Odelius, M.; Ogden, T.; Réhault, J.; Helbing, J.

    2013-03-01

    The hydration dynamics of aqueous nitrate, NO3-(aq), is studied by 2D-IR spectroscopy, UV-IR- and UV-UV transient absorption spectroscopy. The experimental results are compared to Car-Parinello molecular dynamics (MD) simulations. The 2D-IR measurements and MD simulations of the non-degenerate asymmetric stretch vibrations of nitrate reveal an intermodal energy exchange occurring on a 0.2 ps time scale related to hydrogen bond fluctuations. The transient absorption measurements find that the nitrate ions rotate in 2 ps. The MD simulations indicate that the ion rotation is associated with the formation of new hydrogen bonds. The 2 ps rotation time thus indicates that the hydration shell of aqueous nitrate is rather labile.

  19. Probing the Spatial Structure of a Molecular Attosecond Electron Wave Packet Using Shaped Recollision Trajectories

    NASA Astrophysics Data System (ADS)

    Niikura, Hiromichi; Wörner, Hans Jakob; Villeneuve, D. M.; Corkum, P. B.

    2011-08-01

    Using orthogonally polarized 800 nm and 400 nm laser pulses, we have generated high harmonics in ethane (C2H6). We observe that the intensity of each harmonic order modulates with the attosecond delay between the two laser fields. The modulation period of the low even harmonics is twice that of the period of modulation of the other harmonics. By comparing with theoretical calculation, we show that the double periodicity is a result of the electron wave packet motion in the valence shell of C2H6 on the attosecond time-scale. Our method is a general approach to measuring internal electron dynamics which does not require molecular alignment, making it applicable to more complex molecules than previous approaches.

  20. Probing Nuclear Motion by Frequency Modulation of Molecular High-Order Harmonic Generation

    NASA Astrophysics Data System (ADS)

    Bian, Xue-Bin; Bandrauk, André D.

    2014-11-01

    Molecular high-order harmonic generation (MHOHG) in a non-Born-Oppenheimer treatment of H2 + , D2 + , is investigated by numerical simulations of the corresponding time-dependent Schrödinger equations in full dimensions. As opposed to previous studies on amplitude modulation of intracycle dynamics in MHOHG, we demonstrate redshifts as frequency modulation (FM) of intercycle dynamics in MHOHG. The FM is induced by nuclear motion using intense laser pulses. Compared to fixed-nuclei approximations, the intensity of MHOHG is much higher due to the dependence of enhanced ionization on the internuclear distance. The width and symmetry of the spectrum of each harmonic in MHOHG encode rich information on the dissociation process of molecules at the rising and falling parts of the laser pulses, which can be used to retrieve the nuclear dynamics. Isotope effects are studied to confirm the FM mechanism.

  1. Probing nuclear motion by frequency modulation of molecular high-order harmonic generation.

    PubMed

    Bian, Xue-Bin; Bandrauk, André D

    2014-11-01

    Molecular high-order harmonic generation (MHOHG) in a non-Born-Oppenheimer treatment of H(2)(+), D(2)(+), is investigated by numerical simulations of the corresponding time-dependent Schrödinger equations in full dimensions. As opposed to previous studies on amplitude modulation of intracycle dynamics in MHOHG, we demonstrate redshifts as frequency modulation (FM) of intercycle dynamics in MHOHG. The FM is induced by nuclear motion using intense laser pulses. Compared to fixed-nuclei approximations, the intensity of MHOHG is much higher due to the dependence of enhanced ionization on the internuclear distance. The width and symmetry of the spectrum of each harmonic in MHOHG encode rich information on the dissociation process of molecules at the rising and falling parts of the laser pulses, which can be used to retrieve the nuclear dynamics. Isotope effects are studied to confirm the FM mechanism. PMID:25415907

  2. Electromagnetic probes of molecular motors in the electron transport chains of mitochondria and chloroplasts

    NASA Astrophysics Data System (ADS)

    Miller, J. H., Jr.; Nawarathna, D.; Vajrala, V.; Gardner, J.; Widger, W. R.

    2005-12-01

    We report on measurements of harmonics generated by whole cells, mitochondria, and chloroplasts in response to applied sinusoidal electric fields. The frequency- and amplitude-dependence of the induced harmonics exhibit features that correlate with physiological processes. Budding yeast (S. cerevisiae) cells produce numerous harmonics, the amplitudes of which depend strongly on frequency. When the second or third harmonic amplitude is plotted vs. applied frequency, we observe two peaks, around 3 kHz and 12 kHz, which are suppressed by respiratory inhibitors. We observe similar peaks when measuring the harmonic response of B. indicas, a relative of the mitochondrial ancestor. In uncoupled mitochondria, in which most of the electron transport chain is active but the ATP-synthase molecular turbine is inactive, only one (lower frequency) of the two peaks is present. Finally, we find that harmonics generated by chloroplasts depend dramatically on incident light, and vanish in the absence of light.

  3. ALMA probes the molecular gas reservoirs in the changing-look Seyfert galaxy Mrk 590

    NASA Astrophysics Data System (ADS)

    Koay, J. Y.; Vestergaard, M.; Casasola, V.; Lawther, D.; Peterson, B. M.

    2016-01-01

    We investigate if the active galactic nucleus (AGN) of Mrk 590, whose supermassive black hole was until recently highly accreting, is turning off due to a lack of central gas to fuel it. We analyse new subarcsecond resolution Atacama Large Millimetre/submilllimetre Array maps of the 12CO(3-2) line and 344 GHz continuum emission in Mrk 590. We detect no 12CO(3-2) emission in the inner 150 pc, constraining the central molecular gas mass to M(H2) ≲ 1.6 × 105 M⊙, no more than a typical giant molecular gas cloud, for a CO luminosity to gas mass conversion factor of αCO ˜ 0.8 M⊙ (K km s- 1 pc2)- 1. However, there is still potentially enough gas to fuel the black hole for another 2.6 × 105 yr assuming Eddington-limited accretion. We therefore cannot rule out that the AGN may just be experiencing a temporary feeding break, and may turn on again in the near future. We discover a ring-like structure at a radius of ˜1 kpc, where a gas clump exhibiting disturbed kinematics and located just ˜200 pc west of the AGN, may be refuelling the centre. Mrk 590 does not have significantly less gas than other nearby AGN host galaxies at kpc scales, confirming that gas reservoirs at these scales provide no direct indication of on-going AGN activity and accretion rates. Continuum emission detected in the central 150 pc likely originates from warm AGN-heated dust, although contributions from synchrotron and free-free emission cannot be ruled out.

  4. Advancing molecular-guided surgery through probe development and testing in a moderate cost evaluation pipeline

    NASA Astrophysics Data System (ADS)

    Pogue, Brian W.; Paulsen, Keith D.; Hull, Sally M.; Samkoe, Kimberley S.; Gunn, Jason; Hoopes, Jack; Roberts, David W.; Strong, Theresa V.; Draney, Daniel; Feldwisch, Joachim

    2015-03-01

    Molecular guided oncology surgery has the potential to transform the way decisions about resection are done, and can be critically important in areas such as neurosurgery where the margins of tumor relative to critical normal tissues are not readily apparent from visual or palpable guidance. Yet there are major financial barriers to advancing agents into clinical trials with commercial backing. We observe that development of these agents in the standard biological therapeutic paradigm is not viable, due to the high up front financial investment needed and the limitations in the revenue models of contrast agents for imaging. The hypothesized solution to this problem is to develop small molecular biologicals tagged with an established fluorescent reporter, through the chemical agent approval pathway, targeting a phase 0 trials initially, such that the initial startup phase can be completely funded by a single NIH grant. In this way, fast trials can be completed to de-risk the development pipeline, and advance the idea of fluorescence-guided surgery (FGS) reporters into human testing. As with biological therapies the potential successes of each agent are still moderate, but this process will allow the field to advance in a more stable and productive manner, rather than relying upon isolated molecules developed at high cost and risk. The pathway proposed and tested here uses peptide synthesis of an epidermal growth factor receptor (EGFR)-binding Affibody molecules, uniquely conjugated to IRDye 800CW, developed and tested in academic and industrial laboratories with well-established records for GMP production, fill and finish, toxicity testing, and early phase clinical trials with image guidance.

  5. Advancing Molecular-Guided Surgery through probe development and testing in a moderate cost evaluation pipeline

    PubMed Central

    Pogue, Brian W; Paulsen, Keith D; Hull, Sally M.; Samkoe, Kimberly S.; Gunn, Jason; Hoopes, Jack; Roberts, David W.; Strong, Theresa V.; Draney, Daniel; Feldwisch, Joachim

    2015-01-01

    Molecular guided oncology surgery has the potential to transform the way decisions about resection are done, and can be critically important in areas such as neurosurgery where the margins of tumor relative to critical normal tissues are not readily apparent from visual or palpable guidance. Yet there are major financial barriers to advancing agents into clinical trials with commercial backing. We observe that development of these agents in the standard biological therapeutic paradigm is not viable, due to the high up front financial investment needed and the limitations in the revenue models of contrast agents for imaging. The hypothesized solution to this problem is to develop small molecular biologicals tagged with an established fluorescent reporter, through the chemical agent approval pathway, targeting a phase 0 trials initially, such that the initial startup phase can be completely funded by a single NIH grant. In this way, fast trials can be completed to de-risk the development pipeline, and advance the idea of fluorescence-guided surgery (FGS) reporters into human testing. As with biological therapies the potential successes of each agent are still moderate, but this process will allow the field to advance in a more stable and productive manner, rather than relying upon isolated molecules developed at high cost and risk. The pathway proposed and tested here uses peptide synthesis of an epidermal growth factor receptor (EGFR)-binding Affibody molecules, uniquely conjugated to IRDye 800CW, developed and tested in academic and industrial laboratories with well-established records for GMP production, fill & finish, toxicity testing, and early phase clinical trials with image guidance. PMID:25914500

  6. Probing the origins of aromatase inhibitory activity of disubstituted coumarins via QSAR and molecular docking

    PubMed Central

    Worachartcheewan, Apilak; Suvannang, Naravut; Prachayasittikul, Supaluk; Prachayasittikul, Virapong; Nantasenamat, Chanin

    2014-01-01

    This study investigated the quantitative structure-activity relationship (QSAR) of imidazole derivatives of 4,7-disubstituted coumarins as inhibitors of aromatase, a potential therapeutic protein target for the treatment of breast cancer. Herein, a series of 3,7- and 4,7-disubstituted coumarin derivatives (1-34) with R1 and R2 substituents bearing aromatase inhibitory activity were modeled as a function of molecular and quantum chemical descriptors derived from low-energy conformer geometrically optimized at B3LYP/6-31G(d) level of theory. Insights on origins of aromatase inhibitory activity was afforded by the computed set of 7 descriptors comprising of F10[N-O], Inflammat-50, Psychotic-80, H-047, BELe1, B10[C-O] and MAXDP. Such significant descriptors were used for QSAR model construction and results indicated that model 4 afforded the best statistical performance. Good predictive performance were achieved as verified from the internal (comprising the training and the leave-one-out cross-validation (LOO-CV) sets) and external sets affording the following statistical parameters: R2Tr = 0.9576 and RMSETr = 0.0958 for the training set; Q2CV = 0.9239 and RMSECV = 0.1304 for the LOO-CV set as well as Q2Ext = 0.7268 and RMSEExt = 0.2927 for the external set. Significant descriptors showed correlation with functional substituents, particularly, R1 in governing high potency as aromatase inhibitor. Molecular docking calculations suggest that key residues interacting with the coumarins were predominantly lipophilic or non-polar while a few were polar and positively-charged. Findings illuminated herein serve as the impetus that can be used to rationally guide the design of new aromatase inhibitors. PMID:26417339

  7. High sensitivity of diamond resonant microcantilevers for direct detection in liquids as probed by molecular electrostatic surface interactions.

    PubMed

    Bongrain, Alexandre; Agnès, Charles; Rousseau, Lionel; Scorsone, Emmanuel; Arnault, Jean-Charles; Ruffinatto, Sébastien; Omnès, Franck; Mailley, Pascal; Lissorgues, Gaëlle; Bergonzo, Philippe

    2011-10-01

    Resonant microcantilevers have demonstrated that they can play an important role in the detection of chemical and biological agents. Molecular interactions with target species on the mechanical microtransducers surface generally induce a change of the beam's bending stiffness, resulting in a shift of the resonance frequency. In most biochemical sensor applications, cantilevers must operate in liquid, even though damping deteriorates the vibrational performances of the transducers. Here we focus on diamond-based microcantilevers since their transducing properties surpass those of other materials. In fact, among a wide range of remarkable features, diamond possesses exceptional mechanical properties enabling the fabrication of cantilever beams with higher resonant frequencies and Q-factors than when made from other conventional materials. Therefore, they appear as one of the top-ranked materials for designing cantilevers operating in liquid media. In this study, we evaluate the resonator sensitivity performances of our diamond microcantilevers using grafted carboxylated alkyl chains as a tool to investigate the subtle changes of surface stiffness as induced by electrostatic interactions. Here, caproic acid was immobilized on the hydrogen-terminated surface of resonant polycrystalline diamond cantilevers using a novel one-step grafting technique that could be also adapted to several other functionalizations. By varying the pH of the solution one could tune the -COO(-)/-COOH ratio of carboxylic acid moieties immobilized on the surface, thus enabling fine variations of the surface stress. We were able to probe the cantilevers resonance frequency evolution and correlate it with the ratio of -COO(-)/-COOH terminations on the functionalized diamond surface and consequently the evolution of the electrostatic potential over the cantilever surface. The approach successfully enabled one to probe variations in cantilevers bending stiffness from several tens to hundreds of

  8. Probing the origins of human acetylcholinesterase inhibition via QSAR modeling and molecular docking.

    PubMed

    Simeon, Saw; Anuwongcharoen, Nuttapat; Shoombuatong, Watshara; Malik, Aijaz Ahmad; Prachayasittikul, Virapong; Wikberg, Jarl E S; Nantasenamat, Chanin

    2016-01-01

    Alzheimer's disease (AD) is a chronic neurodegenerative disease which leads to the gradual loss of neuronal cells. Several hypotheses for AD exists (e.g., cholinergic, amyloid, tau hypotheses, etc.). As per the cholinergic hypothesis, the deficiency of choline is responsible for AD; therefore, the inhibition of AChE is a lucrative therapeutic strategy for the treatment of AD. Acetylcholinesterase (AChE) is an enzyme that catalyzes the breakdown of the neurotransmitter acetylcholine that is essential for cognition and memory. A large non-redundant data set of 2,570 compounds with reported IC50 values against AChE was obtained from ChEMBL and employed in quantitative structure-activity relationship (QSAR) study so as to gain insights on their origin of bioactivity. AChE inhibitors were described by a set of 12 fingerprint descriptors and predictive models were constructed from 100 different data splits using random forest. Generated models afforded R (2), [Formula: see text] and [Formula: see text] values in ranges of 0.66-0.93, 0.55-0.79 and 0.56-0.81 for the training set, 10-fold cross-validated set and external set, respectively. The best model built using the substructure count was selected according to the OECD guidelines and it afforded R (2), [Formula: see text] and [Formula: see text] values of 0.92 ± 0.01, 0.78 ± 0.06 and 0.78 ± 0.05, respectively. Furthermore, Y-scrambling was applied to evaluate the possibility of chance correlation of the predictive model. Subsequently, a thorough analysis of the substructure fingerprint count was conducted to provide informative insights on the inhibitory activity of AChE inhibitors. Moreover, Kennard-Stone sampling of the actives were applied to select 30 diverse compounds for further molecular docking studies in order to gain structural insights on the origin of AChE inhibition. Site-moiety mapping of compounds from the diversity set revealed three binding anchors encompassing both hydrogen bonding and van der Waals

  9. Single-molecular surface-enhanced resonance Raman scattering as a quantitative probe of local electromagnetic field: The case of strong coupling between plasmonic and excitonic resonance

    NASA Astrophysics Data System (ADS)

    Itoh, Tamitake; Yamamoto, Yuko S.; Tamaru, Hiroharu; Biju, Vasudevanpillai; Wakida, Shin-ichi; Ozaki, Yukihiro

    2014-05-01

    We investigate electromagnetic coupling between plasmonic and molecular electronic resonances using single-molecular surface-enhanced resonance Raman scattering (SERRS) from single silver nanoparticle dimers. When dimers exhibit SERRS activity, their elastic light scattering spectra show two lines, which are temporally closing toward each other. The higher energy line eventually disappears at the time of SERRS quenching. A coupled-oscillator model composed of plasmonic and molecular electronic resonances consistently reproduces the above interesting results by decreasing coupling energy, indicating that SERRS can be a quantitative probe for strong coupling between the two resonances.

  10. Probing self assembly in biological mixed colloids by SANS, deuteration and molecular manipulation

    SciTech Connect

    Hjelm, R.P.; Thiyagarajan, P.; Hoffman, A.; Alkan-Onyuksel, H.

    1994-12-31

    Small-angle neutron scattering was used to obtain information on the form and molecular arrangement of particles in mixed colloids of bile salts with phosphatidylcholine, and bile salts with monoolein. Both types of systems showed the same general characteristics. The particle form was highly dependent on total lipid concentration. At the highest concentrations the particles were globular mixed micelles with an overall size of 50{Angstrom}. As the concentration was reduced the mixed micelles elongated, becoming rodlike with diameter about 50{Angstrom}. The rods had a radial core-shell structure in which the phosphatidylcholine or monoolein fatty tails were arranged radially to form the core with the headgroups pointing outward to form the shell. The bile salts were at the interface between the shell and core with the hydrophilic parts facing outward as part of the shell. The lengths of the rods increased and became more polydispersed with dilution. At sufficiently low concentrations the mixed micelles transformed into single bilayer vesicles. These results give insight on the physiological function of bile and on the rules governing the self assembly of bile particles in the hepatic duct and the small intestine.

  11. Mg2+-sensing mechanism of Mg2+ transporter MgtE probed by molecular dynamics study

    PubMed Central

    Ishitani, Ryuichiro; Sugita, Yuji; Dohmae, Naoshi; Furuya, Noritaka; Hattori, Motoyuki; Nureki, Osamu

    2008-01-01

    Proper regulation of the intracellular ion concentration is essential to maintain life and is achieved by ion transporters that transport their substrates across the membrane in a strictly regulated manner. MgtE is a Mg2+ transporter that may function in the homeostasis of the intracellular Mg2+ concentration. A recent crystallographic study revealed that its cytosolic domain undergoes a Mg2+-dependent structural change, which is proposed to gate the ion-conducting pore passing through the transmembrane domain. However, the dynamics of Mg2+ sensing, i.e., how MgtE responds to the change in the intracellular Mg2+ concentration, remained elusive. Here we performed molecular dynamics simulations of the MgtE cytosolic domain. The simulations successfully reproduced the structural changes of the cytosolic domain upon binding or releasing Mg2+, as well as the ion selectivity. These results suggested the roles of the N and CBS domains in the cytosolic domain and their respective Mg2+ binding sites. Combined with the current crystal structures, we propose an atomically detailed model of Mg2+ sensing by MgtE. PMID:18832160

  12. Probing of molecular replication and accumulation in shallow heat gradients through numerical simulations.

    PubMed

    Keil, Lorenz; Hartmann, Michael; Lanzmich, Simon; Braun, Dieter

    2016-07-27

    How can living matter arise from dead matter? All known living systems are built around information stored in RNA and DNA. To protect this information against molecular degradation and diffusion, the second law of thermodynamics imposes the need for a non-equilibrium driving force. Following a series of successful experiments using thermal gradients, we have shown that heat gradients across sub-millimetre pores can drive accumulation, replication, and selection of ever longer molecules, implementing all the necessary parts for Darwinian evolution. For these lab experiments to proceed with ample speed, however, the temperature gradients have to be quite steep, reaching up to 30 K per 100 μm. Here we use computer simulations based on experimental data to show that 2000-fold shallower temperature gradients - down to 100 K over one metre - can still drive the accumulation of protobiomolecules. This finding opens the door for various environments to potentially host the origins of life: volcanic, water-vapour, or hydrothermal settings. Following the trajectories of single molecules in simulation, we also find that they are subjected to frequent temperature oscillations inside these pores, facilitating e.g. template-directed replication mechanisms. The tilting of the pore configuration is the central strategy to achieve replication in a shallow temperature gradient. Our results suggest that shallow thermal gradients across porous rocks could have facilitated the formation of evolutionary machines, significantly increasing the number of potential sites for the origin of life on young rocky planets. PMID:27153345

  13. Probing ice-nucleation processes on the molecular level using second harmonic generation spectroscopy

    NASA Astrophysics Data System (ADS)

    Abdelmonem, A.; Lützenkirchen, J.; Leisner, T.

    2015-08-01

    We present and characterize a novel setup to apply second harmonic generation (SHG) spectroscopy in total internal reflection geometry (TIR) to heterogeneous freezing research. It allows to monitor the evolution of water structuring at solid surfaces at low temperatures prior to heterogeneous ice nucleation. Apart from the possibility of investigating temperature dependence, a major novelty in our setup is the ability of measuring sheet-like samples in TIR geometry in a direct way. As a main experimental result, we find that our method can discriminate between good and poor ice nucleating surfaces. While at the sapphire basal plane, which is known to be a poor ice nucleator, no structural rearrangement of the water molecules is found prior to freezing, the basal plane surface of mica, an analogue to ice active mineral dust surfaces, exhibits a strong change in the nonlinear optical properties at temperatures well above the freezing transition. This is interpreted as a pre-activation, i.e. an increase in the local ordering of the interfacial water which is expected to facilitate the crystallization of ice at the surface. The results are in line with recent predictions by molecular dynamics simulations on a similar system.

  14. Pore-spanning lipid membrane under indentation by a probe tip: a molecular dynamics simulation study.

    PubMed

    Huang, Chen-Hsi; Hsiao, Pai-Yi; Tseng, Fan-Gang; Fan, Shih-Kang; Fu, Chien-Chung; Pan, Rong-Long

    2011-10-01

    We study the indentation of a free-standing lipid membrane suspended over a nanopore on a hydrophobic substrate by means of molecular dynamics simulations. We find that in the course of indentation the membrane bends at the point of contact and the fringes of the membrane glide downward intermittently along the pore edges and stop gliding when the fringes reach the edge bottoms. The bending continues afterward, and the large strain eventually induces a phase transition in the membrane, transformed from a bilayered structure to an interdigitated structure. The membrane is finally ruptured when the indentation goes deep enough. Several local physical quantities in the pore regions are calculated, which include the tilt angle of lipid molecules, the nematic order, the included angle, and the distance between neighboring lipids. The variations of these quantities reveal many detailed, not-yet-specified local structural transitions of lipid molecules under indentation. The force-indentation curve is also studied and discussed. The results make a connection between the microscopic structure and the macroscopic properties and provide deep insight into the understanding of the stability of a lipid membrane spanning over nanopore. PMID:21859109

  15. Molecular Self-Probing Spectroscopy with High Harmonic Generation at Long Wavelengths

    NASA Astrophysics Data System (ADS)

    Camper, A.; Schoun, S. B.; Agostini, P.; Salieres, Pascal; Caillat, J.; Lucchese, R. R.; Dimauro, L.

    2015-05-01

    We used laser driven sub-femtosecond electronic wave packet (EWP) recollision to generate high-order harmonics (HHG) of a 1.3 μm laser pulse in aligned molecules. We performed a tomographic investigation of N2 [ItataniNature2004, HaesslerNatPhys2010, VozziNatPhys2011, DivekiNJP2012] by characterizing the HHG yield and spectral phase of the attosecond emission for different recollision angles of EWP with respect to the main axis of the angular distribution of the molecules. Thanks to the high degree of alignment and to the fine spectral sampling, our XUV quantum phase measurements [SchounPRL2014] reveal subtle features in the recombination dipole moment of N2. We interpret the latter within the Quantitative Rescattering Theory [LePRA2009] and emphasize the effect of the EWP scattering on the ion Coulombic potential and of the shape resonance in the X channel of N2 on HHG [LucchesePRA1982]. Compared to previous results at 800 nm, our experiment is deeper into the tunneling regime and only one ionization channel is enough to explain what we observed. Our results shine a new light on imaging molecular orbitals using laser-driven photo-recombination processes.

  16. Probing the molecular interstellar medium of M82 with Herschel-SPIRE spectroscopy

    NASA Astrophysics Data System (ADS)

    Panuzzo, P.; Rangwala, N.; Rykala, A.; Isaak, K. G.; Glenn, J.; Wilson, C. D.; Auld, R.; Baes, M.; Barlow, M. J.; Bendo, G. J.; Bock, J. J.; Boselli, A.; Bradford, M.; Buat, V.; Castro-Rodríguez, N.; Chanial, P.; Charlot, S.; Ciesla, L.; Clements, D. L.; Cooray, A.; Cormier, D.; Cortese, L.; Davies, J. I.; Dwek, E.; Eales, S. A.; Elbaz, D.; Fulton, T.; Galametz, M.; Galliano, F.; Gear, W. K.; Gomez, H. L.; Griffin, M.; Hony, S.; Levenson, L. R.; Lu, N.; Madden, S.; O'Halloran, B.; Okumura, K.; Oliver, S.; Page, M. J.; Papageorgiou, A.; Parkin, T. J.; Pérez-Fournon, I.; Pohlen, M.; Polehampton, E. T.; Rigby, E. E.; Roussel, H.; Sacchi, N.; Sauvage, M.; Schulz, B.; Schirm, M. R. P.; Smith, M. W. L.; Spinoglio, L.; Stevens, J. A.; Srinivasan, S.; Symeonidis, M.; Swinyard, B.; Trichas, M.; Vaccari, M.; Vigroux, L.; Wozniak, H.; Wright, G. S.; Zeilinger, W. W.

    2010-07-01

    We present the observations of the starburst galaxy M82 taken with the Herschel SPIRE Fourier-transform spectrometer. The spectrum (194-671 μm) shows a prominent CO rotational ladder from J = 4-3 to 13-12 emitted by the central region of M82. The fundamental properties of the gas are well constrained by the high J lines observed for the first time. Radiative transfer modeling of these high-S/N 12CO and 13CO lines strongly indicates a very warm molecular gas component at ~500 K and pressure of ~3×106 K cm-3, in good agreement with the H2 rotational lines measurements from Spitzer and ISO. We suggest that this warm gas is heated by dissipation of turbulence in the interstellar medium (ISM) rather than X-rays or UV flux from the straburst. This paper illustrates the promise of the SPIRE FTS for the study of the ISM of nearby galaxies. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.

  17. Molecular force probe measurement of antigen I/II-matrix protein interactions.

    PubMed

    Soell, Martine; Hemmerlé, Joseph; Hannig, Matthias; Haïkel, Youssef; Sano, Hidehiko; Selimovic, Denis

    2010-12-01

    Viridans streptococci possess a family of immunologically and structurally related cell-surface proteins, termed antigen I/II, which may function as adhesins and enable oral streptococci to adhere to saliva-coated surfaces and matrix proteins. Here we used atomic force microscopy in the molecular force mode to measure the specific interaction forces between antigen I/II and two matrix proteins, collagen and fibronectin. These matrix proteins provide important binding sites for adherence of oral streptococcal in dentinal caries and endocarditis, respectively. Antigen I/II-coated cantilever tips were brought into contact with collagen- or fibronectin-coated silica coverslips. For the protein I/II-fibronectin interaction experiments, the mean strength of the last ruptures was 216 pN, with most of the detachments located around 125 pN. In antigen I/II-collagen interaction experiments, the mean strength of the last rupture forces corresponded to 136 pN, with the most frequent unbinding force around 75 pN. Thus, our findings definitely suggest that, under the present experimental conditions, antigen I/II binds more strongly to fibronectin than to type I collagen. This might be of relevance for the attachment of viridians streptococci to surfaces exposed to strong hydrodynamic shearing forces under in vivo conditions. PMID:21083620

  18. Probing the origins of human acetylcholinesterase inhibition via QSAR modeling and molecular docking

    PubMed Central

    Shoombuatong, Watshara; Malik, Aijaz Ahmad; Prachayasittikul, Virapong; Wikberg, Jarl E.S.

    2016-01-01

    {mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}${Q}_{\\mathrm{CV }}^{2}$\\end{document}QCV2 and \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}${Q}_{\\mathrm{Ext}}^{2}$\\end{document}QExt2 values of 0.92 ± 0.01, 0.78 ± 0.06 and 0.78 ± 0.05, respectively. Furthermore, Y-scrambling was applied to evaluate the possibility of chance correlation of the predictive model. Subsequently, a thorough analysis of the substructure fingerprint count was conducted to provide informative insights on the inhibitory activity of AChE inhibitors. Moreover, Kennard–Stone sampling of the actives were applied to select 30 diverse compounds for further molecular docking studies in order to gain structural insights on the origin of AChE inhibition. Site-moiety mapping of compounds from the diversity set revealed three binding anchors encompassing both hydrogen bonding and van der Waals interaction. Molecular docking revealed that compounds 13, 5 and 28 exhibited the lowest binding energies of −12.2, −12.0 and −12.0 kcal/mol, respectively, against human AChE, which is modulated by hydrogen bonding, π–π stacking and hydrophobic interaction inside the binding pocket. These information may be used as guidelines for the design of novel and robust AChE inhibitors. PMID:27602288

  19. Probing the binding mechanism of Mnk inhibitors by docking and molecular dynamics simulations.

    PubMed

    Kannan, Srinivasaraghavan; Poulsen, Anders; Yang, Hai Yan; Ho, Melvyn; Ang, Shi Hua; Eldwin, Tan Sum Wai; Jeyaraj, Duraiswamy Athisayamani; Chennamaneni, Lohitha Rao; Liu, Boping; Hill, Jeffrey; Verma, Chandra S; Nacro, Kassoum

    2015-01-13

    Mitogen-activated protein kinases-interacting kinase 1 and 2 (Mnk1/2) activate the oncogene eukaryotic initiation factor 4E (eIF4E) by phosphorylation. High level of phosphorylated eIF4E is associated with various types of cancers. Inhibition of Mnk prevents eIF4E phosphorylation, making them potential therapeutic targets for cancer. Recently, we have designed and synthesized a series of novel imidazopyridine and imidazopyrazine derivatives that inhibit Mnk1/2 kinases with a potency in the nanomolar to micromolar range. In the current work we model the inhibition of Mnk kinase activity by these inhibitors using various computational approaches. Combining homology modeling, docking, molecular dynamics simulations, and free energy calculations, we find that all compounds bind similarly to the active sites of both kinases with their imidazopyridine and imidazopyrazine cores anchored to the hinge regions of the kinases through hydrogen bonds. In addition, hydrogen bond interactions between the inhibitors and the catalytic Lys78 (Mnk1), Lys113 (Mnk2) and Ser131 (Mnk1), Ser166 (Mnk2) appear to be important for the potency and stability of the bound conformations of the inhibitors. The computed binding free energies (ΔGPred) of these inhibitors are in accord with experimental bioactivity data (pIC50) with correlation coefficients (r(2)) of 0.70 and 0.68 for Mnk1 and Mnk2 respectively. van der Waals energies and entropic effects appear to dominate the binding free energy (ΔGPred) for each Mnk-inhibitor complex studied. The models suggest that the activities of these small molecule inhibitors arise from interactions with multiple residues in the active sites, particularly with the hydrophobic residues. PMID:25431995

  20. Probing molecular interaction between concanavalin A and mannose ligands by means of SFM.

    PubMed

    Lekka, M; Laidler, P; Dulińska, J; Łabedź, M; Pyka, G

    2004-11-01

    Recently, the scanning force microscope (SFM) has been widely used for direct monitoring of specific interactions between biologically active molecules. Such studies have employed the SFM liquid-cell setup, which allows measurements to be made in the native environment with force resolution down to a tenth of a picoNewton. In this study, the ligand-receptor strength of monoclonal anti-human prostatic acid phosphatase and prostatic acid phosphatase, representing an antigen-antibody system with a single type of interaction, was determined. Then, the interaction force occurring between concanavalin A and the carbohydrate component of the glycoproteins arylsulfatase A and carboxypeptidase Y was measured. High mannose-type glycans were sought on the human prostate carcinoma cell surface. Application of an analysis based on the Poisson distribution of the number of bonds formed in all these measured systems allowed the strength of the molecular interaction to be calculated. The values of the force acting between two single molecules were 530+/-25, 790+/-32, and 940+/-39 pN between prostatic acid phosphatase and monoclonal anti-human prostatic acid phosphatase, between concanavalin A and arylsulfatase A, and between concanavalin A and carboxypeptidase Y, respectively. The value calculated from data collected for the force between concanavalin A and mannose-containing ligands present on the surface of human prostate carcinoma cells was smaller, 116+/-17 pN. The different values of the binding force between concanavalin A and mannose-containing ligands were attributed to the structural changes of the carbohydrate components. PMID:15138737

  1. Molecular Probes of the Mechanism of Cytochrome P450. Oxygen Traps a Substrate Radical Intermediate

    PubMed Central

    Cooper, Harriet L. R.; Groves, John T.

    2010-01-01

    The diagnostic substrate tetramethylcyclopropane (TMCP) has been reexamined as a substrate with three drug- and xenobiotic-metabolizing cytochrome P450 enzymes, human CYP2E1, CYP3A4 and rat CYP2B1. The major hydroxylation product in all cases was the unrearranged primary alcohol along with smaller amounts of a rearranged tertiary alcohol. Significantly, another ring-opened product, diacetone alcohol, was also observed. With CYP2E1 this product accounted for 20% of the total turnover. Diacetone alcohol also was detected as a product from TMCP with a biomimetic model catalyst, FeTMPyP, but not with a ruthenium porphyrin catalyst. Lifetimes of the intermediate radicals were determined from the ratios of rearranged and unrearranged products to be 120, 13 and 1 ps for CYP2E1, CYP3A4 and CYP2B1, respectively, corresponding to rebound rates of 0.9×1010 s−1, 7.2×1010 s−1 and 1.0×1012 s−1. For the model iron porphyrin, FeTMPyP, a radical lifetime of 81 ps and a rebound rate of 1.2×1010 s−1 were determined. These apparent radical lifetimes are consistent with earlier reports with a variety of CYP enzymes and radical clock substrates, however, the large amounts of diacetone alcohol with CYP2E1 and the iron porphyrin suggest that for these systems a considerable amount of the intermediate carbon radical is trapped by molecular oxygen. These results add to the view that cage escape of the intermediate carbon radical in [FeIV-OH •R] can compete with cage collapse to form a CO bond. The results could be significant with regard to our understanding of iron-catalyzed C-H hydroxylation, the observation of P450-dependent peroxidation and the development of oxidative stress, especially for CYP2E1. PMID:21075070

  2. The stable isotopic composition of molecular hydrogen in the tropopause region probed by the CARIBIC aircraft

    NASA Astrophysics Data System (ADS)

    Batenburg, A. M.; Schuck, T. J.; Baker, A. K.; Zahn, A.; Brenninkmeijer, C. A. M.; Röckmann, T.

    2012-05-01

    More than 450 air samples that were collected in the upper troposphere - lower stratosphere (UTLS) region by the CARIBIC aircraft (Civil Aircraft for the Regular Investigation of the atmosphere Based on an Instrument Container) have been analyzed for molecular hydrogen (H2) mixing ratios (χ(H2)) and H2 isotopic composition (deuterium content, δD). More than 120 of the analyzed samples contained air from the lowermost stratosphere (LMS). These show that χ(H2) does not vary appreciably with O3-derived height above the thermal tropopause (TP), whereas δD does increase with height. The isotope enrichment is caused by H2 production and destruction processes that enrich the stratospheric H2 reservoir in deuterium (D); the exact shapes of the profiles are mainly determined by mixing of stratospheric with tropospheric air. Tight negative correlations are found between δD and the mixing ratios of methane (χ(CH4)) and nitrous oxide (χ(N2O)), as a result of the relatively long lifetimes of these three species. The correlations are described by δD[‰]=-0.35 · χ(CH4)[ppb]+768 and δD[‰]=-1.90· χ(N2O)[ppb]+745. These correlations are similar to previously published results and likely hold globally for the LMS. Samples that were collected from the Indian subcontinent up to 40° N before, during and after the summer monsoon season show no significant seasonal change in χ(H2), but δD is up to 12.3‰ lower in the July, August and September monsoon samples. This δD decrease is correlated with the χ(CH4) increase in these samples. The significant correlation with χ(CH4) and the absence of a perceptible χ(H2) increase that accompanies the δD decrease indicates that microbial production of very D-depleted H2 in the wet season may contribute to this phenomenon. Some of the samples have very high χ(H2) and very low δD values, which indicates a pollution effect. Aircraft engine exhaust plumes are a suspected cause, since the effect mostly occurs in samples

  3. The stable isotopic composition of molecular hydrogen in the tropopause region probed by the CARIBIC aircraft

    NASA Astrophysics Data System (ADS)

    Batenburg, A. M.; Schuck, T. J.; Baker, A. K.; Zahn, A.; Brenninkmeijer, C. A. M.; Röckmann, T.

    2012-01-01

    More than 450 air samples that were collected in the upper troposphere - lower stratosphere (UTLS) region around the tropopause (TP) by the CARIBIC aircraft (Civil Aircraft for the Regular Investigation of the Atmosphere Based on an Instrument Container) have been analyzed for molecular hydrogen (H2) mixing ratios (m(H2)) and H2 isotopic composition (deuterium content, δD). More than 120 of the analysed samples consisted of air from the lowermost stratosphere (LMS). These show that m(H2) does not vary appreciably with O3-derived height above the thermal TP, whereas δD does increase with height. The isotope enrichment is caused by competing H2 production and destruction processes that enrich the stratospheric H2 reservoir in deuterium (D); the exact shapes of the profiles are mainly determined by mixing of stratospheric with tropospheric air. Tight negative correlations are found between δD and the mixing ratios of methane (CH4) and nitrous oxide (N2O), as a result of the relatively long lifetimes of these three species. The correlations are described by δ D [‰]=-0.35 · m(CH4)[ppb]+768 and δD [‰]=-1.90 · m(N2O)[ppb]+745. These correlations are similar to previously published results and likely hold globally. Samples that were collected from the Indian subcontinent up to 40° N before, during and after the summer monsoon season show no significant seasonal change in m(H2), but δD is up to 15‰ lower in the July, August and September monsoon samples. This δD lowering is correlated with m(CH4) increase. The significant correlation with m(CH4) and the absence of a perceptible m(H2) increase that accompanies the δD lowering indicates that microbial production of very D-depleted H2 in the wet season may contribute to this phenomenon. Some of the samples have very high m(H2) and very low δD values, which indicates a pollution effect. Aircraft engine exhaust plumes are a suspected cause, since the effect mostly occurs in samples collected close to airports

  4. Probing the hydrogen equilibrium and kinetics in zeolite imidazolate frameworks via molecular dynamics and quasi-elastic neutron scattering experiments

    NASA Astrophysics Data System (ADS)

    Pantatosaki, Evangelia; Jobic, Hervé; Kolokolov, Daniil I.; Karmakar, Shilpi; Biniwale, Rajesh; Papadopoulos, George K.

    2013-01-01

    The problem of simulating processes involving equilibria and dynamics of guest sorbates within zeolitic imidazolate frameworks (ZIF) by means of molecular dynamics (MD) computer experiments is of growing importance because of the promising role of ZIFs as molecular "traps" for clean energy applications. A key issue for validating such an atomistic modeling attempt is the possibility of comparing the MD results, with real experiments being able to capture analogous space and time scales to the ones pertained to the computer experiments. In the present study, this prerequisite is fulfilled through the quasi-elastic neutron scattering technique (QENS) for measuring self-diffusivity, by elaborating the incoherent scattering signal of hydrogen nuclei. QENS and MD experiments were performed in parallel to probe the hydrogen motion, for the first time in ZIF members. The predicted and measured dynamics behaviors show considerable concentration variation of the hydrogen self-diffusion coefficient in the two topologically different ZIF pore networks of this study, the ZIF-3 and ZIF-8. Modeling options such as the flexibility of the entire matrix versus a rigid framework version, the mobility of the imidazolate ligand, and the inclusion of quantum mechanical effects in the potential functions were examined in detail for the sorption thermodynamics and kinetics of hydrogen and also of deuterium, by employing MD combined with Widom averaging towards studying phase equilibria. The latter methodology ensures a rigorous and efficient way for post-processing the dynamics trajectory, thereby avoiding stochastic moves via Monte Carlo simulation, over the large number of configurational degrees of freedom a nonrigid framework encompasses.

  5. Probing the hydrogen equilibrium and kinetics in zeolite imidazolate frameworks via molecular dynamics and quasi-elastic neutron scattering experiments.

    PubMed

    Pantatosaki, Evangelia; Jobic, Hervé; Kolokolov, Daniil I; Karmakar, Shilpi; Biniwale, Rajesh; Papadopoulos, George K

    2013-01-21

    The problem of simulating processes involving equilibria and dynamics of guest sorbates within zeolitic imidazolate frameworks (ZIF) by means of molecular dynamics (MD) computer experiments is of growing importance because of the promising role of ZIFs as molecular "traps" for clean energy applications. A key issue for validating such an atomistic modeling attempt is the possibility of comparing the MD results, with real experiments being able to capture analogous space and time scales to the ones pertained to the computer experiments. In the present study, this prerequisite is fulfilled through the quasi-elastic neutron scattering technique (QENS) for measuring self-diffusivity, by elaborating the incoherent scattering signal of hydrogen nuclei. QENS and MD experiments were performed in parallel to probe the hydrogen motion, for the first time in ZIF members. The predicted and measured dynamics behaviors show considerable concentration variation of the hydrogen self-diffusion coefficient in the two topologically different ZIF pore networks of this study, the ZIF-3 and ZIF-8. Modeling options such as the flexibility of the entire matrix versus a rigid framework version, the mobility of the imidazolate ligand, and the inclusion of quantum mechanical effects in the potential functions were examined in detail for the sorption thermodynamics and kinetics of hydrogen and also of deuterium, by employing MD combined with Widom averaging towards studying phase equilibria. The latter methodology ensures a rigorous and efficient way for post-processing the dynamics trajectory, thereby avoiding stochastic moves via Monte Carlo simulation, over the large number of configurational degrees of freedom a nonrigid framework encompasses. PMID:23343292

  6. Probing the initial stages of molecular organization of oligo(p-phenylenevinylene) assemblies with monolayer protected gold nanoparticles.

    PubMed

    Kumar, Vattakattu R Rajeev; Sajini, Vadukumpulli; Sreeprasad, Theruvakkattil S; Praveen, Vakayil K; Ajayaghosh, Ayyappanpillai; Pradeep, Thalappil

    2009-06-01

    Thiol-protected gold nanoparticles (GNPs) have been used to probe the initial stages of the molecular organization of oligo(p-phenylenevinylene) (OPV) gelators. The hybrid materials prepared by the self-assembly of OPVs and GNPs are characterized by optical microscopy, fluorescence microscopy, scanning electron microscopy, transmission electron microscopy, and atomic force microscopy. GNPs are located preferentially on the sides of the OPV structures, which implies the presence of alkyl chains at the edges, which makes the assemblies hydrophobic. TEM analyses at the early stages of self-assembly show tapes that have a width of 4 nm, which upon further self-assembly, form fibrils through hydrogen bonding. The experiment was performed with GNPs protected with dodecane and octadecane thiols. The existence of tapes, ribbons, fibrils, and fibers were confirmed by nanoparticle marking. Based on the experimental data, we have proposed a hierarchical model for the self-assembly of OPV molecules. The presence of nanoparticles does not alter the morphology or electronic properties of the OPV structures, as revealed by microscopic and spectroscopic studies. PMID:19462383

  7. High potency olfactory receptor agonists discovered by virtual high-throughput screening: molecular probes for receptor structure and olfactory function

    PubMed Central

    Triballeau, Nicolas; Van Name, Eric; Laslier, Guillaume; Cai, Diana; Paillard, Guillaume; Sorensen, Peter W.; Hoffmann, Rémy; Bertrand, Hugues-Olivier; Ngai, John; Acher, Francine C.

    2008-01-01

    The detection and discrimination of diverse chemical structures by the vertebrate olfactory system is accomplished by the recognition of odorous ligands by their cognate receptors. In the present study we used a computational high-throughput screening strategy to discover novel high affinity agonists of an olfactory G protein-coupled receptor tuned to recognize amino acid ligands. Functional testing of the top candidates validated several agonists with potencies higher than any of the receptor’s known natural ligands. Computational modeling revealed molecular interactions involved in ligand recognition by this receptor, and further highlighted interactions that have been conserved in evolutionarily divergent amino acid receptors. Significantly, the top compounds display robust activities as odorants in vivo, and include a natural product that may be used to signal the presence of bacteria in the aquatic environment. Our virtual screening approach should be applicable to the identification of new bioactive molecules for probing the structure of chemosensory receptors and the function of chemosensory systems in vivo. PMID:19081373

  8. Unfolding stabilities of two paralogous proteins from Naja naja naja (Indian cobra) as probed by molecular dynamics simulations.

    PubMed

    Gorai, Biswajit; Sivaraman, Thirunavukkarasu

    2013-09-01

    Structurally similar but functionally different two paralogous proteins, CTX1 (a cardiotoxin) and LNTX2 (an alpha-neurotoxin), from venom of Naja naja naja have been homology modeled and subjected to molecular dynamics (MD) simulations at four different temperatures (298 K, 310 K, 373 K & 473 K) under close quarters of physiological conditions. Each MD simulation was performed for 25 ns and trajectory structures stored at every 25 ps were used to probe various structural events occurring in the temperature-induced unfolding of the proteins. Notwithstanding their similar scaffolds, the two proteins are drastically differing in their unfolding stabilities from each other. The structural orders of flexibilities for the CTX1 and LNTX2 were found to be loop II > loop III > loop I > C-terminal and C-terminal > loop I > loop III > loop II, respectively. Based on the comprehensive analyses of the simulation data and studies on the various structural interactions of all cardiotoxins (CTXs) and alpha-neurotoxins (NTXs) for which three-dimensional structures determined by experimental techniques are available to date, we have herein proposed a hypothesis ('CN network') rationalizing the differential stabilities of the CTXs and NTXs belonging to a three-finger toxin superfamily of snake venoms. PMID:23791667

  9. Gold Nanoparticle-Based Surface-Enhanced Raman Scattering for Noninvasive Molecular Probing of Embryonic Stem Cell Differentiation

    PubMed Central

    Sathuluri, Ramachandra Rao; Yoshikawa, Hiroyuki; Shimizu, Eiichi; Saito, Masato; Tamiya, Eiichi

    2011-01-01

    This study reports the use of gold nanoparticle-based surface-enhanced Raman scattering (SERS) for probing the differentiation of mouse embryonic stem (mES) cells, including undifferentiated single cells, embryoid bodies (EBs), and terminally differentiated cardiomyocytes. Gold nanoparticles (GNPs) were successfully delivered into all 3 mES cell differentiation stages without affecting cell viability or proliferation. Transmission electron microscopy (TEM) confirmed the localization of GNPs inside the following cell organelles: mitochondria, secondary lysosome, and endoplasmic reticulum. Using bright- and dark-field imaging, the bright scattering of GNPs and nanoaggregates in all 3 ES cell differentiation stages could be visualized. EB (an early differentiation stage) and terminally differentiated cardiomyocytes both showed SERS peaks specific to metabolic activity in the mitochondria and to protein translation (amide I, amide II, and amide III peaks). These peaks have been rarely identified in undifferentiated single ES cells. Spatiotemporal changes observed in the SERS spectra from terminally differentiated cardiomyocyte tissues revealed local and dynamic molecular interactions as well as transformations during ES cell differentiation. PMID:21829653

  10. A new silver nanochain SERS analytical platform to detect trace hexametaphosphate with a rhodamine S molecular probe.

    PubMed

    Shang, Guangyun; Li, Chongning; Wen, Guiqing; Zhang, Xinghui; Liang, Aihui; Jiang, Zhiliang

    2016-05-01

    Using AgNO3 as the precursor, stable silver nanochain (AgNC) sols, orange-red in color, were prepared using hydrazine hydrate. A strong surface plasmon resonance Rayleigh scattering (RRS) peak occurred at 420 nm plus two surface plasmon resonance (SPR) absorption peaks at 410 nm and 510 nm. Rhodamine S (RhS) cationic dye was absorbed on the as-prepared AgNC substrate to obtain a RhS-AgNC surface-enhanced Raman scattering (SERS) nanoprobe that exhibited a strong SERS peak at 1506 cm(-1) and a strong RRS peak at 375 nm. Upon addition of the analyte sodium hexametaphosphate (HP), it reacted with RhS, which resulted in a decrease in the SERS and RRS peaks that was studied in detail. The decreased SERS and RRS intensities correlated linearly with HP concentration in the range of 0.0125-0.3 µmol/L and 0.05-1.0 µmol/L, with a detection limit of 6 nmol/L and 20 nmol/L HP respectively. Due to advantages of high sensitivity, good selectivity and simple operation, the RhS molecular probes were used to determine HP concentration in real samples. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26280554

  11. Subcellular integrities in Chroococcidiopsis sp. CCMEE 029 survivors after prolonged desiccation revealed by molecular probes and genome stability assays.

    PubMed

    Billi, Daniela

    2009-01-01

    Desiccation-tolerant cells must either protect their cellular components from desiccation-induced damage and/or repair it upon rewetting. Subcellular damage to the anhydrobiotic cyanobacterium Chroococcidiopsis sp. CCMEE 029 stored in the desiccated state for 4 years was evaluated at the single-cell level using fluorescent DNA strand breakage labelling, membrane integrity and potential related molecular probes, oxidant-sensing fluorochrome and redox dye. Covalent modifications of dried genomes were assessed by testing their suitability as PCR template. Results suggest that desiccation survivors avoid/and or limit genome fragmentation and genome covalent modifications, preserve intact plasma membranes and phycobiliprotein autofluorescence, exhibit spatially-reduced ROS accumulation and dehydrogenase activity upon rewetting. Damaged cells undergo genome fragmentation, loss of plasma membrane potential and integrity, phycobiliprotein bleaching, whole-cell ROS accumulation and lack respiratory activity upon rewetting. The co-occurrence of live and dead cells within dried aggregates of Chroococcidiopsis confirms that desiccation resistance is not a simple process and that subtle modifications to the cellular milieu are required to dry without dying. It rises also intriguing questions about the triggers of dead cells in response to drying. The capability of desiccation survivors to avoid and/or reduce subcellular damage, shows that protection mechanisms are relevant in the desiccation tolerance of this cyanobacterium. PMID:18931823

  12. Direct Monitoring of γ-Glutamyl Transpeptidase Activity In Vivo Using a Hyperpolarized (13) C-Labeled Molecular Probe.

    PubMed

    Nishihara, Tatsuya; Yoshihara, Hikari A I; Nonaka, Hiroshi; Takakusagi, Yoichi; Hyodo, Fuminori; Ichikawa, Kazuhiro; Can, Emine; Bastiaansen, Jessica A M; Takado, Yuhei; Comment, Arnaud; Sando, Shinsuke

    2016-08-26

    The γ-glutamyl transpeptidase (GGT) enzyme plays a central role in glutathione homeostasis. Direct detection of GGT activity could provide critical information for the diagnosis of several pathologies. We propose a new molecular probe, γ-Glu-[1-(13) C]Gly, for monitoring GGT activity in vivo by hyperpolarized (HP) (13) C magnetic resonance (MR). The properties of γ-Glu-[1-(13) C]Gly are suitable for in vivo HP (13) C metabolic analysis since the chemical shift between γ-Glu-[1-(13) C]Gly and its metabolic product, [1-(13) C]Gly, is large (4.3 ppm) and the T1 of both compounds is relatively long (30 s and 45 s, respectively, in H2 O at 9.4 T). We also demonstrate that γ-Glu-[1-(13) C]Gly is highly sensitive to in vivo modulation of GGT activity induced by the inhibitor acivicin. PMID:27483206

  13. Nano-confined water in the interlayers of hydrocalumite: Reorientational dynamics probed by neutron spectroscopy and molecular dynamics computer simulations

    NASA Astrophysics Data System (ADS)

    Kalinichev, A. G.; Faraone, A.; Udovic, T.; Kolesnikov, A. I.; de Souza, N. R.; Reinholdt, M. X.; Kirkpatrick, R.

    2008-12-01

    Layered double hydroxides (LDHs, anionic clays) represent excellent model systems for detailed molecular- level studies of the structure, dynamics, and energetics of nano-confined water in mineral interlayers and nano-pores, because LDH interlayers can have a well-defined structures and contain H2O molecules and a wide variety of anions in structurally well-defined positions and coordinations. [Ca2Al(OH)6]Cl·2H2O, also known as hydrocalumite or Friedel's salt, has a well- ordered Ca,Al distribution in the hydroxide layer and a very high degree of H2O,Cl ordering in the interlayer. It is also one of the only LDH phase for which a single crystal structure refinement is available. Thus, it is currently the best model compound for understanding the structure and dynamical behavior of interlayer and surface species in other, less-ordered, LDHs. We investigated the structural and dynamic behavior of water in the interlayers of hydrocalumite using inelastic (INS) and quasielastic (QENS) neutron scattering and molecular dynamics computer simulations. The comperehensive neutron scattering studies were performed for one fully hydrated and one dehydrated sample of hydrocalumite using several complementary instruments (HFBS, DCS and FANS at NCNR; HRMECS and QENS at IPNS) at temperatures above and below the previously discovered order-disorder interlayer phase transition. Together the experimental and molecular modeling results capture the important details of the dynamics of nano-confined water and the effects of the orientational ordering of H2O molecules above and below the phase transition. They provide otherwise unobtainable experimental information about the transformation of H2O librational and diffusional modes across the order-disorder phase transition and significantly add to our current understanding of the structure and dynamics of water in LDH phases based on the earlier NMR, IR, X-ray, and calorimetric measurements. The approach can now be extended to probe the

  14. Systematic Discovery of Molecular Probes Targeting Multiple Non-orthosteric and Spatially Distinct Sites in the Botulinum Neurotoxin Subtype A (BoNT/A)

    PubMed Central

    Dadgar, Saedeh; Floriano, Wely B.

    2015-01-01

    The development of molecular probes targeting proteins has traditionally relied on labeling compounds already known to bind to the protein of interest. These known ligands bind to orthosteric or allosteric sites in their target protein as a way to control their activity. Binding pockets other than known orthosteric or allosteric sites may exist that are large enough to accommodate a ligand without significantly disrupting protein activity. Such sites may provide opportunities to discriminate between subtypes or other closely related proteins, since they are under less evolutionary pressure to be conserved. The Protein Scanning with Virtual Ligand Screening (PSVLS) approach was previously used to identify a novel inhibitor and a fluorescent probe against the catalytic site of the botulinum neurotoxin subtype A (BoNT/A). PSVLS screens compound databases against multiple sites within a target protein, and the results for all the sites probed against BoNT/A, not only the catalytic site, are available online. Here, we analyze the PSVLS data for multiple sites in order to identify molecular probes with affinity for binding pockets other than the catalytic site of BoNT/A. BoNT/A is a large protein with a light (LC) and a heavy (HC) chain that can be assayed separately. We used scintillation proximity assay (SPA) to test experimentally 5 probe candidates predicted computationally to have affinity for different non-orthosteric binding regions within the HC and LC, and one compound predicted not to have affinity for either domain. The binding profiles obtained experimentally confirmed the targeting of multiple and spatially distinct pockets within BoNT/A. Moreover, inhibition assay results indicate that some of these probes do not significantly interfere with the catalytic activity of BoNT/A. PMID:25745992

  15. Cloning, sequencing, and use as a molecular probe of a gene encoding an aminoglycoside 6'-N-acetyltransferase of broad substrate profile.

    PubMed Central

    Terán, F J; Suárez, J E; Mendoza, M C

    1991-01-01

    A gene coding for an aminoglycoside 6'-N-acetyltransferase that was able to modify amikacin was cloned from a plasmid isolated from a clinical strain of Enterobacter cloacae. Sequencing of a 955-bp segment which mediates the modifying activity revealed a single open reading frame of 432 nucleotides that predicted a polypeptide of 144 amino acid residues with a molecular weight of 16,021. Putative ribosomal binding sites and -10 and -35 sequences were located at the 5' end of the gene. The size of the polypeptide was confirmed through minicell analysis of the expression products of plasmids containing the sequence. The use of the gene as a molecular probe revealed its specificity toward strains harboring genes coding for related enzymes. This probe is therefore useful for epidemiological studies. Images PMID:2069376

  16. Herschel/HIFI Legacy Survey of HF and H2O in the Galaxy: Probing Diffuse Molecular Cloud Chemistry

    NASA Astrophysics Data System (ADS)

    Sonnentrucker, Paule G.; Wolfire, Mark; Neufeld, David A.; Flagey, Nicolas; Gerin, Maryvonne; Goldsmith, Paul F.; Lis, Darek; Monje, Raquel

    2015-08-01

    We combine Herschel observations of a total of 13 sources to construct the most uniform survey of HF and H2O in our Galactic disk. Both molecules are detected in absorption along all sight lines. The high spectral resolution of the Heterodyne Instrument for the Far-Infrared (HIFI) allows us to compare the HF and H2O distributions in 47 diffuse cloud components sampling the disk. We find that the HF and H2O velocity distributions follow each other almost perfectly and we establish that HF and H2O probe the same gas-phase volume. Our observations corroborate theoretical predictions that HF is a sensitive tracer of H2 in diffuse clouds, down to molecular fractions of only a few percent. We use HF as a surrogate tracer of H2 to study the variations of H2O column density -relative to HF- within the Galactic disk diffuse gas. We find that the N(H2O)-to-N(HF) ratio shows a narrow distribution with a median value of 1.51. Our results therefore add weight to the previous suggestion that H2O can also be used as tracer of H2- within a factor of 2.5- in the diffuse ISM- in the absence of HF or CH observations. We show that the measured variation of about a factor 2.5 around the median is driven by true local variations in the H2O column density throughout the disk. The latter variability allows us to test our theoretical understanding of the chemistry of oxygen-bearing molecules in the diffuse gas. We will show that both gas-phase and grain-surface chemistry are required to reproduce our H2O observations. While most chemical pathways involve gas phase reactions alone in the diffuse ISM, we will demonstrate that our survey confirms that grain surface chemistry can play a significant role in the production of some molecular species, such as gas phase H2O, in this low-density environment.

  17. Probing the molecular dimensions of general anaesthetic target sites in tadpoles (Xenopus laevis) and model systems using cycloalcohols.

    PubMed Central

    Curry, S.; Moss, G. W.; Dickinson, R.; Lieb, W. R.; Franks, N. P.

    1991-01-01

    1. The series of cycloalcohols C6, C7, C8 and C10 have been used to probe the molecular dimensions of a variety of general anaesthetic target sites. 2. The general anaesthetic EC50 concentrations of the cycloalcohols were determined for tadpoles (Xenopus laevis). All of the cycloalcohols tested were found to be potent general anaesthetics (on average EC50/Csat = 0.03). 3. The effects of the cycloalcohols on highly purified luciferase enzymes from fireflies (Photinus pyralis) and bacteria (Vibrio harveyi) were also investigated. Both enzymes were inhibited competitively, with the cycloalcohols competing with firefly luciferin for binding to the firefly enzyme and with n-decanal for binding to the bacterial enzyme. 4. The binding site on the firefly enzyme could accommodate two molecules of cycloalcohols C6 and C7 but only a single molecule of the larger cycloalcohols (C8 and C10), implying a volume of the binding site of about 250 cm3 mol-1. In contrast, the binding site on the bacterial luciferase could bind only a single cycloalcohol molecule between C6 and C10. 5. While all of the cycloalcohols were potent inhibitors of the firefly luciferase enzyme (on average EC50/Csat = 0.015), they were very weak inhibitors of the bacterial luciferase enzyme (on average EC50/Csat = 0.12). Since both enzymes bind long-chain aliphatic n-alcohols tightly, the differing affinities of the cycloalcohols for the two enzymes is probably a consequence of geometrical factors. 6. The cycloalcohols produced very small effects on lipid bilayers. At EC50 concentrations which produce general anaesthesia, lipid bilayer phase transitions were shifted, on average, by only 0.43 degrees C.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:2043920

  18. A Herschel/HIFI Legacy Survey of HF and H2O in the Galaxy: Probing Diffuse Molecular Cloud Chemistry

    NASA Astrophysics Data System (ADS)

    Sonnentrucker, P.; Wolfire, M.; Neufeld, D. A.; Flagey, N.; Gerin, M.; Goldsmith, P.; Lis, D.; Monje, R.

    2015-06-01

    We combine Herschel observations for a total of 12 sources to construct the most uniform survey of HF and H2O in our Galactic disk. Both molecules are detected in absorption along all sight lines. The high spectral resolution of the Heterodyne Instrument for the Far-infrared (HIFI) allows us to compare the HF and H2O distributions in 47 diffuse cloud components sampling the disk. We find that the HF and H2O velocity distributions follow each other almost perfectly and establish that HF and H2O probe the same gas-phase volume. Our observations corroborate theoretical predictions that HF is a sensitive tracer of H2 in diffuse clouds, down to molecular fractions of only a few percent. Using HF to trace H2 in our sample, we find that the N(H2O)-to-N(HF) ratio shows a narrow distribution with a median value of 1.51. Our results further suggest that H2O might be used as a tracer of H2—within a factor of 2.5—in the diffuse interstellar medium (ISM). We show that the measured factor of ˜2.5 variation around the median is driven by true local variations in the H2O abundance relative to H2 throughout the disk. The latter variability allows us to test our theoretical understanding of the chemistry of oxygen-bearing molecules in the diffuse gas. We show that both gas-phase and grain-surface chemistry are required to reproduce our H2O observations. This survey thus confirms that grain surface reactions can play a significant role in the chemistry occurring in the diffuse ISM ({{n}H} ≤slant 1000 cm-3). Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.

  19. Characterization of sorbent properties of soil organic matter and carbonaceous geosorbents using n-alkanes and cycloalkanes as molecular probes

    SciTech Connect

    Satoshi Endo; Peter Grathwohl; Stefan B. Haderlein; Torsten C. Schmidt

    2009-01-15

    Nonspecific interactions and modes (i.e., adsorption vs absorption) of sorption by noncondensed, amorphous organic phases (here termed organic matter; OM) in soils and by rigid, aromatic, and condensed phases (termed carbonaceous geosorbents; CGs) were investigated using n-alkanes and cycloalkanes as molecular probes. Sorption isotherms of and cyclooctane from water for seven CGs (charcoal, lignite coke, activated carbon, graphite, partially oxidized graphite, diesel soot, bituminous coal), four sorbents with a predominance of OM (lignite, peat, two sapric soils), and two soils containing OM and high amounts of CGs were measured in batch systems. The peat and the sapric soils showed extensively linear sorption, while the CGs exhibited highly nonlinear and strong (K{sub oc} values being up to 105 times those for the OM-rich materials at low concentrations) sorption for the alkanes studied, showing that enhanced sorption by CGs can occur to completely apolar sorbates that do not undergo any specific interaction. The n-octane-to-cyclooctane sorption coefficient ratios for adsorption to CGs were {ge}1, being distinctly different from those for absorption to the OM-rich materials. The measured sorption isotherms and the CG compositions in the soils determined by quantitative petrography analysis suggest, however, that CGs occurring in soils may be far less effective sorbents than the reference CGs used in the sorption experiments at least for nonspecifically interacting sorbates, probably because of competitive sorption and/or pore blocking by natural OM. The presented approaches and results offer a basis for interpreting sorption data for other organic compounds, as nonspecific interactions and sorption modes are relevant for any compound. 47 refs., 4 figs., 2 tabs.

  20. Nanoscopic electrode molecular probes

    DOEpatents

    Krstic, Predrag S.; Meunier, Vincent

    2012-05-22

    The present invention relates to a method and apparatus for enhancing the electron transport property measurements of a molecule when the molecule is placed between chemically functionalized carbon-based nanoscopic electrodes to which a suitable voltage bias is applied. The invention includes selecting a dopant atom for the nanoscopic electrodes, the dopant atoms being chemically similar to atoms present in the molecule, and functionalizing the outer surface and terminations of the electrodes with the dopant atoms.

  1. Improving the visualization of fluorescently tagged nanoparticles and fluorophore-labeled molecular probes by treatment with CuSO(4) to quench autofluorescence in the rat inner ear.

    PubMed

    Zhang, Ya; Zhang, Weikai; Johnston, Alexander H; Newman, Tracey A; Pyykkö, Ilmari; Zou, Jing

    2010-10-01

    Fluorescent tags and fluorophore-conjugated molecular probes have been extensively employed in histological studies to demonstrate nanoparticle distribution in inner ear cell populations. However, autofluorescence that exists in the rodent cochleae disturbs visualization of the fluorescent tags and fluorophore labeling. In the present work, we aimed to improve the visualization of fluorescently tagged nanoparticles and fluorophore-labeled molecular probes by treatment with CuSO(4) to quench autofluorescence in the rat inner ear. The in vivo study was performed on eight- to nine-month-old rats using confocal laser scanning microscopy, and the in vitro study was carried out with DiI-tagged poly(ethylene glycol) and poly(capro-lactone) polymersomes and different fluorescent-labeling agents using a spectrofluorometer. The nanoparticles were intratympanically administered using either an osmotic pump or transtympanic injection. Abundant autofluorescence was detected in spiral ganglion cells (SGCs), stria marginal cells, spiral ligament fibrocytes (SL) and the subcuticular cytoplasm of inner hair cells (IHCs). Sparsely distributed faint autofluorescence was also visualized in outer hair cells (OHCs). The autofluorescence was eliminated by treatment with 1 mM CuSO(4) (in 0.01 M ammonium acetate buffer) for 70-90 min, while the fluorescent tag in the nanoparticle was absolutely preserved and the labeling fluorescence signals of the molecular probes were mostly retained. PMID:20659540

  2. Cystic Fibrosis Transmembrane Conductance Regulator: Using Differential Reactivity toward Channel-Permeant and Channel-Impermeant Thiol-Reactive Probes To Test a Molecular Model for the Pore†

    PubMed Central

    2009-01-01

    The sixth transmembrane segment (TM6) of the CFTR chloride channel has been intensively investigated. The effects of amino acid substitutions and chemical modification of engineered cysteines (cysteine scanning) on channel properties strongly suggest that TM6 is a key component of the anion-conducting pore, but previous cysteine-scanning studies of TM6 have produced conflicting results. Our aim was to resolve these conflicts by combining a screening strategy based on multiple, thiol-directed probes with molecular modeling of the pore. CFTR constructs were screened for reactivity toward both channel-permeant and channel-impermeant thiol-directed reagents, and patterns of reactivity in TM6 were mapped onto two new, molecular models of the CFTR pore: one based on homology modeling using Sav1866 as the template and a second derived from the first by molecular dynamics simulation. Comparison of the pattern of cysteine reactivity with model predictions suggests that nonreactive sites are those where the TM6 side chains are occluded by other TMs. Reactive sites, in contrast, are generally situated such that the respective amino acid side chains either project into the predicted pore or lie within a predicted extracellular loop. Sites where engineered cysteines react with both channel-permeant and channel-impermeant probes occupy the outermost extent of TM6 or the predicted TM5−6 loop. Sites where cysteine reactivity is limited to channel-permeant probes occupy more cytoplasmic locations. The results provide an initial validation of two, new molecular models for CFTR and suggest that molecular dynamics simulation will be a useful tool for unraveling the structural basis of anion conduction by CFTR. PMID:19754156

  3. Molecular diffusion in disordered interfacial media as probed by pulsed field gradients and nuclear magnetic relaxation dispersion

    NASA Astrophysics Data System (ADS)

    Levitz, P.; Korb, J.-P.; Bryant, R. G.

    1999-10-01

    We address the question of probing the fluid dynamics in disordered interfacial media by Pulsed field gradient (PFG) and Magnetic relaxation dispersion (MRD) techniques. We show that the PFG method is useful to separate the effects of morphology from the connectivity in disordered macroporous media. We propose simulations of molecular dynamics and spectral density functions, J(ω), in a reconstructed mesoporous medium for different limiting conditions at the pore surface. An algebraic form is found for J(ω) in presence of a surface diffusion and a local exploration of the pore network. A logarithmic form of J(ω) is found in presence of a pure surface diffusion. We present magnetic relaxation dispersion experiments (MRD) for water and acetone in calibrated mesoporous media to support the main results of our simulations and theories. Nous présentons les avantages respectifs des méthodes de gradients de champs pulsés (PFG) et de relaxation magnétique nucléaire en champs cyclés (MRD) pour sonder la dynamique moléculaire dans les milieux interfaciaux désordonnés. La méthode PFG est utile pour séparer la morphologie et la connectivité dans des milieux macroporeux. Des simulations de diffusion moléculaire et de densité spectrale J(ω) en milieux mésoporeux sont présentées dans différentes conditions limites aux interfaces des pores. Nous trouvons une forme de dispersion algébrique de J(ω) pour une diffusion de surface assistée d'une exploration locale du réseau de pores et une forme logarithmique dans le cas d'une simple diffusion de surface. Les résultats expérimentaux de la méthode MRD pour de l'eau et de l'acétone dans des milieux mésoporeux calibrés supportent les résultats principaux de nos simulations et théories.

  4. Molecular cytogenetic analysis of Inv Dup(15) chromosomes, using probes specific for the Pradar-Willi/Angelman syndrome region: Clinical implications

    SciTech Connect

    Leana-Cox, J. ); Jenkins, L. ); Palmer, C.G.; Plattner, R. ); Sheppard, L. ); Flejter, W.L. ); Zackowski, J. ); Tsien, F. ); Schwartz, S. )

    1994-05-01

    Twenty-seven cases of inverted duplications of chromosome 15 (inv dup[15]) were investigated by FISH with two DNA probes specific for the Prader-Willi syndrome/Angelman syndrome (PWS/AS) region on proximal 15q. Sixteen of the marker chromosomes displayed two copies of each probe, while in the remaining 11 markers no hybridization was observed. A significant association was found between the presence of this region and an abnormal phenotype (P<.01). This is the largest study to date of inv dup(15) chromosomes, that uses molecular cytogenetic methods and is the first to report a significant association between the presence of a specific chromosomal region in such markers and an abnormal phenotype. 30 refs., 1 fig., 4 tabs.

  5. Binding of hydroxyquinoline probes to human serum albumin: combining molecular modeling and Förster's resonance energy transfer spectroscopy to understand flexible ligand binding.

    PubMed

    Abou-Zied, Osama K; Al-Lawatia, Najla; Elstner, Marcus; Steinbrecher, Thomas B

    2013-01-31

    Human serum albumin (HSA) is the most abundant protein in blood plasma. It has high relevance for the lipid metabolism, and its ability to bind a large variety of natural and pharmaceutical compounds makes it a crucial determinant of drug pharmaco-kinetics and -dynamics. The drug binding properties of HSA can be characterized by spectroscopic analysis of bound probe molecules. We have recently characterized the subdomain IIA binding site of HSA using three hydroxyquinoline derivatives. In this work, we extend our study by combining data from energy transfer experiments, ligand docking, and long molecular dynamics (MD) simulations. Multiple possible binding locations are found within the subdomain IIA site, and their solvent accessibility and interactions with ligands are analyzed in detail. Binding pockets appear well hydrated during simulations, with ligands in direct contact to water molecules at all times. Binding free energies in good agreement to experiment are calculated. The HSA apoprotein is found to exhibit significant conformational flexibility over 250 ns of simulation time, but individual domains remain structurally stable. Two rotamers of Trp214 were observed on a time scale longer than 50 ns in the MD simulations, supporting the experimental observation of two fluorescence lifetime components. The flexible protein structure and heterogeneous nature of its binding sites explain the ability of HSA to act as a versatile molecular transporter. The combination of experimental and computational molecular distance information allows the conclusion that hydroxyquinoline probes bind in a binding mode similar to the anticoagulant drug warfarin. PMID:23297700

  6. Characterization of subdomain IIA binding site of human serum albumin in its native, unfolded, and refolded states using small molecular probes.

    PubMed

    Abou-Zied, Osama K; Al-Shihi, Othman I K

    2008-08-13

    Subdomain IIA binding site of human serum albumin (HSA) was characterized by examining the change in HSA fluorescence in the native, unfolded, and refolded states. The study was carried out in the absence and presence of small molecular probes using steady-state and time-resolved fluorescence measurements. 2-Pyridone, 3-pyridone, and 4-pyridone bear similar molecular structures to those found in many drugs and are used here as probes. They are found to specifically bind in subdomain IIA and cause a reduction in the fluorescence intensity and lifetime of the Trp-214 residue in native HSA which is located in the same subdomain. The efficiency of energy transfer from Trp-214 fluorescence to the probes was found to depend on the degree of the spectral overlap between the donor's fluorescence and the acceptor's absorption. After probe binding in subdomain IIA, the distance between the donor and acceptor was calculated using Forster theory. The calculated quenching rate constants and binding constants were also shown to depend on the degree of spectral overlap. The results point to a static quenching mechanism operating in the complexes. Denaturation of HSA in the presence of guanidine hydrochloride (GdnHCl) starts at [GdnHCl] > 1.0 M and is complete at [GdnHCl] > or = 6.0 M. Upon unfolding, two fluorescence peaks were observed. One peak was assigned to the fluorescence of Trp-214 in a polar environment, and the other peak was assigned to tyrosine fluorescence. A reduction of the fluorescence intensity of the two peaks upon binding of the probes to the denatured HSA indicates that Tyr-263 in subdomain IIA is one of the tyrosine residues responsible for the second fluorescence peak. The results were confirmed by measuring the fluorescence spectra and lifetimes of denatured HSA at different excitation wavelengths, and of L-tryptophan and L-tyrosine free in buffer. The measured lifetimes of denatured HSA are typical of tryptophan in a polar environment and are slightly

  7. [Investigation on the spectral characteristics and existing state of a substituted 3H-indole molecular probe in triton X-100 reverse micelle].

    PubMed

    Luo, Jun-jian; Li, Jian; Shen, Xing-hai; Gao, Hong-cheng

    2005-02-01

    The interactions between a fluorescent molecular probe, i. e., [2-(p-hexylamino) phenyl-3, 3-dimethyl-5-ethoxycarbonyl-3H-indole] methyldioctadecylammonium iodide (A) and Triton X-100/heptane/hexanol/water reverse micelle have been investigated by spectroscopy. Micropolarity of the environment, fluorescence anisotropy parameter and the pH effect of A in Triton X-100 reverse micelle were determined. Furthermore, the state of water in reverse micellar systems was studied by FTIR. According to the above experimental results, some information on the structure of Triton X-100 reverse micelle was obtained and the probable site of A in this system was discussed. PMID:15852849

  8. Molecular imaging of human tumor cells that naturally overexpress type 2 cannabinoid receptors using a quinolone-based near-infrared fluorescent probe

    NASA Astrophysics Data System (ADS)

    Wu, Zhiyuan; Shao, Pin; Zhang, Shaojuan; Ling, Xiaoxi; Bai, Mingfeng

    2014-07-01

    Cannabinoid CB2 receptors (CB2R) hold promise as therapeutic targets for treating diverse diseases, such as cancers, neurodegenerative diseases, pain, inflammation, osteoporosis, psychiatric disorders, addiction, and immune disorders. However, the fundamental role of CBR in the regulation of diseases remains unclear, largely due to a lack of reliable imaging tools for the receptors. The goal of this study was to develop a CBR-targeted molecular imaging probe and evaluate the specificity of the probe using human tumor cells that naturally overexpress CBR. To synthesize the CBR-targeted probe (NIR760-Q), a conjugable CBR ligand based on the quinolone structure was first prepared, followed by bioconjugation with a near-infrared (NIR) fluorescent dye, NIR760. In vitro fluorescence imaging and competitive binding studies showed higher uptake of NIR760-Q than free NIR760 dye in Jurkat human acute T-lymphoblastic leukemia cells. In addition, the high uptake of NIR760-Q was significantly inhibited by the blocking agent, 4-quinolone-3-carboxamide, indicating specific binding of NIR760-Q to the target receptors. These results indicate that the NIR760-Q has potential in diagnostic imaging of CBR positive cancers and elucidating the role of CBR in the regulation of disease progression.

  9. Binding hotspots on K-Ras: consensus ligand binding sites and other reactive regions from probe-based molecular dynamics analysis

    PubMed Central

    Prakash, Priyanka; Hancock, John F.; Gorfe, Alemayehu A.

    2015-01-01

    We have used probe-based molecular dynamics (pMD) simulations to search for interaction hotspots on the surface of the therapeutically highly relevant oncogenic K-Ras G12D. Combining the probe-based query with an ensemble-based pocket identification scheme and an analysis of existing Ras-ligand complexes, we show that (i) pMD is a robust and cost-effective strategy for binding site identification, (ii) all four of the previously reported ligand binding sites are suitable for structure-based ligand design, and (iii) in some cases probe binding and expanded sampling of configurational space enable pocket expansion and increase the likelihood of site identification. Furthermore, by comparing the distribution of hotspots in non-pocket-like regions with known protein- and membrane-interacting interfaces, we propose that pMD has the potential to predict surface patches responsible for protein-biomolecule interactions. These observations have important implications for future drug design efforts and will facilitate the search for potential interfaces responsible for the proposed transient oligomerization or interaction of Ras with other biomolecules in the cellular milieu. PMID:25740554

  10. The study of a curcumin-resembling molecular probe for the pH-responsive fluorometric assay and application in cell imaging.

    PubMed

    Xiang, Decheng; Meng, Qinghua; Liu, Heng; Lan, Minbo; Wei, Gang

    2016-01-01

    A molecular probe of DibOH (2,6-bis(4-hydroxybenzylidene)cyclohexanone) designed as the ameliorant to the curcumin was prepared in which one enol unit was removed to avoid the intramolecular hydrogen bond and thus more rigidity and better coplanarity were achieved. Deprotonation of the phenolic hydroxyl group led to the negative charge and the intramolecular charge transfer (ICT) functioned accordingly. The DibOH probe in basic conditions exhibited the absorption peak at 468 nm, which indicated a red shift of 183 nm relative to that in acid conditions and was visible as a brown color to naked eyes. The ratio of fluorescence intensity at 612 nm to that at 520 nm (I612/I520) was calculated and a clear correlation with the pH value was obtained. The density functional theory (DFT) was performed on theoretical investigation of the acidic and basic forms of DibOH. The DibOH probe was evaluated in fluorescent imaging of human breast cancer cells (MCF-7) wherein the heterogeneous distribution of the intracellular pH microenvironment was observed. PMID:26695339

  11. Ratiometric Molecular Probes Based on Dual Emission of a Blue Fluorescent Coumarin and a Red Phosphorescent Cationic Iridium(III) Complex for Intracellular Oxygen Sensing

    PubMed Central

    Yoshihara, Toshitada; Murayama, Saori; Tobita, Seiji

    2015-01-01

    Ratiometric molecular probes RP1 and RP2 consisting of a blue fluorescent coumarin and a red phosphorescent cationic iridium complex connected by a tetra- or octaproline linker, respectively, were designed and synthesized for sensing oxygen levels in living cells. These probes exhibited dual emission with good spectral separation in acetonitrile. The photorelaxation processes, including intramolecular energy transfer, were revealed by emission quantum yield and lifetime measurements. The ratios (RI=(Ip/If)) between the phosphorescence (Ip) and fluorescence (If) intensities showed excellent oxygen responses; the ratio of RI under degassed and aerated conditions (RI0/RI) was 20.3 and 19.6 for RP1 and RP2. The introduction of the cationic Ir (III) complex improved the cellular uptake efficiency compared to that of a neutral analogue with a tetraproline linker. The emission spectra of the ratiometric probes internalized into living HeLa or MCF-7 cells could be obtained using a conventional microplate reader. The complex RP2 with an octaproline linker provided ratios comparable to the ratiometric measurements obtained using a microplate reader: the ratio of the RI value of RP2 under hypoxia (2.5% O2) to that under normoxia (21% O2) was 1.5 and 1.7 for HeLa and MCF-7 cells, respectively. Thus, the intracellular oxygen levels of MCF-7 cells could be imaged by ratiometric emission measurements using the complex RP2. PMID:26066988

  12. Luminescence of W(CO){sub 4}(4-Me-phen) in photosensitive thin films: A molecular probe of acrylate polymerization

    SciTech Connect

    Rawlins, K.A.; Lees, A.J.; Fuerniss, S.J.; Papathomas, K.I.

    1996-07-01

    The complex W(CO){sub 4}(4-Me-phen) (4-Me-phen = 4-methyl-1,10-phenanthroline) has been determined to be luminescent and act as a spectroscopic probe in UV-curable trimethylolpropane triacrylate/poly(methyl methacrylate) thin films. Electronic absorption and luminescence characteristics have been measured for this complex in room-temperature solutions and low-temperature (80 K) glasses and in 10 mil thin films of the unexposed and exposed acrylate resins. In each environment dual luminescence bands were observed which are attributed to triplet-centered metal-to-ligand charge-transfer ({sup 3}MLCT) excited states. For the unexposed photoresist these transitions were recorded at 520 and 750 nm and in the exposed material these are moved to 525 and 715 nm, respectively. The lowest energy emission band undergoes a substantial blue-shift and intensified greatly on polymerization; this phenomenon provides a useful molecular probe of the acrylate cross-linking process. These changes in emission characteristics are associated with a rigidochromic effect imparted on the lowest lying and solvent sensitive b{sub 2} {yields} b{sub 2}({pi}*) {sup 3}MLCT electronically excited state in this complex. The complex W(CO){sub 5}(4-CN-py) (4-CN-py = 4-cyanopyridine) was also investigated as a spectroscopic probe in the acrylate system but appears unsuitable for this purpose as it was found to degrade significantly in the resin. 20 refs., 6 figs.

  13. Molecular cytogenetic analysis of the crucian carp, Carassius carassius (Linnaeus, 1758) (Teleostei, Cyprinidae), using chromosome staining and fluorescence in situ hybridisation with rDNA probes

    PubMed Central

    Spoz, Aneta; Boron, Alicja; Porycka, Katarzyna; Karolewska, Monika; Ito, Daisuke; Abe, Syuiti; Kirtiklis, Lech; Juchno, Dorota

    2014-01-01

    Abstract The crucian carp Carassius carassius (Linnaeus, 1758) is a species with restricted and decreasing distribution in Europe. Six males and six females of the species from the Baltic Sea basin in Poland were examined to show sequentially CMA3/AgNO3 staining pattern, DAPI staining, and, for the first time in literature, molecular cytogenetic analysis using double-colour fluorescence in situ hybridisation (FISH) with 28S and 5S rDNA probes. The karyotype consisted of 20 m, 36 sm and 44 sta chromosomes, NF=156. The AgNO3 stained NORs were most frequently located terminally in the short arms of two sm and two sta elements, and CMA3-positive sites were also observed suggesting abundant GC-rich repetitive DNA in the regions. Other CMA3-positive sites in the short arms of six to ten sm and sta chromosomes were detected. The results based on 28S rDNA FISH confirmed the location of rDNA sites. DAPI-negative staining of NORs suggested the scarcity of AT-rich DNA in the regions. FISH with 5S rDNA probe revealed 8–14 loci (ten and 12 in respectively 49 and 29% of metaphases). They were located in two sm and eight to ten sta chromosomes and six of them were larger than others. Simultaneously, mapping of the two rDNA families on the chromosomes of C. carassius revealed that both 28S and 5S rDNA probes were located in different chromosomes. Molecular cytogenetic data of C. carassius presented here for the first time give an important insight into the structure of chromosomes of this polyploid and declining species and may be useful in its systematics. PMID:25349674

  14. Novel super-resolution capable mitochondrial probe, MitoRed AIE, enables assessment of real-time molecular mitochondrial dynamics

    PubMed Central

    Lo, Camden Yeung-Wah; Chen, Sijie; Creed, Sarah Jayne; Kang, Miaomiao; Zhao, Na; Tang, Ben Zhong; Elgass, Kirstin Diana

    2016-01-01

    Mitochondria and mitochondrial dynamics play vital roles in health and disease. With the intricate nanometer-scale structure and rapid dynamics of mitochondria, super-resolution microscopy techniques possess great un-tapped potential to significantly contribute to understanding mitochondrial biology and kinetics. Here we present a novel mitochondrial probe (MitoRed AIE) suitable for live mitochondrial dynamics imaging and single particle tracking (SPT), together with a multi-dimensional data analysis approach to assess local mitochondrial (membrane) fluidity. The MitoRed AIE probe localizes primarily to mitochondrial membranes, with 95 ms fluorophore on-time delivering 106 photons/ms, characteristics which we exploit to demonstrate live cell 100 fps 3D time-lapse tracking of mitochondria. Combining our experimental and analytical approaches, we uncover mitochondrial dynamics at unprecedented time scales. This approach opens up a new regime into high spatio-temporal resolution dynamics in many areas of mitochondrial biology. PMID:27492961

  15. Molecular epidemiology of Vibrio cholerae O1 isolated in Nepal by southern hybridization with a cholera toxin gene probe.

    PubMed

    Yamamoto, K; Shrestha, J; Iida, T; Yoh, M; Honda, T

    1995-06-01

    A cholera epidemic broke out in 1992 due to Vibrio cholerae O1 biotype El Tor in the eastern and southern belt of Nepal mainly among the Bhutanese refugees. Restriction fragment profiles (RFP) of DNA fragments of V. cholerae O1 isolates hybridized with an enzyme-labelled oligonucleotide probe for cholera toxin gene (ctx) by Southern Hybridization were compared. The probe hybridized with the 13- and 8-kb fragments of PstI-digested total DNA in all isolates observed in the epidemic. This RFP in the Nepalese strain was not observed in the strains isolated during other epidemics but was observed in the strains isolated from the exported marine products from Taiwan and Thailand. PMID:7594311

  16. Novel super-resolution capable mitochondrial probe, MitoRed AIE, enables assessment of real-time molecular mitochondrial dynamics.

    PubMed

    Lo, Camden Yeung-Wah; Chen, Sijie; Creed, Sarah Jayne; Kang, Miaomiao; Zhao, Na; Tang, Ben Zhong; Elgass, Kirstin Diana

    2016-01-01

    Mitochondria and mitochondrial dynamics play vital roles in health and disease. With the intricate nanometer-scale structure and rapid dynamics of mitochondria, super-resolution microscopy techniques possess great un-tapped potential to significantly contribute to understanding mitochondrial biology and kinetics. Here we present a novel mitochondrial probe (MitoRed AIE) suitable for live mitochondrial dynamics imaging and single particle tracking (SPT), together with a multi-dimensional data analysis approach to assess local mitochondrial (membrane) fluidity. The MitoRed AIE probe localizes primarily to mitochondrial membranes, with 95 ms fluorophore on-time delivering 106 photons/ms, characteristics which we exploit to demonstrate live cell 100 fps 3D time-lapse tracking of mitochondria. Combining our experimental and analytical approaches, we uncover mitochondrial dynamics at unprecedented time scales. This approach opens up a new regime into high spatio-temporal resolution dynamics in many areas of mitochondrial biology. PMID:27492961

  17. A New Topological Index for Molecular Probes Used in Inverse Gas Chromatography for the Surface Nanorugosity Evaluation

    PubMed

    Brendlé; Papirer

    1997-10-01

    Inverse gas chromatography is currently used for the determination of the surface properties of divided solids by probing the surface with alkanes or polar molecules of known properties. This paper suggests the use of a new topological index for the description of the probe's (alkanes) geometry and hence of their accessibility to the solid's surface. The proposed index (chiT) derives from the well known Wiener index. The application of chiT for the determination of the dispersive component of the surface energy of pyrogenic silica, but also for the evaluation of the geometric heterogeneity of lamellar silica, is described. Further, goethite and zirconia samples were submitted to similar analysis. Copyright 1997 Academic Press. Copyright 1997Academic Press PMID:9367599

  18. Optical probes for molecular-guided surgery: Using photomedicine to prevent recurrence in the surgical bed (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Spring, Bryan Q.; Sears, R. Bryan; Zheng, Lei Z.; Mai, Zhiming; Watanabe, Reika; Villa, Elizabeth; Hasan, Tayyaba

    2016-03-01

    Residual tumor deposits missed by conventional treatments frequently seed local and distal recurrence utilizing a network of molecular signaling mechanisms. Beyond providing contrast for molecular-guided surgery, this talk will highlight new concepts in phototherapy to address residual cancer cells in danger zones of recurrence, including selective treatment of microscopic disease using molecular-targeted, activatable immunoconjugates, and photo-initiated release of multikinase inhibitors that suppress multiple modes of tumor escape using optically active nanoparticles. These new approaches support an expanded role for the use of light in fluorescence-guided surgery—for phototherapy and for focused drug release to maximize tumor debulking with suppression of disease recurrence.

  19. Molecular imaging of biothiols and in vitro diagnostics based on an organic chromophore bearing a terbium hybrid probe.

    PubMed

    Zhou, Zhan; Wang, Qianming; Zhang, Cheng Cheng; Gao, Jinwei

    2016-04-25

    In this research, a novel terbium-based luminescent hybrid inorganic/organic probe was designed and synthesized. Mesoporous silica nanospheres dispersed in water were used as the appropriate host for the covalently linked lanthanide-containing organic structures. The lanthanide structure was linked to a sulfonate ester unit, which, in the presence of biothiols, was cleaved to result in terbium emission. The hybrid probe exhibited the capabilities of quantitative determination and detection limits for biothiols were presented (36.8 nM for Cys, 32.5 nM for GSH, and 34.7 nM for Hcy). Evaluation of luminescence changes in cell culture demonstrated that this smart probe is cell membrane permeable and selectively lights up in the presence of cysteine and glutathione in human embryonic kidney cells and human lung adenocarcinoma cells. This variation in the presence of biothiols can be controlled by the treatment with N-methylmaleimide. The narrow line-like bands and long-lived excited states of this terbium luminescent sensor allows the discrimination of scattering signals and interfering fluorescence derived from biological tissues. PMID:27041001

  20. Probing the molecular weight distributions of non-boiling petroleum fractions by Ag+ electrospray ionization mass spectrometry.

    PubMed

    Roussis, Stilianos G; Proulx, Richard

    2004-01-01

    This work explores the possibility of Ag+ electrospray ionization mass spectrometry (ESI-MS) to determine the molecular weight distributions of non-boiling petroleum fractions. Information about the molecular weight distributions is needed for fundamental studies on the nature of heavy crude oils and bitumens and for the development of novel recovery and processing methods. The method does not depend on thermal processes for the introduction of the fractions into the gas phase of the mass spectrometer, which is a considerable advantage over most other ionization methods. The Ag+ electrospray mass spectra of the fractions analyzed by using a toluene/methanol/cyclohexane (60:28:12%) solvent system display bimodal distributions in the ranges m/z approximately 300 to approximately 3000 and m/z 3000 to approximately 20,000. The abundances of the high molecular weight peak distributions can be reduced by in-source collisional activation experiments. Comparisons with the results obtained for model heteroatom-containing compounds (molecular weight < 600 Da) and high molecular weight polystyrene standards (up to one million Da) indicate that the majority of the structures in the saturate, naphthenoaromatic and polar aromatic fractions, and a significant portion of the asphaltenes, are small molecules. However, a considerable portion of the asphaltenes and some portion of the other fractions contain high molecular weight structures bound by covalent or strong non-covalent bonds. The results obtained by the Ag+ ESI method in this study for the saturate, aromatic, and polar fractions in a bitumen are in qualitative agreement with published molecular weight average results obtained for Cold Lake bitumen fractions analyzed by conventional gel permeation chromatography and field desorption mass spectrometry. Further work is needed to study the nature of the bonds and the interactions of the molecules in the asphaltene fractions by Ag+ ESI-MS. PMID:15282776

  1. The Evolutionary Connection Bewtween z~2-3 Submillimeter Galaxies and AGN as Probed by Molecular Gas Excitation

    NASA Astrophysics Data System (ADS)

    Sharon, Chelsea E.; Riechers, Dominik A.; Carilli, Chris Luke; Hodge, Jacqueline; Walter, Fabian

    2016-01-01

    Theoretical work has suggested that active galactic nuclei (AGN) play an important role in quenching star formation in massive galaxies. Direct evidence for AGN affecting the molecular ISM has so far been limited to detections of molecular outflows in low-redshift systems and extreme excitation regions which represent a tiny fraction of the total gas. Indirect evidence for AGN's impact on their host galaxies' cold gas phase may be provided by measurements of the gas excitation and dynamics. At z~2-3, the peak epoch of star formation and AGN activity, previous observations of the CO(1-0) line revealed that submillimeter galaxies (SMGs) have multi-phase molecular gas, including substantial reservoirs of cold-phase gas. However, the entirety of the molecular gas in AGN-host galaxies appears highly excited, potentially supporting an evolutionary connection between these two populations. I will present a new VLA sample that nearly doubles the number of CO(1-0) detections in z~2-3 SMGs and AGN-host galaxies that allows us to better compare the cold gas properties of these systems and further investigate evidence for the effects of AGN on the star-forming molecular gas.

  2. Genetic Variability in Probe Binding Regions Explains False Negative Results of a Molecular Assay for the Detection of Dengue Virus.

    PubMed

    Koo, Carmen; Kaur, Simrandeep; Teh, Zhi-Yong; Xu, Helen; Nasir, Amna; Lai, Yee-Ling; Khan, Erum; Ng, Lee-Ching; Hapuarachchi, Hapuarachchige C

    2016-07-01

    Dengue fever is currently the most prevalent disease caused by mosquito-borne flaviviruses. Despite being potentially fatal, there are no specific antiviral therapies for Dengue virus (DENV) infections. Therefore, early, accurate, and rapid diagnosis plays an important role in proper patient management. In this study, we evaluated the performance of a probe-based real-time RT-PCR (rRT-PCR) assay against that of a conventional RT-PCR assay in three sample cohorts from Pakistan (n = 94) and Singapore (first cohort; n = 559, second cohort; n = 123). The Pakistan cohort also included a comparison with virus isolation. The rRT-PCR assay showed relatively lower overall sensitivity (20.2%) in the Pakistan cohort than that in first (90.8%) and second (80.5%) Singapore cohorts. Surprisingly, the overall sensitivity of rRT-PCR assay was lower compared with the virus isolation (26.6%) among Pakistan samples, indicating a high percentage (79.8%) of false negatives due to rRT-PCR assay. The analysis of sequences of failed and successful DENV isolates indicated mismatches in probe binding regions as the likely cause of rRT-PCR assay failure. Our observations testify the importance of utilizing a combination of methods for dengue diagnostics and surveillance. We emphasize that a thorough understanding of the genetic composition of local DENV populations as well as regular monitoring of the performance and reviewing of probe/primer sequences are essential to maintain a consistently high diagnostic accuracy of PCR-based assays. PMID:27172387

  3. Classical Wolf-Hirschhorn Syndrome confirmed molecularly despite normal results using commercially available probes: Redefinition of critical region

    SciTech Connect

    Zackai, E.H.; McDonald-McGinn, D.M.; Spinner, N.

    1994-09-01

    Wolf-Hirschhorn Syndrome, WHS, (4p-) is a clinically recognized entity where the deletion ranges from one half of the short arm of 4p to being subtle and cytogenetically undetectable. Because such variations do not result in significant differences in the WMS phenotype it has been suggested that them is a critical region involved in the distal portion of chromosome 4, within 4p16.3. This has been recently localized to a 2.5 Mb segment 100-300 kb from the telomere. A cosmid probe, pC847.351, that maps to distal 4p16.3 (locus D4F26) is commercially available for diagnostic use. We present a child with classical feature of Wolf-Hirschhorn Syndrome whose chromosome analyses, including high resolution banding, looking specifically at the 4p region, were normal, and in whom FISH using the commercially available cosmid probe for the 4p16.3 region did not demonstrate a deletion. Insistence on the clinician`s part that the child`s features were classic for WHS prompted further investigation. Four additional cosmid clones distal to the HD gene were tested by FISH on metaphase chromosomes from the proband. Cosmids representing the loci D4S95 and D4S43, which are {approximately}3.5 and 2.5 Mb, Respectively, proximal to D4F26 were present. However, cosmids for the loci D4S98 and FGFR3, which are within 100 kb of each other and {approximately}300 kb distal to D4S43 were deleted. This deletion is the smallest reported to date in a patient with typical WHS. Previous studies of patients both lacking the WHS phenotype and deleted using cosmid probe pC847.351 have suggested that the most distal region (150 kb) of 4p16.3 is not part of the WHS critical region. This is confirmed by our study. Estabrooks` report, together with our case, suggests redefinition of the WHS critical region proximal to D4F26 and distal to D4S43. We caution against ruling out WHS with the above probe since there may be other cases where the most distal region is intact.

  4. The accumulation mechanism of the hypoxia imaging probe “FMISO” by imaging mass spectrometry: possible involvement of low-molecular metabolites

    PubMed Central

    Masaki, Yukiko; Shimizu, Yoichi; Yoshioka, Takeshi; Tanaka, Yukari; Nishijima, Ken-ichi; Zhao, Songji; Higashino, Kenichi; Sakamoto, Shingo; Numata, Yoshito; Yamaguchi, Yoshitaka; Tamaki, Nagara; Kuge, Yuji

    2015-01-01

    18F-fluoromisonidazole (FMISO) has been widely used as a hypoxia imaging probe for diagnostic positron emission tomography (PET). FMISO is believed to accumulate in hypoxic cells via covalent binding with macromolecules after reduction of its nitro group. However, its detailed accumulation mechanism remains unknown. Therefore, we investigated the chemical forms of FMISO and their distributions in tumours using imaging mass spectrometry (IMS), which visualises spatial distribution of chemical compositions based on molecular masses in tissue sections. Our radiochemical analysis revealed that most of the radioactivity in tumours existed as low-molecular-weight compounds with unknown chemical formulas, unlike observations made with conventional views, suggesting that the radioactivity distribution primarily reflected that of these unknown substances. The IMS analysis indicated that FMISO and its reductive metabolites were nonspecifically distributed in the tumour in patterns not corresponding to the radioactivity distribution. Our IMS search found an unknown low-molecular-weight metabolite whose distribution pattern corresponded to that of both the radioactivity and the hypoxia marker pimonidazole. This metabolite was identified as the glutathione conjugate of amino-FMISO. We showed that the glutathione conjugate of amino-FMISO is involved in FMISO accumulation in hypoxic tumour tissues, in addition to the conventional mechanism of FMISO covalent binding to macromolecules. PMID:26582591

  5. Application of the Steady-State Variable Nutation Angle Method for Faster Determinations of Long T1s—An Approach Useful for the Design of Hyperpolarized MR Molecular Probes

    PubMed Central

    Jupin, Marc; Gamliel, Ayelet; Hovav, Yonatan; Sosna, Jacob; Gomori, J Moshe; Katz-Brull, Rachel

    2015-01-01

    In the dissolution-dynamic nuclear polarization technique, molecular probes with long T1s are preferred. 13C nuclei of small molecules with no directly bonded protons or sp3 13C nuclei with proton positions substituted by deuterons may fulfill this requirement. The T1 determination of such new molecular probes is crucial for the success of the hyperpolarized observation. Although the inversion-recovery approach remained by and large the standard for T1 measurements, we show here that the steady-state variable nutation angle approach is faster and may be better suited for the determination of relatively long T1s in thermal equilibrium. Specifically, the T1 of a new molecular probe, [uniformly labeled (UL)-13C6, UL-2H8]2-deoxy-d-glucose, is determined here and compared to that of [UL-13C6, UL-2H7]d-glucose. PMID:26560856

  6. Molecular Imaging of Labile Iron(II) Pools in Living Cells with a Turn-On Fluorescent Probe

    PubMed Central

    Au-Yeung, Ho Yu; Chan, Jefferson; Chantarojsiri, Teera; Chang, Christopher J.

    2013-01-01

    Iron is an essential metal for living organisms, but misregulation of its homeostasis at the cellular level can trigger detrimental oxidative and/or nitrosative stress and damage events. Motivated to help study the physiological and pathological consequences of biological iron regulation, we now report a reaction-based strategy for monitoring labile Fe2+ pools in aqueous solution and in living cells. Iron Probe 1 (IP1) exploits a bioinspired, iron-mediated oxidative C–O bond cleavage reaction to achieve a selective turn-on response to Fe2+ over a range of cellular metal ions in their bioavailable forms. We show that this first-generation chemical tool for fluorescence Fe2+ detection can visualize changes in exchangeable iron stores in living cells upon iron supplementation or depletion, including labile iron pools at endogenous, basal levels. Moreover, IP1 can be used to identify reversible expansion of labile iron pools by stimulation with vitamin C or the iron regulatory hormone hepcidin, providing a starting point for further investigations of iron signaling and stress events in living systems as well as future probe development. PMID:24063668

  7. Phenotyping hepatocellular metabolism using uniformly labeled carbon-13 molecular probes and LC-HRMS stable isotope tracing.

    PubMed

    Meissen, John K; Pirman, David A; Wan, Min; Miller, Emily; Jatkar, Aditi; Miller, Russell; Steenwyk, Rick C; Blatnik, Matthew

    2016-09-01

    Metabolite stable isotope tracing is a powerful bioanalytical strategy that has the potential to unravel phenotypic markers of early pharmaceutical efficacy by monitoring enzymatic incorporation of carbon-13 atoms into targeted pathways over time. The practice of probing biological systems with carbon-13 labeled molecules using broad MS-based screens has been utilized for many years in academic laboratories but has had limited application in the pharmaceutical R&D environment. The goal of this work was to establish a LCMS analytical workflow that was capable of monitoring carbon-13 isotope changes in glycolysis, the TCA and urea cycles, and non-essential amino acid metabolism. This work applies a standardized protein precipitation with 80% cold methanol and two distinct reverse-phase ion-pair liquid chromatography methods coupled to either a positive- or negative-ion mode high-resolution accurate mass spectrometry screening method. The data herein combines thousands of single-point peak integrations into a novel metabolite network map as a visualization aid to probe and monitor stable isotope incorporation in murine hepatocytes using uniformly labeled (13)C6 glucose, (13)C3 lactate, and (13)C5 glutamine. This work also demonstrates that nitrogen metabolism may have a large influence on the TCA cycle and gluconeogenic carbon fluxes in hepatocyte cell culture. PMID:27343766

  8. Probing the Sequence of Conformationally-Induced Polarity Changes in the Molecular Chaperonin GroEL with Fluorescence Spectroscopy

    PubMed Central

    Kim, So Yeon; Semyonov, Alexander N.; Twieg, Robert J.; Horwich, Arthur L.; Frydman, Judith; Moerner, W. E.

    2006-01-01

    Hydrophobic interactions play a major role in binding non-native substrate proteins in the central cavity of the bacterial chaperonin GroEL. The sequence of local conformational changes by which GroEL and its cofactor GroES assist protein folding can be explored using the polarity-sensitive fluorescence probe Nile Red. A specific single-cysteine mutant of GroEL (Cys261), whose cysteine is located inside the central cavity at the apical region of the protein, was covalently labeled with synthetically prepared Nile Red maleimide (NR). Bulk fluorescence spectra of Cys261-NR were measured to examine the effects of binding of the stringent substrate, malate dehydrogenase (MDH), GroES, and nucleotide on the local environment of the probe. After binding denatured substrate, the fluorescence intensity increased by 32±7%, suggesting enhanced hydrophobicity at the position of the label. On the other hand, in the presence of ATP, the fluorescence intensity decreased by 13±3%, implying increased local polarity. In order to explore the sequence of local polarity changes, substrate, GroES, and various nucleotides were added in different orders; the resulting changes in emission intensity provide insight into the sequence of conformational changes occurring during GroEL-mediated protein folding. PMID:16375456

  9. A curcumin-based molecular probe for near-infrared fluorescence imaging of tau fibrils in Alzheimer's disease.

    PubMed

    Park, Kwang-Su; Seo, Yujin; Kim, Mi Kyoung; Kim, Kyungdo; Kim, Yun Kyung; Choo, Hyunah; Chong, Youhoon

    2015-12-14

    In recent years, there has been growing interest in the near-infrared (NIR) fluorescence imaging of tau fibrils for the early diagnosis of Alzheimer's disease (AD). In order to develop a curcumin-based NIR fluorescent probe for tau fibrils, structural modification of the curcumin scaffold was attempted by combining the following rationales: the curcumin derivative should preserve its binding affinity to tau fibrils, and, upon binding to tau fibrils, the probe should show favorable fluorescence properties. To meet these requirements, we designed a novel curcumin scaffold with various aromatic substituents. Among the series, the curcumin derivative with a (4-dimethylamino-2,6-dimethoxy)phenyl moiety showed a significant change in its fluorescence properties (22.9-fold increase in quantum yield; Kd, 0.77 μM; λem, 620 nm; Φ, 0.32) after binding to tau fibrils. In addition, fluorescence imaging of tau-green fluorescent protein-transfected SHSY-5Y cells with confirmed that detected tau fibrils in live cells. PMID:26488450

  10. Exploring a 2-Naphthoic Acid Template for the Structure-Based Design of P2Y14 Receptor Antagonist Molecular Probes

    PubMed Central

    2015-01-01

    The P2Y14 receptor (P2Y14R), one of eight P2Y G protein-coupled receptors (GPCR), is involved in inflammatory, endocrine, and hypoxic processes and is an attractive pharmaceutical target. The goal of this research is to develop high-affinity P2Y14R fluorescent probes based on the potent and highly selective antagonist 4-(4-(piperidin-4-yl)-phenyl)-7-(4-(trifluoromethyl)-phenyl)-2-naphthoic acid (6, PPTN). A model of hP2Y14R based on recent hP2Y12R X-ray structures together with simulated antagonist docking suggested that the piperidine ring is suitable for fluorophore conjugation while preserving affinity. Chain-elongated alkynyl or amino derivatives of 6 for click or amide coupling were synthesized, and their antagonist activities were measured in hP2Y14R-expressing CHO cells. Moreover, a new Alexa Fluor 488 (AF488) containing derivative 30 (MRS4174, Ki = 80 pM) exhibited exceptionally high affinity, as compared to 13 nM for the alkyne precursor 22. A flow cytometry assay employing 30 as a fluorescent probe was used to quantify specific binding to P2Y14R. Known P2Y receptor ligands inhibited binding of 30 with properties consistent with their previously established receptor selectivities and affinities. These results illustrate that potency in this series of 2-naphthoic acid derivatives can be preserved by chain functionalization, leading to highly potent fluorescent molecular probes for P2Y14R. Such conjugates will be useful tools in expanding the SAR of this receptor, which still lacks chemical diversity in its collective ligands. This approach demonstrates the predictive power of GPCR homology modeling and the relevance of newly determined X-ray structures to GPCR medicinal chemistry. PMID:25299434

  11. A novel nanocatalytic SERS detection of trace human chorionic gonadotropin using labeled-free Vitoria blue 4R as molecular probe.

    PubMed

    Wen, Guiqing; Liang, Xiaojing; Liu, Qingye; Liang, Aihui; Jiang, Zhiliang

    2016-11-15

    In pH 7.4 Na2HPO4-NaH2PO4 buffer solution containing the peptide probes for human chorionic gonadotropin (hCG), silver nanoparticles (AgNPs) were aggregated to big AgNPs clusters that exhibited very weak catalytic effect on the gold nanoparticle reaction of H2O2-HAuCl4. When hCG was present in the peptide probe solution, the AgNPs did not aggregate and it had strong catalytic effect on the gold nanoparticle reaction with a strong resonance Rayleigh scattering (RRS) peak at 370nm and a strong surface enhanced Raman scattering (SERS) peak at 1615cm(-1) in the presence of molecular probe of Victoria blue 4R (VB4R). With the increase of the hCG concentration, the catalysis enhanced due to the nanocatalyst of AgNPs increasing, and the RRS intensity increased at 370nm. The increased RRS intensity was linear to the hCG concentration in 0.05-10ng/mL, with a linear regression equation of ΔI370nm=409.8C +294. And the SERS intensity at 1615cm(-1) increased linearly with the hCG concentration in the range of 0.05-20ng/mL, with a linear regression equation of ΔI1615cm-1=142C+134. Based on this, two new methods of nanocatalytic SERS and RRS were proposed for the determination of trace hCG. PMID:27208477

  12. New fluorescence probe for Fe³⁺ with bis-rhodamine and its application as a molecular logic gate.

    PubMed

    Yan, Fanyong; Zheng, Tancheng; Guo, Shanshan; Shi, Dechao; Han, Ziyi; Zhou, Siyushan; Chen, Li

    2015-12-01

    A bis-rhodamine based fluorescent probe R1 for naked-eye detection of Fe(3+) with enhanced sensitivity compared to a mono-rhodamine derivative that shows selectivity for Hg(2+), has been synthesized. The 1:1 stoichiometric structure of R1 and Fe(3+) is confirmed using a Job's plot estimation and density functional theory calculations. The reversibility of R1 is verified through its spectral response toward Fe(3+) and S(2-) titration experiments. Using Fe(3+) and S(2-) as chemical inputs and the fluorescence intensity signal as outputs, R1 can be utilized as an INHIBIT logic gate at molecular level. Fluorescent imaging for Fe(3+) in living HL-7702 cells have also been successfully performed. PMID:26184473

  13. A simple and cost-effective molecular diagnostic system and DNA probes synthesized by light emitting diode photolithography

    NASA Astrophysics Data System (ADS)

    Oleksandrov, Sergiy; Kwon, Jung Ho; Lee, Ki-chang; Sujin-Ku; Paek, Mun Cheol

    2014-09-01

    This work introduces a novel chip to be used in the future as a simple and cost-effective method for creating DNA arrays using light emission diode (LED) photolithography. The DNA chip platform contains 24 independent reaction sites, which allows for the testing of a corresponding amount of patients' samples in hospital. An array of commercial UV LEDs and lens systems was combined with a microfluidic flow system to provide patterning of 24 individual reaction sites, each with 64 independent probes. Using the LED array instead of conventional laser exposure systems or micro-mirror systems significantly reduces the cost of equipment. The microfluidic system together with microfluidic flow cells drastically reduces the amount of used reagents, which is important due to the high cost of commercial reagents. The DNA synthesis efficiency was verified by fluorescence labeling and conventional hybridization.

  14. Probing the interaction of a therapeutic flavonoid, pinostrobin with human serum albumin: multiple spectroscopic and molecular modeling investigations.

    PubMed

    Feroz, Shevin R; Mohamad, Saharuddin B; Bakri, Zarith S D; Malek, Sri N A; Tayyab, Saad

    2013-01-01

    Interaction of a pharmacologically important flavonoid, pinostrobin (PS) with the major transport protein of human blood circulation, human serum albumin (HSA) has been examined using a multitude of spectroscopic techniques and molecular docking studies. Analysis of the fluorescence quenching data showed a moderate binding affinity (1.03 × 10(5) M(-1) at 25°C) between PS and HSA with a 1∶1 stoichiometry. Thermodynamic analysis of the binding data (ΔS = +44.06 J mol(-1) K(-1) and ΔH = -15.48 kJ mol(-1)) and molecular simulation results suggested the involvement of hydrophobic and van der Waals forces, as well as hydrogen bonding in the complex formation. Both secondary and tertiary structural perturbations in HSA were observed upon PS binding, as revealed by intrinsic, synchronous, and three-dimensional fluorescence results. Far-UV circular dichroism data revealed increased thermal stability of the protein upon complexation with PS. Competitive drug displacement results suggested the binding site of PS on HSA as Sudlow's site I, located at subdomain IIA, and was well supported by the molecular modelling data. PMID:24116089

  15. Probing the Interaction of a Therapeutic Flavonoid, Pinostrobin with Human Serum Albumin: Multiple Spectroscopic and Molecular Modeling Investigations

    PubMed Central

    Feroz, Shevin R.; Mohamad, Saharuddin B.; Bakri, Zarith S. D.; Malek, Sri N. A.; Tayyab, Saad

    2013-01-01

    Interaction of a pharmacologically important flavonoid, pinostrobin (PS) with the major transport protein of human blood circulation, human serum albumin (HSA) has been examined using a multitude of spectroscopic techniques and molecular docking studies. Analysis of the fluorescence quenching data showed a moderate binding affinity (1.03 × 105 M−1 at 25°C) between PS and HSA with a 1∶1 stoichiometry. Thermodynamic analysis of the binding data (ΔS = +44.06 J mol−1 K−1 and ΔH = −15.48 kJ mol−1) and molecular simulation results suggested the involvement of hydrophobic and van der Waals forces, as well as hydrogen bonding in the complex formation. Both secondary and tertiary structural perturbations in HSA were observed upon PS binding, as revealed by intrinsic, synchronous, and three-dimensional fluorescence results. Far-UV circular dichroism data revealed increased thermal stability of the protein upon complexation with PS. Competitive drug displacement results suggested the binding site of PS on HSA as Sudlow’s site I, located at subdomain IIA, and was well supported by the molecular modelling data. PMID:24116089

  16. Confinement effects on excitation energies and regioselectivity as probed by the Fukui function and the molecular electrostatic potential

    NASA Astrophysics Data System (ADS)

    Borgoo, Alex; Tozer, David; Geerlings, Paul; de Proft, Frank

    2009-03-01

    When a molecule is placed as a guest inside a zeolite pore, its electronic structure will be altered, among others by the effect of the so-called ``confinement". It has been established that the compression of the molecular orbitals influences a system's reactivity. In this work we use a simple potential barrier method to quantify the importance of confinement effects on chemical reactivity. In the first part, excitation energies and molecular orbital energy gaps are evaluated for molecules placed in cavities of different sizes. Our results for ethylene and formaldehyde reveal an increase in excitation energy and the gap between the occupied and the unoccupied levels. In the case of the larger molecules naphthalene and anthracene, the HOMO-LUMO gap shows very little sensitivity to the confinement. To investigate the role of confinement effects on local aspects of chemical reactivity and on regioselectivity, we evaluated its effect on the Fukui function and the molecular electrostatic potential, reactivity indices that are central in the description of orbital and charge controlled reactions. The results indicate that confinement can influence the regioselectivity and that the reactivity of anions is expected to change, due to the artificial binding of the exess electron.

  17. Probe assembly

    SciTech Connect

    Avera, C.J.

    1981-01-06

    A hand-held probe assembly, suitable for monitoring a radioactive fibrinogen tracer, is disclosed comprising a substantially cylindrically shaped probe handle having an open end. The probe handle is adapted to be interconnected with electrical circuitry for monitoring radioactivity that is sensed or detected by the probe assembly. Mounted within the probe handle is a probe body assembly that includes a cylindrically shaped probe body inserted through the open end of the probe handle. The probe body includes a photomultiplier tube that is electrically connected with a male connector positioned at the rearward end of the probe body. Mounted at the opposite end of the probe body is a probe head which supports an optical coupler therewithin. The probe head is interconnected with a probe cap which supports a detecting crystal. The probe body assembly, which consists of the probe body, the probe head, and the probe cap is supported within the probe handle by means of a pair of compressible o-rings which permit the probe assembly to be freely rotatable, preferably through 360*, within the probe handle and removable therefrom without requiring any disassembly.

  18. Trimodal color-fluorescence-polarization endoscopy aided by a tumor selective molecular probe accurately detects flat lesions in colitis-associated cancer

    NASA Astrophysics Data System (ADS)

    Charanya, Tauseef; York, Timothy; Bloch, Sharon; Sudlow, Gail; Liang, Kexian; Garcia, Missael; Akers, Walter J.; Rubin, Deborah; Gruev, Viktor; Achilefu, Samuel

    2014-12-01

    Colitis-associated cancer (CAC) arises from premalignant flat lesions of the colon, which are difficult to detect with current endoscopic screening approaches. We have developed a complementary fluorescence and polarization reporting strategy that combines the unique biochemical and physical properties of dysplasia and cancer for real-time detection of these lesions. Using azoxymethane-dextran sodium sulfate (AOM-DSS) treated mice, which recapitulates human CAC and dysplasia, we show that an octapeptide labeled with a near-infrared (NIR) fluorescent dye selectively identified all precancerous and cancerous lesions. A new thermoresponsive sol-gel formulation allowed topical application of the molecular probe during endoscopy. This method yielded high contrast-to-noise ratios (CNR) between adenomatous tumors (20.6±1.65) and flat lesions (12.1±1.03) and surrounding uninvolved colon tissue versus CNR of inflamed tissues (1.62±0.41). Incorporation of nanowire-filtered polarization imaging into NIR fluorescence endoscopy shows a high depolarization contrast in both adenomatous tumors and flat lesions in CAC, reflecting compromised structural integrity of these tissues. Together, the real-time polarization imaging provides real-time validation of suspicious colon tissue highlighted by molecular fluorescence endoscopy.

  19. Comprehensive Screening of Gene Copy Number Aberrations in Formalin-Fixed, Paraffin-Embedded Solid Tumors Using Molecular Inversion Probe-Based Single-Nucleotide Polymorphism Array.

    PubMed

    Singh, Rajesh R; Mehrotra, Meenakshi; Chen, Hui; Almohammedsalim, Alaa A; Sahin, Ayesagul; Bosamra, Alex; Patel, Keyur P; Routbort, Mark J; Lu, Xinyan; Ronald, Abraham; Mishra, Bal Mukund; Virani, Shumaila; Medeiros, L Jeffrey; Luthra, Rajyalakshmi

    2016-09-01

    Gene copy number aberrations (CNAs) represent a major class of cancer-related genomic alterations that drive solid tumors. Comprehensive and sensitive detection of CNAs is challenging because of often low quality and quantity of DNA isolated from the formalin-fixed, paraffin-embedded (FFPE) solid tumor samples. Here, in a clinical molecular diagnostic laboratory, we tested the utility and validated a molecular inversion probe-based (MIP) array to routinely screen for CNAs in solid tumors. Using low-input FFPE DNA, the array detects genome-wide CNAs with a special focus on 900 cancer-related genes. A cohort of 76 solid tumors of various types and tumor cellularity (20% to 100%), and four cancer cell lines were used. These harbored CNAs in clinically important genes (ERBB2, EGFR, FGFR1, KRAS, MYC) as detected by orthogonal techniques like next-generation sequencing or fluorescence in situ hybridization. Results of the MIP array were concordant with results from orthogonal techniques, and also provided additional information regarding the allelic nature of the CNAs. Limit-of-detection and assay reproducibility studies showed a high degree of sensitivity and reproducibility of detection, respectively. FFPE compatibility, ability to detect CNAs with high sensitivity, accuracy, and provide valuable information such as loss of heterozygosity along with relatively short turnaround times makes the MIP array a desirable clinical platform for routine screening of solid tumors in a clinical laboratory. PMID:27392636

  20. Trimodal color-fluorescence-polarization endoscopy aided by a tumor selective molecular probe accurately detects flat lesions in colitis-associated cancer

    PubMed Central

    Charanya, Tauseef; York, Timothy; Bloch, Sharon; Sudlow, Gail; Liang, Kexian; Garcia, Missael; Akers, Walter J.; Rubin, Deborah; Gruev, Viktor; Achilefu, Samuel

    2014-01-01

    Abstract. Colitis-associated cancer (CAC) arises from premalignant flat lesions of the colon, which are difficult to detect with current endoscopic screening approaches. We have developed a complementary fluorescence and polarization reporting strategy that combines the unique biochemical and physical properties of dysplasia and cancer for real-time detection of these lesions. Using azoxymethane-dextran sodium sulfate (AOM-DSS) treated mice, which recapitulates human CAC and dysplasia, we show that an octapeptide labeled with a near-infrared (NIR) fluorescent dye selectively identified all precancerous and cancerous lesions. A new thermoresponsive sol-gel formulation allowed topical application of the molecular probe during endoscopy. This method yielded high contrast-to-noise ratios (CNR) between adenomatous tumors (20.6±1.65) and flat lesions (12.1±1.03) and surrounding uninvolved colon tissue versus CNR of inflamed tissues (1.62±0.41). Incorporation of nanowire-filtered polarization imaging into NIR fluorescence endoscopy shows a high depolarization contrast in both adenomatous tumors and flat lesions in CAC, reflecting compromised structural integrity of these tissues. Together, the real-time polarization imaging provides real-time validation of suspicious colon tissue highlighted by molecular fluorescence endoscopy. PMID:25473883

  1. Molecular beam studies of unimolecular and bimolecular chemical reaction dynamics using VUV synchrotron radiation as a product probe

    SciTech Connect

    Blank, D.A.

    1997-08-01

    This dissertation describes the use of a new molecular beam apparatus designed to use tunable VUV synchrotron radiation for photoionization of the products from scattering experiments. The apparatus was built at the recently constructed Advanced Light Source at Lawrence Berkeley National Laboratory, a third generation 1-2 GeV synchrotron radiation source. The new apparatus is applied to investigations of the dynamics of unimolecular reactions, photodissociation experiments, and bimolecular reactions, crossed molecular beam experiments. The first chapter describes the new apparatus and the VUV radiation used for photoionization. This is followed by a number of examples of the many advantages provided by using VUV photoionization in comparison with the traditional technique of electron bombardment ionization. At the end of the chapter there is a discussion of the data analysis employed in these scattering experiments. The remaining four chapters are complete investigations of the dynamics of four chemical systems using the new apparatus and provide numerous additional examples of the advantages provided by VUV photoionizaiton of the products. Chapters 2-4 are photofragment translational spectroscopy studies of the photodissociation dynamics of dimethyl sulfoxide, acrylonitrile, and vinyl chloride following absorption at 193 mn. All of these systems have multiple dissociation channels and provide good examples of the ability of the new apparatus to unravel the complex UV photodissociation dynamics that can arise in small polyatomic molecules.

  2. Molecular gels in the gas phase? Gelator-gelator and gelator-solvent interactions probed by vibrational spectroscopy.

    PubMed

    Lozada-Garcia, Rolando; Mu, Dan; Plazanet, Marie; Çarçabal, Pierre

    2016-08-10

    Benzylidene glucose (BzGlc) is a member of the benzylidene glycoside family. These molecules have the ability to form molecular physical gels. These materials are formed when gelator molecules create a non-covalently bound frame where solvent molecules are trapped. Since the gel formation process and its properties are determined by the subtle balance between non-covalent forces, it is difficult to anticipate them. Quantitative and qualitative understanding of the gelator-gelator and gelator-solvent interactions is needed to better control these materials for important potential applications. We have used gas phase vibrational spectroscopy and theoretical chemistry to study the conformational choices of BzGlc, its dimer and the complexes it forms with water or toluene. To interpret the vibrational spectra we have used the dispersion corrected functional B97D which we have calibrated for the calculation of OH stretching frequencies. Even at the most basic molecular level, it is possible to interrogate a large range of non-covalent interactions ranging from OH → OH hydrogen bonding, to OH → π, and CH → π, all being at the center of gel properties at the macroscopic level. PMID:27443393

  3. Probing molecular geometry of solids by nuclear magnetic resonance spin exchange at the n=0 rotational-resonance condition

    NASA Astrophysics Data System (ADS)

    Tekely, Piotr; Gardiennet, Carole; Potrzebowski, Marek J.; Sebald, Angelika; Reichert, Detlef; Luz, Zeev

    2002-05-01

    Exploration of the molecular geometry in rotating powder solids on the basis of magnetization exchange between spins with identical isotropic chemical shifts but differing chemical shielding tensor orientations is demonstrated experimentally. For this we take advantage of the potential of the ODESSA (one-dimensional exchange spectroscopy by sidebands alternation) experiment for the accurate measurement of spin exchange rate constants. We also report the observation of oscillatory behavior of the rotor-driven magnetization exchange at this so-called n=0 rotational-resonance condition which, in contrast to n=1,2,3,… rotational-resonance conditions, takes place at nearly arbitrary magic-angle spinning frequencies. The sensitivity of the longitudinal exchange decays to the relevant physical parameters of the spin system under conditions of rotor-driven and proton-driven magnetization exchange is discussed theoretically and demonstrated experimentally. Several 13C and 31P spin-exchange measurements have been performed on a series of model compounds covering a broad range of internuclear distances between carboxyl carbon atoms, and on a series of phosphorylated amino acids with different internuclear distances between phosphorus sites. The capacity of the ODESSA experiment for an unambiguous recognition of distinct internuclear distances is demonstrated. Potential applications of such measurements involve the exploration of intermolecular distances and the determination of the mutual orientation of neighboring molecular fragments in polycrystalline and noncrystalline solids.

  4. Star-forming regions of the Aquila rift cloud complex. II. Turbulence in molecular cores probed by NH3 emission

    NASA Astrophysics Data System (ADS)

    Levshakov, S. A.; Henkel, C.; Reimers, D.; Wang, M.

    2014-07-01

    Aims: We intend to derive statistical properties of stochastic gas motion inside the dense, low-mass star-forming molecular cores that are traced by NH3(1, 1) and (2, 2) emission lines. Methods: We use the spatial two-point autocorrelation (ACF) and structure functions calculated from maps of the radial velocity fields. Results: The observed ammonia cores are characterized by complex intrinsic motions of stochastic nature. The measured kinetic temperature ranges between 8.8 K and 15.1 K. From NH3 excitation temperatures of 3.5-7.3 K, we determine H2 densities with typical values of nH2~ (1-6) × 104 cm-3. The ammonia abundance, X = [NH3]/[H2], varies from 2 × 10-8 to 1.5 × 10-7. We find oscillating ACFs, which eventually decay to zero with increasing lags on scales of 0.04 ≲ ℓ ≲ 0.5 pc. The current paradigm supposes that the star-formation process is controlled by the interplay between gravitation and turbulence with the latter preventing molecular cores from a rapid collapse due to their own gravity. Thus, oscillating ACFs may indicate a damping of the developed turbulent flows surrounding the dense but less turbulent core, a transition to dominating gravitational forces and, hence, to gravitational collapse. Appendix A is available in electronic form at http://www.aanda.org

  5. Probing non-covalent interactions with a second generation energy decomposition analysis using absolutely localized molecular orbitals.

    PubMed

    Horn, Paul R; Mao, Yuezhi; Head-Gordon, Martin

    2016-08-17

    An energy decomposition analysis (EDA) separates a calculated interaction energy into as many interpretable contributions as possible; for instance, permanent and induced electrostatics, Pauli repulsions, dispersion and charge transfer. The challenge is to construct satisfactory definitions of all terms in the chemically relevant regime where fragment densities overlap, rendering unique definitions impossible. Towards this goal, we present an improved EDA for Kohn-Sham density functional theory (DFT) with properties that have previously not been simultaneously attained. Building on the absolutely localized molecular orbital (ALMO)-EDA, this second generation ALMO-EDA is variational and employs valid antisymmetric electronic wavefunctions to produce all five contributions listed above. These contributions moreover all have non-trivial complete basis set limits. We apply the EDA to the water dimer, the T-shaped and parallel-displaced benzene dimer, the p-biphthalate dimer "anti-electrostatic" hydrogen bonding complex, the biologically relevant binding of adenine and thymine in stacked and hydrogen-bonded configurations, the triply hydrogen-bonded guanine-cytosine complex, the interaction of Cl(-) with s-triazine and with the 1,3-dimethyl imidazolium cation, which is relevant to the study of ionic liquids, and the water-formaldehyde-vinyl alcohol ter-molecular radical cationic complex formed in the dissociative photoionization of glycerol. PMID:27492057

  6. Probing environment fluctuations by two-dimensional electronic spectroscopy of molecular systems at temperatures below 5 K

    SciTech Connect

    Rancova, Olga; Abramavicius, Darius; Jankowiak, Ryszard

    2015-06-07

    Two-dimensional (2D) electronic spectroscopy at cryogenic and room temperatures reveals excitation energy relaxation and transport, as well as vibrational dynamics, in molecular systems. These phenomena are related to the spectral densities of nuclear degrees of freedom, which are directly accessible by means of hole burning and fluorescence line narrowing approaches at low temperatures (few K). The 2D spectroscopy, in principle, should reveal more details about the fluctuating environment than the 1D approaches due to peak extension into extra dimension. By studying the spectral line shapes of a dimeric aggregate at low temperature, we demonstrate that 2D spectra have the potential to reveal the fluctuation spectral densities for different electronic states, the interstate correlation of static disorder and, finally, the time scales of spectral diffusion with high resolution.

  7. Molecular recognition of curcumin (Indian Ayurvedic medicine) by the supramolecular probe, p-t-butyl calix(8)arene

    NASA Astrophysics Data System (ADS)

    Meenakshi, C.; Jayabal, P.; Ramakrishnan, V.

    2014-06-01

    The thermodynamic property of the host-guest complexes formed between the curcumin, component of Indian Ayurvedic medicine turmeric, a drug molecule, with the supra molecule, p-t-butyl calix(8)arene was studied. p-t-Butyl calix(8)arene has been used as a host molecule and curcumin as a guest molecule. Optical absorption spectral studies were carried out to investigate the molecular recognition properties of p-t-butyl calix(8)arene with curcumin. The stochiometry of the host-guest complexes formed and the binding constant were determined. An interesting 1:1 and 4:1 stochiometric host-guest complexes were formed. Job's continuous method of variation and Benesi-Hildebrand expression were used for the determination of binding constant and the stochiometry of the host-guest complex formed.

  8. Density Structure of the SGR B2 Molecular Cloud Probed by Low-J Lines of CS

    NASA Astrophysics Data System (ADS)

    Minh, Y. C.; Hjalmarson, Å.

    1999-01-01

    We have observed the CS (2-1) and (3-2), and 13CS (2-1) transitions toward the Galactic Center molecular cloud Sgr B2 which consists of several clumps with different chemical properties. We have newly identified a cloud at 30 km s-1 from a CS (2-1) optical depth map. This cloud lies 1.5' South from the Sgr B2 (M) position and has a diameter of ~2.5 pc and a total column density of 7 × 1023 cm-2 assuming optically thin emission of the 13CS (2-1) line. Towards the 2'N Cloud no evidence for a density enhancement is found, which suggests that the strong emission from HNCO and HCO+2 is due to chemical effects. The main isotopic CS lines show broad wing components similar to previous studies, but we find rotational temperatures Trot(CS) < 10 K at this region

  9. Probing thermal stability of the β-lactoglobulin-oleic acid complex by fluorescence spectroscopy and molecular modeling

    NASA Astrophysics Data System (ADS)

    Simion (Ciuciu), Ana-Maria; Aprodu, Iuliana; Dumitrașcu, Loredana; Bahrim, Gabriela Elena; Alexe, Petru; Stănciuc, Nicoleta

    2015-09-01

    Bovine β-lactoglobulin is able to interact with different bioactive compounds, thus being an important candidate in the development of delivery systems with improved functionality. The heat induced changes in the β-lactoglobulin-oleic acid complex were examined by means of fluorescence spectroscopy and molecular modeling techniques. Fluorescence spectroscopy results indicated a rigid protein structure in the temperature range 25-70 °C, whereas at temperatures over 75 °C, the rearrangements of the polypeptide chains led to higher exposure of hydrophobic residues. The most significant increase of the accessible surface area with temperature increase was identified in case of Tyr99 and Tyr102. The phase diagram method indicated an all or none transition between two conformations. Due to conformational changes, no contact between Ile56 or Lys60 and the fatty acid could be identified at 85 °C, but new non-bonding interaction were established with Ile12 and Val15. The results obtained in this study provide important details about thermal induced changes in the conformation of β-lactoglobulin-oleic acid complex. Significant conformational changes were registered above 75 °C, suggesting the possibility of obtaining highly functional complexes between whey proteins and natural unsaturated fatty acids.

  10. Probing the Molecular Interactions between CXC Chemokine Receptor 4 (CXCR4) and an Arginine-Based Tripeptidomimetic Antagonist (KRH-1636).

    PubMed

    Zachariassen, Zack G; Karlshøj, Stefanie; Haug, Bengt Erik; Rosenkilde, Mette M; Våbenø, Jon

    2015-10-22

    We here report an experimentally verified binding mode for the known tripeptidomimetic CXCR4 antagonist KRH-1636 (1). A limited SAR study based on the three functionalities of 1 was first conducted, followed by site-directed mutagenesis studies. The receptor mapping showed that both the potency and affinity of 1 were dependent on the transmembrane residues His(113), Asp(171), Asp(262), and His(281) and also suggested the involvement of Tyr(45) and Gln(200) (potency) and Tyr(116) and Glu(288) (affinity). Molecular docking of 1 to an X-ray structure of CXCR4 showed that the l-Arg guanidino group of 1 forms polar interactions with His(113) and Asp(171) and the (pyridin-2-ylmethyl)amino moiety is anchored by Asp(262) and His(281), whereas the naphthalene ring is tightly packed in a hydrophobic subpocket formed by the aromatic side chains of Trp(94), Tyr(45), and Tyr(116). The detailed picture of ligand-receptor interactions provided here will assist in structure-based design and further development of small-molecule peptidomimetic CXCR4 antagonists. PMID:26397724

  11. Probing the ATP-induced conformational flexibility of the PcrA helicase protein using molecular dynamics simulation.

    PubMed

    Mhashal, Anil R; Choudhury, Chandan Kumar; Roy, Sudip

    2016-03-01

    Helicases are enzymes that unwind double-stranded DNA (dsDNA) into its single-stranded components. It is important to understand the binding and unbinding of ATP from the active sites of helicases, as this knowledge can be used to elucidate the functionality of helicases during the unwinding of dsDNA. In this work, we investigated the unbinding of ATP and its effect on the active-site residues of the helicase PcrA using molecular dynamic simulations. To mimic the unbinding process of ATP from the active site of the helicase, we simulated the application of an external force that pulls ATP from the active site and computed the free-energy change during this process. We estimated an energy cost of ~85 kJ/mol for the transformation of the helicase from the ATP-bound state (1QHH) to the ATP-free state (1PJR). Unbinding led to conformational changes in the residues of the protein at the active site. Some of the residues at the ATP-binding site were significantly reoriented when the ATP was pulled. We observed a clear competition between reorientation of the residues and energy stabilization by hydrogen bonds between the ATP and active-site residues. We also checked the flexibility of the PcrA protein using a principal component analysis of domain motion. We found that the ATP-free state of the helicase is more flexible than the ATP-bound state. PMID:26860503

  12. The Ar-HCO{sup +} and He-HCO{sup +} molecular complexes. Theoretical probe of the experimental data

    SciTech Connect

    Nowek, A.; Leszczynski, J.

    1996-12-31

    A number of ab initio correlated levels of theory, up to MP4(SDTQ), CCSD(T), and QCISD(T), have been employed in studies on molecular geometry and stability of the Ar-HCO{sup +} and He-HCO{sup +} complexes. At the applied levels of theory, the predicted interaction energies (corrected for the BSSE and ZPE) for Ar-HCO{sup +} range from -3.21 kcal/mol to -4.21 kcal /mol and for He-HCO{sup +} vary from -0.12 kcal/mol (-42 cm{sup -1}) to -0.37 kcal/mol (-130 cm{sup -1}). The optimized Ar-H distance agree very well with the experimentally determined value, whereas when step-by-step higher-level methods and basis sets are applied, the He-H distance, (1.9156 {angstrom} at QCISD(T)/aug-cc-pVTZ) dramatically retreats from the experimental value of 2.00 {angstrom}.

  13. Molecular interactions in the ionic liquid emim acetate and water binary mixtures probed via NMR spin relaxation and exchange spectroscopy.

    PubMed

    Allen, Jesse J; Bowser, Sage R; Damodaran, Krishnan

    2014-05-01

    Interactions of ionic liquids (ILs) with water are of great interest for many potential IL applications. 1-Ethyl-3-methylimidazolium (emim) acetate, in particular, has shown interesting interactions with water including hydrogen bonding and even chemical exchange. Previous studies have shown the unusual behavior of emim acetate when in the presence of 0.43 mole fraction of water, and a combination of NMR techniques is used herein to investigate the emim acetate-water system and the unusual behavior at 0.43 mole fraction of water. NMR relaxometry techniques are used to describe the effects of water on the molecular motion and interactions of emim acetate with water. A discontinuity is seen in nuclear relaxation behavior at the concentration of 0.43 mole fraction of water, and this is attributed to the formation of a hydrogen bonded network. EXSY measurements are used to determine the exchange rates between the H2 emim proton and water, which show a complex dependence on the concentration of the mixture. The findings support and expand our previous results, which suggested the presence of an extended hydrogen bonding network in the emim acetate-water system at concentrations close to 0.50 mole fraction of H2O. PMID:24654003

  14. Probing molecular packing at engineered interfaces in organic field effect transistor and its correlation with charge carrier mobility.

    PubMed

    Maheshwari, Priya; Mukherjee, Saurabh; Bhattacharya, Debarati; Sen, Shashwati; Tokas, Raj Bahadur; Honda, Yoshihide; Basu, Saibal; Padma, Narayanan; Pujari, Pradeep Kumar

    2015-05-20

    Surface engineering of SiO2 dielectric using different self-assembled monolayer (SAM) has been carried out, and its effect on the molecular packing and growth behavior of copper phthalocyanine (CuPc) has been studied. A correlation between the growth behavior and performance of organic field effect transistors is examined. Depth profiling using positron annihilation and X-ray reflectivity techniques has been employed to characterize the interface between CuPc and the modified and/or unmodified dielectric. We observe the presence of structural defects or disorder due to disorientation of CuPc molecules on the unmodified dielectric and ordered arrangement on the modified dielectrics, consistent with the high charge carrier mobility in organic field effect transistors in the latter. The study also highlights the sensitivity of these techniques to the packing of CuPc molecules on SiO2 modified using different SAMs. Our study also signifies the sensitivity and utility of these two techniques in the characterization of buried interfaces in organic devices. PMID:25922969

  15. Vibrational spectroscopy of an algal Phot-LOV1 domain probes the molecular changes associated with blue-light reception.

    PubMed

    Ataka, K; Hegemann, P; Heberle, J

    2003-01-01

    The LOV1 domain of the blue light Phot1-receptor (phototropin homolog) from Chlamydomonas reinhardtii has been studied by vibrational spectroscopy. The FMN modes of the dark state of LOV1 were identified by preresonance Raman spectroscopy and assigned to molecular vibrations. By comparing the blue-light-induced FTIR difference spectrum with the preresonance Raman spectrum, most of the differences are due to FMN modes. Thus, we exclude large backbone changes of the protein that might occur during the phototransformation of the dark state LOV1-447 into the putative signaling state LOV1-390. Still, the presence of smaller amide difference bands cannot be excluded but may be masked by overlapping FMN modes. The band at 2567 cm(-1) is assigned to the S-H stretching vibration of C57, the residue that forms the transient thio-adduct with the chromophore FMN. The occurrence of this band is evidence that C57 is protonated in the dark state of LOV1. This result challenges conclusions from the homologous LOV2 domain from oat that the thiolate of the corresponding cysteine is the reactive species. PMID:12524299

  16. Effect of Sequence Variation on the Mechanical Response of Amyloid Fibrils Probed by Steered Molecular Dynamics Simulation

    PubMed Central

    Ndlovu, Hlengisizwe; Ashcroft, Alison E.; Radford, Sheena E.; Harris, Sarah A.

    2012-01-01

    The mechanical failure of mature amyloid fibers produces fragments that act as seeds for the growth of new fibrils. Fragmentation may also be correlated with cytotoxicity. We have used steered atomistic molecular dynamics simulations to study the mechanical failure of fibrils formed by the amyloidogenic fragment of human amylin hIAPP20-29 subjected to force applied in a variety of directions. By introducing systematic variations to this peptide sequence in silico, we have also investigated the role of the amino-acid sequence in determining the mechanical stability of amyloid fibrils. Our calculations show that the force required to induce mechanical failure depends on the direction of the applied stress and upon the degree of structural order present in the β-sheet assemblies, which in turn depends on the peptide sequence. The results have implications for the importance of sequence-dependent mechanical properties on seeding the growth of new fibrils and the role of breakage events in cytotoxicity. PMID:22325282

  17. Probing Difference in Binding Modes of Inhibitors to MDMX by Molecular Dynamics Simulations and Different Free Energy Methods.

    PubMed

    Shi, Shuhua; Zhang, Shaolong; Zhang, Qinggang

    2015-01-01

    The p53-MDMX interaction has attracted extensive attention of anti-cancer drug development in recent years. This current work adopted molecular dynamics (MD) simulations and cross-correlation analysis to investigate conformation changes of MDMX caused by inhibitor bindings. The obtained information indicates that the binding cleft of MDMX undergoes a large conformational change and the dynamic behavior of residues obviously change by the presence of different structural inhibitors. Two different methods of binding free energy predictions were employed to carry out a comparable insight into binding mechanisms of four inhibitors PMI, pDI, WK23 and WW8 to MDMX. The data show that the main factor controlling the inhibitor bindings to MDMX arises from van der Waals interactions. The binding free energies were further divided into contribution of each residue and the derived information gives a conclusion that the hydrophobic interactions, such as CH-CH, CH-π and π-π interactions, are responsible for the inhibitor associations with MDMX. PMID:26513747

  18. Probing Difference in Binding Modes of Inhibitors to MDMX by Molecular Dynamics Simulations and Different Free Energy Methods

    PubMed Central

    Shi, Shuhua; Zhang, Shaolong; Zhang, Qinggang

    2015-01-01

    The p53-MDMX interaction has attracted extensive attention of anti-cancer drug development in recent years. This current work adopted molecular dynamics (MD) simulations and cross-correlation analysis to investigate conformation changes of MDMX caused by inhibitor bindings. The obtained information indicates that the binding cleft of MDMX undergoes a large conformational change and the dynamic behavior of residues obviously change by the presence of different structural inhibitors. Two different methods of binding free energy predictions were employed to carry out a comparable insight into binding mechanisms of four inhibitors PMI, pDI, WK23 and WW8 to MDMX. The data show that the main factor controlling the inhibitor bindings to MDMX arises from van der Waals interactions. The binding free energies were further divided into contribution of each residue and the derived information gives a conclusion that the hydrophobic interactions, such as CH-CH, CH-π and π-π interactions, are responsible for the inhibitor associations with MDMX. PMID:26513747

  19. Probing the molecular forces involved in binding of selected volatile flavour compounds to salt-extracted pea proteins.

    PubMed

    Wang, Kun; Arntfield, Susan D

    2016-11-15

    Molecular interactions between heterologous classes of flavour compounds with salt-extracted pea protein isolates (PPIs) were determined using various bond disrupting agents followed by GC/MS analysis. Flavour bound by proteins decreased in the order: dibutyl disulfide>octanal>hexyl acetate>2-octanone=benzaldehyde. Benzaldehyde, 2-octanone and hexyl acetate interacted non-covalently with PPIs, whereas octanal bound PPIs via covalent and non-covalent forces. Dibutyl disulfide reacted with PPIs covalently, as its retention was not diminished by urea and guanidine hydrochloride. Using propylene glycol, H-bonding and ionic interactions were implicated for hexyl acetate, benzaldehyde, and 2-octanone. A protein-destabilising salt (Cl3CCOONa) reduced bindings for 2-octanone, hexyl acetate, and benzaldehyde; however, retention for octanal and dibutyl disulfide increased. Conversely, a protein-stabilising salt (Na2SO4) enhanced retention for benzaldehyde, 2-octanone, hexyl acetate and octanal. Formation of a volatile flavour by-product, 1-butanethiol, from dibutyl disulfide when PPIs were treated with dithiothreitol indicated occurrence of sulfhydryl-disulfide interchange reactions. PMID:27283627

  20. Probing immobilization mechanism of alpha-chymotrypsin onto carbon nanotube in organic media by molecular dynamics simulation.

    PubMed

    Zhang, Liyun; Xiao, Xiuchan; Yuan, Yuan; Guo, Yanzhi; Li, Menglong; Pu, Xuemei

    2015-01-01

    The enzyme immobilization has been adopted to enhance the activity and stability of enzymes in non-aqueous enzymatic catalysis. However, the activation and stabilization mechanism has been poorly understood on experiments. Thus, we used molecular dynamics simulation to study the adsorption of α-chymotrypsin (α-ChT) on carbon nanotube (CNT) in aqueous solution and heptane media. The results indicate that α-ChT has stronger affinity with CNT in aqueous solution than in heptane media, as confirmed by more adsorption atoms, larger contact area and higher binding free energies. Although the immobilization causes significant structure deviations from the crystal one, no significant changes in secondary structure of the enzyme upon adsorption are observed in the two media. Different from aqueous solution, the stabilization effects on some local regions far from the surface of CNT were observed in heptane media, in particular for S1 pocket, which should contribute to the preservation of specificity reported by experiments. Also, CNT displays to some extent stabilization role in retaining the catalytic H-bond network of the active site in heptane media, which should be associated with the enhanced activity of enzymes. The observations from the work can provide valuable information for improving the catalytic properties of enzymes in non-aqueous media. PMID:25787884

  1. Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding

    PubMed Central

    Abriata, Luciano A.; Dal Peraro, Matteo

    2015-01-01

    Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin’s noncovalent dimerization equilibrium to assess the potential of atomistic simulations to reproduce reversible protein-protein binding, by running submicrosecond simulations of systems with multiple copies of the protein at millimolar concentrations. The simulations essentially fail because they lead to aggregates, yet they reproduce some specificity in the binding interfaces as observed in known covalent and noncovalent ubiquitin dimers. Following similar observations in literature we hint at electrostatics and water descriptions as the main liable force field elements, and propose that their optimization should consider observables relevant to multi-protein systems and unfolded proteins. Within limitations, analysis of binding events suggests salient features of protein-protein recognition and binding, to be retested with improved force fields. Among them, that specific configurations of relative direction and orientation seem to trigger fast binding of two molecules, even over 50 Å distances; that conformational selection can take place within surface-to-surface distances of 10 to 40 Å i.e. well before actual intermolecular contact; and that establishment of contacts between molecules further locks their conformations and relative orientations. PMID:26023027

  2. Green's function-stochastic methods framework for probing nonlinear evolution problems: Burger's equation, the nonlinear Schroedinger's equation, and hydrodynamic organization of near-molecular-scale vorticity

    SciTech Connect

    Keanini, R.G.

    2011-04-15

    Research Highlights: > Systematic approach for physically probing nonlinear and random evolution problems. > Evolution of vortex sheets corresponds to evolution of an Ornstein-Uhlenbeck process. > Organization of near-molecular scale vorticity mediated by hydrodynamic modes. > Framework allows calculation of vorticity evolution within random strain fields. - Abstract: A framework which combines Green's function (GF) methods and techniques from the theory of stochastic processes is proposed for tackling nonlinear evolution problems. The framework, established by a series of easy-to-derive equivalences between Green's function and stochastic representative solutions of linear drift-diffusion problems, provides a flexible structure within which nonlinear evolution problems can be analyzed and physically probed. As a preliminary test bed, two canonical, nonlinear evolution problems - Burgers' equation and the nonlinear Schroedinger's equation - are first treated. In the first case, the framework provides a rigorous, probabilistic derivation of the well known Cole-Hopf ansatz. Likewise, in the second, the machinery allows systematic recovery of a known soliton solution. The framework is then applied to a fairly extensive exploration of physical features underlying evolution of randomly stretched and advected Burger's vortex sheets. Here, the governing vorticity equation corresponds to the Fokker-Planck equation of an Ornstein-Uhlenbeck process, a correspondence that motivates an investigation of sub-sheet vorticity evolution and organization. Under the assumption that weak hydrodynamic fluctuations organize disordered, near-molecular-scale, sub-sheet vorticity, it is shown that these modes consist of two weakly damped counter-propagating cross-sheet acoustic modes, a diffusive cross-sheet shear mode, and a diffusive cross-sheet entropy mode. Once a consistent picture of in-sheet vorticity evolution is established, a number of analytical results, describing the motion

  3. In Vivo Detection of Oxidation-Specific Epitopes in Atherosclerotic Lesions Using Bio-Compatible Mn(II) Molecular Magnetic Imaging Probes

    PubMed Central

    Briley-Saebo, Karen C.; Hoang, Tuyen; Saeboe, Alexander M.; Cho, Young Seok; Ryu, Sung Kee; Volkava, Eugenia; Dickson, Stephen; Leibundgut, Gregor; Weisner, Philipp; Green, Simone; Casanada, Florence; Miller, Yury I.; Shaw, Walter; Witztum, Joseph L; Fayad, Zahi A.; Tsimikas, Sotirios

    2012-01-01

    Objectives To evaluate the in vivo magnetic resonance (MR) imaging efficacy of manganese (Mn(II)) molecular imaging probes targeted to oxidation-specific epitopes (OSE). Background OSE are critical in the initiation, progression and de-stabilization of atherosclerotic plaques. Gadolinium (Gd(III)) based MR imaging agents can be associated with systemic toxicity. Mn is an endogenous, bio-compatible, paramagnetic metal ion that has poor MR efficacy when chelated, but strong efficacy when released within cells. Methods Multimodal Mn-micelles were generated to contain rhodamine for confocal microscopy and conjugated with either the murine monoclonal IgG antibody MDA2 targeted to malondialdehyde (MDA)-lysine epitopes or the human single-chain Fv antibody fragment IK17 targeted to MDA-like epitopes (‘targeted micelles”). Micelle formulations were characterized in vitro and in vivo and their MR efficacy (9.4 Tesla) evaluated in apoE−/− and LDLR−/− mice (0.05 mmol Mn/Kg dose) (total of 120 mice for all experiments). In vivo competitive inhibition studies were performed to evaluate target specificity. Untargeted, MDA2-Gd and IK17-Gd micelles (0.075 mmol Gd/Kg) were included as controls. Results In vitro studies demonstrated that targeted Mn-micelles accumulate in macrophages when pre-exposed to MDA-LDL with ~10X increase in longitudinal relativity. Following intravenous injection, strong MR signal enhancement was observed 48–72 hours after administration of targeted Mn-micelles, with co-localization within intraplaque macrophages. Co-injection of free MDA2 with the MDA2-Mn micelles resulted in full suppression of MR signal in the arterial wall confirming target specificity. Similar MR efficacy was noted in apoE−/− and LDLR−/− mice with aortic atherosclerosis. No significant differences in MR efficacy were noted between targeted Mn and Gd micelles. Conclusions This study demonstrates that bio-compatible multimodal Mn-based molecular imaging probes

  4. Development of a One-Step Probe Based Molecular Assay for Rapid Immunodiagnosis of Infection with M. tuberculosis Using Dried Blood Spots

    PubMed Central

    Blauenfeldt, Thomas; Heyckendorf, Jan; Graff Jensen, Sidse; Lange, Christoph; Drabe, Camilla; Hermansen, Thomas S.; de Thurah, Lena; Lillebaek, Troels; Eugen-Olsen, Jesper; Seersholm, Niels; Hoff, Søren; Bonde, Jesper; Ruhwald, Morten

    2014-01-01

    Background Antigen specific release of IP-10 is the most promising alternative marker to IFN-γ for infection with M. tuberculosis. Compared to Interferon-γ release assays (IGRA), IP-10 is released in high levels enabling novel approaches such as field friendly dried blood spots (DBS) and molecular detection. Aim To develop a robust IP-10 based molecular assay for the diagnosis of infection with M. tubercuolsis from whole blood and DBS. Method We developed a one-step probe based multiplex RT-qPCR assay for detecting IP-10 and IFN-γ mRNA expression from whole blood and DBS samples. The assay was validated and applied for the diagnosis of M. tuberculosis infection in DBS samples from 43 patients with confirmed TB, 13 patients with latent TB and 96 presumed uninfected controls. In parallel, IP-10 and INF-γ levels were measured in Quantiferon (QFT-TB) plasma supernatants. Results IP-10 mRNA upregulation was detectable at 4 hours after stimulation (6 fold upregulation) peaking at 8 hours (108 fold upregulation). IFN-γ expression occurred in concert but levels were lower (peak 6.7 fold upregulation). IP-10 gene expression level was significantly higher in patients with tuberculosis (median 31.2, IQR 10.7–67.0) and persons with latent tuberculosis infection (LTBI) (41.2, IQR 9.8–64.9) compared to healthy controls (1.6, IQR 1.1–2.4; p<0.0001). The IP-10 mRNA and protein based tests had comparable diagnostic accuracy to QFT-TB, sensitivity (85% and 88% vs 85%) and specificity (96% and 96% vs 97%, p = ns.). Conclusion We developed a rapid, robust and accurate molecular immunodiagnostic test for M. tuberculosis infection. By combining DBS based sample acquisition, mail or currier based sample transport with centralized molecular detection, this immunodiagnostic test concept can reduce the local technological requirements everywhere and make it possible to offer highly accurate immunodiagnostic tests in low resource settings. PMID:25184553

  5. The bandmerged Planck Early Release Compact Source Catalogue: probing sub-structure in the molecular gas at high Galactic latitude

    NASA Astrophysics Data System (ADS)

    Chen, X.; Chary, R.; Pearson, T. J.; McGehee, P.; Fowler, J. W.; Helou, G.

    2016-06-01

    The Planck Early Release Compact Source Catalogue (ERCSC) includes nine lists of highly reliable sources, individually extracted at each of the nine Planck frequency channels. To facilitate the study of the Planck sources, especially their spectral behaviour across the radio/infrared frequencies, we provide a `bandmerged' catalogue of the ERCSC sources. This catalogue consists of 15 191 entries, with 79 sources detected in all nine frequency channels of Planck and 6818 sources detected in only one channel. We describe the bandmerging algorithm, including the various steps used to disentangle sources in confused regions. The multifrequency matching allows us to develop spectral energy distributions of sources between 30 and 857 GHz, in particular across the 100 GHz band, where the energetically important CO J = 1→0 line enters the Planck bandpass. We find ˜3σ-5σ evidence for contribution to the 100 GHz intensity from foreground CO along the line of sight to 147 sources with |b|>{30°}. The median excess contribution is 4.5 ± 0.9 per cent of their measured 100 GHz flux density which cannot be explained by calibration or beam uncertainties. This translates to 0.5 ± 0.1 K km s-1 of CO which must be clumped on the scale of the Planck 100 GHz beam, i.e. ˜10 arcmin. If this is due to a population of low-mass (˜15 M⊙) molecular gas clumps, the total mass in these clumps may be more than 2000 M⊙. Further, high-spatial-resolution, ground-based observations of the high-latitude sky will help shed light on the origin of this diffuse, clumpy CO emission.

  6. Novel Fluorescent Antagonist as a Molecular Probe in A3 Adenosine Receptor Binding Assays Using Flow Cytometry

    PubMed Central

    Kozma, Eszter; Kumar, T. Santhosh; Federico, Stephanie; Phan, Khai; Balasubramanian, Ramachandran; Gao, Zhan-Guo; Paoletta, Silvia; Moro, Stefano; Spalluto, Giampiero; Jacobson, Kenneth A.

    2012-01-01

    The physiological role of the A3 adenosine receptor (AR) was explored in cardiac ischaemia, inflammatory diseases and cancer. We report a new fluorophore-conjugated human (h) A3AR antagonist for application to cell-based assays in ligand discovery and for receptor imaging. Fluorescent pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidin-5-ylamine (pyrazolo-triazolo-pyrimidine, PTP) and triazolo[1,5-c]quinazolin-5-yl)amine (triazolo-quinazoline, TQ) AR antagonists were compared. A chain-extended and click-conjugated Alexa Fluor-488 TQ derivative (MRS5449) displayed a radioligand binding Ki value of 6.4 ± 2.5 nM in hA3AR-expressing CHO cell membranes. MRS5449 antagonized hA3AR agonist-induced inhibition of cyclic AMP accumulation in a concentration-dependent manner (KB 4.8 nM). Using flow cytometry (FCM), MRS5449 saturated hA3ARs with very high specific-to-nonspecific binding ratio with an equilibrium binding constant 5.15 nM, comparable to the Kd value of 6.65 nM calculated from kinetic experiments. Ki values of known AR antagonists in inhibition of MRS5449 binding in whole cell FCM were consistent with radioligand binding in membranes, but agonist binding was 5–20 fold weaker than obtained with agonist radioligand [125I]I-AB-MECA. Further binding analysis of MRS5549 suggested multiple agonist binding states of the A3AR. Molecular docking predicted binding modes of these fluorescent antagonists. Thus, MRS5449 is a useful tool for hA3AR characterization. PMID:22402302

  7. A study of dynamical processes in the Orion KL region using ALMA—probing molecular outflow and inflow

    SciTech Connect

    Wu, Yuefang; Liu, Tie; Qin, Sheng-Li

    2014-08-20

    This work reports high spatial resolution observations toward the Orion KL region with high critical density lines of CH{sub 3}CN (12{sub 4}-11{sub 4}) and CH{sub 3}OH (8{sub –1,8}-7{sub 0,7}), as well as a continuum at ∼1.3 mm band. The observations were made using the Atacama Large Millimeter/Submillimeter Array with a spatial resolution of ∼1.''5 and sensitivity of about 0.07 K and ∼0.18 K for continuum and line, respectively. The observational results showed that the gas in the Orion KL region consists of jet-propelled cores at the ridge and dense cores east and south of the region that are shaped like a wedge ring. The outflow has multiple lobes, which may originate from an explosive ejection, and is not driven by young stellar objects. Four infrared bubbles were found in the Spitzer/IRAC emissions. These bubbles, the distributions of the previously found H{sub 2} jets, the young stellar objects, and molecular gas suggest that BN is the explosive center. The burst time was estimated to be ≤1300 yr. At the same time, signatures of gravitational collapse toward Source I and the hot core were detected with material infall velocities of 1.5 km s{sup –1} and ∼0.6 km s{sup –1}, corresponding to mass accretion rates of 1.2 × 10{sup –3} M {sub ☉}/yr and 8.0 × 10{sup –5} M {sub ☉}/yr, respectively. These observations may support the belief that high-mass stars form via the accretion model, similar to their low-mass counterparts.

  8. Strong electric fields at a prototypical oxide/water interface probed by ab initio molecular dynamics: MgO(001).

    PubMed

    Laporte, Sara; Finocchi, Fabio; Paulatto, Lorenzo; Blanchard, Marc; Balan, Etienne; Guyot, François; Saitta, Antonino Marco

    2015-08-21

    We report a density-functional theory (DFT)-based study of the interface of bulk water with a prototypical oxide surface, MgO(001), and focus our study on the often-overlooked surface electric field. In particular, we observe that the bare MgO(001) surface, although charge-neutral and defectless, has an intense electric field on the Å scale. The MgO(001) surface covered with 1 water monolayer (1 ML) is investigated via a supercell accounting for the experimentally-observed (2 × 3) reconstruction, stable at ambient temperature, and in which two out of six water molecules are dissociated. This 1 ML-hydrated surface is also found to have a high, albeit short-ranged, normal component of the field. Finally, the oxide/water interface is studied via room-temperature ab initio molecular dynamics (AIMD) using 34 H2O molecules between two MgO(001) surfaces. To our best knowledge this is the first AIMD study of the MgO(001)/liquid water interface in which all atoms are treated using DFT and including several layers above the first adsorbed layer. We observe that the surface electric field, averaged over the AIMD trajectories, is still very strong on the fully-wet surface, peaking at about 3 V Å(-1). Even in the presence of bulk-like water, the structure of the first layer in contact with the surface remains similar to the (2 × 3)-reconstructed ice ad-layer on MgO(001). Moreover, we observe proton exchange within the first layer, and between the first and second layers - indeed, the O-O distances close to the surface are found to be distributed towards shorter distances, a property which has been shown to directly promote proton transfer. PMID:26193818

  9. UV laser photoactivation of hexachloroplatinate bound to individual nucleobases in vacuo as molecular level probes of a model photopharmaceutical.

    PubMed

    Matthews, Edward; Sen, Ananya; Yoshikawa, Naruo; Bergström, Ed; Dessent, Caroline E H

    2016-06-01

    Isolated molecular clusters of adenine, cytosine, thymine and uracil bound to hexachloroplatinate, PtCl6(2-), have been studied using laser electronic photodissociation spectroscopy to investigate photoactivation of a platinum complex in the vicinity of a nucleobase. These metal complex-nucleobase clusters represent model systems for identifying the fundamental photochemical processes occurring in photodynamic platinum drug therapies that target DNA. This is the first study to explore the specific role of a strongly photoactive platinum compound in the aggregate complex. Each of the clusters studied displays a broadly similar absorption spectra, with a strong λmax ∼ 4.6 eV absorption band and a subsequent increase in the absorption intensity towards higher spectral-energy. The absorption bands are traced to ligand-to-metal-charge-transfer excitations on the PtCl6(2-) moiety within the cluster, and result in Cl(-)·nucleobase and PtCl5(-) as primary photofragments. These results demonstrate how selective photoexcitation can drive distinctive photodecay channels for a model photo-pharmaceutical. In addition, cluster absorption due to excitation of nucleobase-centred chromophores is observed in the region around 5 eV. For the uracil cluster, photofragments consistent with ultrafast decay of the excited state and vibrational predissociation on the ground-state surface are observed. However, this decay channel becomes successively weaker on going from thymine to cytosine to adenine, due to differential coupling of the excited states to the electron detachment continuum. These effects demonstrate the distinctive photophysical characteristics of the different nucleobases, and are discussed in the context of the recently recorded photoelectron spectra of theses clusters. PMID:27198464

  10. Fundamental Science for Geologic Carbon Sequestration: Molecular Probes for Understanding Wet CO2 Interaction with Caprock Minerals (Invited)

    NASA Astrophysics Data System (ADS)

    Rosso, K. M.; White, D.; Murphy, E. M.; Hu, J.; Hoyt, D. W.; Wang, Z.; Lea, A. S.; Schaef, H. T.; McGrail, P.

    2009-12-01

    Capture and storage of carbon dioxide and other greenhouse gases in deep geologic formations represents one of the most promising options for minimizing the impacts of greenhouse gases on climate change. A critical issue is to demonstrate in a scientifically defensible manner that CO2 will remain stored over the long-term in the geological formation where it is injected. With regards to mineral-fluid interaction, the majority of previous research has focused on mineral reactivity in aqueous solutions containing CO2. However, at the caprock-fluid interface, interaction with the supercritical CO2 (scCO2) phase itself may become more important as the buoyant plume slowly displaces or dessicates residual aqueous solution. Mechanisms of mineral interfacial reactions with wet or water-saturated CO2 are unknown. The measurement of kinetic and thermodynamic data for mineral transformation reactions in these fluids present unique challenges. New experimental tools under development at Pacific Northwest National Laboratory are enabling in situ characterization of mineral transformation processes in scCO2/H2O fluids with molecular resolution. 29Si and 13C magic angle sample spinning nuclear magnetic resonance spectroscopy of metal carbonation reactions of model magnesium silicate minerals (e.g., Mg2SiO4 forsterite) in scCO2 shows initial transformation to MgCO3 magnesite within 20 hours at 80 atm and 80°C only when water is present for nucleophilic attack on Mg-O-Si. High pressure infrared spectroscopy detects unique spectral signatures for H2O and D2O dissolved in trace quantities (<0.08M) in scCO2 and clearly shows carbonate species as reaction intermediates for forsterite transformation to magnesite. A high-pressure atomic force microscope is under development that will enable in situ site-specific measurements of metal carbonate nucleation and growth rates on mineral surfaces in contact with scCO2 fluids. High-pressure x-ray diffraction will enable phase identification

  11. Comparative Evaluation of Sloppy Molecular Beacon and Dual-Labeled Probe Melting Temperature Assays to Identify Mutations in Mycobacterium tuberculosis Resulting in Rifampin, Fluoroquinolone and Aminoglycoside Resistance.

    PubMed

    Roh, Sandy S; Smith, Laura E; Lee, Jong Seok; Via, Laura E; Barry, Clifton E; Alland, David; Chakravorty, Soumitesh

    2015-01-01

    Several molecular assays to detect resistance to Rifampin, the Fluoroquinolones, and Aminoglycosides in Mycobacterium tuberculosis (M. tuberculosis) have been recently described. A systematic approach for comparing these assays in the laboratory is needed in order to determine the relative advantage of each assay and to decide which ones should be advanced to evaluation. We performed an analytic comparison of a Sloppy Molecular Beacon (SMB) melting temperature (Tm) assay and a Dual labeled probe (DLP) Tm assay. Both assays targeted the M. tuberculosis rpoB, gyrA, rrs genes and the eis promoter region. The sensitivity and specificity to detect mutations, analytic limit of detection (LOD) and the detection of heteroresistance were tested using a panel of 56 clinical DNA samples from drug resistant M. tuberculosis strains. Both SMB and DLP assays detected 29/29 (100%) samples with rpoB RRDR mutations and 3/3 (100%) samples with eis promoter mutations correctly. The SMB assay detected all 17/17 gyrA mutants and 22/22 rrs mutants, while the DLP assay detected 16/17 (94%) gyrA mutants and 12/22 (55%) rrs mutants. Both assays showed comparable LODs for detecting rpoB and eis mutations; however, the SMB assay LODs were at least two logs better for detecting wild type and mutants in gyrA and rrs targets. The SMB assay was also moderately better at detecting heteroresistance. In summary, both assays appeared to be promising methods to detect drug resistance associated mutations in M. tuberculosis; however, the relative advantage of each assay varied under each test condition. PMID:25938476

  12. A cost-effective sandwich electrochemiluminescence immunosensor for ultrasensitive detection of HIV-1 antibody using magnetic molecularly imprinted polymers as capture probes.

    PubMed

    Zhou, Jing; Gan, Ning; Li, Tianhua; Hu, Futao; Li, Xing; Wang, Lihong; Zheng, Lei

    2014-04-15

    In this report, a rapid and cost-effective sandwich electrochemiluminescence (ECL) immunosensor was constructed for the ultrasensitive detection of human immunodeficiency virus type 1 antibody (anti-HIV-1) using magnetic molecularly imprinted polymers (MMIPs) as capture probes by combining surface and epitope imprinting techniques and antigen conjugated with horseradish peroxidase (HRP-HIV-1) as labels. First, 3-aminobenzeneboronic acid (APBA) was used as the functional monomer and cross-linking reagent, which was polymerized on the surface of silicate-coated magnetic iron oxide nanoparticles (Fe3O4@SiO2 NPs) in the presence of human immunoglobulin G (HIgG), as the template exhibiting the same Fc region but different Fab region to anti-HIV-1 after the addition of the initiator, ammonium persulfate. This process resulted in grafting a hydrophilic molecularly imprinted polymer (MIP) film on the Fe3O4@SiO2 NPs. Thus, MMIPs, which could be reused after eluting the template, were used to recognize and enrich ultra-trace levels of anti-HIV-1. Subsequently, a novel sandwich ECL immunosensor was formed through the immunoreaction between MMIPs conjugated with varied concentrations of anti-HIV-1 and HRP-HIV-1. By the catalysis of HRP immobilized onto HRP-HIV-1 on the ECL system of Luminol-H2O2, a linear response range of the anti-HIV-1 dilution ratio (standard positive serum) was achieved from 1:20,000 to 1:50, with a detection limit of 1:60,000 (S/N=3). The developed method provides a low-cost, simple, and sensitive way for the early diagnosis of HIV infected patients. PMID:24280050

  13. Probing the Atomic and Molecular Inventory of a Beta-Pic Analog, the Young, Edge-On Debris Disk of HD32297

    NASA Astrophysics Data System (ADS)

    Redfield, Seth

    2009-07-01

    Edge-on, optically thin, debris disks provide unique opportunities to probe physical properties of the disk itself. Using the host star as the background source, trace atomic and molecular disk species can be detected in absorption. Redfield {2007} found that the recently discovered edge-on system, HD32297, has the strongest NaI absorption feature of any known debris disk, 5 times the level observed toward beta Pic, the canonical edge-on debris disk. Roberge et al. {2006} compiled the only comprehensive chemical inventory of a debris disk, using beta Pic, and found that carbon was surprisingly overabundant, which has important implications for the physical structure and support of a stable gas disk. What is severely lacking are comparison observations to determine if such an abundance pattern is typical of debris disk systems. HD32297 represents the best opportunity to make such a comparative study and perform a comprehensive gas inventory of a debris disk, due to its high NaI column density. The UV is critical for this work due to the large number of strong transitions {almost 50 ions and molecules are accessible} that are located in, and often only in, the UV. These observations will provide a much needed comparison dataset for addressing the gas chemistry of debris disk systems that are at the critical stage, near the end of planet formation, and in the process of clearing their interplanetary environments.

  14. Using EPR spectroscopy as a unique probe of molecular-scale reorganization and solvation in self-assembled gel-phase materials.

    PubMed

    Caragheorgheopol, Agneta; Edwards, William; Hardy, John G; Smith, David K; Chechik, Victor

    2014-08-01

    We describe the synthesis of spin-labeled bis-ureas which coassemble with bis-urea gelators and report on self-assembly as detected using electron paramagnetic resonance spectroscopy (EPR). Specifically, EPR detects the gel-sol transition and allows us to quantify how much spin-label is immobilized within the gel fibers and how much is present in mobile solvent pools-as controlled by temperature, gelator structure, and thermal history. EPR is also able to report on the initial self-assembly processes below the gelation threshold which are not macroscopically visible and appears to be more sensitive than NMR to intermediate-sized nongelating oligomeric species. By studying dilute solutions of gelator molecules and using either single or double spin-labels, EPR allows quantification of the initial steps of the hierarchical self-assembly process in terms of cooperativity and association constant. Finally, EPR enables us to estimate the degree of gel-fiber solvation by probing the distances between spin-labels. Comparison of experimental data against the predicted distances assuming the nanofibers are only composed of gelator molecules indicates a significant difference, which can be assigned to the presence of a quantifiable number of explicit solvent molecules. In summary, EPR provides unique data and yields powerful insight into how molecular-scale mobility and solvation impact on assembly of supramolecular gels. PMID:25017326

  15. Surface potential modification of molecular beam epitaxially grown SrTiO3-δ/Si(001) measured by Kelvin Force Probe Microscopy

    NASA Astrophysics Data System (ADS)

    Cottier, Ryan; Currie, Alexander; Theodoropoulou, Nikoleta; Texas State University Team

    2014-03-01

    SrTiO3 (STO) films have been grown by molecular beam epitaxy on p-Si(001), n-Si(001), and STO(001) substrates. The STO/Si films were of high crystalline quality as determined by x-ray diffraction (XRD) and TEM and ranged in thickness from 3.6 to 60 nm as measured by x-ray reflectivity (XRR). The partial pressure of oxygen (O2) was varied during growth to induce oxygen vacancies within the STO structure. Through additional XRD and magnetotransport studies, we estimate that for the lowest O2 pressure the oxygen deficiency is δ = 0.02. The surface potential of the films was modified through the use of a conducting atomic force microscopy (AFM) tip by scanning regions of the STO surface in contact mode with a DC bias on the tip (referred to as `writing'). Regions were written with either positive or negative voltage and then analyzed by Kelvin Force Probe Microscopy (KFPM). Following this writing mode, KFPM revealed a retained surface potential of the same polarity used in writing. The ability of the films to be written and read through this method depended on the growth O2 partial pressure with higher O2 pressures demonstrating weaker surface potential modification. The results agree with other studies regarding the drift and diffusion of charged O2 vacancies in STO. Funded by NSF Career Award, DMR-1255629.

  16. Vacancy-type defects in Mg-doped GaN grown by ammonia-based molecular beam epitaxy probed using a monoenergetic positron beam

    NASA Astrophysics Data System (ADS)

    Uedono, Akira; Malinverni, Marco; Martin, Denis; Okumura, Hironori; Ishibashi, Shoji; Grandjean, Nicolas

    2016-06-01

    Vacancy-type defects in Mg-doped GaN were probed using a monoenergetic positron beam. GaN films with a thickness of 0.5-0.7 μm were grown on GaN/sapphire templates using ammonia-based molecular beam epitaxy and characterized by measuring Doppler broadening spectra. Although no vacancies were detected in samples with a Mg concentration [Mg] below 7 × 1019 cm-3, vacancy-type defects were introduced starting at above [Mg] = 1 × 1020 cm-3. The major defect species was identified as a complex between Ga vacancy (VGa) and multiple nitrogen vacancies (VNs). The introduction of vacancy complexes was found to correlate with a decrease in the net acceptor concentration, suggesting that the defect introduction is closely related to the carrier compensation. We also investigated Mg-doped GaN layers grown using In as the surfactant. The formation of vacancy complexes was suppressed in the subsurface region (≤80 nm). The observed depth distribution of defects was attributed to the thermal instability of the defects, which resulted in the introduction of vacancy complexes during the deposition process.

  17. Use of molecular beacons to probe for messenger RNA release from ribosomes during 5'-translational blockage by consecutive low-usage codons in Escherichia coli

    NASA Astrophysics Data System (ADS)

    Gao, Wenwu; Tyagi, Sanjay; Kramer, Fred R.; Goldman, Emanuel

    2000-03-01

    In `5'-translational blockage,' significantly reduced yields of proteins are synthesized in Escherichia coli when consecutive low-usage codons are inserted near translation starts of messages (with reduced or no effect when these same codons are inserted downstream). We tested the hypothesis that ribosomes encountering these low-usage codons prematurely release the mRNA. RNA from polysome gradients was fractionated into pools of polysomes, monosomes and ribosomes-free. New hybridization probes, called `molecular beacons,' and standard slot-blots, were used to detect test messages containing either consecutive low-usage AGG (arginine) or synonymous high-usage CGU insertions near the 5' end. The results show an approximately twofold increase in the ratio of free to bound mRNA when the low-usage codons were present compared to high-usage codons. In contrast, there was no difference in the ratio of free to bound mRNA when consecutive low-usage CUA or high-usage CUG (leucine) codons were inserted, or when the arginine codons were inserted near the 3' end. These data indicate that at least some mRNA is released from ribosomes during 5'-translational blockage by arginine but not leucine codons, and they support proposals that premature termination of translation can occur in some conditions in vivo in the absence of a stop codon.

  18. Foldable polymers as probes

    DOEpatents

    Li, Alexander D. Q.; Wang, Wei

    2007-07-03

    Disclosed herein are novel probes, which can be used to detect and identify target molecules of interest in a sample. The disclosed probes can be used to monitor conformational changes induced by molecular recognition events in addition to providing signaling the presence and/or identity of a target molecule. Methods, including solid phase synthesis techniques, for making probe molecules that exhibit changes in their optical properties upon target molecule binding are described in the disclosure. Also disclosed herein are novel chromophore moieties, which have tailored fluorescent emission spectra.

  19. Foldable polymers as probes

    DOEpatents

    Li, Alexander D. Q.; Wang, Wei

    2009-07-07

    Disclosed herein are novel probes, which can be used to detect and identify target molecules of interest in a sample. The disclosed probes can be used to monitor conformational changes induced by molecular recognition events in addition to providing signaling the presence and/or identity of a target molecule. Methods, including solid phase synthesis techniques, for making probe molecules that exhibit changes in their optical properties upon target molecule binding are described in the disclosure. Also disclosed herein are novel chromophore moieties, which have tailored fluorescent emission spectra.

  20. Probing Allosteric Inhibition Mechanisms of the Hsp70 Chaperone Proteins Using Molecular Dynamics Simulations and Analysis of the Residue Interaction Networks.

    PubMed

    Stetz, Gabrielle; Verkhivker, Gennady M

    2016-08-22

    Although molecular mechanisms of allosteric regulation in the Hsp70 chaperones have been extensively studied at both structural and functional levels, the current understanding of allosteric inhibition of chaperone activities by small molecules is still lacking. In the current study, using a battery of computational approaches, we probed allosteric inhibition mechanisms of E. coli Hsp70 (DnaK) and human Hsp70 proteins by small molecule inhibitors PET-16 and novolactone. Molecular dynamics simulations and binding free energy analysis were combined with network-based modeling of residue interactions and allosteric communications to systematically characterize and compare molecular signatures of the apo form, substrate-bound, and inhibitor-bound chaperone complexes. The results suggested a mechanism by which the allosteric inhibitors may leverage binding energy hotspots in the interaction networks to stabilize a specific conformational state and impair the interdomain allosteric control. Using the network-based centrality analysis and community detection, we demonstrated that substrate binding may strengthen the connectivity of local interaction communities, leading to a dense interaction network that can promote an efficient allosteric communication. In contrast, binding of PET-16 to DnaK may induce significant dynamic changes and lead to a fractured interaction network and impaired allosteric communications in the DnaK complex. By using a mechanistic-based analysis of distance fluctuation maps and allosteric propensities of protein residues, we determined that the allosteric network in the PET-16 complex may be small and localized due to the reduced communication and low cooperativity of the substrate binding loops, which may promote the higher rates of substrate dissociation and the decreased substrate affinity. In comparison with the significant effect of PET-16, binding of novolactone to HSPA1A may cause only moderate network changes and preserve allosteric

  1. Spectrophotometric probe

    DOEpatents

    Prather, W.S.; O'Rourke, P.E.

    1994-08-02

    A support structure is described bearing at least one probe for making spectrophotometric measurements of a fluid using a source of light and a spectrophotometer. The probe includes a housing with two optical fibers and a planoconvex lens. A sleeve bearing a mirror surrounds the housing. The lens is separated from the mirror by a fixed distance, defining an interior space for receiving a volume of the fluid sample. A plurality of throughholes extending through the sleeve communicate between the sample volume and the exterior of the probe, all but one hole bearing a screen. A protective jacket surrounds the probe. A hollow conduit bearing a tube is formed in the wall of the probe for venting any air in the interior space when fluid enters. The probe is held at an acute angle so the optic fibers carrying the light to and from the probe are not bent severely on emergence from the probe. 3 figs.

  2. Spectrophotometric probe

    DOEpatents

    Prather, William S.; O'Rourke, Patrick E.

    1994-01-01

    A support structure bearing at least one probe for making spectrophotometric measurements of a fluid using a source of light and a spectrophotometer. The probe includes a housing with two optical fibers and a planoconvex lens. A sleeve bearing a mirror surrounds the housing. The lens is separated from the mirror by a fixed distance, defining an interior space for receiving a volume of the fluid sample. A plurality of throughholes extending through the sleeve communicate between the sample volume and the exterior of the probe, all but one hole bearing a screen. A protective jacket surrounds the probe. A hollow conduit bearing a tube is formed in the wall of the probe for venting any air in the interior space when fluid enters. The probe is held at an acute angle so the optic fibers carrying the light to and from the probe are not bent severely on emergence from the probe.

  3. Design, synthesis, and biological evaluation of 4-(5-dimethylamino-naphthalene-1-sulfon-amido)-3-(4-iodophenyl)butanoic acid as a novel molecular probe for apoptosis imaging

    SciTech Connect

    Zeng, Wenbin; Miao, Weimin; Le Puil, Michael; Shi, Guangqing; Biggerstaff, John; Kabalka, George W.; Townsend, David

    2010-07-30

    Research highlights: {yields} Annexin V is the gold standard probe for imaging apoptosis. {yields} Unfavorable profiles of Annexin V make it difficult to apply in the clinic. {yields} A novel small-molecular probe DNSBA was designed as an alternative to Annexin V. {yields} DNSBA specifically and selectively detect apoptotic cancer cells at all stages. {yields} DNSBA is a potential SPECT and PET agent when labeled with radioiodine. -- Abstract: Apoptosis (programmed cell death) plays a crucial role in the pathogenesis of many disorders, thus the detection of apoptotic cells can provide the physician with important information to further therapeutic strategies and would substantially advance patient care. A small molecule, 4-(5-dimethylamino-naphthalene-1-sulfonamido)-3-(4-iodo-phenyl)butanoic acid (DNSBA), was designed as a novel probe for imaging apoptosis and synthesized with good yield. The biological characterization demonstrated that DNSBA can be used to specifically and selectively detect apoptotic cancer cells at all stages. DNSBA is also designed as a potential SPECT and PET probe when labeled with radioiodine (I-123, -124, and -131).

  4. Mechanosensitive membrane probes.

    PubMed

    Dal Molin, Marta; Verolet, Quentin; Soleimanpour, Saeideh; Matile, Stefan

    2015-04-13

    This article assembles pertinent insights behind the concept of planarizable push-pull probes. As a response to the planarization of their polarized ground state, a red shift of their excitation maximum is expected to report on either the disorder, the tension, or the potential of biomembranes. The combination of chromophore planarization and polarization contributes to various, usually more complex processes in nature. Examples include the color change of crabs or lobsters during cooking or the chemistry of vision, particularly color vision. The summary of lessons from nature is followed by an overview of mechanosensitive organic materials. Although often twisted and sometimes also polarized, their change of color under pressure usually originates from changes in their crystal packing. Intriguing exceptions include the planarization of several elegantly twisted phenylethynyl oligomers and polymers. Also mechanosensitive probes in plastics usually respond to stretching by disassembly. True ground-state planarization in response to molecular recognition is best exemplified with the binding of thoughtfully twisted cationic polythiophenes to single- and double-stranded oligonucleotides. Molecular rotors, en vogue as viscosity sensors in cells, operate by deplanarization of the first excited state. Pertinent recent examples are described, focusing on λ-ratiometry and intracellular targeting. Complementary to planarization of the ground state with twisted push-pull probes, molecular rotors report on environmental changes with quenching or shifts in emission rather than absorption. The labeling of mechanosensitive channels is discussed as a bioengineering approach to bypass the challenge to create molecular mechanosensitivity and use biological systems instead to sense membrane tension. With planarizable push-pull probes, this challenge is met not with twistome screening, but with "fluorescent flippers," a new concept to insert large and bright monomers into oligomeric

  5. In situ molecular hybridization for detection of Aleutian mink disease parvovirus DNA by using strand-specific probes: identification of target cells for viral replication in cell cultures and in mink kits with virus-induced interstitial pneumonia.

    PubMed Central

    Alexandersen, S; Bloom, M E; Wolfinbarger, J; Race, R E

    1987-01-01

    Strand-specific hybridization probes were utilized in in situ molecular hybridization specifically to localize replicative form DNA of Aleutian mink disease parvovirus (ADV). Throughout in vitro infection, duplex replicative form DNA of ADV was located in the cell nuclei. Single-stranded virion DNA and capsid proteins were present in the nuclei early in infection, but were later translocated to the cytoplasm. In neonatal mink, ADV causes acute interstitial pneumonia, and replicative forms of viral DNA were found predominantly in alveolar type II cells of the lung. Viral DNA was also found in other organs, but strand-specific probes made it possible to show that most of this DNA represented virus sequestration. In addition, glomerular immune complexes containing intact virions were detected, suggesting that ADV virions may have a role in the genesis of ADV-induced glomerulonephritis. Images PMID:3037104

  6. Optical probe

    DOEpatents

    Hencken, Kenneth; Flower, William L.

    1999-01-01

    A compact optical probe is disclosed particularly useful for analysis of emissions in industrial environments. The instant invention provides a geometry for optically-based measurements that allows all optical components (source, detector, rely optics, etc.) to be located in proximity to one another. The geometry of the probe disclosed herein provides a means for making optical measurements in environments where it is difficult and/or expensive to gain access to the vicinity of a flow stream to be measured. Significantly, the lens geometry of the optical probe allows the analysis location within a flow stream being monitored to be moved while maintaining optical alignment of all components even when the optical probe is focused on a plurality of different analysis points within the flow stream.

  7. Development and Application of Multiple-Probe Scanning Probe Microscopes

    SciTech Connect

    Nakayama, T.; Kubo, O.; Shingaya, Y.; Higuchi, S.; Hasegawa, T.; Jiang, C. S.; Okuda, T.; Kuwahara, Y.; Takami, K.; Aono, M.

    2012-04-03

    the research of advanced materials based on nanoscience and nanotechnology, it is often desirable to measure nanoscale local electrical conductivity at a designated position of a given sample. For this purpose, multiple-probe scanning probe microscopes (MP-SPMs), in which two, three or four scanning tunneling microscope (STM) or atomic force microscope (AFM) probes are operated independently, have been developed. Each probe in an MP-SPM is used not only for observing high-resolution STM or AFM images but also for forming an electrical contact enabling nanoscale local electrical conductivity measurement. The world's first double-probe STM (DP-STM) developed by the authors, which was subsequently modified to a triple-probe STM (TP-STM), has been used to measure the conductivities of one-dimensional metal nanowires and carbon nanotubes and also two-dimensional molecular films. A quadruple-probe STM (QP-STM) has also been developed and used to measure the conductivity of two-dimensional molecular films without the ambiguity of contact resistance between the probe and sample. Moreover, a quadruple-probe AFM (QP-AFM) with four conductive tuning-fork-type self-detection force sensing probes has been developed to measure the conductivity of a nanostructure on an insulating substrate. A general-purpose computer software to control four probes at the same time has also been developed and used in the operation of the QP-AFM. These developments and applications of MP-SPMs are reviewed in this paper.

  8. A differentially selective molecular probe for detection of trivalent ions (Al(3+), Cr(3+) and Fe(3+)) upon single excitation in mixed aqueous medium.

    PubMed

    Paul, Sima; Manna, Abhishek; Goswami, Shyamaprosad

    2015-07-14

    A chemosensor was developed which could selectively detect and differentiate trivalent metal ions (Al(3+), Cr(3+) and Fe(3+)) upon single excitation at two different wavelengths in aqueous medium. This probe selectively detects trivalent ions in the presence of different metal ions in aqueous medium. It shows an excellent performance in the "dipstick" method. PMID:26051708

  9. Diagnostic Molecular Mycobacteriology in Regions With Low Tuberculosis Endemicity: Combining Real-time PCR Assays for Detection of Multiple Mycobacterial Pathogens With Line Probe Assays for Identification of Resistance Mutations.

    PubMed

    Deggim-Messmer, Vanessa; Bloemberg, Guido V; Ritter, Claudia; Voit, Antje; Hömke, Rico; Keller, Peter M; Böttger, Erik C

    2016-07-01

    Molecular assays have not yet been able to replace time-consuming culture-based methods in clinical mycobacteriology. Using 6875 clinical samples and a study period of 35months we evaluated the use of PCR-based assays to establish a diagnostic workflow with a fast time-to-result of 1-2days, for 1. detection of Mycobacterium tuberculosis complex (MTB), 2. detection and identification of nontuberculous mycobacteria (NTM), and 3. identification of drug susceptible MTB. MTB molecular-based detection and culture gave concordant results for 97.7% of the specimens. NTM PCR-based detection and culture gave concordant results for 97.0% of the specimens. Defining specimens on the basis of combined laboratory data as true positives or negatives with discrepant results resolved by clinical chart reviews, we calculated sensitivity, specificity, PPV and NPV for PCR-based MTB detection as 84.7%, 100%, 100%, and 98.7%; the corresponding values for culture-based MTB detection were 86.3%, 100%, 100%, and 98.8%. PCR-based detection of NTM had a sensitivity of 84.7% compared to 78.0% of that of culture-based NTM detection. Molecular drug susceptibility testing (DST) by line-probe assay was found to predict phenotypic DST results in MTB with excellent accuracy. Our findings suggest a diagnostic algorithm to largely replace lengthy culture-based techniques by rapid molecular-based methods. PMID:27333026

  10. Conductivity Probe

    NASA Technical Reports Server (NTRS)

    2008-01-01

    The Thermal and Electrical Conductivity Probe (TECP) for NASA's Phoenix Mars Lander took measurements in Martian soil and in the air.

    The needles on the end of the instrument were inserted into the Martian soil, allowing TECP to measure the propagation of both thermal and electrical energy. TECP also measured the humidity in the surrounding air.

    The needles on the probe are 15 millimeters (0.6 inch) long.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  11. Comparison of DC and AC Transport in 1.5-7.5 nm Oligophenylene Imine Molecular Wires across Two Junction Platforms: Eutectic Ga-In versus Conducting Probe Atomic Force Microscope Junctions.

    PubMed

    Sangeeth, C S Suchand; Demissie, Abel T; Yuan, Li; Wang, Tao; Frisbie, C Daniel; Nijhuis, Christian A

    2016-06-15

    We have utilized DC and AC transport measurements to measure the resistance and capacitance of thin films of conjugated oligophenyleneimine (OPI) molecules ranging from 1.5 to 7.5 nm in length. These films were synthesized on Au surfaces utilizing the imine condensation chemistry between terephthalaldehyde and 1,4-benzenediamine. Near edge X-ray absorption fine structure (NEXAFS) spectroscopy yielded molecular tilt angles of 33-43°. To probe DC and AC transport, we employed Au-S-OPI//GaOx/EGaIn junctions having contact areas of 9.6 × 10(2) μm(2) (10(9) nm(2)) and compared to previously reported DC results on the same OPI system obtained using Au-S-OPI//Au conducting probe atomic force microscopy (CP-AFM) junctions with 50 nm(2) areas. We found that intensive observables agreed very well across the two junction platforms. Specifically, the EGaIn-based junctions showed: (i) a crossover from tunneling to hopping transport at molecular lengths near 4 nm; (ii) activated transport for wires >4 nm in length with an activation energy of 0.245 ± 0.008 eV for OPI-7; (iii) exponential dependence of conductance with molecular length with a decay constant β = 2.84 ± 0.18 nm(-1) (DC) and 2.92 ± 0.13 nm(-1) (AC) in the tunneling regime, and an apparent β = 1.01 ± 0.08 nm(-1) (DC) and 0.99 ± 0.11 nm(-1) (AC) in the hopping regime; (iv) previously unreported dielectric constant of 4.3 ± 0.2 along the OPI wires. However, the absolute resistances of Au-S-OPI//GaOx/EGaIn junctions were approximately 100 times higher than the corresponding CP-AFM junctions due to differences in metal-molecule contact resistances between the two platforms. PMID:27172452

  12. A combined spectroscopic, docking and molecular dynamics simulation approach to probing binding of a Schiff base complex to human serum albumin

    NASA Astrophysics Data System (ADS)

    Fani, N.; Bordbar, A. K.; Ghayeb, Y.

    2013-02-01

    The molecular mechanism of a Schiff base complex ((E)-((E)-2-(3-((E)-((E)-3(mercapto (methylthio) methylene)cyclopentylidene) amino) propylimino) cyclopentylidene) (methylthio) methanethiol) binding to Human Serum Albumin (HSA) was investigated by fluorescence quenching, absorption spectroscopy, molecular docking and molecular dynamics (MD) simulation procedures. The fluorescence emission of HSA was quenched by this Schiff base complex that has been analyzed for estimation of binding parameters. The titration of Schiff base solution by various amount of HSA was also followed by UV-Vis absorption spectroscopy and the corresponding data were analyzed by suitable models. The results revealed that this Schiff base has an ability to bind strongly to HSA and formed 1:1 complex. Energy transfer mechanism of quenching was discussed and the value of 5.45 ± 0.06 nm was calculated as the mean distance between the bound complex and the Trp residue. This is implying the high possibility of energy transfer from HSA to this Schiff base complex. Molecular docking results indicated that the main active binding site for this Schiff base complex is site III in subdomain IB. Moreover, MD simulation results suggested that this Schiff base complex can interact with HSA, without affecting the secondary structure of HSA but probably with a slight modification of its tertiary structure. MD simulations, molecular docking and experimental data reciprocally supported each other.

  13. Validation of a simple and fast method to quantify in vitro mineralization with fluorescent probes used in molecular imaging of bone

    SciTech Connect

    Moester, Martiene J.C.; Schoeman, Monique A.E.; Oudshoorn, Ineke B.; Beusekom, Mara M. van; Mol, Isabel M.; Kaijzel, Eric L.; Löwik, Clemens W.G.M.; Rooij, Karien E. de

    2014-01-03

    Highlights: •We validate a simple and fast method of quantification of in vitro mineralization. •Fluorescently labeled agents can detect calcium deposits in the mineralized matrix of cell cultures. •Fluorescent signals of the probes correlated with Alizarin Red S staining. -- Abstract: Alizarin Red S staining is the standard method to indicate and quantify matrix mineralization during differentiation of osteoblast cultures. KS483 cells are multipotent mouse mesenchymal progenitor cells that can differentiate into chondrocytes, adipocytes and osteoblasts and are a well-characterized model for the study of bone formation. Matrix mineralization is the last step of differentiation of bone cells and is therefore a very important outcome measure in bone research. Fluorescently labelled calcium chelating agents, e.g. BoneTag and OsteoSense, are currently used for in vivo imaging of bone. The aim of the present study was to validate these probes for fast and simple detection and quantification of in vitro matrix mineralization by KS483 cells and thus enabling high-throughput screening experiments. KS483 cells were cultured under osteogenic conditions in the presence of compounds that either stimulate or inhibit osteoblast differentiation and thereby matrix mineralization. After 21 days of differentiation, fluorescence of stained cultures was quantified with a near-infrared imager and compared to Alizarin Red S quantification. Fluorescence of both probes closely correlated to Alizarin Red S staining in both inhibiting and stimulating conditions. In addition, both compounds displayed specificity for mineralized nodules. We therefore conclude that this method of quantification of bone mineralization using fluorescent compounds is a good alternative for the Alizarin Red S staining.

  14. Benzofuroxan as a thiol-specific reactivity probe. Kinetics of its reactions with papain, ficin, bromelain and low-molecular-weight thiols.

    PubMed Central

    Shipton, M; Brocklehurst, K

    1977-01-01

    1. The characteristics of benzofuroxan (benzofurazan 1-oxide, benzo-2-oxa-1,3-diazole N-oxide) that relate to its application as a reactivity probe for the study of environments of thiol groups are discussed. 2. To establish a kinetic and mechanistic basis for its use as a probe, a kinetic study of its reaction with 2-mercaptoethanol was carried out. 3. This reaction appears to proceed by a rate-determining attack of the thiolate ion on one of the electrophilic centres of benzofuroxan (possibly C-6) to provide a low steady-state concentration of an intermediate adduct; rapid reaction of this adduct with a second molecule of thiol gives the disulphide and o-benzoquinone dioxime. 4. The effects of the different types of environment that proteins can provide on the kinetic characteristics of reactions of thiol groups with benzofuroxan are delineated. 5. Benzofuroxan was used as a thiolspecific reactivity probe to investigate the active centres of papain (EC 3.4.22.2), ficin (EC 3.4.22.3) and bromelain (EC 3.4.22.4). The results support the concept that the active centres of all three enzymes either contain a nucleophilic thiolate ion whose formation is characterized by a pKa of 3-4 and whose reaction with an electrophile can be assisted by interaction of a site of high electron density in the electrophile with active-centre imidazolium ion of pKa 8-9, or can provide such ions by protonic redistribution in enzyme-reagent or enzyme-substrate complexes. PMID:23765

  15. Pollution Probe.

    ERIC Educational Resources Information Center

    Chant, Donald A.

    This book is written as a statement of concern about pollution by members of Pollution Probe, a citizens' anti-pollution group in Canada. Its purpose is to create public awareness and pressure for the eventual solution to pollution problems. The need for effective government policies to control the population explosion, conserve natural resources,…

  16. Molecular interactions of a model bile salt and porcine bile with (1,3:1,4)-β-glucans and arabinoxylans probed by (13)C NMR and SAXS.

    PubMed

    Gunness, Purnima; Flanagan, Bernadine M; Mata, Jitendra P; Gilbert, Elliot P; Gidley, Michael J

    2016-04-15

    Two main classes of interaction between soluble dietary fibres (SDFs), such as (1,3:1,4)-β-D-glucan (βG) and arabinoxylan (AX) and bile salt (BS) or diluted porcine bile, were identified by (13)C NMR and small angle X-ray scattering (SAXS). Small chemical shift differences of BS NMR resonances were consistent with effective local concentration or dilution of BS micelles mostly by βG, suggesting dynamic interactions; whilst the reduced line widths/intensities observed were mostly caused by wheat AX and the highest molecular size and concentrations of βG. SAXS showed evidence of changes in βG but not AX in the presence of BS micelles, at >13 nm length scale consistent with molecular level interactions. Thus intermolecular interactions between SDF and BS depend on both SDF source and its molecular weight and may occur alone or in combination. PMID:26617003

  17. Molecular characterization of Mycobacterium avium complex isolates giving discordant results in AccuProbe tests by PCR-restriction enzyme analysis, 16S rRNA gene sequencing, and DT1-DT6 PCR.

    PubMed Central

    Devallois, A; Picardeau, M; Paramasivan, C N; Vincent, V; Rastogi, N

    1997-01-01

    Based on cultural and biochemical tests, a total of 84 strains (72 clinical and 12 environmental isolates from the Caribbean Isles, Europe, and the Indian subcontinent) were identified as members of the Mycobacterium avium complex (MAC). They were further characterized with MAC, M. avium, and M. intracellulare probes of the AccuProbe system, and this was followed by selective amplification of DT6 and DT1 sequences. Seventy isolates gave concordant results; 63 were identified as M. avium, 5 were identified as M. intracellulare, and 24 remained untypeable by both methods. Fourteen isolates gave discrepant results, as they were DT1 positive but gave negative results by the M. intracellulare AccuProbe test. Consequently, a detailed molecular analysis of all DT1-positive isolates (14 discrepant strains plus 5 M. intracellulare strains) was performed by PCR-restriction analysis (PRA) of the hsp65 gene and 16S rRNA gene sequencing. The results confirmed the reported heterogeneity of M. intracellulare, as only 6 of 19 isolates (32%) gave PRA results compatible with published M. intracellulare profiles while the rest of the isolates were grouped in four previously unpublished profiles. 16S rRNA gene sequencing showed that only 8 of 19 isolates (42%) were related to M. intracellulare IWGMT 90247 (EMBL accession no. X88917), the rest being related to MCRO19 (EMBL accession no. X93030) and MIWGTMR10 (EMBL accession no. X88915). In conclusion, we have characterized a significant number of MAC isolates which were not identified by the AccuProbe test, PRA, or 16S rRNA sequencing. However, all of them were identifiable by DT1-DT6 PCR (they were DT6 negative and DT1 positive) and could be tentatively identified as M. intracellulare based on previously published observations. It is noteworthy that the majority of such isolates (14 of 19) were from the Indian subcontinent, with 12 of 14 being environmental isolates. Our study confirms the marked heterogeneity of M. intracellulare

  18. Length of hydrocarbon chain influences location of curcumin in liposomes: Curcumin as a molecular probe to study ethanol induced interdigitation of liposomes.

    PubMed

    El Khoury, Elsy; Patra, Digambara

    2016-05-01

    Using fluorescence quenching of curcumin in 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) liposomes by brominated derivatives of fatty acids, the location of curcumin has been studied, which indicates length of hydrocarbon chain has an effect on the location of curcumin in liposomes. Change of fluorescence intensity of curcumin with temperature in the presence of liposomes helps to estimate the phase transition temperature of these liposomes, thus, influence of cholesterol on liposome properties has been studied using curcumin as a molecule probe. The cooperativity due to the interactions between the hydrocarbon chains during melting accelerates the phase transition of DPPC liposomes in the presence of high percentage of cholesterol whereas high percentage of cholesterol generates a rather rigid DMPC liposome over a wide range of temperatures. We used ethanol to induce interdigitation between the hydrophobic chains of the lipids and studied this effect using curcumin as fluorescence probe. As a result of interdigitation, curcumin fluorescence is quenched in liposomes. The compact arrangement of the acyl chains prevents curcumin from penetrating deep near the midplane. In the liquid crystalline phase ethanol introduces a kind of order to the more fluid liposome, and does not leave space for curcumin to be inserted away from water. PMID:26945646

  19. Measurement Of Molecular Mobilities Of Polymers

    NASA Technical Reports Server (NTRS)

    Kim, Soon Sam; Tsay, Fun-Dow

    1989-01-01

    New molecular-probe technique used to measure molecular mobility of polymer. Method based on use of time-resolved electron-spin resonance (ESR) spectroscopy to monitor decay of transient nutation amplitudes from photoexcited triplet states of probe molecules with which polymer is doped. The higher molecular mobility of polymer matrix, the faster nutation amplitudes of the probe molecules decay.

  20. Mapping Cannabinoid 1 Receptor Allosteric Site(s): Critical Molecular Determinant and Signaling Profile of GAT100, a Novel, Potent, and Irreversibly Binding Probe.

    PubMed

    Laprairie, Robert B; Kulkarni, Abhijit R; Kulkarni, Pushkar M; Hurst, Dow P; Lynch, Diane; Reggio, Patricia H; Janero, David R; Pertwee, Roger G; Stevenson, Lesley A; Kelly, Melanie E M; Denovan-Wright, Eileen M; Thakur, Ganesh A

    2016-06-15

    One of the most abundant G-protein coupled receptors (GPCRs) in brain, the cannabinoid 1 receptor (CB1R), is a tractable therapeutic target for treating diverse psychobehavioral and somatic disorders. Adverse on-target effects associated with small-molecule CB1R orthosteric agonists and inverse agonists/antagonists have plagued their translational potential. Allosteric CB1R modulators offer a potentially safer modality through which CB1R signaling may be directed for therapeutic benefit. Rational design of candidate, druglike CB1R allosteric modulators requires greater understanding of the architecture of the CB1R allosteric endodomain(s) and the capacity of CB1R allosteric ligands to tune the receptor's information output. We have recently reported the synthesis of a focused library of rationally designed, covalent analogues of Org27569 and PSNCBAM-1, two prototypic CB1R negative allosteric modulators (NAMs). Among the novel, pharmacologically active CB1R NAMs reported, the isothiocyanate GAT100 emerged as the lead by virtue of its exceptional potency in the [(35)S]GTPγS and β-arrestin signaling assays and its ability to label CB1R as a covalent allosteric probe with significantly reduced inverse agonism in the [(35)S]GTPγS assay as compared to Org27569. We report here a comprehensive functional profiling of GAT100 across an array of important downstream cell-signaling pathways and analysis of its potential orthosteric probe-dependence and signaling bias. The results demonstrate that GAT100 is a NAM of the orthosteric CB1R agonist CP55,940 and the endocannabinoids 2-arachidonoylglycerol and anandamide for β-arrestin1 recruitment, PLCβ3 and ERK1/2 phosphorylation, cAMP accumulation, and CB1R internalization in HEK293A cells overexpressing CB1R and in Neuro2a and STHdh(Q7/Q7) cells endogenously expressing CB1R. Distinctively, GAT100 was a more potent and efficacious CB1R NAM than Org27569 and PSNCBAM-1 in all signaling assays and did not exhibit the inverse

  1. Lateral distribution of NBD-PC fluorescent lipid analogs in membranes probed by molecular dynamics-assisted analysis of Förster Resonance Energy Transfer (FRET) and fluorescence quenching.

    PubMed

    Loura, Luís M S

    2012-01-01

    Förster resonance energy transfer (FRET) is a powerful tool used for many problems in membrane biophysics, including characterization of the lateral distribution of lipid components and other species of interest. However, quantitative analysis of FRET data with a topological model requires adequate choices for the values of several input parameters, some of which are difficult to obtain experimentally in an independent manner. For this purpose, atomistic molecular dynamics (MD) simulations can be potentially useful as they provide direct detailed information on transverse probe localization, relative probe orientation, and membrane surface area, all of which are required for analysis of FRET data. This is illustrated here for the FRET pairs involving 1,6-diphenylhexatriene (DPH) as donor and either 1-palmitoyl,2-(6-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino] hexanoyl)- sn-glycero-3-phosphocholine (C6-NBD-PC) or 1-palmitoyl,2-(12-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino]dodecanoyl)-sn-glycero-3-phosphocholine (C12-NBD-PC) as acceptors, in fluid vesicles of 1,2-dipalmitoyl-sn-3-glycerophosphocholine (DPPC, 50 °C). Incorporation of results from MD simulations improves the statistical quality of model fitting to the experimental FRET data. Furthermore, the decay of DPH in the presence of moderate amounts of C12-NBD-PC (>0.4 mol%) is consistent with non-random lateral distribution of the latter, at variance with C6-NBD-PC, for which aggregation is ruled out up to 2.5 mol% concentration. These conclusions are supported by analysis of NBD-PC fluorescence self-quenching. Implications regarding the relative utility of these probes in membrane studies are discussed. PMID:23203080

  2. Stable Isotope Probing of an Algal Bloom To Identify Uncultivated Members of the Rhodobacteraceae Associated with Low-Molecular-Weight Polycyclic Aromatic Hydrocarbon Degradation▿

    PubMed Central

    Gutierrez, Tony; Singleton, David R.; Aitken, Michael D.; Semple, Kirk T.

    2011-01-01

    Polycyclic aromatic hydrocarbon (PAH)-degrading bacteria associated with an algal bloom in Tampa Bay, FL, were investigated by stable isotope probing (SIP) with uniformly labeled [13C]naphthalene. The dominant sequences in clone libraries constructed from 13C-enriched bacterial DNA (from naphthalene enrichments) were identified as uncharacterized members of the family Rhodobacteraceae. Quantitative PCR primers targeting the 16S rRNA gene of these uncultivated organisms were used to determine their abundance in incubations amended with unlabeled naphthalene and phenanthrene, both of which showed substantial increases in gene copy numbers during the experiments. As demonstrated by this work, the application of uniformly 13C-labeled PAHs in SIP experiments can successfully be used to identify novel PAH-degrading bacteria in marine waters. PMID:21926219

  3. A bimodal molecular imaging probe based on chitosan encapsulated magneto-fluorescent nanocomposite offers biocompatibility, visualization of specific cancer cells in vitro and lung tissues in vivo.

    PubMed

    Walia, Shanka; Sharma, Supriya; Markand Kulurkar, Pankaj; Patial, Vikram; Acharya, Amitabha

    2016-02-10

    Multifunctional hybrid nanocomposite material, consists of chitosan encapsulated iron oxide (as MRI contrasting agent), CdS (as fluorescent probe) nanoparticles and podophyllotoxin (as anticancer drug) was synthesized and characterized. The TEM studies suggested the size of the NPs to be in the range of 80-100 nm. These nanocomposites were treated with different cancer cell lines viz., KB, C6 and A549 cells. Fluorescence imaging and Perl's Prussian blue staining confirmed the presence of these nanocomposites inside both KB and C6 cells but not in A549 cells. Cytotoxicity experiments revealed that these biopolymer coated nanocomposites showed minimal toxicity towards cancerous cells. Further the intraperitoneal administration of one of the nanoformulations to Wistar rats suggested deposition of these nanocomposites in the lungs. The hematological, biochemical and histopathological analysis confirmed that these nanocomposites are safe to use as a novel dual mode imaging material. PMID:26680315

  4. Array of Synthetic Oligonucleotides to Generate Unique Multi-Target Artificial Positive Controls and Molecular Probe-Based Discrimination of Liposcelis Species

    PubMed Central

    Arif, Mohammad; Opit, George; Mendoza-Yerbafría, Abigail; Dobhal, Shefali; Li, Zhihong; Kučerová, Zuzana; Ochoa-Corona, Francisco M.

    2015-01-01

    Several species of the genus Liposcelis are common insect pests that cause serious qualitative and quantitative losses to various stored grains and processed grain products. They also can contaminate foods, transmit pathogenic microorganisms and cause allergies in humans. The common occurrence of multi-species infestations and the fact that it is difficult to identify and discriminate Liposcelis spp. make accurate, rapid detection and discriminatory tools absolutely necessary for confirmation of their identity. In this study, PCR primers and probes specific to different Liposcelis spp. were designed based on nucleotide sequences of the cytochrome oxidase 1 (CO1) gene. Primer sets ObsCo13F/13R, PeaCo15F/14R, BosCO7F/7R, BruCo5F/5R, and DecCo11F/11R were used to specifically detect Liposcelis obscura Broadhead, Liposcelis pearmani Lienhard, Liposcelis bostrychophila Badonnel, Liposcelis brunnea Motschulsky and Liposcelis decolor (Pearman) in multiplex endpoint PCRs, which amplified products of 438-, 351-, 191-, 140-, and 87-bp, respectively. In multiplex TaqMan qPCR assays, orange, yellow, red, crimson and green channels corresponding to reporter dyes 6-ROXN, HEX, Cy5, Quasar705 and 6-FAM specifically detected L. obscura, L. brunnea, L. bostrychophila, L. pearmani and L. decolor, respectively. All developed primer and probe sets allowed specific amplification of corresponding targeted Liposcelis species. The development of multiplex endpoint PCR and multiplex TaqMan qPCR will greatly facilitate psocid identification and their management. The use of APCs will streamline and standardize PCR assays. APC will also provide the opportunity to have all positive controls in a single tube, which reduces maintenance cost and labor, but increases the accuracy and reliability of the assays. These novel methods from our study will have applications in pest management, biosecurity, quarantine, food safety, and routine diagnostics. PMID:26086728

  5. Metal-Directed Self-Assembly of a Polyoxometalate-Based Molecular Triangle: Using Powerful Analytical Tools to Probe the Chemical Structure of Complex Supramolecular Assemblies.

    PubMed

    Izzet, Guillaume; Macdonell, Andrew; Rinfray, Corentin; Piot, Madeleine; Renaudineau, Séverine; Derat, Etienne; Abécassis, Benjamin; Afonso, Carlos; Proust, Anna

    2015-12-21

    A polyoxometalate-based molecular triangle has been synthesized through the metal-driven self-assembly of covalent organic/inorganic hybrid oxo-clusters with remote pyridyl binding sites. The new metallomacrocycle was unambiguously characterized by using a combination of (1)H NMR spectroscopy, 2D diffusion NMR spectroscopy (DOSY), electrospray ionization travelling wave ion mobility mass spectrometry (ESI-TWIM-MS), small-angle X-ray scattering (SAXS) and molecular modelling. The collision cross-sections obtained from TWIM-MS and the hydrodynamic radii derived from DOSY are in good agreement with the geometry-optimized structures obtained by using theoretical calculations. Furthermore, SAXS was successfully employed and proved to be a powerful technique for characterizing such large supramolecular assemblies. PMID:26602994

  6. Probing Molecular Interactions of Asphaltenes in Heptol Using a Surface Forces Apparatus: Implications on Stability of Water-in-Oil Emulsions.

    PubMed

    Zhang, Ling; Shi, Chen; Lu, Qingye; Liu, Qingxia; Zeng, Hongbo

    2016-05-17

    The behaviors and molecular interactions of asphaltenes are related to many challenging issues in oil production. In this study, the molecular interaction mechanism of asphaltenes in Heptol solvents of varying toluene/n-heptane ratio were directly measured using a surface forces apparatus (SFA). The results showed that the interactions between asphaltene surfaces gradually changed from pure repulsion to weak adhesion as the weight ratio of toluene (ω) in Heptol decreased from ω = 1 to 0. The measured repulsion was mainly due to the steric interactions between swelling asphaltene molecules and/aggregates. The micropipet technique was applied to test the stability of two water-in-oil emulsion droplets attached to glass pipettes. A computer-controlled 4-roll mill fluidic device was also built in-house to investigate the interaction of free-suspending water-in-oil emulsions under dynamic flow conditions. Both micropipet and 4-roll mill fluidic tests demonstrate that asphaltenes adsorbed at oil/water interfaces play a critical role in stabilizing the emulsion drops, in agreement with the repulsion measured between asphaltene surfaces in toluene using SFA, and that interfacial sliding or shearing is generally required to destabilize the protective interfacial apshaltene layers which facilitates the coalescence of emulsion drops. Our results provide insights into the fundamental understanding of molecular interaction mechanisms of asphaltenes in organic solvents and stabilization/destabilization behaviors of water-in-oil emulsions with asphaltenes. PMID:27128395

  7. Solid-state NMR as a probe of anion binding: molecular dynamics and associations in a [5]polynorbornane bisurea host complexed with terephthalate.

    PubMed

    Rawal, Aditya; Hook, James M; Robson, Ryan N; Gunzelmann, Daniel; Pfeffer, Frederick M; O'Dell, Luke A

    2015-09-14

    A range of solid-state NMR techniques is used to characterise a molecular host:guest complex consisting of a [5]polynorbornane bisurea host binding a terephthalate dianion guest. Detailed information is obtained on the molecular dynamics and associations from the point of view of both the host and guest molecules. The formation of the complex in the solid state is confirmed using (1)H 2D exchange NMR, and the 180° flipping of the (2)H-labelled terephthalate guest and its eventual expulsion from the complex at elevated temperatures are quantified using variable-temperature (2)H spin-echo experiments. Two-dimensional (1)H-(13)C HETCOR spectra obtained under fast magic angle spinning conditions (60 kHz) show a high resolution despite the poor crystallinity of the solid complex, and clearly reveal changes in the rigidity of the host molecule when complexed. Short-range intra- and intermolecular (1)H-(1)H proximities are also detected using 2D SQ-DQ correlation methods, providing insight into the molecular packing in the solid phase. PMID:26239510

  8. Visualizing genomes with Oligopaint FISH probes

    PubMed Central

    Beliveau, Brian J.; Apostolopoulos, Nicholas; Wu, Chao-ting

    2014-01-01

    Oligopaint probes are fluorescently-labeled, single-stranded DNA oligonucleotides that can be used to visualize genomic regions ranging in size from tens of kilobases to many megabases. This unit details how Oligopaint probes can be synthesized using basic molecular biological techniques as well as provides protocols for FISH, 3D-FISH, and sample preparation. PMID:24510436

  9. Probing the molecular mechanism of cerium oxide nanoparticles in protecting against the neuronal cytotoxicity of Aβ1-42 with copper ions.

    PubMed

    Zhao, Yaqin; Xu, Qiming; Xu, Wei; Wang, Dandan; Tan, Jason; Zhu, Cuiqing; Tan, Xiangshi

    2016-07-13

    The molecular mechanism of CeONP in protecting against neuronal cytotoxicity from amyloid peptides and copper ions was investigated systematically by photoluminescence of [Ru(phen)2dppz](2+), morphology of TEM, mass spectroscopy, cell viability assay, ROS fluorescence assay, and EPR. The results revealed that CeONPs reduced Aβ1-42 aggregation, protected from neurotoxicity of ROS induced by Cu(2+) + Aβ1-42via blocking the production of free radicals and scavenging the radicals with Ce(3+)/Ce(4+) catalytic cycles, which provides a valuable insight into CeONPs as a therapeutic intervention in oxidative damage in Alzheimer's disease. PMID:26662372

  10. Novel Molecular Beacon Probe-Based Real-Time RT-PCR Assay for Diagnosis of Crimean-Congo Hemorrhagic Fever Encountered in India

    PubMed Central

    Kamboj, Aman; Pateriya, Atul Kumar; Mishra, Anamika; Ranaware, Pradip; Kulkarni, Diwakar D.; Raut, Ashwin Ashok

    2014-01-01

    Crimean-Congo hemorrhagic fever (CCHF) is an emerging zoonotic disease in India and requires immediate detection of infection both for preventing further transmission and for controlling the infection. The present study describes development, optimization, and evaluation of a novel molecular beacon-based real-time RT-PCR assay for rapid, sensitive, and specific diagnosis of Crimean-Congo hemorrhagic fever virus (CCHFV). The developed assay was found to be a better alternative to the reported TaqMan assay for routine diagnosis of CCHF. PMID:24877102

  11. Manipulating the charge state of Au clusters on rutile TiO2(110) single crystal surfaces through molecular reactions probed by infrared spectroscopy.

    PubMed

    Cao, Yunjun; Hu, Shujun; Yu, Min; Wang, Tingting; Huang, Shiming; Yan, Shishen; Xu, Mingchun

    2016-07-14

    The charge state of Au clusters deposited on rutile TiO2(110) single crystal surfaces was studied by UHV-FTIRS using CO as a probe. The as-deposited Au clusters on oxidized TiO2(110) surfaces are electrically neutral and are identified by the 2105-2112 cm(-1) vibrational frequency of adsorbed CO depending on Au coverage. Annealing Au/TiO2(110) in a moderate O2 atmosphere at 400 K blue shifts the CO vibrational frequency by only 2-3 cm(-1) both on bare TiO2(110) surfaces and on Au clusters. However, NO exposure blue shifts the CO vibrational frequency by 16-26 cm(-1) for CO adsorbed on Au atoms near the interface and by 3-4 cm(-1) for CO adsorbed on top of Au clusters. As the acceptors of the intense charge transfer from Au, the Oa atoms generated through (NO)2→ N2O + Oa reactions on the small fraction of the bare TiO2(110) surface reside around the Au/TiO2(110) interface perimeter, causing the neutral Au(0) to be cationic Au(δ+) states. This is a new approach to manipulate the charge state of Au clusters on oxide surfaces, which may be helpful in regulating the catalytic redox reactions on oxide supported metal systems. PMID:27306113

  12. Temperature-dependences of the kinetics of reactions of papain and actinidin with a series of reactivity probes differing in key molecular recognition features

    PubMed Central

    Gul, Sheraz; Mellor, Geoffrey W.; Thomas, Emrys W.; Brocklehurst, Keith

    2006-01-01

    The temperature-dependences of the second-order rate constants (k) of the reactions of the catalytic site thiol groups of two cysteine peptidases papain (EC 3.4.22.2) and actinidin (EC 3.4.22.14) with a series of seven 2-pyridyl disulphide reactivity probes (R-S-S-2-Py, in which R provides variation in recognition features) were determined at pH 6.7 at temperatures in the range 4–30 °C by stopped-flow methodology and were used to calculate values of ΔS‡, ΔH‡ and ΔG‡. The marked changes in ΔS‡ from negative to positive in the papain reactions consequent on provision of increase in the opportunities for key non-covalent recognition interactions may implicate microsite desolvation in binding site–catalytic site signalling to provide a catalytically relevant transition state. The substantially different behaviour of actinidin including apparent masking of changes in ΔH‡ by an endothermic conformational change suggests a difference in mechanism involving kinetically significant conformational change. PMID:16445383

  13. Molecular cytogenetic analysis of the Appenine endemic cyprinid fish Squalius lucumonis and three other Italian leuciscines using chromosome banding and FISH with rDNA probes.

    PubMed

    Rossi, Anna Rita; Milana, Valentina; Hett, Anne Kathrin; Tancioni, Lorenzo

    2012-12-01

    Karyotype and other chromosomal characteristics of the Appenine endemic cyprinid fish, Toscana stream chub Squalius lucumonis, were analysed using conventional banding and FISH with 45S and 5S rDNA probes. The diploid chromosome number (2n = 50) and karyotype characteristics including pericentromeric heterochromatic blocks and GC-rich CMA(3)-positive sites corresponding to both positive Ag-NORs and 45S rDNA loci on the short arms of a single medium-sized submetacentric chromosome pair were consistent with those found in most European leuciscine cyprinids. On other hand, 5S rDNA FISH in the Toscana stream chub and three other Italian leuciscines, S. squalus, Rutilus rubilio and Telestes muticellus, revealed a species-specific hybridization pattern, i.e. signals on four (S. lucumonis), three (S. squalus and R. rubilio) and two (T. muticellus) chromosome pairs. Whereas all the species shared the 5S rDNA loci on the largest subtelocentric chromosome pair, a "leuciscine" cytotaxonomic marker, S. lucumonis showed both classes of rDNA loci tandem aligned on the short arms of chromosome pair No. 12. The present findings suggest that the observed high variability of 5S rDNA loci provides a powerful tool for investigation of karyotype differentiation in karyologically conservative leuciscine fishes. PMID:23238894

  14. Probing the binding mechanisms of α-tocopherol to trypsin and pepsin using isothermal titration calorimetry, spectroscopic, and molecular modeling methods.

    PubMed

    Li, Xiangrong; Ni, Tianjun

    2016-06-01

    α-Tocopherol is a required nutrient for a variety of biological functions. In this study, the binding of α-tocopherol to trypsin and pepsin was investigated using isothermal titration calorimetry (ITC), steady-state and time-resolved fluorescence measurements, circular dichroism (CD) spectroscopy, and molecular modeling methods. Thermodynamic investigations reveal that α-tocopherol binds to trypsin/pepsin is synergistically driven by enthalpy and entropy. The fluorescence experimental results indicate that α-tocopherol can quench the fluorescence of trypsin/pepsin through a static quenching mechanism. The binding ability of α-tocopherol with trypsin/pepsin is in the intermediate range, and one molecule of α-tocopherol combines with one molecule of trypsin/pepsin. As shown by circular dichroism (CD) spectroscopy, α-tocopherol may induce conformational changes of trypsin/pepsin. Molecular modeling displays the specific binding site and gives information about binding forces and α-tocopherol-tryptophan (Trp)/tyrosine (Tyr) distances. In addition, the inhibition rate of α-tocopherol on trypsin and pepsin was studied. The study provides a basic data set for clarifying the binding mechanisms of α-tocopherol with trypsin and pepsin and is helpful for understanding its biological activity in vivo. PMID:27094449

  15. Characterization of molecular channel in photodissociation of SOCl2 at 248 nm: Cl2 probing by cavity ring-down absorption spectroscopy.

    PubMed

    Chen, Bo-Jung; Tsai, Po-Yu; Huang, Ting-Kang; Xia, Zhu-Hong; Lin, King-Chuen; Chiou, Chuei-Jhih; Sun, Bing-Jian; Chang, A H H

    2015-03-28

    A primary elimination channel of the chlorine molecule in the one-photon dissociation of SOCl2 at 248 nm was investigated using cavity ring-down absorption spectroscopy (CRDS). By means of spectral simulation, the ratio of the vibrational population in the v = 0, 1, and 2 levels was evaluated to be 1 : (0.10 ± 0.02) : (0.009 ± 0.005), corresponding to a Boltzmann vibrational temperature of 340 ± 30 K. The Cl2 molecular channel was obtained with a quantum yield of 0.4 ± 0.2 from the X(1)A' ground state of SOCl2via internal conversion. The dissociation mechanism differs from a prior study where a smaller yield of <3% was obtained, initiated from the 2(1)A' excited state. Temperature-dependence measurements of the Cl2 fragment turn out to support our mechanism. With the aid of ab initio potential energy calculations, two dissociation routes to the molecular products were found, including one synchronous dissociation pathway via a three-center transition state (TS) and the other sequential dissociation pathway via a roaming-mediated isomerization TS. The latter mechanism with a lower energy barrier dominates the dissociation reaction. PMID:25715942

  16. Diffusion and molecular interactions in a methanol/polyimide system probed by coupling time-resolved FTIR spectroscopy with gravimetric measurements

    PubMed Central

    Musto, Pellegrino; Galizia, Michele; La Manna, Pietro; Pannico, Marianna; Mensitieri, Giuseppe

    2013-01-01

    In this contribution the diffusion of methanol in a commercial polyimide (PMDA-ODA) is studied by coupling gravimetric measurements with in-situ, time-resolved FTIR spectroscopy. The spectroscopic data have been treated with two complementary techniques, i.e., difference spectroscopy (DS) and least-squares curve fitting (LSCF). These approaches provided information about the overall diffusivity, the nature of the molecular interactions among the system components and the dynamics of the various molecular species. Additional spectroscopic measurements on thin film samples (about 2 μm) allowed us to identify the interaction site on the polymer backbone and to propose likely structures for the H-bonding aggregates. Molar absorptivity values from a previous literature report allowed us to estimate the population of first-shell and second-shell layers of methanol in the polymer matrix. In terms of diffusion kinetics, the gravimetric and spectroscopic estimates of the diffusion coefficients were found to be in good agreement with each other and with previous literature reports. A Fickian behavior was observed throughout, with diffusivity values markedly affected by the total concentration of sorbed methanol. PMID:24809042

  17. Probing Origin of Binding Difference of inhibitors to MDM2 and MDMX by Polarizable Molecular Dynamics Simulation and QM/MM-GBSA Calculation

    NASA Astrophysics Data System (ADS)

    Chen, Jianzhong; Wang, Jinan; Zhang, Qinggang; Chen, Kaixian; Zhu, Weiliang

    2015-11-01

    Binding abilities of current inhibitors to MDMX are weaker than to MDM2. Polarizable molecular dynamics simulations (MD) followed by Quantum mechanics/molecular mechanics generalized Born surface area (QM//MM-GBSA) calculations were performed to investigate the binding difference of inhibitors to MDM2 and MDMX. The predicted binding free energies not only agree well with the experimental results, but also show that the decrease in van der Walls interactions of inhibitors with MDMX relative to MDM2 is a main factor of weaker bindings of inhibitors to MDMX. The analyses of dihedral angles based on MD trajectories suggest that the closed conformation formed by the residues M53 and Y99 in MDMX leads to a potential steric clash with inhibitors and prevents inhibitors from arriving in the deep of MDMX binding cleft, which reduces the van der Waals contacts of inhibitors with M53, V92, P95 and L98. The calculated results using the residue-based free energy decomposition method further prove that the interaction strength of inhibitors with M53, V92, P95 and L98 from MDMX are obviously reduced compared to MDM2. We expect that this study can provide significant theoretical guidance for designs of potent dual inhibitors to block the p53-MDM2/MDMX interactions.

  18. The Release of Trapped Gases from Amorphous Solid Water Films: I. “Top-Down” Crystallization-Induced Crack Propagation Probed using the Molecular Volcano

    SciTech Connect

    May, Robert A.; Smith, R. Scott; Kay, Bruce D.

    2013-03-14

    In this (Paper I) and the companion paper (Paper II) we investigate the mechanisms for the release of trapped gases from underneath of amorphous solid water (ASW) films. In prior work, we reported the episodic release of trapped gases in concert with the crystallization ASW, a phenomenon that we termed the "molecular volcano". The observed abrupt desorption is due to the formation of cracks that span the film to form a connected pathway for release. In this paper we utilize the "molecular volcano" desorption peak to characterize the formation of crystallization-induced cracks. We find that the crack length and distribution are independent of the trapped gas (Ar, Kr, Xe, CH4, N2, O2 or CO). Selective placement of the inert gas layer is used to show that cracks form near the top of the film and propagate downward into the film. Isothermal experiments reveal that, after some induction time, cracks propagate linearly in time with an Arrhenius dependent velocity corresponding to an activation energy of 54 kJ/mol. This value is consistent with the crystallization growth rate reported by others and establishes a direct connection between crystallization growth rate and the crack propagation rate. A two-step model in which nucleation and crystallization occurs in an induction zone near the top of the film followed by the propagation of a crystallization/crack front into the film is in good agreement with the temperature programmed desorption results.

  19. Probing Origin of Binding Difference of inhibitors to MDM2 and MDMX by Polarizable Molecular Dynamics Simulation and QM/MM-GBSA Calculation

    PubMed Central

    Chen, Jianzhong; Wang, Jinan; Zhang, Qinggang; Chen, Kaixian; Zhu, Weiliang

    2015-01-01

    Binding abilities of current inhibitors to MDMX are weaker than to MDM2. Polarizable molecular dynamics simulations (MD) followed by Quantum mechanics/molecular mechanics generalized Born surface area (QM//MM-GBSA) calculations were performed to investigate the binding difference of inhibitors to MDM2 and MDMX. The predicted binding free energies not only agree well with the experimental results, but also show that the decrease in van der Walls interactions of inhibitors with MDMX relative to MDM2 is a main factor of weaker bindings of inhibitors to MDMX. The analyses of dihedral angles based on MD trajectories suggest that the closed conformation formed by the residues M53 and Y99 in MDMX leads to a potential steric clash with inhibitors and prevents inhibitors from arriving in the deep of MDMX binding cleft, which reduces the van der Waals contacts of inhibitors with M53, V92, P95 and L98. The calculated results using the residue-based free energy decomposition method further prove that the interaction strength of inhibitors with M53, V92, P95 and L98 from MDMX are obviously reduced compared to MDM2. We expect that this study can provide significant theoretical guidance for designs of potent dual inhibitors to block the p53-MDM2/MDMX interactions. PMID:26616018

  20. Infrared absorption by molecular gases as a probe of nanoporous silica xerogel and molecule-surface collisions: Low-pressure results

    NASA Astrophysics Data System (ADS)

    Vander Auwera, J.; Ngo, N. H.; El Hamzaoui, H.; Capoen, B.; Bouazaoui, M.; Ausset, P.; Boulet, C.; Hartmann, J.-M.

    2013-10-01

    Transmission spectra of gases confined (but not adsorbed) within the pores of a 1.4-cm-thick silica xerogel sample have been recorded between 2.5 and 5 μm using a high-resolution Fourier transform spectrometer. This was done for pure CO, CO2, N2O, H2O, and CH4 at room temperature and pressures of a few hectopascals. Least-squares fits of measured absorption lines provide the optical-path lengths within the confined (LC) and free (LF) gas inside the absorption cell and the half width at half maximum ΓC of the lines of the confined gases. The values of LC and LF retrieved using numerous transitions of all studied species are very consistent. Furthermore, LC is in satisfactory agreement with values obtained from independent measurements, thus showing that reliable information on the open porosity volume can be retrieved from an optical experiment. The values of ΓC, here resulting from collisions of the molecules with the inner surfaces of the xerogel pores, are practically independent of the line for each gas and inversely proportional to the square root of the probed-molecule molar mass. This is a strong indication that, for the studied transitions, a single collision of a molecule with a pore surface is sufficient to change its rotational state. A previously proposed simple model, used for the prediction of the line shape, leads to satisfactory agreement with the observations. It also enables a determination of the average pore size, bringing information complementary to that obtained from nitrogen adsorption porosimetry.

  1. LAT1 targeted delivery of methionine based imaging probe derived from M(III) metal ions for early diagnosis of proliferating tumours using molecular imaging modalities.

    PubMed

    Hazari, Puja Panwar; Prakash, Surbhi; Meena, Virendra K; Jaswal, Ambika; Khurana, Harleen; Mishra, Surabhi Kirti; Bhonsle, Hemanth Kumar; Singh, Lokendra; Mishra, Anil K

    2015-01-01

    We investigated the potential of DTPA-bis(Methionine), a target specific amino acid based probe for detection of L-type amino acid transporters (LAT1) known to over express in proliferating tumours using multimodality imaging. The ligand, DTPA-bis(Met) was readily converted to lanthanide complexes and was found capable of targeting cancer cells using multimodality imaging. DTPA-bis(Met) complexes were synthesized and characterized by mass spectroscopy. MR longitudinal relaxivity, r₁ = 4.067 ± 0.31 mM⁻¹s⁻¹ and transverse relaxivity, r₂ = 8.61 ± 0.07 mM⁻¹s⁻¹ of Gd(III)-DTPA-bis(Met) were observed at pH 7.4 at 7 T. Bright, localized fluorescence of Eu(III)-DTPA-bis(Met) was observed with standard microscopy and displacement studies indicated ligand functionality. K(D) value determined for Eu(III)-DTPA-bis(Met) on U-87 MG cells was found to be 17.3 pM and showed appreciable fluorescence within the cells. Radio HPLC showed a radiochemical purity more than 95% (specific activity = 400-500 MBq/μmol, labelling efficiency 78 %) for ⁶⁸Ga(III)-DTPA-bis(Met). Pre-treatment of xenografted U-87 MG athymic mice with ⁶⁸Ga(III)-DTPA-bis(Met) following unlabelled L-methionine administration reduced tumour uptake by 10-folds in Micro PET. These data support the specific binding of ⁶⁸Ga(III)-DTPA-bis(Met) to the LAT1 transporter. To summarize, this agent possesses high stability in biological environment and exhibits effective interaction with its LAT1 transporters giving high accumulation in tumour area, excellent tumour/non-tumour ratio and low non-specific retention in vivo. PMID:25329672

  2. Structure-Function Analysis of Mammalian CYP2B Enzymes Using 7-Substituted Coumarin Derivatives as Probes: Utility of Crystal Structures and Molecular Modeling in Understanding Xenobiotic Metabolism.

    PubMed

    Shah, Manish B; Liu, Jingbao; Huo, Lu; Zhang, Qinghai; Dearing, M Denise; Wilderman, P Ross; Szklarz, Grazyna D; Stout, C David; Halpert, James R

    2016-04-01

    Crystal structures of CYP2B35 and CYP2B37 from the desert woodrat were solved in complex with 4-(4-chlorophenyl)imidazole (4-CPI). The closed conformation of CYP2B35 contained two molecules of 4-CPI within the active site, whereas the CYP2B37 structure demonstrated an open conformation with three 4-CPI molecules, one within the active site and the other two in the substrate access channel. To probe structure-function relationships of CYP2B35, CYP2B37, and the related CYP2B36, we tested the O-dealkylation of three series of related substrates-namely, 7-alkoxycoumarins, 7-alkoxy-4-(trifluoromethyl)coumarins, and 7-alkoxy-4-methylcoumarins-with a C1-C7 side chain. CYP2B35 showed the highest catalytic efficiency (kcat/KM) with 7-heptoxycoumarin as a substrate, followed by 7-hexoxycoumarin. In contrast, CYP2B37 showed the highest catalytic efficiency with 7-ethoxy-4-(trifluoromethyl)coumarin (7-EFC), followed by 7-methoxy-4-(trifluoromethyl)coumarin (7-MFC). CYP2B35 had no dealkylation activity with 7-MFC or 7-EFC. Furthermore, the new CYP2B-4-CPI-bound structures were used as templates for docking the 7-substituted coumarin derivatives, which revealed orientations consistent with the functional studies. In addition, the observation of multiple -Cl and -NH-π interactions of 4-CPI with the aromatic side chains in the CYP2B35 and CYP2B37 structures provides insight into the influence of such functional groups on CYP2B ligand binding affinity and specificity. To conclude, structural, computational, and functional analysis revealed striking differences between the active sites of CYP2B35 and CYP2B37 that will aid in the elucidation of new structure-activity relationships. PMID:26826176

  3. Probing the Properties of the Molecular Adlayers on Metal Substrates: Scanning Tunneling Microscopy Study of Amine Adsorption on Gold(111) and Graphene Nanoislands on Cobalt(0001)

    NASA Astrophysics Data System (ADS)

    Zhou, Hui

    In this thesis, we present our findings on two major topics, both of which are studies of molecules on metal surfaces by scanning tunneling microscopy (STM). The first topic is on adsorption of a model amine compound, 1,4-benzenediamine (BDA), on the reconstructed Au(111) surface, chosen for its potential application as a molecular electronic device. The molecules were deposited in the gas phase onto the substrate in the vacuum chamber. Five different patterns of BDA molecules on the surface at different coverages, and the preferred adsorption sites of BDA molecules on reconstructed Au(111) surface, were observed. In addition, BDA molecules were susceptible to tip-induced movement, suggesting that BDA molecules on metal surfaces can be a potential candidate in STM molecular manipulations. We also studied graphene nanoislands on Co(0001) in the hope of understanding interaction of expitaxially grown graphene and metal substrates. This topic can shed a light on the potential application of graphene as an electronic device, especially in spintronics. The graphene nanoislands were formed by annealing contorted hexabenzocoronene (HBC) on the Co(0001) surface. In our experiments, we have determined atop registry of graphene atoms with respect to the underlying Co surface. We also investigated the low-energy electronic structures of graphene nanoislands by scanning tunneling spectroscopy. The result was compared with a first-principle calculation using density functional theory (DFT) which suggested strong coupling between graphene pi-bands and cobalt d-electrons. We also observed that the islands exhibit zigzag edges, which exhibits unique electronic structures compared with the center areas of the islands.

  4. Herschel Survey of Galactic OH+, H2O+, and H3O+: Probing the Molecular Hydrogen Fraction and Cosmic-Ray Ionization Rate

    NASA Astrophysics Data System (ADS)

    Indriolo, Nick; Neufeld, D. A.; Gerin, M.; Schilke, P.; Benz, A. O.; Winkel, B.; Menten, K. M.; Chambers, E. T.; Black, John H.; Bruderer, S.; Falgarone, E.; Godard, B.; Goicoechea, J. R.; Gupta, H.; Lis, D. C.; Ossenkopf, V.; Persson, C. M.; Sonnentrucker, P.; van der Tak, F. F. S.; van Dishoeck, E. F.; Wolfire, Mark G.; Wyrowski, F.

    2015-02-01

    In diffuse interstellar clouds the chemistry that leads to the formation of the oxygen-bearing ions OH+, H2O+, and H3O+ begins with the ionization of atomic hydrogen by cosmic rays, and continues through subsequent hydrogen abstraction reactions involving H2. Given these reaction pathways, the observed abundances of these molecules are useful in constraining both the total cosmic-ray ionization rate of atomic hydrogen (ζH) and molecular hydrogen fraction (f_H_2). We present observations targeting transitions of OH+, H2O+, and H3O+ made with the Herschel Space Observatory along 20 Galactic sight lines toward bright submillimeter continuum sources. Both OH+ and H2O+ are detected in absorption in multiple velocity components along every sight line, but H3O+ is only detected along 7 sight lines. From the molecular abundances we compute f_H_2 in multiple distinct components along each line of sight, and find a Gaussian distribution with mean and standard deviation 0.042 ± 0.018. This confirms previous findings that OH+ and H2O+ primarily reside in gas with low H2 fractions. We also infer ζH throughout our sample, and find a lognormal distribution with mean log (ζH) = -15.75 (ζH = 1.78 × 10-16 s-1) and standard deviation 0.29 for gas within the Galactic disk, but outside of the Galactic center. This is in good agreement with the mean and distribution of cosmic-ray ionization rates previously inferred from H_3^+ observations. Ionization rates in the Galactic center tend to be 10-100 times larger than found in the Galactic disk, also in accord with prior studies. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.

  5. Probing Molecular Associations of Secondary Organic Aerosol (SOA) Samples from CalNex 2010 with Nano-DESI High-Resolution Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    O'Brien, R. E.; Nguyen, T. B.; Laskin, A.; Laskin, J.; Hayes, P. L.; Liu, S.; Jimenez, J. L.; Russell, L. M.; Nizkorodov, S.; Goldstein, A. H.

    2012-12-01

    This project focuses on analyzing the identities of molecules that comprise oligomers in size resolved aerosol fractions. Since oligomers are generally too large and polar to be measured by typical GC/MS analysis, soft ionization with high resolution mass spectrometry is used to extend the range of observable compounds. Samples collected during CalNex 2010 in Bakersfield and Los Angeles and secondary organic aerosol (SOA) produced in a photochemical chamber by photooxidation of diesel (DSL) fuel and isoprene (ISO) under humid, high-NOx conditions have been analyzed with nanospray desorption electrospray ionization (nano-DESI) and a high-resolution Orbitrap mass spectrometer. The nano-DESI is a soft ionization technique that allows molecular ions to be observed and the Orbitrap has sufficient resolution to determine the elemental composition of almost all species above the detection limit. A large fraction of SOA is made up of high molecular weight oligomers which are thought to form through acid catalyzed reactions of photo-chemically processed volatile organic compounds (VOC). The formation of oligomers is influenced by the VOCs available, the amount of atmospheric sulfate and nitrate, and the magnitude of photo-chemical processing, among other potential influences. We present the elemental composition of chemical species in size resolved SOA samples with six-hour time resolution, providing the first time resolved data set for the study of these oligomers in atmospheric samples. We present a comparison of the degree of overlap between the ambient and chamber experiments as a novel method to examine sources for this fraction of SOA. Possible formation pathways and sources of observed compounds are analyzed by comparison to other concurrent measurements at the site.

  6. Global Fold of Human Cannabinoid Type 2 Receptor Probed by Solid-State 13C-, 15N-MAS NMR and Molecular Dynamics Simulations

    PubMed Central

    Kimura, Tomohiro; Vukoti, Krishna; Lynch, Diane L.; Hurst, Dow P.; Grossfield, Alan; Pitman, Michael C.; Reggio, Patricia H.; Yeliseev, Alexei A.; Gawrisch, Klaus

    2014-01-01

    The global fold of human cannabinoid type 2 (CB2) receptor in the agonist-bound active state in lipid bilayers was investigated by solid-state 13C- and 15N magic-angle spinning (MAS) NMR, in combination with chemical-shift prediction from a structural model of the receptor obtained by microsecond-long molecular dynamics (MD) simulations. Uniformly 13C-, and 15N-labeled CB2 receptor was expressed in milligram quantities by bacterial fermentation, purified, and functionally reconstituted into liposomes. 13C MAS NMR spectra were recorded without sensitivity enhancement for direct comparison of Cα, Cβ, and C=O bands of superimposed resonances with predictions from protein structures generated by MD. The experimental NMR spectra matched the calculated spectra reasonably well indicating agreement of the global fold of the protein between experiment and simulations. In particular, the 13C chemical shift distribution of Cα resonances was shown to be very sensitive to both the primary amino acid sequence and the secondary structure of CB2. Thus the shape of the Cα band can be used as an indicator of CB2 global fold. The prediction from MD simulations indicated that upon receptor activation a rather limited number of amino acid residues, mainly located in the extracellular loop 2 and the second half of intracellular loop 3, change their chemical shifts significantly (≥1.5 ppm for carbons and ≥5.0 ppm for nitrogens). Simulated two-dimensional 13Cα(i)-13C=O(i) and 13C=O(i)-15NH(i+1) dipolar-interaction correlation spectra provide guidance for selective amino-acid labeling and signal assignment schemes to study the molecular mechanism of activation of CB2 by solid-state MAS NMR. PMID:23999926

  7. A Total Molecular Gas Mass Census in Z ˜ 2–3 Star-forming Galaxies: Low-J CO Excitation Probes of Galaxies’ Evolutionary States

    NASA Astrophysics Data System (ADS)

    Sharon, Chelsea E.; Riechers, Dominik A.; Hodge, Jacqueline; Carilli, Chris L.; Walter, Fabian; Weiß, Axel; Knudsen, Kirsten K.; Wagg, Jeff

    2016-08-01

    We present CO(1–0) observations obtained at the Karl G. Jansky Very Large Array for 14 z˜ 2 galaxies with existing CO(3–2) measurements, including 11 galaxies that contain active galactic nuclei (AGNs) and three submillimeter galaxies (SMGs). We combine this sample with an additional 15 z˜ 2 galaxies from the literature that have both CO(1–0) and CO(3–2) measurements in order to evaluate differences in CO excitation between SMGs and AGN host galaxies, to measure the effects of CO excitation on the derived molecular gas properties of these populations, and to look for correlations between the molecular gas excitation and other physical parameters. With our expanded sample of CO(3–2)/CO(1–0) line ratio measurements, we do not find a statistically significant difference in the mean line ratio between SMGs and AGN host galaxies as can be found in the literature; we instead find {r}{3,1}=1.03+/- 0.50 for AGN host galaxies and {r}{3,1}=0.78+/- 0.27 for SMGs (or {r}{3,1}=0.90+/- 0.40 for both populations combined). We also do not measure a statistically significant difference between the distributions of the line ratios for these populations at the p = 0.05 level, although this result is less robust. We find no excitation dependence on the index or offset of the integrated Schmidt–Kennicutt relation for the two CO lines, and we obtain indices consistent with N = 1 for the various subpopulations. However, including low-z “normal” galaxies increases our best-fit Schmidt–Kennicutt index to N˜ 1.2. While we do not reproduce correlations between the CO line width and luminosity, we do reproduce correlations between CO excitation and star-formation efficiency.

  8. Small molecular probes for G-protein-coupled C5a receptors: conformationally constrained antagonists derived from the C terminus of the human plasma protein C5a.

    PubMed

    Wong, A K; Finch, A M; Pierens, G K; Craik, D J; Taylor, S M; Fairlie, D P

    1998-08-27

    . These results indicate that potent C5a antagonists can be developed by targeting site 2 alone of the C5a receptor and define a novel pharmacophore for developing powerful receptor probes or drug candidates. PMID:9719594

  9. Recent Progress in Fluorescent Imaging Probes.

    PubMed

    Pak, Yen Leng; Swamy, K M K; Yoon, Juyoung

    2015-01-01

    Due to the simplicity and low detection limit, especially the bioimaging ability for cells, fluorescence probes serve as unique detection methods. With the aid of molecular recognition and specific organic reactions, research on fluorescent imaging probes has blossomed during the last decade. Especially, reaction based fluorescent probes have been proven to be highly selective for specific analytes. This review highlights our recent progress on fluorescent imaging probes for biologically important species, such as biothiols, reactive oxygen species, reactive nitrogen species, metal ions including Zn(2+), Hg(2+), Cu(2+) and Au(3+), and anions including cyanide and adenosine triphosphate (ATP). PMID:26402684

  10. Recent Progress in Fluorescent Imaging Probes

    PubMed Central

    Pak, Yen Leng; Swamy, K. M. K.; Yoon, Juyoung

    2015-01-01

    Due to the simplicity and low detection limit, especially the bioimaging ability for cells, fluorescence probes serve as unique detection methods. With the aid of molecular recognition and specific organic reactions, research on fluorescent imaging probes has blossomed during the last decade. Especially, reaction based fluorescent probes have been proven to be highly selective for specific analytes. This review highlights our recent progress on fluorescent imaging probes for biologically important species, such as biothiols, reactive oxygen species, reactive nitrogen species, metal ions including Zn2+, Hg2+, Cu2+ and Au3+, and anions including cyanide and adenosine triphosphate (ATP). PMID:26402684

  11. Probing the smallest molecular model of MoS2 catalyst: S2 units in the MoS(-/0 (n = 1-5) clusters.

    PubMed

    Wang, Bin; Wu, Ni; Zhang, Xiao-Bin; Huang, Xin; Zhang, Yong-Fan; Chen, Wen-Kai; Ding, Kai-Ning

    2013-07-11

    Density functional theory (DFT) and coupled cluster theory (CCSD(T)) calculations are carried out to investigate the electronic and structural properties of a series of monomolybdenum sulfide clusters, MoSn(-/0) (n = 1-5). Generalized Koopmans' theorem is applied to predict the vertical detachment energies and simulate the photoelectron spectra (PES). We found that the additional sulfur atoms have a tendency to successively occupy the terminal sites in the sequential sulfidation until the Mo reaches its maximum oxidation sate of +6. After that, the polysulfide ligands (viz., S2 and S3) emerge in the MoS4 and MoS5(-/0) clusters. The MoS4 (C2, (1)A) is predicted to be the ground state and may be used as a neutral model for the sulfur-rich edge sites of the fresh MoS2 catalysts. Molecular orbital analyses are performed to analyze the chemical bonding in the monomolybdenum sulfide clusters and to elucidate their electronic and structural evolution. PMID:23767784

  12. Probing the Catalytic Mechanism Involved in the Isocitrate Lyase Superfamily: Hybrid Quantum Mechanical/Molecular Mechanical Calculations on 2,3-Dimethylmalate Lyase.

    PubMed

    Jongkon, Nathjanan; Chotpatiwetchkul, Warot; Gleeson, M Paul

    2015-09-01

    The isocitrate lyase (ICL) superfamily catalyzes the cleavage of the C(2)-C(3) bond of various α-hydroxy acid substrates. Members of the family are found in bacteria, fungi, and plants and include ICL itself, oxaloacetate hydrolase (OAH), 2-methylisocitrate lyase (MICL), and (2R,3S)-dimethylmalate lyase (DMML) among others. ICL and related targets have been the focus of recent studies to treat bacterial and fungal infections, including tuberculosis. The catalytic process by which this family achieves C(2)-C(3) bond breaking is still not clear. Extensive structural studies have been performed on this family, leading to a number of plausible proposals for the catalytic mechanism. In this paper, we have applied quantum mechanical/molecular mechanical (QM/MM) methods to the most recently reported family member, DMML, to assess whether any of the mechanistic proposals offers a clear energetic advantage over the others. Our results suggest that Arg161 is the general base in the reaction and Cys124 is the general acid, giving rise to a rate-determining barrier of approximately 10 kcal/mol. PMID:26224328

  13. A molecular dynamics simulation study of the α-relaxation in a 1,4-polybutadiene melt as probed by the coherent dynamic structure factor

    NASA Astrophysics Data System (ADS)

    Smith, Grant D.; Bedrov, Dmitry; Paul, Wolfgang

    2004-09-01

    The dynamic coherent structure factor Scoh(q,t) for a 1,4-polybutadiene (PBD) melt has been investigated using atomistic molecular dynamics simulations. The relaxation of Scoh(q,t) at q=1.44 Å-1 and q=2.72 Å-1, corresponding to the first and second peaks in the static structure factor for PBD, was studied in detail over a wide range of temperature. It was found that time-temperature superposition holds for the α-relaxation for both q values over a wide temperature range and that the α-relaxation can be well described by a stretched (Kohlrauch-William-Watts) exponential with temperature independent but q dependent amplitude and stretching exponent. The α-relaxation times for both q values were found to exhibit the same non-Arrhenius temperature dependence, indicating that the same physical processes are responsible for relaxation on both length scales. The α-relaxation time was found to depend strongly upon the dynamical range of data utilized in determining the relaxation time, accounting for qualitative discrepancies between α-relaxation times reported here and those extracted for PBD from experimentally measured Scoh(q,t).

  14. Cloning, overexpression, and characterization of a novel thermostable penicillin G acylase from Achromobacter xylosoxidans: probing the molecular basis for its high thermostability.

    PubMed

    Cai, Gang; Zhu, Songcheng; Yang, Sheng; Zhao, Guoping; Jiang, Weihong

    2004-05-01

    The gene encoding a novel penicillin G acylase (PGA), designated pgaW, was cloned from Achromobacter xylosoxidans and overexpressed in Escherichia coli. The pgaW gene contains an open reading frame of 2586 nucleotides. The deduced protein sequence encoded by pgaW has about 50% amino acid identity to several well-characterized PGAs, including those of Providencia rettgeri, Kluyvera cryocrescens, and Escherichia coli. Biochemical studies showed that the optimal temperature for this novel PGA (PGA650) activity is greater than 60 degrees C and its half-life of inactivation at 55 degrees C is four times longer than that of another previously reported thermostable PGA from Alcaligenes faecalis (R. M. D. Verhaert, A. M. Riemens, J. V. R. Laan, J. V. Duin, and W. J. Quax, Appl. Environ. Microbiol. 63:3412-3418, 1997). To our knowledge, this is the most thermostable PGA ever characterized. To explore the molecular basis of the higher thermostability of PGA650, homology structural modeling and amino acid composition analyses were performed. The results suggested that the increased number of buried ion pair networks, lower N and Q contents, excessive arginine residues, and remarkably high content of proline residues in the structure of PGA650 could contribute to its high thermostability. The unique characteristic of higher thermostability of this novel PGA provides some advantages for its potential application in industry. PMID:15128530

  15. Gold Nanoparticle Internal Structure and Symmetry Probed by Unified Small-Angle X-ray Scattering and X-ray Diffraction Coupled with Molecular Dynamics Analysis.

    PubMed

    Fleury, Blaise; Cortes-Huerto, Robinson; Taché, Olivier; Testard, Fabienne; Menguy, Nicolas; Spalla, Olivier

    2015-09-01

    Shape and size are known to determine a nanoparticle's properties. Hardly ever studied in synthesis, the internal crystal structure (i.e., particle defects, crystallinity, and symmetry) is just as critical as shape and size since it directly impacts catalytic efficiency, plasmon resonance, and orients anisotropic growth of metallic nanoparticles. Hence, its control cannot be ignored any longer in today's research and applications in nanotechnology. This study implemented an unprecedented reliable measurement combining these three structural aspects. The unified small-angle X-ray scattering and diffraction measurement (SAXS/XRD) was coupled with molecular dynamics to allow simultaneous determination of nanoparticles' shape, size, and crystallinity at the atomic scale. Symmetry distribution (icosahedra-Ih, decahedra-Dh, and truncated octahedra-TOh) of 2-6 nm colloidal gold nanoparticles synthesized in organic solvents was quantified. Nanoparticle number density showed the predominance of Ih, followed by Dh, and little, if any, TOh. This result contradicts some theoretical predictions and highlights the strong effect of the synthesis environment on structure stability. We foresee that this unified SAXS/XRD analysis, yielding both statistical and quantitative counts of nanoparticles' symmetry distribution, will provide new insights into nanoparticle formation, growth, and assembly. PMID:26263393

  16. The cytotoxic effect of Eucheuma serra agglutinin (ESA) on cancer cells and its application to molecular probe for drug delivery system using lipid vesicles.

    PubMed

    Sugahara, T; Ohama, Y; Fukuda, A; Hayashi, M; Kawakubo, A; Kato, K

    2001-07-01

    Eucheuma serra agglutinin (ESA) derived from a marine red alga, Eucheuma serra, is a lectin that specifically binds to mannose-rich carbohydrate chains. ESA is a monomeric molecule, with a molecular weight of29,000. ESA induced cell death against several cancer cell lines, such as colon cancer Colo201 cells and cervix cancer HeLa cells. DNA ladder detection and the induction of caspase-3 activity suggested that the cell death induced by ESA against cancer cells was apoptosis. ESA bound to the cell surface of Colo201 cells in the sugar chain dependent manner. This means that the binding of ESA to the cell surface is specific for mannose-rich sugar chains recognized by ESA. The binding of ESA to the cell surface of Colo201 cells was slightly suppressed by the high concentrations of serum because of the competition with serum components possessing the mannose-rich sugar chain motifs. On the other hand, a lipid vesicle is a very useful microcapsule constructed by multilamellar structure,and adopted as drug or gene carrier. ESA was immobilized on the surface of the lipid vesicles to apply the lipid vesicles to cancer specific drug delivery system. ESA-immobilized lipid vesicles were effectively bound to cancer cell lines compared with plane vesicles. PMID:19003319

  17. Probing Molecular Associations of Field-Collected and Laboratory-Generated SOA with Nano-DESI High-Resolution Mass Spectrometry

    SciTech Connect

    O'Brien, Rachel E.; Nguyen, Tran B.; Laskin, Alexander; Laskin, Julia; Hayes, Patrick L.; Liu, Shang; Jimenez, Jose L.; Russell, Lynn M.; Nizkorodov, Sergey; Goldstein, Allen H.

    2013-01-30

    Aerosol samples from the 2010 CalNex field study in Bakersfield (BF) and Los Angeles (LA) were analyzed using positive mode nanospray-desorption electrospray ionization mass spectrometry (nano-DESI-MS). Secondary organic aerosol (SOA) produced in a photochemical chamber by photooxidation of diesel (DSL) fuel and isoprene (ISO) under humid, high-NOx conditions, was analyzed for comparison. Three groups of organic compounds with zero, one, or two nitrogen atoms in their molecular formulas (0N, 1N, 2N) were compared in detail. The composition of ambient SOA exhibited greater overlap with DSL than with ISO. The overlap of the chamber experiments with the BF data was relatively consistent throughout the day while the overlap with LA data increased significantly in the noon-6pm sample, consistent with the SOA plume arriving from downtown Los Angeles. BF samples were more oxidized, contained more organic nitrogen, and had more overlap with the chamber data compared to LA samples. The addition of gaseous ammonia (NH3) to the DSL experiment was necessary to generate many of the 2N compounds observed in BF. This analysis demonstrates that DSL and ISO were important sources but cannot account for all of the observed ambient compounds indicating that other sources of organics were also likely important.

  18. Probing the solvent shell with 195Pt chemical shifts: density functional theory molecular dynamics study of Pt(II) and Pt(IV) anionic complexes in aqueous solution.

    PubMed

    Truflandier, Lionel A; Autschbach, Jochen

    2010-03-17

    Ab initio molecular dynamics (aiMD) simulations based on density functional theory (DFT) were performed on a set of five anionic platinum complexes in aqueous solution. (195)Pt nuclear magnetic shielding constants were computed with DFT as averages over the aiMD trajectories, using the two-component relativistic zeroth-order regular approximation (ZORA) in order to treat relativistic effects on the Pt shielding tensors. The chemical shifts obtained from the aiMD averages are in good agreement with experimental data. For Pt(II) and Pt(IV) halide complexes we found an intermediate solvent shell interacting with the complexes that causes pronounced solvent effects on the Pt chemical shifts. For these complexes, the magnitude of solvent effects on the Pt shielding constant can be correlated with the surface charge density. For square-planar Pt complexes the aiMD simulations also clearly demonstrate the influence of closely coordinated non-equatorial water molecules on the Pt chemical shift, relating the structure of the solution around the complex to the solvent effects on the metal NMR chemical shift. For the complex [Pt(CN)(4)](2-), the solvent effects on the Pt shielding constant are surprisingly small. PMID:20166712

  19. Probing the dynamics of polyatomic multichannel elementary reactions by crossed molecular beam experiments with soft electron-ionization mass spectrometric detection.

    PubMed

    Casavecchia, Piergiorgio; Leonori, Francesca; Balucani, Nadia; Petrucci, Raffaele; Capozza, Giovanni; Segoloni, Enrico

    2009-01-01

    In this Perspective we highlight developments in the field of chemical reaction dynamics. Focus is on the advances recently made in the investigation of the dynamics of elementary multichannel radical-molecule and radical-radical reactions, as they have become possible using an improved crossed molecular beam scattering apparatus with universal electron-ionization mass spectrometric detection and time-of-flight analysis. These improvements consist in the implementation of (a) soft ionization detection by tunable low-energy electrons which has permitted us to reduce interfering signals originating from dissociative ionization processes, usually representing a major complication, (b) different beam crossing-angle set-ups which have permitted us to extend the range of collision energies over which a reaction can be studied, from very low (a few kJ mol(-1), as of interest in astrochemistry or planetary atmospheric chemistry) to quite high energies (several tens of kJ mol(-1), as of interest in high temperature combustion systems), and (c) continuous supersonic sources for producing a wide variety of atomic and molecular radical reactant beams. Exploiting these new features it has become possible to tackle the dynamics of a variety of polyatomic multichannel reactions, such as those occurring in many environments ranging from combustion and plasmas to terrestrial/planetary atmospheres and interstellar clouds. By measuring product angular and velocity distributions, after having suppressed or mitigated, when needed, the problem of dissociative ionization of interfering species (reactants, products, background gases) by soft ionization detection, essentially all primary reaction products can be identified, the dynamics of each reaction channel characterized, and the branching ratios determined as a function of collision energy. In general this information, besides being of fundamental relevance, is required for a predictive description of the chemistry of these

  20. Probing the importance of hydrogen bonds in the active site of the subtilisin nattokinase by site-directed mutagenesis and molecular dynamics simulation.

    PubMed

    Zheng, Zhong-liang; Ye, Mao-qing; Zuo, Zhen-yu; Liu, Zhi-gang; Tai, Keng-chang; Zou, Guo-lin

    2006-05-01

    Hydrogen bonds occurring in the catalytic triad (Asp32, His64 and Ser221) and the oxyanion hole (Asn155) are very important to the catalysis of peptide bond hydrolysis by serine proteases. For the subtilisin NK (nattokinase), a bacterial serine protease, construction and analysis of a three-dimensional structural model suggested that several hydrogen bonds formed by four residues function to stabilize the transition state of the hydrolysis reaction. These four residues are Ser33, Asp60, Ser62 and Thr220. In order to remove the effect of these hydrogen bonds, four mutants (Ser33-->Ala33, Asp60-->Ala60, Ser62-->Ala62, and Thr220-->Ala220) were constructed by site-directed mutagenesis. The results of enzyme kinetics indicated that removal of these hydrogen bonds increases the free-energy of the transition state (DeltaDeltaG(T)). We concluded that these hydrogen bonds are more important for catalysis than for binding the substrate, because removal of these bonds mainly affects the kcat but not the K(m) values. A substrate, SUB1 (succinyl-Ala-Ala-Pro-Phe-p-nitroanilide), was used during enzyme kinetics experiments. In the present study we have also shown the results of FEP (free-energy perturbation) calculations with regard to the binding and catalysis reactions for these mutant subtilisins. The calculated difference in FEP also suggested that these four residues are more important for catalysis than binding of the substrate, and the simulated values compared well with the experimental values from enzyme kinetics. The results of MD (molecular dynamics) simulations further demonstrated that removal of these hydrogen bonds partially releases Asp32, His64 and Asn155 so that the stability of the transition state decreases. Another substrate, SUB2 (H-D-Val-Leu-Lys-p-nitroanilide), was used for FEP calculations and MD simulations. PMID:16411898

  1. Probing the importance of hydrogen bonds in the active site of the subtilisin nattokinase by site-directed mutagenesis and molecular dynamics simulation

    PubMed Central

    Zheng, Zhong-liang; Ye, Mao-qing; Zuo, Zhen-yu; Liu, Zhi-gang; Tai, Keng-chang; Zou, Guo-lin

    2006-01-01

    Hydrogen bonds occurring in the catalytic triad (Asp32, His64 and Ser221) and the oxyanion hole (Asn155) are very important to the catalysis of peptide bond hydrolysis by serine proteases. For the subtilisin NK (nattokinase), a bacterial serine protease, construction and analysis of a three-dimensional structural model suggested that several hydrogen bonds formed by four residues function to stabilize the transition state of the hydrolysis reaction. These four residues are Ser33, Asp60, Ser62 and Thr220. In order to remove the effect of these hydrogen bonds, four mutants (Ser33→Ala33, Asp60→Ala60, Ser62→Ala62, and Thr220→Ala220) were constructed by site-directed mutagenesis. The results of enzyme kinetics indicated that removal of these hydrogen bonds increases the free-energy of the transition state (ΔΔGT). We concluded that these hydrogen bonds are more important for catalysis than for binding the substrate, because removal of these bonds mainly affects the kcat but not the Km values. A substrate, SUB1 (succinyl-Ala-Ala-Pro-Phe-p-nitroanilide), was used during enzyme kinetics experiments. In the present study we have also shown the results of FEP (free-energy perturbation) calculations with regard to the binding and catalysis reactions for these mutant subtilisins. The calculated difference in FEP also suggested that these four residues are more important for catalysis than binding of the substrate, and the simulated values compared well with the experimental values from enzyme kinetics. The results of MD (molecular dynamics) simulations further demonstrated that removal of these hydrogen bonds partially releases Asp32, His64 and Asn155 so that the stability of the transition state decreases. Another substrate, SUB2 (H-D-Val-Leu-Lys-p-nitroanilide), was used for FEP calculations and MD simulations. PMID:16411898

  2. Investigation of a Calcium-Responsive Contrast Agent in Cellular Model Systems: Feasibility for Use as a Smart Molecular Probe in Functional MRI

    PubMed Central

    2014-01-01

    Responsive or smart contrast agents (SCAs) represent a promising direction for development of novel functional MRI (fMRI) methods for the eventual noninvasive assessment of brain function. In particular, SCAs that respond to Ca2+ may allow tracking neuronal activity independent of brain vasculature, thus avoiding the characteristic limitations of current fMRI techniques. Here we report an in vitro proof-of-principle study with a Ca2+-sensitive, Gd3+-based SCA in an attempt to validate its potential use as a functional in vivo marker. First, we quantified its relaxometric response in a complex 3D cell culture model. Subsequently, we examined potential changes in the functionality of primary glial cells following administration of this SCA. Monitoring intracellular Ca2+ showed that, despite a reduction in the Ca2+ level, transport of Ca2+ through the plasma membrane remained unaffected, while stimulation with ATP induced Ca2+-transients suggested normal cellular signaling in the presence of low millimolar SCA concentrations. SCAs merely lowered the intracellular Ca2+ level. Finally, we estimated the longitudinal relaxation times (T1) for an idealized in vivo fMRI experiment with SCA, for extracellular Ca2+ concentration level changes expected during intense neuronal activity which takes place upon repetitive stimulation. The values we obtained indicate changes in T1 of around 1–6%, sufficient to be robustly detectable using modern MRI methods in high field scanners. Our results encourage further attempts to develop even more potent SCAs and appropriate fMRI protocols. This would result in novel methods that allow monitoring of essential physiological processes at the cellular and molecular level. PMID:24712900

  3. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    NASA Astrophysics Data System (ADS)

    Zheng, Wenjun; Glenn, Paul

    2015-01-01

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  4. Probing the binding of Cu(2+) ions to a fragment of the Aβ(1-42) polypeptide using fluorescence spectroscopy, isothermal titration calorimetry and molecular dynamics simulations.

    PubMed

    Makowska, Joanna; Żamojć, Krzysztof; Wyrzykowski, Dariusz; Żmudzińska, Wioletta; Uber, Dorota; Wierzbicka, Małgorzata; Wiczk, Wiesław; Chmurzyński, Lech

    2016-09-01

    Steady-state and time-resolved fluorescence quenching measurements supported by isothermal titration calorimetry (ITC) and molecular dynamics simulations (MD), with the NMR-derived restraints, were used to investigate the interactions of Cu(2+) ions with a fragment of the Aβ(1-42) polypeptide, Aβ(5-16) with the following sequence: Ac-Arg-His-Asp-Ser-Gly-Tyr-Glu-Val-His-His-Gln-Lys-NH2, denoted as HZ1. The studies presented in this paper, when compared with our previous results (Makowska et al., Spectrochim. Acta A 153: 451-456), show that the affinity of the peptide to metal ions is conformation-dependent. All the measurements were carried out in 20mM 2-(N-morpholino)ethanesulfonic acid (MES) buffer solution, pH6.0. The Stern-Volmer equations, along with spectroscopic observations, were used to determine the quenching and binding parameters. The obtained results unequivocally suggest that Cu(2+) ions quench the fluorescence of HZ1 only through a static quenching mechanism, in contrast to the fragment from the N-terminal part of the FPB28 protein, with sequence Ac-Tyr-Lys-Thr-Ala-Asp-Gly-Lys-Thr-Tyr- NH2 (D9) and its derivative with a single point mutation: Ac-Tyr-Lys-Thr-Ala-Asn-Gly-Lys-Thr-Tyr- NH2 (D9_M), where dynamic quenching occurred. The thermodynamic parameters (ΔITCH, ΔITCS) for the interactions between Cu(2+) ions and the HZ1 peptide were determined from the calorimetric data. The conditional thermodynamic parameters suggest that, under the experimental conditions, the formation of the Cu(2+)-HZ1 complex is both an enthalpy and entropy driven process. PMID:27398680

  5. Simple and Sensitive Molecularly Imprinted Polymer - Mn-Doped ZnS Quantum Dots Based Fluorescence Probe for Cocaine and Metabolites Determination in Urine.

    PubMed

    Chantada-Vázquez, María Pilar; Sánchez-González, Juan; Peña-Vázquez, Elena; Tabernero, María Jesús; Bermejo, Ana María; Bermejo-Barrera, Pilar; Moreda-Piñeiro, Antonio

    2016-03-01

    A new molecularly imprinted polymer (MIP)-based fluorescent artificial receptor has been prepared by anchoring a selective MIP for cocaine (COC) on the surface of polyethylene glycol (PEG) modified Mn-doped ZnS quantum dots (QDs). The prepared material combines the high selectivity attributed to MIPs and the sensitive fluorescent property of the Mn-doped ZnS QDs. Simple and low cost methods have therefore been optimized for assessing cocaine abuse in urine by monitoring the fluorescence quenching when the template (COC) and also metabolites from COC [benzoylecgonine (BZE) and ecgonine methyl ester (EME)] are present. Fluorescence quenching was not observed when performing experiments with other drugs of abuse (and their metabolites) or when using nonimprinted polymer (NIP)-coated QDs. Under optimized operating conditions (1.5 mL of 200 mg L(-1) MIP-coated QDs solution, pH 5.5, and 15 min before fluorescence scanning) two analytical methods were developed/validated. One of the procedures (direct method) consisted of urine sample 1:20 dilution before fluorescence measurements. The method has been found to be fast, precise, and accurate, but the standard addition technique for performing the analysis was required because of the existence of matrix effect. The second procedure performed a solid phase extraction (SPE) first, avoiding matrix effect and allowing external calibration. The limits of detection of the methods were 0.076 mg L(-1) (direct method) and 0.0042 mg L(-1) (SPE based method), which are lower than the cutoff values for confirmative conclusions regarding cocaine abuse. PMID:26857857

  6. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    SciTech Connect

    Zheng, Wenjun Glenn, Paul

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  7. SO and CS observations of molecular clouds. II. Analysis and modelling of the abundance ratios - probing O_2/CO with SO/CS?

    NASA Astrophysics Data System (ADS)

    Nilsson, A.; Hjalmarson, Å.; Bergman, P.; Millar, T. J.

    2000-06-01

    We here analyse the observational SO and CS data presented in Nilsson et al. (\\cite{2000A&A...XXX..XXXN}). The SO/CS integrated intensity ratio maps are presented for 19 molecular clouds, together with tables of relevant ratios at strategic positions, where we have also observed 34SO and/or C34S. The SO/CS abundance ratio as calculated from an LTE analysis is highly varying within and between the sources. Our isotopomer observations and Monte Carlo simulations verify that this is not an artifact due to optical depth problems. The variation of the maximum SO/CS abundance ratio between the clouds is 0.2-7. The largest variations within a cloud are found for the most nearby objects, possibly indicating resolution effects. We have also performed time dependent chemical simulations. We compare the simulations with our observed SO/CS abundance ratios and suggest a varying oxygen to carbon initial abundance, differing temporal evolution, density differences and X-ray sources associated with young stellar objects as possible explanations to the variations. In particular, the observed variation of the maximum SO/CS abundance ratio between the clouds can be explained by using initial O/C+ abundance ratios in the range 1.3-2.5. We finally derive a relationship between the SO/CS and O_2/CO abundance ratios, which may be used as a guide to find the most promising interstellar O_2 search targets. Table 1 and Figs. 4 to 21 are only available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/Abstract.html)

  8. Probing the Probes: Fitness Factors For Small Molecule Tools

    PubMed Central

    Workman, Paul; Collins, Ian

    2010-01-01

    Chemical probes for interrogating biological processes are of considerable current interest. Cell permeable small molecule tools have a major role in facilitating the functional annotation of the human genome, understanding both physiological and pathological processes, and validating new molecular targets. To be valuable, chemical tools must satisfy necessary criteria and recent publications have suggested objective guidelines for what makes a useful chemical probe. Although recognizing that such guidelines may be valuable, we caution against overly restrictive rules that may stifle innovation in favor of a “fit-for-purpose” approach. Reviewing the literature and providing examples from the cancer field, we recommend a series of “fitness factors” to be considered when assessing chemical probes. We hope this will encourage innovative chemical biology research while minimizing the generation of poor quality and misleading biological data, thus increasing understanding of the particular biological area, to the benefit of basic research and drug discovery. PMID:20609406

  9. Probing the configurational space of a metalloprotein core: an ab initio molecular dynamics study of Duo Ferro 1 binuclear Zn cofactor.

    PubMed

    Papoian, Garegin A; DeGrado, William F; Klein, Michael L

    2003-01-15

    We present three theoretical models of various degree of completeness to explore the chemical phase space available to the Glu4His2Zn2 cofactor found in the four-helix bundle of de novo designed metalloprotein Duo Ferro 1. We have found that the planewave DFT geometry optimization of 94-atom Model I, which contains both the protein scaffold constraints as well as the second shell hydrogen bonding network, reproduces the crystal structure bonding with remarkable accuracy (0.34 A). Surprisingly, the geometry optimization of 66-atom Model II (lacking the second shell hydrogen bonding) and 48-atom Model III (being also free of the protein scaffold constraints) still result in the fidelity with the crystallographic structure (RMSDs 0.29 and 0.34 A, respectively). To examine whether these structures are close to the global minimum as well as to investigate various conformational transitions to which the di-Zn cofactor may be susceptible to, we have carried out a 10 ps Car-Parrinello Molecular Dynamics (CPMD) simulation of Model III. We suggest that weak hydrogen bonds between imidazole hydrogens and carboxylate oxygens modulate the dynamical behavior of the system. One part of the molecule was found to be rigid due to the particular H(imidazole)-O(carboxylate) interaction restricting both the motion of the imidazole ring as well as the terminal carboxylate conformational mobility. The second half of the system was very flexible demonstrating a coupling of a transient formation of H(imidazole)-O(carboxylate) bonds with the spinning of the imidazole ring and syn-anti isomerization of the terminal carboxylate group. In addition, two low-energy snapshots from the 10 ps CPMD run were quenched, and their geometries were optimized, leading to two new isomers 48 kJ/mol lower in energy than the one associated with the crystal structure. We suggest that periodic quenching of the CPMD simulation snapshots of a minimalist model may be used as an efficient method to generate a large

  10. Scanning probe image wizard: A toolbox for automated scanning probe microscopy data analysis

    NASA Astrophysics Data System (ADS)

    Stirling, Julian; Woolley, Richard A. J.; Moriarty, Philip

    2013-11-01

    We describe SPIW (scanning probe image wizard), a new image processing toolbox for SPM (scanning probe microscope) images. SPIW can be used to automate many aspects of SPM data analysis, even for images with surface contamination and step edges present. Specialised routines are available for images with atomic or molecular resolution to improve image visualisation and generate statistical data on surface structure.

  11. Hydrodynamic ultrasonic probe

    DOEpatents

    Day, Robert A.; Conti, Armond E.

    1980-01-01

    An improved probe for in-service ultrasonic inspection of long lengths of a workpiece, such as small diameter tubing from the interior. The improved probe utilizes a conventional transducer or transducers configured to inspect the tubing for flaws and/or wall thickness variations. The probe utilizes a hydraulic technique, in place of the conventional mechanical guides or bushings, which allows the probe to move rectilinearly or rotationally while preventing cocking thereof in the tube and provides damping vibration of the probe. The probe thus has lower friction and higher inspection speed than presently known probes.

  12. Hyperpolarized NMR Probes for Biological Assays

    PubMed Central

    Meier, Sebastian; Jensen, Pernille R.; Karlsson, Magnus; Lerche, Mathilde H.

    2014-01-01

    During the last decade, the development of nuclear spin polarization enhanced (hyperpolarized) molecular probes has opened up new opportunities for studying the inner workings of living cells in real time. The hyperpolarized probes are produced ex situ, introduced into biological systems and detected with high sensitivity and contrast against background signals using high resolution NMR spectroscopy. A variety of natural, derivatized and designed hyperpolarized probes has emerged for diverse biological studies including assays of intracellular reaction progression, pathway kinetics, probe uptake and export, pH, redox state, reactive oxygen species, ion concentrations, drug efficacy or oncogenic signaling. These probes are readily used directly under natural conditions in biofluids and are often directly developed and optimized for cellular assays, thus leaving little doubt about their specificity and utility under biologically relevant conditions. Hyperpolarized molecular probes for biological NMR spectroscopy enable the unbiased detection of complex processes by virtue of the high spectral resolution, structural specificity and quantifiability of NMR signals. Here, we provide a survey of strategies used for the selection, design and use of hyperpolarized NMR probes in biological assays, and describe current limitations and developments. PMID:24441771

  13. Monoclonals and DNA probes in diagnostic and preventative medicine

    SciTech Connect