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Sample records for cellulose-specific molecular probes

  1. Microscopic analysis of corn fiber using starch- and cellulose-specific molecular probes.

    PubMed

    Porter, Stephanie E; Donohoe, Bryon S; Beery, Kyle E; Xu, Qi; Ding, Shi-You; Vinzant, Todd B; Abbas, Charles A; Himmel, Michael 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. 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.

  3. 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

  4. Techniques for molecular imaging probe design.

    PubMed

    Reynolds, Fred; Kelly, Kimberly A

    2011-12-01

    Molecular imaging allows clinicians to visualize disease-specific molecules, thereby providing relevant information in the diagnosis and treatment of patients. With advances in genomics and proteomics and underlying mechanisms of disease pathology, the number of targets identified has significantly outpaced the number of developed molecular imaging probes. There has been a concerted effort to bridge this gap with multidisciplinary efforts in chemistry, proteomics, physics, material science, and biology--all essential to progress in molecular imaging probe development. In this review, we discuss target selection, screening techniques, and probe optimization with the aim of developing clinically relevant molecularly targeted imaging agents.

  5. Techniques for Molecular Imaging Probe Design

    PubMed Central

    Reynolds, Fred; Kelly, Kimberly A.

    2011-01-01

    Molecular imaging allows clinicians to visualize disease specific molecules, thereby providing relevant information in the diagnosis and treatment of patients. With advances in genomics and proteomics and underlying mechanisms of disease pathology, the number of targets identified has significantly outpaced the number of developed molecular imaging probes. There has been a concerted effort to bridge this gap with multidisciplinary efforts in chemistry, proteomics, physics, material science, and biology; all essential to progress in molecular imaging probe development. In this review, we will discuss target selection, screening techniques and probe optimization with the aim of developing clinically relevant molecularly targeted imaging agents. PMID:22201532

  6. 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

  7. Molecular probe technology detects bacteria without culture

    PubMed Central

    2012-01-01

    Background Our ultimate goal is to detect the entire human microbiome, in health and in disease, in a single reaction tube, and employing only commercially available reagents. To that end, we adapted molecular inversion probes to detect bacteria using solely a massively multiplex molecular technology. This molecular probe technology does not require growth of the bacteria in culture. Rather, the molecular probe technology requires only a sequence of forty sequential bases unique to the genome of the bacterium of interest. In this communication, we report the first results of employing our molecular probes to detect bacteria in clinical samples. Results While the assay on Affymetrix GenFlex Tag16K arrays allows the multiplexing of the detection of the bacteria in each clinical sample, one Affymetrix GenFlex Tag16K array must be used for each clinical sample. To multiplex the clinical samples, we introduce a second, independent assay for the molecular probes employing Sequencing by Oligonucleotide Ligation and Detection. By adding one unique oligonucleotide barcode for each clinical sample, we combine the samples after processing, but before sequencing, and sequence them together. Conclusions Overall, we have employed 192 molecular probes representing 40 bacteria to detect the bacteria in twenty-one vaginal swabs as assessed by the Affymetrix GenFlex Tag16K assay and fourteen of those by the Sequencing by Oligonucleotide Ligation and Detection assay. The correlations among the assays were excellent. PMID:22404909

  8. Chemomechanics with Molecular Force Probes

    DTIC Science & Technology

    2010-03-30

    Prescribed by ANSI Std Z39-18 quantified by pressure, and its effect on the reaction rate is governed by the reaction’s volume of acti- vation, ΔV‡ [8...into chemomechanical coupling. Covalent bond rearrange- ments involve large energy changes, making them particularly attractive as the basis of novel...scales related, from the macroscopic force that accounts for large -scale dis- tortion in material in response to an external load down to molecular

  9. Using molecular rotors to probe gelation.

    PubMed

    Raeburn, Jaclyn; Chen, Lin; Awhida, Salmah; Deller, Robert C; Vatish, Manu; Gibson, Matthew I; Adams, Dave J

    2015-05-14

    A series of fluorescent probes, including a number of molecular rotors, have been used to follow the self-assembly of dipeptide-based low molecular weight gelators. We show that these probes can be used to gain an insight into the assembly process. Thioflavin T, a commonly used stain for β-sheets, appears to act as a molecular rotor in these gelling systems, with the fluorescence data closely matching that of other rotors. The molecular rotor was incorporated into an assay system with glucose oxidase to enable glucose-concentration specific gelation and hence generating a fluorescent output. Applying this system to urine from patients with various levels of glycosuria (a symptom of diabetes), it was found to provide excellent correlation with different clinical assessments of diabetes. This demonstrates a new concept in gelation-linked biosensing for a real clinical problem.

  10. 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

  11. 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

  12. Probing the molecular determinants of fluorinase specificity.

    PubMed

    Yeo, W L; Chew, X; Smith, D J; Chan, K P; Sun, H; Zhao, H; Lim, Y H; Ang, E L

    2017-02-23

    Molecular determinants of FlA1 fluorinase specificity were probed using 5'-chloro-5'-deoxyadenosine (5'-ClDA) analogs as substrates and FlA1 active site mutants. Modifications at F213 or A279 residues are beneficial towards these modified substrates, including 5'-chloro-5'-deoxy-2-ethynyladenosine, ClDEA (>10-fold activity improvement), and conferred novel activity towards substrates not readily accepted by wild-type FlA1.

  13. Molecular Optical Imaging with Radioactive Probes

    PubMed Central

    Liu, Hongguang; Ren, Gang; Miao, Zheng; Zhang, Xiaofen; Tang, Xiaodong; Han, Peizhen; Gambhir, Sanjiv S.; Cheng, Zhen

    2010-01-01

    Background Optical imaging (OI) techniques such as bioluminescence and fluorescence imaging have been widely used to track diseases in a non-invasive manner within living subjects. These techniques generally require bioluminescent and fluorescent probes. Here we demonstrate the feasibility of using radioactive probes for in vivo molecular OI. Methodology/Principal Findings By taking the advantages of low energy window of light (1.2–3.1 eV, 400–1000 nm) resulting from radiation, radionuclides that emit charged particles such as β+ and β− can be successfully imaged with an OI instrument. In vivo optical images can be obtained for several radioactive probes including 2-deoxy-2-[18F]fluoro-D-glucose ([18F]FDG), Na18F, Na131I, 90YCl3 and a 90Y labeled peptide that specifically target tumors. Conclusions/Significance These studies demonstrate generalizability of radioactive OI technique. It provides a new molecular imaging strategy and will likely have significant impact on both small animal and clinical imaging. PMID:20208993

  14. 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

  15. A quantum spin-probe molecular microscope.

    PubMed

    Perunicic, V S; Hill, C D; Hall, L T; Hollenberg, L C L

    2016-10-11

    Imaging the atomic structure of a single biomolecule is an important challenge in the physical biosciences. Whilst existing techniques all rely on averaging over large ensembles of molecules, the single-molecule realm remains unsolved. Here we present a protocol for 3D magnetic resonance imaging of a single molecule using a quantum spin probe acting simultaneously as the magnetic resonance sensor and source of magnetic field gradient. Signals corresponding to specific regions of the molecule's nuclear spin density are encoded on the quantum state of the probe, which is used to produce a 3D image of the molecular structure. Quantum simulations of the protocol applied to the rapamycin molecule (C51H79NO13) show that the hydrogen and carbon substructure can be imaged at the angstrom level using current spin-probe technology. With prospects for scaling to large molecules and/or fast dynamic conformation mapping using spin labels, this method provides a realistic pathway for single-molecule microscopy.

  16. A quantum spin-probe molecular microscope

    NASA Astrophysics Data System (ADS)

    Perunicic, V. S.; Hill, C. D.; Hall, L. T.; Hollenberg, L. C. L.

    2016-10-01

    Imaging the atomic structure of a single biomolecule is an important challenge in the physical biosciences. Whilst existing techniques all rely on averaging over large ensembles of molecules, the single-molecule realm remains unsolved. Here we present a protocol for 3D magnetic resonance imaging of a single molecule using a quantum spin probe acting simultaneously as the magnetic resonance sensor and source of magnetic field gradient. Signals corresponding to specific regions of the molecule's nuclear spin density are encoded on the quantum state of the probe, which is used to produce a 3D image of the molecular structure. Quantum simulations of the protocol applied to the rapamycin molecule (C51H79NO13) show that the hydrogen and carbon substructure can be imaged at the angstrom level using current spin-probe technology. With prospects for scaling to large molecules and/or fast dynamic conformation mapping using spin labels, this method provides a realistic pathway for single-molecule microscopy.

  17. A quantum spin-probe molecular microscope

    PubMed Central

    Perunicic, V. S.; Hill, C. D.; Hall, L. T.; Hollenberg, L.C.L.

    2016-01-01

    Imaging the atomic structure of a single biomolecule is an important challenge in the physical biosciences. Whilst existing techniques all rely on averaging over large ensembles of molecules, the single-molecule realm remains unsolved. Here we present a protocol for 3D magnetic resonance imaging of a single molecule using a quantum spin probe acting simultaneously as the magnetic resonance sensor and source of magnetic field gradient. Signals corresponding to specific regions of the molecule's nuclear spin density are encoded on the quantum state of the probe, which is used to produce a 3D image of the molecular structure. Quantum simulations of the protocol applied to the rapamycin molecule (C51H79NO13) show that the hydrogen and carbon substructure can be imaged at the angstrom level using current spin-probe technology. With prospects for scaling to large molecules and/or fast dynamic conformation mapping using spin labels, this method provides a realistic pathway for single-molecule microscopy. PMID:27725630

  18. 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.

  19. MOLECULAR PROBES FOR EXTRACELLULAR ADENOSINE RECEPTORS

    PubMed Central

    Jacobson, Kenneth A.; Ukena, Dieter; Padgett, William; Kirk, Kenneth L.; Daly, John W.

    2012-01-01

    Derivatives of adenosine receptor agonists (N6-phenyladenosines) and antagonists (1,3-dialkyl-8-phenylxanthines) bearing functionalized chains suitable for attachment to other molecules have been reported [Jacobson et al., J. med. Chem. 28, 1334 and 1341 (1985)]. The “functionalized congener” approach has been extended to the synthesis of spectroscopic and other probes for adenosine receptors that retain high affinity (Ki ~ 10−9 −10−8 M) in A1-receptor binding. The probes have been synthesized from an antagonist xanthine amine congener (XAC) and an adenosine amine congener (ADAC). [3H]ADAC has been synthesized and found to bind highly specifically to A1-adenosine receptors of rat and calf cerebral cortical membranes with KD values of 1.4 and 0.34 nM respectively. The higher affinity in the bovine brain, seen also with many of the probes derived from ADAC and XAC, is associated with phenyl substituents. The spectroscopic probes contain a reporter group attached at a distal site of the functionalized chain. These bifunctional ligands may contain a spin label (e.g. the nitroxyl radical TEMPO) for electron spin resonance spectroscopy, or a fluorescent dye, including fluorescein and 4-nitrobenz-2-oxa-1,3-diazole (NBD), or labels for 19F nuclear magnetic resonance spectroscopy. Potential applications of the spectroscopic probes in characterization of adenosine receptors are discussed. PMID:3036153

  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. Molecular probes for the in vivo imaging of cancer

    PubMed Central

    Alford, Raphael; Ogawa, Mikako; Choyke, Peter L.

    2012-01-01

    Advancements in medical imaging have brought about unprecedented changes in the in vivo assessment of cancer. Positron emission tomography, single photon emission computed tomography, optical imaging, and magnetic resonance imaging are the primary tools being developed for oncologic imaging. These techniques may still be in their infancy, as recently developed chemical molecular probes for each modality have improved in vivo characterization of physiologic and molecular characteristics. Herein, we discuss advances in these imaging techniques, and focus on the major design strategies with which molecular probes are being developed. PMID:19823742

  2. 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.

  3. 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.

  4. Molecular modulated cysteine-selective fluorescent probe.

    PubMed

    Jung, Hyo Sung; Pradhan, Tuhin; Han, Ji Hye; Heo, Kyung Jun; Lee, Joung Hae; Kang, Chulhun; Kim, Jong Seung

    2012-11-01

    We have synthesized a series of coumarins (1-3) that can emit fluorescence in a turn-on manner through a Michael-type reaction with thiol-containing compounds. The only difference among the coumarins is the position of a carboxyl group on its benzene ring moiety near the double-bond conjugated coumarin. Their selectivity for Cys, GSH, and Hcy as well as the associated fluorogenic mechanism were illustrated by fluorescence spectroscopy, DFT calculations, and kinetic studies. All isomers prefer Cys over GSH in the reaction from 48.6 (probe 3) to 111-fold (probe 1) as demonstrated in a second order kinetics. The high selectivity of probe 1 to Cys might be achieved since the ortho carboxyl group on its benzene ring prefers a less negatively charged nucleophile. During intracellular Cys detection using 1, a possible interference by a large amount of GSH in the HepG2 cells was evaluated. The cells were treated with l-buthionine sulfoximine (BSO), an inhibitor of γ-glutamylcysteine synthetase, providing an experimental condition where the cells could not synthesize GSH from Cys or other species. Then, the fluorescence intensity of 1 in HepG2 cells under BSO-H(2)O(2) treatment was strongly enhanced by N-acetylcysteine (NAC), a precursor of Cys, implicating that the fluorescence signal from the cells is mainly associated with changes in intracellular [Cys] rather than that in intracellular [GSH].

  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. Instrumentation and probes for molecular and cellular imaging.

    PubMed

    Lecchi, M; Ottobrini, L; Martelli, C; Del Sole, A; Lucignani, G

    2007-06-01

    Molecular and cellular imaging is a branch of biomedical sciences that combines the use of imaging instrumentation and biotechnology to characterize molecular and cellular processes in living organisms in normal and pathologic conditions. The two merging areas of research behind molecular and cellular imaging are detection technology, i.e. scanners and imaging devices, and development of tracers, contrast agents and reporter probes that make imaging with scanners and devices possible. Several in vivo imaging instruments currently used in human studies, such as computer tomography, ultrasound, magnetic resonance, positron emission tomography and single photon emission computed tomography, have been rescaled for small animal studies, while other methods initially used for in vitro evaluation, such as bioluminescence and fluorescence, have been refined for in vivo imaging. Conventional imaging relies on the use of non specific contrast agents and classical probes; however, newly developed targeted contrast agents and activable ''smart'' imaging probes for so-called ''targeted imaging'' have demonstrated high specificity and high signal to noise ratio in small animal studies. This review focuses on basic recent findings in the technical aspects of molecular and cellular imaging modalities (equipment, targeted probe and contrast agents and applied combinations of instrumentation and probe) with particular attention to the choice of the future: the multimodal imaging approach.

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

    DOE PAGES

    Lee, Ida; Evans, Barbara R.; Foston, Marcus B.; ...

    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.

  9. Diffusion of molecular probes and proteins in hydrogels

    NASA Astrophysics Data System (ADS)

    Raccis, Riccardo; Roskamp, Robert; Brunsen, Annette; Menges, Bernhard; Jonas, Ulrich; Knoll, Wolfgang; Fytas, George

    2009-03-01

    We employ fluorescence correlation spectroscopy to study the diffusion of molecular probes (Cy5) and dye-tagged proteins (Cy5-AntiMouse, hydrodynamic radius 10nm and Alexa488-Streptavidin, 4nm) in surface-attached poly-N-isopropylacrylamide (PNIPAAm) and dextran based hydrogel layers. The diffusion process depends on the crosslinking density and the presence of electrostatic and steric interactions. The protein penetration into the hydrogel layer occurs close to the isoelectric point but the local probe concentration and diffusion rate diminish with increasing penetration depth. Mesh size characterization of the hydrogels is inferred from the diffusivity and the concentration profile of fluorescent probes with different size, with the molecular free dye diffusing deeper into the gel.

  10. Surface modification: how nanoparticles assemble to molecular imaging probes

    NASA Astrophysics Data System (ADS)

    Tan, Huilong; Yu, Lun; Gao, Feng; Liao, Weihua; Wang, Wei; Zeng, Wenbin

    2013-12-01

    Nanomaterials have attracted widespread attention due to their unique chemical and physical properties, such as size-dependent optical, magnetic, or catalytic properties, thus have the great potential application, especially in the fields of new materials and devices. The emergence of nanoparticle-based probe has led to important innovations in molecular imaging field. Several types of nanoparticles have been employed for molecular imaging application, including Au/Ag nanoparticles, upconversion nanoparticles (UCNPs), quantum dots, dye-doped nanoparticles, magnetic nanoparticles (MNPs), etc. The preparation of nanoparticle-based probe for molecular imaging routinely includes three steps: synthesis, surface modification, and bioconjugation, among which surface modification plays an important role for the whole procedure. Surface modification usually possesses the safety, biocompatibility, stability, hydrophilicity, and terminal functional groups for further conjugation. This review aims to outline the surface modification of how nanoparticles assemble to probes, focusing on the developments of two widely used nanoparticles, UCNPs and MNPs. Recent advances of different types of linkers, a core component for surface modification, are summarized. It shows the intimate relationship between chemistry and nanoscience. Finally, perspectives and challenges of nanoparticle-based probe in the field of molecular imaging are expected.

  11. Advanced Molecular Probes for Sequence-Specific DNA Recognition

    NASA Astrophysics Data System (ADS)

    Bertucci, Alessandro; Manicardi, Alex; Corradini, Roberto

    DNA detection can be achieved using the Watson-Crick base pairing with oligonucleotides or oligonucleotide analogs, followed by generation of a physical or chemical signal coupled with a transducer device. The nature of the probe is an essential feature which determines the performances of the sensing device. Many synthetic processes are presently available for "molecular engineering" of DNA probes, enabling label-free and PCR-free detection to be performed. Furthermore, many DNA analogs with improved performances are available and are under development; locked nucleic acids (LNA), peptide nucleic acids (PNA) and their analogs, morpholino oligonucleotides (MO) and other modified probes have shown improved properties of affinity and selectivity in target recognition compared to those of simple DNA probes. The performances of these probes in sensing devices, and the requirements for detection of unamplified DNA will be discussed in this chapter. Chemistry and architectures for conjugation of probes to reporter units, surfaces and nanostructures will also be discussed. Examples of probes used in ultrasensitive detection of unamplified DNA are listed.

  12. 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

  13. 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.

  14. Probing (macro)molecular transport through cell walls.

    PubMed

    Kilcher, Giona; Delneri, Daniela; Duckham, Craig; Tirelli, Nicola

    2008-01-01

    We here report a study on the passive permeability of hydrophobic probes through the cell wall of Saccharomyces cerevisiae. In this study we have prepared a series of fluorescent probes with similar chemical composition and molecular weight ranging from a few hundreds to a few thousands of g mol(-1). Their permeation into the cell body exhibits a clear MW cut-off and the underlying mechanism is governed by the permeation of individual molecules rather than aggregates. We also show that it is possible to reversibly alter the cell wall permeation properties without compromising the essence of its structure, by modifying the polarity/dielectric constant of the wall through solvent exchange.

  15. Engineering imaging probes and molecular machines for nanomedicine.

    PubMed

    Tong, Sheng; Cradick, Thomas J; Ma, Yan; Dai, Zhifei; Bao, Gang

    2012-10-01

    Nanomedicine is an emerging field that integrates nanotechnology, biomolecular engineering, life sciences and medicine; it is expected to produce major breakthroughs in medical diagnostics and therapeutics. Due to the size-compatibility of nano-scale structures and devices with proteins and nucleic acids, the design, synthesis and application of nanoprobes, nanocarriers and nanomachines provide unprecedented opportunities for achieving a better control of biological processes, and drastic improvements in disease detection, therapy, and prevention. Recent advances in nanomedicine include the development of functional nanoparticle based molecular imaging probes, nano-structured materials as drug/gene carriers for in vivo delivery, and engineered molecular machines for treating single-gene disorders. This review focuses on the development of molecular imaging probes and engineered nucleases for nanomedicine, including quantum dot bioconjugates, quantum dot-fluorescent protein FRET probes, molecular beacons, magnetic and gold nanoparticle based imaging contrast agents, and the design and validation of zinc finger nucleases (ZFNs) and TAL effector nucleases (TALENs) for gene targeting. The challenges in translating nanomedicine approaches to clinical applications are discussed.

  16. Molecular Probes in Marine Ecology: Concepts, Techniques and Applications.

    DTIC Science & Technology

    1991-08-16

    bacterial Woody Hastings: bioluminescence . 20 Wed. Paul Dunlap: The lux genes in bacteria : organization, structure, and expression. 21 Thurs. Chuck...probes for microbial identification. Ken Nealson: Taxonomy physiology and distribution of marine bioluminescent bacteria . 10 Tues. Ann Bucklin: Allozymic...cuponsored with the microbiology course, the first of these being on bioluminescence and symbiosis on July 7, and the second on molecular approaches to

  17. 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.

  18. 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

  19. A Pan-GTPase Inhibitor as a Molecular Probe.

    PubMed

    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.

  20. Ultrafast Molecular Dynamics probed by Vacuum Ultraviolet Pulses

    NASA Astrophysics Data System (ADS)

    Cryan, James; Champenois, Elio; Shivaram, Niranjan; Wright, Travis; Yang, Chan-Shan; Falcone, Roger; Belkacem, Ali

    2014-05-01

    We present time-resolved measurements of the relaxation dynamics in small molecular systems (CO2 and C2H4) following ultraviolet (UV) photo-excitation. We probe these excitations through photoionization and velocity map imaging (VMI) spectroscopy. Vacuum and extreme ultraviolet (VUV/XUV) pump and probe pulses are created by exploiting strong-field high harmonic generation (HHG) from our state-of-the-art 30 mJ, 1 kHz laser system. Three dimensional photoelectron and photoion momentum images recorded with our VMI spectrometer reveal non-Born Oppenheimer dynamics in the vicinity of a conical intersection, and allow us track the state of the system as a function of time. We also present initial experiments with the goal of controlling the dynamics near a conical intersection using a strong-field IR pulse. Finally, we will show progress towards measurements of time-resolved molecular frame photoelectron angular distributions (TRMFPADs) by applying our VUV/XUV pulse sequence to an aligned molecular ensemble. Supported by Chemical Sciences, Geosciences and Biosciences division of BES/DOE.

  1. 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.

  2. 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.

  3. Probing single nanometer-scale pores with polymeric molecular rulers

    NASA Astrophysics Data System (ADS)

    Henrickson, Sarah E.; DiMarzio, Edmund A.; Wang, Qian; Stanford, Vincent M.; Kasianowicz, John J.

    2010-04-01

    We previously demonstrated that individual molecules of single-stranded DNA can be driven electrophoretically through a single Staphylococcus aureus α-hemolysin ion channel. Polynucleotides thread through the channel as extended chains and the polymer-induced ionic current blockades exhibit stable modes during the interactions. We show here that polynucleotides can be used to probe structural features of the α-hemolysin channel itself. Specifically, both the pore length and channel aperture profile can be estimated. The results are consistent with the channel crystal structure and suggest that polymer-based "molecular rulers" may prove useful in deducing the structures of nanometer-scale pores in general.

  4. 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

  5. Mesoscale Polymer Dissolution Probed by Raman Spectroscopy and Molecular Simulations

    SciTech Connect

    Chang, Tsun-Mei; Xantheas, Sotiris S.; Vasdekis, Andreas E.

    2016-10-13

    The diffusion of various solvents into a polystyrene (PS) matrix was probed experimentally by monitoring the temporal profiles of the Raman spectra and theoretically from molecular dynamics (MD) simulations of the binary system. The simulation results assist in providing a fundamental, molecular level connection between the mixing/dissolution processes and the difference = solvent – PS in the values of the Hildebrand parameter () between the two components of the binary systems: solvents having similar values of with PS (small ) exhibit fast diffusion into the polymer matrix, whereas the diffusion slows down considerably when the ’s are different (large ). To this end, the Hildebrand parameter was identified as a useful descriptor that governs the process of mixing in polymer – solvent binary systems. The experiments also provide insight into further refinements of the models specific to non-Fickian diffusion phenomena that need to be used in the simulations.

  6. 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.

  7. 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.

  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. 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.

  10. 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

  11. Molecular electrostatics for probing lone pair-π interactions.

    PubMed

    Mohan, Neetha; Suresh, Cherumuttathu H; Kumar, Anmol; Gadre, Shridhar R

    2013-11-14

    An electrostatics-based approach has been proposed for probing the weak interactions between lone pair containing molecules and π deficient molecular systems. For electron-rich molecules, the negative minima in molecular electrostatic potential (MESP) topography give the location of electron localization and the MESP value at the minimum (Vmin) quantifies the electron-rich character of that region. Interactive behavior of a lone pair bearing molecule with electron deficient π-systems, such as hexafluorobenzene, 1,3,5-trinitrobenzene, 2,4,6-trifluoro-1,3,5-triazine and 1,2,4,5-tetracyanobenzene explored within DFT brings out good correlation of the lone pair-π interaction energy (E(int)) with the Vmin value of the electron-rich system. Such interaction is found to be portrayed well with the Electrostatic Potential for Intermolecular Complexation (EPIC) model. On the basis of the precise location of MESP minimum, a prediction for the orientation of a lone pair bearing molecule with an electron deficient π-system is possible in the majority of the cases studied.

  12. Photophysical aspects of molecular probes near nanostructured gold surfaces.

    PubMed

    Ghosh, Sujit Kumar; Pal, Tarasankar

    2009-05-28

    Highly ordered, self-organized assemblies of organic molecules at surfaces of metal particles with sizes in the nanometer regime have been a subject of immense interest in recent years. Amongst the metal nanoparticles, considering the nobility of gold, organic fluoroprobes have often been attached to the surfaces of gold nanoparticles to form an extended network for potential technological applications. These organic-inorganic hybrid nanoassemblies offer an efficient route for the patterning of surfaces with functional nanometer-scale architectures utilizing several non-covalent intermolecular bonding interactions, e.g., hydrogen bonding, coordination bonding, etc. There is a growing recognition of fluorescence spectroscopy to achieve a molecular level understanding of the physical and chemical aspects of the molecule-surface interactions. The fluorophore-bound gold nanoparticles provide a convenient way to examine the mechanistic details of various deactivation pathways of the photoexcited fluoroprobes, such as energy and electron transfer to the particles as well as different types of intermolecular interactions involved in producing the bottom-up assembly of tailored nanostructures with a wide variety of structures and properties. The understanding of electronic absorption and dynamics in nanoparticulate systems is essential before assembling them into devices, which is essentially the future goal of the use of nanostructured systems. It is, therefore, important to elucidate the particle size and distance dependence on the interaction between excited molecular probes and the gold nanoparticles. The potential impact of the derived nanopatterned surfaces ranges from applications in molecular electronics to selective sensors to diagnostic devices. The greatest promise of these systems lies in the potential to tune functional aspects of the supramolecular assemblies at surfaces by manipulation of the interactions governing the derivation of supramolecular function

  13. 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.

  14. 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.

  15. Agonist Derived Molecular Probes for A2A Adenosine Receptors

    PubMed Central

    Jacobson, Kenneth A.; Pannell, Lewis K.; Ji, Xiao-duo; Jarvis, Michael F.; Williams, Michael; Hutchison, Alan J.; Barrington, William W.; Stiles, Gary L.

    2011-01-01

    The adenosine agonist 2-(4-(2-carboxyethyl)phenylethylamino)-5′-N-ethylcarboxamidoadenosine (CGS21680) was recently reported to be selective for the A2A adenosine receptor subtype, which mediates its hypotensive action. To investigate structurelactivity relationships at a distal site, CGS21680 was derivatized using a functionalized congener approach. The carboxylic group of CGS21680 has been esterified to form a methyl ester, which was then treated with ethylenediamine to produce an amine congener. The amine congener was an intermediate for acylation reactions, in which the reactive acyl species contained a reported group, or the precursor for such. For radioiodination, derivatives of p-hydroxyphenylpropionic, 2-thiophenylacetic, and p-aminophenylacetic acids were prepared. The latter derivative (PAPA-APEC) was iodinated electrophilically using [125I]iodide resulting in a radioligand which was used for studies of competition of binding to striatal A, adenosine receptors in bovine brain. A biotin conjugate and an aryl sulfonate were at least 350-fold selective for A, receptors. For spectroscopic detection, a derivative of the stable free radical tetramethyl-1-piperidinyloxy (TEMPO) was prepared. For irreversible inhibition of receptors, meta- and para-phenylenediisothiocyanate groups were incorporated in the analogs. We have demonstrated that binding at A2A receptors is relatively insensitive to distal structural changes at the 2-position, and we report high affinity molecular probes for receptor characterization by radioactive, spectroscopic and affinity labelling methodology. PMID:2561548

  16. Probing Molecular Organization and Electronic Dynamics at Buried Organic Interfaces

    NASA Astrophysics Data System (ADS)

    Roberts, Sean

    2015-03-01

    Organic semiconductors are a promising class of materials due to their ability to meld the charge transport capabilities of semiconductors with many of the processing advantages of plastics. In thin film organic devices, interfacial charge transfer often comprises a crucial step in device operation. As molecular materials, the density of states within organic semiconductors often reflect their intermolecular organization. Truncation of the bulk structure of an organic semiconductor at an interface with another material can lead to substantial changes in the density of states near the interface that can significantly impact rates for interfacial charge and energy transfer. Here, we will present the results of experiments that utilize electronic sum frequency generation (ESFG) to probe buried interfaces in these materials. Within the electric dipole approximation, ESFG is only sensitive to regions of a sample that experience a breakage of symmetry, which occurs naturally at material interfaces. Through modeling of signals measured for thin organic films using a transfer matrix-based formalism, signals from buried interfaces between two materials can be isolated and used to uncover the interfacial density of states.

  17. 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

  18. A hyperpolarized choline molecular probe for monitoring acetylcholine synthesis.

    PubMed

    Allouche-Arnon, Hyla; Gamliel, Ayelet; Barzilay, Claudia M; Nalbandian, Ruppen; Gomori, J Moshe; Karlsson, Magnus; Lerche, Mathilde H; Katz-Brull, Rachel

    2011-01-01

    Choline as a reporter molecule has been investigated by in vivo magnetic resonance for almost three decades. Accumulation of choline metabolites (mainly the phosphorylated forms) had been observed in malignancy in preclinical models, ex-vivo, in vivo and in patients. The combined choline metabolite signal appears in (1) H-MRS of the brain and its relative intensity had been used as a diagnostic factor in various conditions. The advent of spin hyperpolarization methods for in vivo use has raised interest in the ability to follow the physiological metabolism of choline into acetylcholine in the brain. Here we present a stable-isotope labeled choline analog, [1,1,2,2-D(4) ,2-(13) C]choline chloride, that is suitable for this purpose. In this analog, the (13) C position showed 24% polarization in the liquid state, following DNP hyperpolarization. This nucleus also showed a long T(1) (35 s) at 11.8 T and 25 °C, which is a prerequisite for hyperpolarized studies. The chemical shift of this (13) C position differentiates choline and acetylcholine from each other and from the other water-soluble choline metabolites, namely phosphocholine and betaine. Enzymatic studies using an acetyltransferase enzyme showed the synthesis of the deuterated-acetylcholine form at thermal equilibrium conditions and in a hyperpolarized state. Analysis using a comprehensive model showed that the T(1) of the formed hyperpolarized [1,1,2,2-D(4) ,2-(13) C]acetylcholine was 34 s at 14.1 T and 37 °C. We conclude that [1,1,2,2-D(4) ,2-(13) C]choline chloride is a promising new molecular probe for hyperpolarized metabolic studies and discuss the factors related to its possible use in vivo.

  19. Molecular probe for identification of Trichomonas vaginalis DNA.

    PubMed Central

    Rubino, S; Muresu, R; Rappelli, P; Fiori, P L; Rizzu, P; Erre, G; Cappuccinelli, P

    1991-01-01

    Trichomoniasis is one of the most widespread sexually transmitted diseases in the world. Diagnosis can be achieved by several methods, such as direct microscopic observation of vaginal discharge, cell culture, and immunological techniques. A 2.3-kb Trichomonas vaginalis DNA fragment present in strains from diverse geographic areas was cloned and used as a probe to detect T. vaginalis DNA in vaginal discharge by a dot blot hybridization technique. This probe was specific for T. vaginalis DNA. It recognized strains from two regions in Italy (Sardinia, Piemonte) and from Mozambique (Africa). In addition, our probe did not cross-react with bacterial (Escherichia coli, Enterococcus spp., group B streptococci, Gardnerella vaginalis, Neisseria gonorrhoeae, Chlamydia trachomatis, and Lactobacillus spp.), viral (herpes simplex virus type 2), fungal (Candida albicans), protozoan (Entamoeba histolytica, Giardia lamblia, Plasmodium falciparum, Leishmania major, and Leishmania infantum), or human nucleic acids. The probe reacted with Pentatrichomonas hominis and Trichomonas foetus. The limit signal recognized by our probe corresponded to the DNA of 200 T. vaginalis isolates. The 2.3-kb probe was used in a clinical analysis of 98 samples. Of these, 20 samples were found to be positive both with the probe and by cell culture, and only 14 of these were positive by a standard wet mount method. Images PMID:1890171

  20. Relative intermolecular orientation probed via molecular heat transport.

    PubMed

    Chen, Hailong; Bian, Hongtao; Li, Jiebo; Wen, Xiewen; Zheng, Junrong

    2013-07-25

    In this work, through investigating a series of liquid, glassy, and crystalline samples with ultrafast multiple-mode 2D IR and IR transient absorption methods, we demonstrated that the signal anisotropy of vibrational relaxation-induced heat effects is determined by both relative molecular orientations and molecular rotations. If the relative molecular orientations are randomized or molecular rotations are fast compared to heat transfer, the signal anisotropy of heat effects is zero. If the relative molecular orientations are anisotropic and the molecular rotations are slow, the signal anisotropy of heat effects can be nonzero, which is determined by the relative orientations of the energy source mode and the heat sensor mode within the same molecule and in different molecules. We also demonstrated that the correlation between the anisotropy value of heat signal and the relative molecular orientations can be quantitatively calculated.

  1. Use of Sloppy Molecular Beacon Probes for Identification of Mycobacterial Species ▿ †

    PubMed Central

    El-Hajj, Hiyam H.; Marras, Salvatore A. E.; Tyagi, Sanjay; Shashkina, Elena; Kamboj, Mini; Kiehn, Timothy E.; Glickman, Michael S.; Kramer, Fred Russell; Alland, David

    2009-01-01

    We report here the use of novel “sloppy” molecular beacon probes in homogeneous PCR screening assays in which thermal denaturation of the resulting probe-amplicon hybrids provides a characteristic set of amplicon melting temperature (Tm) values that identify which species is present in a sample. Sloppy molecular beacons possess relatively long probe sequences, enabling them to form hybrids with amplicons from many different species despite the presence of mismatched base pairs. By using four sloppy molecular beacons, each possessing a different probe sequence and each labeled with a differently colored fluorophore, four different Tm values can be determined simultaneously. We tested this technique with 27 different species of mycobacteria and found that each species generates a unique, highly reproducible signature that is unaffected by the initial bacterial DNA concentration. Utilizing this general paradigm, screening assays can be designed for the identification of a wide range of species. PMID:19171684

  2. 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.

  3. 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.

  4. [Preparation of magnetic resonance molecular probe for breast cancer detection in vitro].

    PubMed

    Li, Xu-bin; DU, Xiang-ke; Huo, Tian-long; Liu, Xia; Zhang, Sen

    2009-04-18

    To prepare magnetic resonance (MR) molecular probe for somatostain receptor expressed on breast cancer cell membranes and investigate its physico-chemical properties and imaging features in vitro. Molecular probe was prepared through superparamagnetic iron oxide (SPIO) conjugated to somatostatin analog-octreotide (OCT) using chemical method. Its features at different Fe(2+) concentrations were tested by MTT assay and Prussian blue staining respectively. Molecular probes at different Fe(2+) concentration and various numbers of cells labeled with the probe at Fe(2+) concentrations of 20 mg/L were scanned with 1.5 Tesla MR. Resovist was used in control group when labeling cells. Various blue-staining particles were found in the cytoplasms of labeled cells with the molecular probes at different concentrations after Prussion blue staining and there were more particles with the increase of Fe(2+) concentration. The label rate of the probe was 96.15% which was higher than that in control group (80.00%). The bioactivity had no difference between labeled and non-labeled cells (P>0.05). There was remarkable low signal intensity on T(2)-weighed imaging and no evident artifacts for molecular probe when the concentration of Fe(2+) was 20 mg/L. The least number of labeled cells detected by MR in vitro was 6 x 10(6) when the concentration of Fe(2+) was 20 mg/L. Molecular probe, SPIO-OCT, can effectively label breast cells which express SSTR. The reasonable Fe(2+) concentration of labeled cells and imaging was 20 mg/L. There is a correlation between MR signal intensity in vitro and the number of labeled cells.

  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.

  6. Near-infrared Molecular Probes for In Vivo Imaging

    PubMed Central

    Zhang, Xuan; Bloch, Sharon; Akers, Walter; Achilefu, Samuel

    2012-01-01

    Cellular and tissue imaging in the near-infrared (NIR) wavelengths between 700 and 900 nm is advantageous for in vivo because of the low absorption of biological molecules in this region. This Unit presents protocols for small animal imaging using planar and fluorescence lifetime imaging techniques. Included is an overview of NIR fluorescence imaging of cells and small animals using NIR organic fluorophores, nanoparticles, and multimodal imaging probes. The development, advantages, and application of NIR fluorescent probes that have been used for in vivo imaging are also summarized. The use of NIR agents in conjunction with visible dyes and considerations in selecting imaging agents are discussed. We conclude with practical considerations for the use of these dyes in cell and small animal imaging applications. PMID:22470154

  7. Probing molecular junctions using surface plasmon resonance spectroscopy.

    PubMed

    Shimizu, Ken T; Pala, Ragip A; Fabbri, Jason D; Brongersma, Mark L; Melosh, Nicholas A

    2006-12-01

    The optical absorption spectra of nanometer-thick organic films and molecular monolayers sandwiched between two metal contacts have been measured successfully using surface plasmon resonance spectroscopy (SPRS). The electric field within metal-insulator (organic)-metal (MIM) cross-bar junctions created by surface plasmon-polaritons excited on the metal surface allows sensitive measurement of molecular optical properties. Specifically, this spectroscopic technique extracts the real and imaginary indices of the organic layer for each wavelength of interest. The SPRS sensitivity was calculated for several device architectures, metals, and layer thicknesses to optimize the organic film absorptivity measurements. Distinct optical absorption features were clearly observed for R6G layers as thin as a single molecular monolayer between two metal electrodes. This method also enables dynamic measurement of molecular conformation inside metallic junctions, as shown by following the optical switching of a thin spiropyran/polymer film upon exposure to UV light. Finally, optical and electrical measurements can be made simultaneously to study the effect of electrical bias and current on molecular conformation, which may have significant impact in areas such as molecular and organic electronics.

  8. Single and multiple molecular beacon probes for DNA hybridization studies on a silica glass surface

    NASA Astrophysics Data System (ADS)

    Fang, Xiaohong; Liu, Xiaojing; Tan, Weihong

    1999-05-01

    Surface immobilizable molecular beacons have been developed for DNA hybridization studies on a silica glass plate. Molecular beacons are a new class of oligonucleotide probes that have a loop-and-stem structure with a fluorophore and a quencher attached to the two ends of the stem. They only emit intense fluorescence when hybridize to their target molecules. This provides an excellent selectivity for the detection of DNA molecules. We have designed biotinylated molecular beacons which can be immobilized onto a solid surface. The molecular beacon is synthesized using DABCYL as the quencher and an optical stable dye, tetramethylrhodamine, as the fluorophore. Mass spectrometry is used to confirm the synthesized molecular beacon. The molecular beacons have been immobilized onto a silica surface through biotin-avidin binding. The surface immobilized molecular beacons have been used for the detection of target DNA with subnanomolar analytical sensitivity. have also immobilized two different molecular beacons on a silica surface in spatially resolved microscopic regions. The hybridization study of these two different molecular beacon probes has shown excellent selectivity for their target sequences. The newly designed molecular beacons are intended for DNA molecular interaction studies at an interface and for the development of ultrasensitive DNA sensors for a variety of applications including disease diagnosis, disease mechanism studies, new drug development, and in the investigation of molecular interactions between DNA molecules and other interesting biomolecules.

  9. NanoCluster Beacon - A New Molecular Probe for Homogeneous Detection of Nucleic Acid Targets

    DTIC Science & Technology

    2011-02-01

    requires only a single preparation step (i.e. nanocluster formation on NC probes), but because there is no need to remove excess silver ions or...Oligonucleotide-templated nanoclusters consisting of a few atoms of silver (DNA/Ag NCs) have been made into a new molecular probe that “lights up...upon target DNA binding, termed a NanoCluster Beacon (NCB). We discovered that interactions between silver nanoclusters and a proximal, guanine- rich

  10. Observing the Hydration Layer of Trehalose with a Linked Molecular Terahertz Probe.

    PubMed

    Sajadi, Mohsen; Berndt, Falko; Richter, Celin; Gerecke, Mario; Mahrwald, Rainer; Ernsting, Nikolaus P

    2014-06-05

    The terahertz (THz) absorption bands of biomolecular hydration layers are generally swamped by absorption from bulk water. Using the disaccharide trehalose, we show that this limitation can be overcome by attaching a molecular probe. By time-resolving the fluorescence shift of the probe, a local THz spectrum is obtained. From the dependence on temperature and H2O/D2O exchange, it is concluded that the trehalose hydration layer is being observed. The region of dynamic water perturbation by the disaccharide encompasses the probe and is therefore larger than the first two solvation layers.

  11. [Targeted magnetic nanoparticles used as probe for magnetic resonance molecular imaging of tumor].

    PubMed

    Lu, Jing-Jing; Wang, Fang; Jin, Zheng-Yu; Zhong, Ding-Rong

    2009-04-01

    To investigate the feasibility of in vivo tumor detection using magnetic resonance (MR) molecular imaging with targeted magnetic nanoparticles as imaging probe. Targeted probe was synthesized by covalently linking the recombinant human gonadotropin releasing hormone analog (the targeting portion) with the ultrasmall superparamagnetic iron oxide nanoparticles (the imaging portion). The imaging portion served as the control material. The in vitro tumor cell experiment and the in vivo experiment using nude mice bearing tumors were carried out to test the targeting ability of the probe. In the in vitro experiment, the targeting probe and control materials were incubated separately with A549 cells which had high affinity to gonadotropin releasing hormone. Then the cells were taken out and lysed. The resultant solution was then subjected to MR imaging. The T2 value of the solutions was measured and compared. In the in vivo experiment, the targeting probe was administered into nude mice bearing A549 tumors. Dynamic MR imaging was carried out to measure the signal and T2 value of the tumor. The control material was also administered into control group of nude mice, and dynamic magnetic resonance imaging was performed. The T2 value of the tumor in both groups were recorded and compared. Both the in vitro and in vivo experiments proved the targeting ability of targeted probe. Compared with control material, the targeting probe had higher combining ability with tumor cells. MR molecular imaging of tumor can be realized by using targeting magnetic nanoparticles.

  12. Optimally designed nanolayered metal-dielectric particles as probes for massively multiplexed and ultrasensitive molecular assays.

    PubMed

    Kodali, Anil K; Llora, Xavier; Bhargava, Rohit

    2010-08-03

    An outstanding challenge in biomedical sciences is to devise a palette of molecular probes that can enable simultaneous and quantitative imaging of tens to hundreds of species down to ultralow concentrations. Addressing this need using surface-enhanced Raman scattering-based probes is potentially possible. Here, we theorize a rational design and optimization strategy to obtain reproducible probes using nanospheres with alternating metal and reporter-filled dielectric layers. The isolation of reporter molecules from metal surfaces suppresses chemical enhancement, and consequently signal enhancements are determined by electromagnetic effects alone. This strategy synergistically couples interstitial surface plasmons and permits the use of almost any molecule as a reporter by eliminating the need for surface attachment. Genetic algorithms are employed to optimize the layer dimensions to provide controllable enhancements exceeding 11 orders of magnitude and of single molecule sensitivity for nonresonant and resonant reporters, respectively. The strategy also provides several other opportunities, including a facile route to tuning the response of these structures to be spectrally flat and localization of the enhancement within a specific volume inside or outside the probe. The spectrally uniform enhancement for multiple excitation wavelengths and for different shifts enables generalized probes, whereas enhancement tuning permits a large dynamic range by suppression of enhancements from outside the probe. Combined, these theoretical calculations open the door for a set of reproducible and robust probes with controlled sensitivity for molecular sensing over a concentration range of over 20 orders of magnitude.

  13. Engineered Aptamers to Probe Molecular Interactions on the Cell Surface.

    PubMed

    Batool, Sana; Bhandari, Sanam; George, Shanell; Okeoma, Precious; Van, Nabeela; Zümrüt, Hazan E; Mallikaratchy, Prabodhika

    2017-08-29

    Significant progress has been made in understanding the nature of molecular interactions on the cell membrane. To decipher such interactions, molecular scaffolds can be engineered as a tool to modulate these events as they occur on the cell membrane. To guarantee reliability, scaffolds that function as modulators of cell membrane events must be coupled to a targeting moiety with superior chemical versatility. In this regard, nucleic acid aptamers are a suitable class of targeting moieties. Aptamers are inherently chemical in nature, allowing extensive site-specific chemical modification to engineer sensing molecules. Aptamers can be easily selected using a simple laboratory-based in vitro evolution method enabling the design and development of aptamer-based functional molecular scaffolds against wide range of cell surface molecules. This article reviews the application of aptamers as monitors and modulators of molecular interactions on the mammalian cell surface with the aim of increasing our understanding of cell-surface receptor response to external stimuli. The information gained from these types of studies could eventually prove useful in engineering improved medical diagnostics and therapeutics.

  14. Fluorescence probes of spectroscopic and dynamical aspects of molecular photoionization

    NASA Astrophysics Data System (ADS)

    Poliakoff, Erwin D.

    1988-11-01

    Studies were made of vibrationally resolved aspects of shape resonant excitation in the photoionization of N(2)0. This experiment was performed by generating dispersed fluorescence spectra from electronically excited photoions. These results are the first vibrationally resolved results on a polyatomic shape resonance. In vibrationally resolved measurements, different internuclear configurations are probed by sampling alternative vibrational levels of the ion. As a result, the continuum electron behavior can be mapped out most clearly, and the qualitative aspects of the electron ejection can be understood clearly. A central motivation for studying polyatomic shape resonances is that alternative vibrational modes may be explored, revealing facets that are nonexistent for diatomic systems, which are the only systems that have been characterized previously.

  15. 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

  16. Vibrational excitations in molecular layers probed by ballistic electron microscopy

    NASA Astrophysics Data System (ADS)

    Sivasayan Kajen, Rasanayagam; Chandrasekhar, Natarajan; Feng, Xinliang; Müllen, Klaus; Su, Haibin

    2011-10-01

    We demonstrate the information on molecular vibrational modes via the second derivative (d2IB/dV2) of the ballistic electron emission spectroscopy (BEES) current. The proposed method does not create huge fields as in the case of conventional derivative spectroscopy and maintains a zero bias across the device. BEES studies carried out on three different types of large polycyclic aromatic hydrocarbon (PAH) molecular layers show that the d2IB/dV2 spectra consist of uniformly spaced peaks corresponding to vibronic excitations. The peak spacing is found to be identical for molecules within the same PAH family though the BEES onset voltage varies for different molecules. In addition, injection into a particular orbital appears to correspond to a specific vibrational mode as the manifestation of the symmetry principle.

  17. Probing molecular choreography through single-molecule biochemistry.

    PubMed

    van Oijen, Antoine M; Dixon, Nicholas E

    2015-12-01

    Single-molecule approaches are having a dramatic impact on views of how proteins work. The ability to observe molecular properties at the single-molecule level allows characterization of subpopulations and acquisition of detailed kinetic information that would otherwise be hidden in the averaging over an ensemble of molecules. In this Perspective, we discuss how such approaches have successfully been applied to in vitro-reconstituted systems of increasing complexity.

  18. Probing the structural and molecular diversity of tumor vasculature.

    PubMed

    Pasqualini, Renata; Arap, Wadih; McDonald, Donald M

    2002-12-01

    The molecular diversity of the vasculature provides a rational basis for developing targeted diagnostics and therapeutics for cancer. Targeted imaging agents would offer better localization of primary tumors and metastases, and targeted therapies would improve efficacy and reduce side effects. The development of targeted pharmaceuticals requires the identification of specific ligand-receptor pairs, and knowledge of their cellular distribution and accessibility. Using in vivo phage display, a technique by which we can identify organ-specific and disease-specific proteins expressed on the endothelial surface, it is now possible to decipher the molecular signature of blood vessels in normal and diseased tissues. These studies have already led to the identification of peptides that target the normal vasculature of the brain, kidney, pancreas, lung and skin, as well as the abnormal vasculature of tumors, arthritis and atherosclerosis. Membrane dipeptidase in the lungs, interleukin-11 receptor in the prostate, and aminopeptidase N in tumors are examples of molecular targets on blood vessels. Corresponding confocal-microscopic imaging and ultrastructural studies are providing a more complete understanding of the cellular abnormalities of tumor blood vessels, and the distribution and accessibility of potential targets. The combined approach offers a strategy for creating a ligand-receptor map of the human vasculature, and forms a foundation for the development and application of targeted therapies in cancer and other diseases.

  19. Ultrafast X-ray Auger probing of photoexcited molecular dynamics

    DOE PAGES

    McFarland, B. K.; Farrell, J. P.; Miyabe, S.; ...

    2014-06-23

    Here, molecules can efficiently and selectively convert light energy into other degrees of freedom. Disentangling the underlying ultrafast motion of electrons and nuclei of the photoexcited molecule presents a challenge to current spectroscopic approaches. Here we explore the photoexcited dynamics of molecules by an interaction with an ultrafast X-ray pulse creating a highly localized core hole that decays via Auger emission. We discover that the Auger spectrum as a function of photoexcitation—X-ray-probe delay contains valuable information about the nuclear and electronic degrees of freedom from an element-specific point of view. For the nucleobase thymine, the oxygen Auger spectrum shifts towardsmore » high kinetic energies, resulting from a particular C–O bond stretch in the ππ* photoexcited state. A subsequent shift of the Auger spectrum towards lower kinetic energies displays the electronic relaxation of the initial photoexcited state within 200 fs. Ab-initio simulations reinforce our interpretation and indicate an electronic decay to the nπ* state.« less

  20. Ultrafast X-ray Auger probing of photoexcited molecular dynamics

    SciTech Connect

    McFarland, B. K.; Farrell, J. P.; Miyabe, S.; Tarantelli, F.; Aguilar, A.; Berrah, N.; Bostedt, C.; Bozek, J. D.; Bucksbaum, P. H.; Castagna, J. C.; Coffee, R. N.; Cryan, J. P.; Fang, L.; Feifel, R.; Gaffney, K. J.; Glownia, J. M.; Martinez, T. J.; Mucke, M.; Murphy, B.; Natan, A.; Osipov, T.; Petrović, V. S.; Schorb, S.; Schultz, Th.; Spector, L. S.; Swiggers, M.; Tenney, I.; Wang, S.; White, J. L.; White, W.; Gühr, M.

    2014-06-23

    Here, molecules can efficiently and selectively convert light energy into other degrees of freedom. Disentangling the underlying ultrafast motion of electrons and nuclei of the photoexcited molecule presents a challenge to current spectroscopic approaches. Here we explore the photoexcited dynamics of molecules by an interaction with an ultrafast X-ray pulse creating a highly localized core hole that decays via Auger emission. We discover that the Auger spectrum as a function of photoexcitation—X-ray-probe delay contains valuable information about the nuclear and electronic degrees of freedom from an element-specific point of view. For the nucleobase thymine, the oxygen Auger spectrum shifts towards high kinetic energies, resulting from a particular C–O bond stretch in the ππ* photoexcited state. A subsequent shift of the Auger spectrum towards lower kinetic energies displays the electronic relaxation of the initial photoexcited state within 200 fs. Ab-initio simulations reinforce our interpretation and indicate an electronic decay to the nπ* state.

  1. 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

  2. Co-Encapsulating the Fusogenic Peptide INF7 and Molecular Imaging Probes in Liposomes Increases Intracellular Signal and Probe Retention

    PubMed Central

    Martin, Erik W.; Li, Changqing; Lu, Wuyuan; Kao, Joseph P. Y.

    2015-01-01

    Liposomes are promising vehicles to deliver diagnostic and therapeutic agents to cells in vivo. After uptake into cells by endocytosis, liposomes are degraded in the endolysosomal system. Consequently, the encapsulated cargo molecules frequently remain sequestered in endosomal compartments; this limits their usefulness in many applications (e.g. gene delivery). To overcome this, various fusogenic peptides have been developed to facilitate delivery of liposomally-encapsulated molecules into the cytosol. One such peptide is the pH-sensitive influenza-derived peptide INF7. Liposomal delivery of imaging agents is an attractive approach for enabling cell imaging and cell tracking in vivo, but can be hampered by inadequate intracellular accumulation and retention of probes caused by exocytosis (and possible degradation) of endosome-entrapped probes. Such signal loss could be minimized by facilitating escape of probe molecules from endolysosomal compartments into the cytosol. We investigated the ability of co-encapsulated INF7 to release liposomally-delivered rhodamine fluorophores into the cytosol after endosomal acidification/maturation. We co-encapsulated INF7 and fluorescent rhodamine derivatives having vastly different transport properties to show that after endocytosis by CV1 cells, the INF7 peptide is activated by acidic endosomal pH and facilitates efficient release of the fluorescent tracers into the cytosol. Furthermore, we show that INF7-facilitated escape from endosomes markedly enhanced retention of tracers that cannot be actively extruded from the cytosol. Minimizing loss of intracellular probes improves cellular imaging by increasing the signal-to-noise ratio of images and lengthening the time window that imaging can be performed. In particular, this will enhance in vivo electron paramagnetic resonance imaging, an emergent magnetic resonance imaging modality requires exogenous paramagnetic imaging agents and is highly promising for cellular and molecular

  3. 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.

  4. Probing the molecular connectivity of water confined in polymer hydrogels

    NASA Astrophysics Data System (ADS)

    Rossi, B.; Venuti, V.; Mele, A.; Punta, C.; Melone, L.; Crupi, V.; Majolino, D.; Trotta, F.; D'Amico, F.; Gessini, A.; Masciovecchio, C.

    2015-01-01

    The molecular connectivity and the extent of hydrogen-bond patterns of water molecules confined in the polymer hydrogels, namely, cyclodextrin nanosponge hydrogels, are here investigated by using vibrational spectroscopy experiments. The proposed spectroscopic method exploits the combined analysis of the vibrational spectra of polymers hydrated with water and deuterated water, which allows us to separate and selectively investigate the temperature-evolution of the HOH bending mode of engaged water molecules and of the vibrational modes assigned to specific chemical groups of the polymer matrix involved in the physical interactions with water. As main results, we find a strong experimental evidence of a liquid-like behaviour of water molecules confined in the nano-cavities of hydrogel and we observe a characteristic destructuring effect on the hydrogen-bonds network of confined water induced by thermal motion. More interestingly, the extent of this temperature-disruptive effect is found to be selectively triggered by the cross-linking degree of the hydrogel matrix. These results give a more clear picture of the molecular mechanism of water confinement in the pores of nanosponge hydrogel and open the possibility to exploit the spectroscopic method here proposed as investigating tools for water-retaining soft materials.

  5. Probing the molecular connectivity of water confined in polymer hydrogels.

    PubMed

    Rossi, B; Venuti, V; Mele, A; Punta, C; Melone, L; Crupi, V; Majolino, D; Trotta, F; D'Amico, F; Gessini, A; Masciovecchio, C

    2015-01-07

    The molecular connectivity and the extent of hydrogen-bond patterns of water molecules confined in the polymer hydrogels, namely, cyclodextrin nanosponge hydrogels, are here investigated by using vibrational spectroscopy experiments. The proposed spectroscopic method exploits the combined analysis of the vibrational spectra of polymers hydrated with water and deuterated water, which allows us to separate and selectively investigate the temperature-evolution of the HOH bending mode of engaged water molecules and of the vibrational modes assigned to specific chemical groups of the polymer matrix involved in the physical interactions with water. As main results, we find a strong experimental evidence of a liquid-like behaviour of water molecules confined in the nano-cavities of hydrogel and we observe a characteristic destructuring effect on the hydrogen-bonds network of confined water induced by thermal motion. More interestingly, the extent of this temperature-disruptive effect is found to be selectively triggered by the cross-linking degree of the hydrogel matrix. These results give a more clear picture of the molecular mechanism of water confinement in the pores of nanosponge hydrogel and open the possibility to exploit the spectroscopic method here proposed as investigating tools for water-retaining soft materials.

  6. Radionuclide probes for molecular imaging of pancreatic beta-cells.

    PubMed

    Wu, Zhanhong; Kandeel, Fouad

    2010-08-30

    Islet transplantation is a promising treatment option for patients with type 1 diabetes (T1D); however, the fate of the graft over time remains difficult to follow, due to the lack of available tools capable of monitoring graft rejection and inflammation prior to islet graft loss. Due to the challenges imposed by the location of the pancreas and the sparsely dispersed beta-cell population within the pancreas, currently, the clinical verification of beta-cell abnormalities can only be obtained indirectly via metabolic studies, which typically is not possible until after a significant deterioration in islet function has already occurred. The development of non-invasive imaging methods for the assessment of the pancreatic beta-cells, however, offers the potential for the early detection of beta-cell dysfunction prior to the clinical onset of T1D and type 2 diabetes (T2D). Ideal islet imaging agents would have an acceptable residence time in the human body, be capable of providing high-resolution images with minimal uptake in surrounding tissues (e.g., the liver), would not be toxic to islets, and would not require pre-treatment of islets prior to transplantation. A variety of currently available imaging techniques, including magnetic resonance imaging (MRI), bioluminescence imaging (BLI), and nuclear imaging have been tested for the study of beta-cell diseases. In this article, we summarize the recent advances made in nuclear imaging techniques for non-invasive imaging of pancreatic beta-cells. The use of radioactive probes for islet imaging is also discussed. Copyright © 2010 Elsevier B.V. All rights reserved.

  7. Photolytic labeling to probe molecular interactions in lyophilized powders.

    PubMed

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

    2013-12-02

    Local side-chain interactions in lyophilized protein formulations were mapped using solid-state photolytic labeling-mass spectrometry (ssPL-MS). Photoactive amino acid analogues (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 photoleucine (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 electrospray ionization/high-performance liquid chromatography/mass spectrometry (ESI-HPLC-MS), with labeling reaching a plateau at ~30 min, forming up to six labeled populations. Bottom-up MS/MS analysis was able to provide peptide-level 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 acid-level 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.

  8. Molecular detection of bacterial pathogens using microparticle enhanced double-stranded DNA probes.

    PubMed

    Riahi, Reza; Mach, Kathleen E; Mohan, Ruchika; Liao, Joseph C; Wong, Pak Kin

    2011-08-15

    Rapid, specific, and sensitive detection of bacterial pathogens is essential toward clinical management of infectious diseases. Traditional approaches for pathogen detection, however, often require time-intensive bacterial culture and amplification procedures. Herein, a microparticle enhanced double-stranded DNA probe is demonstrated for rapid species-specific detection of bacterial 16S rRNA. In this molecular assay, the binding of the target sequence to the fluorophore conjugated probe thermodynamically displaces the quencher probe and allows the fluorophore to fluoresce. By incorporation of streptavidin-coated microparticles to localize the biotinylated probes, the sensitivity of the assay can be improved by 3 orders of magnitude. The limit of detection of the assay is as few as eight bacteria without target amplification and is highly specific against other common pathogens. Its applicability toward clinical diagnostics is demonstrated by directly identifying bacterial pathogens in urine samples from patients with urinary tract infections.

  9. Ratiometric and near-infrared molecular probes for the detection and imaging of zinc ions.

    PubMed

    Carol, Priya; Sreejith, Sivaramapanicker; Ajayaghosh, Ayyappanpillai

    2007-03-05

    The detection and imaging of Zn2+ in biological samples are of paramount interest owing to the role of this cation in physiological functions. This is possible only with molecular probes that specifically bind to Zn2+ and result in changes in emission properties. A "turn-on" emission or shift in the emission color upon binding to Zn2+ should be ideal for in vivo imaging. In this context, ratiometric and near-IR probes are of particular interest. Therefore, in the area of chemosensors or molecular probes, the design of fluorophores that allow ratiometric sensing or imaging in the near-IR region is attracting the attention of chemists. The purpose of this Focus Review is to highlight recent developments in this area and stress the importance of further research for future applications.

  10. 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.

  11. 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.

  12. Super-resolution surface mapping using the trajectories of molecular probes.

    PubMed

    Walder, Robert; Nelson, Nathaniel; Schwartz, Daniel K

    2011-11-01

    The surface characterization of 'soft' materials presents a significant scientific challenge, particularly under 'wet' in situ conditions where a wide variety of non-covalent interactions may be relevant. Here we introduce a new chemical imaging method, MAPT (mapping using accumulated probe trajectories) that generates images of surface interactions by distributing different aspects of molecular probe trajectories into distinct locations and then combining many trajectories to generate spatial maps. The maps are super-resolution in nature, because they are accumulated from highly localized single-molecule observations. Unlike other super-resolution techniques, which report only photon or point counts, our analysis generates spatial maps of physical quantities (adsorption rate, desorption probability, local surface diffusion coefficient, surface coverage/occupancy) that are directly associated with the molecular interactions between the probe molecule and the surface. We demonstrate the feasibility of this characterization using a surface patterned with various degrees of hydrophobicity.

  13. 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.

  14. Photoexcited State Molecular Structures in Solution Studied by Pump-Probe XAFS

    NASA Astrophysics Data System (ADS)

    Chen, Lin

    2002-03-01

    The photoexcitation causes displacement of electron densities within or among molecules, which consequently leads to nuclear movements. Such nuclear displacements often occur in transient states with short lifetimes. Knowing transient molecular structures during photochemical reactions is important for understanding fundamental aspects of solar energy conversion and storage. Fast x-ray techniques provide direct probes for these transient structures. Using x-ray pulses from the Advanced Photon Source at Argonne, a laser pulse pump, x-ray pulse probe XAFS technique has been developed to capture transient molecular structures in disordered media with nanosecond time resolution. We have carried out several pump-probe XAFS measurements on 1)identifying a transient molecular structure of the photodissociation product of nickel-tetraphenylporphyrin with piperidine axial ligands (NiTPP-L2); 2)determination of the MLCT state structure of Bis(2,9-dimethyl-1,10-phenanthroline) Copper(I) [Cu(I)(dmp)2]+, and 3) triplet state molecular structures of metalloporphyrins. These studies not only prove the feasibility of the technique, but also gain structural information that otherwise will not be available. Future studies include probing transient structures in electron donor-acceptor complexes and optical polarization selected XAFS (OPS-XAFS) using the same technique with a 100-ps time resolution. This work is supported by the Division of Chemical Sciences, Office of Basic Energy Sciences, U. S. Department of Energy, under contract W-31-109-Eng-38.

  15. 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.

  16. 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.

  17. Probing Young Stars' Accretion Flows Using Infrared Molecular Lines

    NASA Astrophysics Data System (ADS)

    Turner, Neal

    We propose to examine how accretion power is released in protostellar disks. We will build models of the formation of the infrared molecular rovibrational lines in the disk surface layers, and apply them to observed spectra to address the following questions: * Do protostellar disk atmospheres have turbulence, outflows, or both? How does this vary with distance from the star? With accretion rate? With stellar mass? * How is the accretion heating distributed through the disk, and what does this imply for the temperatures in the planet-forming material? * Which models of the angular momentum transfer in protostellar disks can explain the flows and heating, and what does this imply about the time history of the accretion? By solving the line transfer problem we will enable interpretation of the rovibrational lines of CO, H2O and other molecules which dominate the near-infrared spectra of many accreting young stars. We will link the spectral lines' shapes to the flow kinematics near the disk surface, and we will link diagnostics including the rotational temperature diagram to proposed accretion heating processes. A non-LTE treatment is essential since the transitions are excited through both thermal collisions and radiative pumping by stellar ultraviolet and disk infrared continuum photons. Furthermore since many of the lines form at very low continuum optical depths, the pumping radiation can arrive either radially or vertically, making a 2-D treatment necessary. This amounts to a challenging line transfer problem, for which we have assembled a team with expertise in two efficient numerical schemes: accelerated Monte Carlo iteration and the coupled escape probability method. Combining non-LTE line transfer modeling with observational investigations as we propose is essential for interpreting the large and growing library of molecular line data from ground-based telescopes, and will make it possible for SOFIA and JWST to reach their potential to determine the basic

  18. Probing Polyoxometalate-Protein Interactions Using Molecular Dynamics Simulations.

    PubMed

    Solé-Daura, Albert; Goovaerts, Vincent; Stroobants, Karen; Absillis, Gregory; Jiménez-Lozano, Pablo; Poblet, Josep M; Hirst, Jonathan D; Parac-Vogt, Tatjana N; Carbó, Jorge J

    2016-10-17

    The molecular interactions between the Ce(IV) -substituted Keggin anion [PW11 O39 Ce(OH2 )4 ](3-) (CeK) and hen egg-white lysozyme (HEWL) were investigated by molecular dynamics simulations. The analysis of CeK was compared with the Ce(IV) -substituted Keggin dimer [(PW11 O39 )2 Ce](10-) (CeK2 ) and the Zr(IV) -substituted Lindqvist anion [W5 O18 Zr(OH2 )(OH)](3-) (ZrL) to understand how POM features such as shape, size, charge, or type of incorporated metal ion influence the POM⋅⋅⋅protein interactions. Simulations revealed two regions of the protein in which the CeK anion interacts strongly: cationic sites formed by Arg21 and by Arg45 and Arg68. The POMs chiefly interact with the side chains of the positively charged (arginines, lysines) and the polar uncharged residues (tyrosines, serines, aspargines) via electrostatic attraction and hydrogen bonding with the oxygen atoms of the POM framework. The CeK anion shows higher protein affinity than the CeK2 and ZrL anions, because it is less hydrophilic and it has the right size and shape for establishing interactions with several residues simultaneously. The larger, more negatively charged CeK2 anion has a high solvent-accessible surface, which is sub-optimal for the interaction, while the smaller ZrL anion is highly hydrophilic and cannot efficiently interact with several residues simultaneously. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. 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

  20. Probing C84-embedded Si Substrate Using Scanning Probe Microscopy and Molecular Dynamics.

    PubMed

    Ho, Mon-Shu; Huang, Chih-Pong; Tsai, Jyun-Hwei; Chou, Che-Fu; Lee, Wen-Jay

    2016-09-28

    This paper reports an array-designed C84-embedded Si substrate fabricated using a controlled self-assembly method in an ultra-high vacuum chamber. The characteristics of the C84-embedded Si surface, such as atomic resolution topography, local electronic density of states, band gap energy, field emission properties, nanomechanical stiffness, and surface magnetism, were examined using a variety of surface analysis techniques under ultra, high vacuum (UHV) conditions as well as in an atmospheric system. Experimental results demonstrate the high uniformity of the C84-embedded Si surface fabricated using a controlled self-assembly nanotechnology mechanism, represents an important development in the application of field emission display (FED), optoelectronic device fabrication, MEMS cutting tools, and in efforts to find a suitable replacement for carbide semiconductors. Molecular dynamics (MD) method with semi-empirical potential can be used to study the nanoindentation of C84-embedded Si substrate. A detailed description for performing MD simulation is presented here. Details for a comprehensive study on mechanical analysis of MD simulation such as indentation force, Young's modulus, surface stiffness, atomic stress, and atomic strain are included. The atomic stress and von-Mises strain distributions of the indentation model can be calculated to monitor deformation mechanism with time evaluation in atomistic level.

  1. X-ray Circular Dichroism Signals: A Unique Probe of Local Molecular Chirality

    DOE PAGES

    Zhang, Yu; Rouxel, Jeremy; Autschbach, Jochen; ...

    2017-09-01

    Core-resonant circular dichroism (CD) signals are induced by molecular chirality and vanish for achiral molecules and racemic mixtures. The highly localized nature of core excitations makes them ideal probes of local chirality within molecules. Simulations of circular dichroism spectra of several molecular families illustrate how these signals vary with the electronic coupling to substitution groups, the distance between the X-ray chromophore and the chiral center, geometry, and chemical structure. Clear insights on the molecular structure are obtained through analysis of the X-ray CD spectra.

  2. Protein conformation and molecular order probed by second-harmonic-generation microscopy

    NASA Astrophysics Data System (ADS)

    Vanzi, Francesco; Sacconi, Leonardo; Cicchi, Riccardo; Pavone, Francesco S.

    2012-06-01

    Second-harmonic-generation (SHG) microscopy has emerged as a powerful tool to image unstained living tissues and probe their molecular and supramolecular organization. In this article, we review the physical basis of SHG, highlighting how coherent summation of second-harmonic response leads to the sensitivity of polarized SHG to the three-dimensional distribution of emitters within the focal volume. Based on the physical description of the process, we examine experimental applications for probing the molecular organization within a tissue and its alterations in response to different biomedically relevant conditions. We also describe the approach for obtaining information on molecular conformation based on SHG polarization anisotropy measurements and its application to the study of myosin conformation in different physiological states of muscle. The capability of coupling the advantages of nonlinear microscopy (micrometer-scale resolution in deep tissue) with tools for probing molecular structure in vivo renders SHG microscopy an extremely powerful tool for the advancement of biomedical optics, with particular regard to novel technologies for molecular diagnostic in vivo.

  3. 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.

  4. Raman probing of molecular interactions of alginate biopolymers with cells

    NASA Astrophysics Data System (ADS)

    Chourpa, Igor; Carpentier, Philippe; Maingault, Philippe; Fetissoff, Franck; Dubois, Pierre

    2000-05-01

    The biological polymers extracted from brown algae, alginates, are novel materials in biotechnology and biomedicine. Their ability to form viscous gels is used to immobilize or encapsulate yeast, enzymes, living cells and drugs. Calcium-alginate fibers are extensively used in wound dressings since exhibit antihaemostatic and healing properties. The problem with alginate-made dressings in surgery is their slow biodegradability: if entrapped within tissues, they can induce a local cellular recruitment with an inflammatory response contemporaneous to the resorption phase. In part, this problem is a consequence of poor solubility of the calcium alginates in water. Although calcium alginate fibers can exchange calcium ions with sodium ions from the wound exudate to create a calcium/sodium alginate fibers, the residual alginates are thought to be not totally degradable in vivo. Rapid and non- destructive characterization of series of the crude alginates and calcium alginate fibers has been performed using Raman spectroscopy with near IR excitation. Study of structural organization of the polymeric chains within calcium alginate fibers have been previously reported as made by confocal Raman multispectral imaging (CRMSI) in visible. Here, the Raman approach has been used to monitor the ion exchange reactions for different types of alginates and their salts in vitro. For in vivo evaluation, histological sections of alginate-treated rat tissue have been analyzed by light microscopy and CRMSI. The in vitro Raman modeling and the histochemical mapping were a necessary precursor for application of the Raman microprobe to follow in a non-invasive way the alginate-cell molecular interactions in rat tissue.

  5. 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

  6. Probing the molecular structure of interfacial films and crystals

    NASA Astrophysics Data System (ADS)

    Wang, Anfeng

    The properties of outside surfaces were found to play an important role in the nucleation and crystallization processes. Thus controlling the surface properties would provide an effective means for crystal engineering. Hydrophobic surface is prepared by self-assembled monolayer (SAM) formation of octadecyltrichlorosilane (OTS) on silicon surface, with the hydrophobicity adjusted by the monolayer coverage. Silicon wafer treated by RCA method is hydrophilic, so are SAMs formed by two amine-terminated organosilanes on silicon. However these three hydrophilic surfaces are unstable, due to contamination of the amine-terminated SAMs and hydrolysis of RCA treated silicon. Polymethine dyes, BDH+Cl- and BDH +ClO4-, are synthesized and characterized by UV spectra and crystal morphology. They have identical UV spectrum in dilute solutions due to the same chromophore, and J-aggregation happens at much higher concentrations. IR spectra are analyzed to monitor the crystallization process of BDH+Cl- OTS SAM surface and the crystallization process of BDH+Cl- on substrates with varying hydrophobicity was monitored by optical microscopy and compared. Due to the extreme flexibility of polysiloxane, silicone surfactants can arrange themselves at the interfaces quickly to adopt configurations with minimum free energy. Polysiloxane is hydrophobic but not oleophilic, which makes them effective emulsifiers and stabilizers in aqueous and nonaqueous media. The interaction between an AFM Si3N4 tip and a hydrophobic surface in silicone polyether (SPE) solution in the presence of ethanol was investigated by Atomic Force Microscopy (AFM) force measurement. ABA triblock type and comb-type SPE surfactants, adsorbed at the liquid-solid interface, provide steric barriers, even with significant addition of ethanol. On the contrary, conventional low-molecular weight and polymeric alkyl surfactants display no steric barrier even in the presence of moderate amount of ethanol. This unique property makes

  7. Probing Molecular Docking in a Charged Model Binding Site

    PubMed Central

    Brenk, Ruth; Vetter, Stefan W.; Boyce, Sarah E.; Goodin, David B.; Shoichet, Brian K.

    2011-01-01

    A model binding site was used to investigate charge–charge interactions in molecular docking. This simple site, a small (180 Å3) engineered cavity in cyctochrome c peroxidase (CCP), is negatively charged and completely buried from solvent, allowing us to explore the balance between electrostatic energy and ligand desolvation energy in a system where many of the common approximations in docking do not apply. A database with about 5300 molecules was docked into this cavity. Retrospective testing with known ligands and decoys showed that overall the balance between electrostatic interaction and desolvation energy was captured. More interesting were prospective docking scre”ens that looked for novel ligands, especially those that might reveal problems with the docking and energy methods. Based on screens of the 5300 compound database, both high-scoring and low-scoring molecules were acquired and tested for binding. Out of 16 new, high-scoring compounds tested, 15 were observed to bind. All of these were small heterocyclic cations. Binding constants were measured for a few of these, they ranged between 20 μM and 60 μM. Crystal structures were determined for ten of these ligands in complex with the protein. The observed ligand geometry corresponded closely to that predicted by docking. Several low-scoring alkyl amino cations were also tested and found to bind. The low docking score of these molecules owed to the relatively high charge density of the charged amino group and the corresponding high desolvation penalty. When the complex structures of those ligands were determined, a bound water molecule was observed interacting with the amino group and a backbone carbonyl group of the cavity. This water molecule mitigates the desolvation penalty and improves the interaction energy relative to that of the “naked” site used in the docking screen. Finally, six low-scoring neutral molecules were also tested, with a view to looking for false negative predictions

  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. Bayesian hierarchical structured variable selection methods with application to molecular inversion probe studies in breast cancer

    PubMed Central

    Zhang, Lin; Baladandayuthapani, Veerabhadran; Mallick, Bani K.; Manyam, Ganiraju C.; Thompson, Patricia A.; Bondy, Melissa L.; Do, Kim-Anh

    2015-01-01

    Summary The analysis of alterations that may occur in nature when segments of chromosomes are copied (known as copy number alterations) has been a focus of research to identify genetic markers of cancer. One high-throughput technique recently adopted is the use of molecular inversion probes (MIPs) to measure probe copy number changes. The resulting data consist of high-dimensional copy number profiles that can be used to ascertain probe-specific copy number alterations in correlative studies with patient outcomes to guide risk stratification and future treatment. We propose a novel Bayesian variable selection method, the hierarchical structured variable selection (HSVS) method, which accounts for the natural gene and probe-within-gene architecture to identify important genes and probes associated with clinically relevant outcomes. We propose the HSVS model for grouped variable selection, where simultaneous selection of both groups and within-group variables is of interest. The HSVS model utilizes a discrete mixture prior distribution for group selection and group-specific Bayesian lasso hierarchies for variable selection within groups. We provide methods for accounting for serial correlations within groups that incorporate Bayesian fused lasso methods for within-group selection. Through simulations we establish that our method results in lower model errors than other methods when a natural grouping structure exists. We apply our method to an MIP study of breast cancer and show that it identifies genes and probes that are significantly associated with clinically relevant subtypes of breast cancer. PMID:25705056

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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

    2016-08-12

    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.

  15. Molecular hybridization with DNA-probes as a laboratory diagnostic test for influenza viruses.

    PubMed

    Pljusnin, A Z; Rozhkova, S A; Nolandt, O V; Bryantseva, E A; Kuznetsov, O K; Noskov, F S

    1987-01-01

    The possibilities of using DNA-copies of different influenza A virus genes cloned with recombinant bacterial plasmids for the detection of virus-specific RNA by molecular dot-hybridization were analyzed. High specificity of RNA identification has been demonstrated and it has been shown expedient to use DNA-probes with high-conservative virus genes (polymerase, nucleoprotein, or matrix) for the detection of influenza A virus subtypes (H1N1, H2N2, H3N2) and probes with corresponding hemagglutinin genes for the differentiation of the subtypes H3N2 and H1N1. The results of nasopharyngeal specimens testing proved the effectiveness of molecular dot-hybridization in epidemiological studies of influenza outbreaks, especially of mixed etiology.

  16. Molecular beacon probes combined with amplification by NASBA enable homogeneous, real-time detection of RNA.

    PubMed Central

    Leone, G; van Schijndel, H; van Gemen, B; Kramer, F R; Schoen, C D

    1998-01-01

    Molecular beacon probes can be employed in a NASBA amplicon detection system to generate a specific fluorescent signal concomitantly with amplification. A molecular beacon, designed to hybridize within the target sequence, was introduced into NASBA reactions that amplify the genomic RNA of potato leafroll virus (PLRV). During amplification, the probe anneals to the antisense RNA amplicon generated by NASBA, producing a specific fluorescent signal that can be monitored in real-time. The assay is rapid, sensitive and specific. As RNA amplification and detection can be carried out in unopened vessels, it minimizes the risk of carry-over contaminations. Robustness has been verified on real-world samples. This homogeneous assay, called AmpliDet RNA, is a significant improvement over current detection methods for NASBA amplicons and is suitable for one-tube applications ranging from high-throughput diagnostics to in vivo studies of biological activities. PMID:9547273

  17. Friction force microscopy as an alternative method to probe molecular interactions

    NASA Astrophysics Data System (ADS)

    Lekka, Małgorzata; Kulik, Andrzej J.; Jeney, Sylvia; Raczkowska, Joanna; Lekki, Janusz; Budkowski, Andrzej; Forró, László

    2005-07-01

    Friction force microscopy was applied to study protein-carbohydrate interactions that are important in many cellular recognition processes. The expression and structure of carbohydrates can be investigated using lectins as molecular probes since they recognize different types of sugar molecules. Lectins (concanavalin A and lentil lectin, recognizing mannose-type carbohydrates) were attached to the probing tip and carboxypeptidase Y (possessing complementary carbohydrates) was immobilized on a modified glass surface using microcontact printing. The results obtained from friction force maps and dependencies on the loading rate (measured in a physiological buffer) were divided in two distinct groups. The first group of results obtained for lectin-protein complexes was assigned to molecular recognition events, whereas the other including all control measurements was attributed to nonspecific interaction. All results presented here indicate that friction force microscopy can be successfully employed to study recognition processes.

  18. microDuMIP: target-enrichment technique for microarray-based duplex molecular inversion probes

    PubMed Central

    Yoon, Jung-Ki; Ahn, Jinwoo; Kim, Han Sang; Han, Soo Min; Jang, Hoon; Lee, Min Goo; Lee, Ji Hyun; Bang, Duhee

    2015-01-01

    Molecular inversion probe (MIP)-based capture is a scalable and effective target-enrichment technology that can use synthetic single-stranded oligonucleotides as probes. Unlike the straightforward use of synthetic oligonucleotides for low-throughput target capture, high-throughput MIP capture has required laborious protocols to generate thousands of single-stranded probes from DNA microarray because of multiple enzymatic steps, gel purifications and extensive PCR amplifications. Here, we developed a simple and efficient microarray-based MIP preparation protocol using only one enzyme with double-stranded probes and improved target capture yields by designing probes with overlapping targets and unique barcodes. To test our strategy, we produced 11 510 microarray-based duplex MIPs (microDuMIPs) and captured 3554 exons of 228 genes in a HapMap genomic DNA sample (NA12878). Under our protocol, capture performance and precision of calling were compatible to conventional MIP capture methods, yet overlapping targets and unique barcodes allowed us to precisely genotype with as little as 50 ng of input genomic DNA without library preparation. microDuMIP method is simpler and cheaper, allowing broader applications and accurate target sequencing with a scalable number of targets. PMID:25414325

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

    PubMed

    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 F(1)-ATPase and the kinesin motor.

  20. Fluorescence microscopy studies of a peripheral-benzodiazepine-receptor-targeted molecular probe for brain tumor imaging

    NASA Astrophysics Data System (ADS)

    Marcu, Laura; Vernier, P. Thomas; Manning, H. Charles; Salemi, Sarah; Li, Aimin; Craft, Cheryl M.; Gundersen, Martin A.; Bornhop, Darryl J.

    2003-10-01

    This study investigates the potential of a new multi-modal lanthanide chelate complex for specifically targeting brain tumor cells. We report here results from ongoing studies of up-take, sub-cellular localization and binding specificity of this new molecular imaging probe. Fluorescence microscopy investigations in living rat C6 glioma tumor cells demonstrate that the new imaging agent has affinity for glioma cells and binds to mitochondria.

  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. Scanning probe microscopy of atoms and molecules on insulating films: from imaging to molecular manipulation.

    PubMed

    Meyer, Gerhard; Gross, Leo; Mohn, Fabian; Repp, Jascha

    2012-01-01

    Scanning tunneling microscopy (STM) and atomic force microscopy (AFM) of single atoms and molecules on ultrathin insulating films have led to a wealth of novel observations and insights. Based on the reduced electronic coupling to the metallic substrate, these techniques allow the charge state of individual atoms to be controlled, orbitals of individual molecules to be imaged and metal-molecule complexes to be built up. Near-contact AFM adds the unique capabilities of imaging and probing the chemical structure of single molecules with atomic resolution. With the help of atomic/molecular manipulation techniques, chemical binding processes and molecular switches can be studied in detail.

  3. Probing Time-Dependent Molecular Dipoles on the Attosecond Time Scale

    NASA Astrophysics Data System (ADS)

    Neidel, Ch.; Klei, J.; Yang, C.-H.; Rouzée, A.; Vrakking, M. J. J.; Klünder, K.; Miranda, M.; Arnold, C. L.; Fordell, T.; L'Huillier, A.; Gisselbrecht, M.; Johnsson, P.; Dinh, M. P.; Suraud, E.; Reinhard, P.-G.; Despré, V.; Marques, M. A. L.; Lépine, F.

    2013-07-01

    Photoinduced molecular processes start with the interaction of the instantaneous electric field of the incident light with the electronic degrees of freedom. This early attosecond electronic motion impacts the fate of the photoinduced reactions. We report the first observation of attosecond time scale electron dynamics in a series of small- and medium-sized neutral molecules (N2, CO2, and C2H4), monitoring time-dependent variations of the parent molecular ion yield in the ionization by an attosecond pulse, and thereby probing the time-dependent dipole induced by a moderately strong near-infrared laser field. This approach can be generalized to other molecular species and may be regarded as a first example of molecular attosecond Stark spectroscopy.

  4. 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.

  5. A new near-infrared absorption and fluorescent probe based on bombesin for molecular imaging

    NASA Astrophysics Data System (ADS)

    Kujala, Naresh; Zhai, Huifang; Smith, Charles; Prasanphanich, Adam; Sieckman, Gary; Hoffman, Timothy; Volkert, Wynn; Ma, Lixin; Yu, Ping

    2009-02-01

    We have developed a series of new dye bombesin conjugates for site-specific absorption and fluorescence imaging of human prostate and breast cancers. Bombesin (BBN), an amphibian analog to the endogenous ligand, binds to the gastrin releasing peptide (GRP) receptors with high specificity and affinity. Previously, we developed an Alexa Fluor 680-GGG-BBN peptide conjugate which demonstrated high binding affinity and specificity for breast cancer cells in the in vitro and in vivo tests (Ref: Ma et al., Molecular Imaging, vol. 6, no. 3, 2007: 171-180). This probe can not be used as an absorption probe in near-infrared imaging because its absorption peak is in the visible wavelength range. In addition, site specific longer wavelength fluorescent probe is desired for in vivo molecular imaging because long wavelength photons penetrate deeper into tissue. The new absorption and fluorescent probe we developed is based on the last eight-residues of BBN, -Q-W-A-V-G-H-L-M-(NH2), and labeled with AlexaFluor750 through a chemical linker, beta-alanine. The new probe, Alexa Fluor 750-BetaAla-BBN(7-14)NH2, exhibits optimal pharmacokinetics for specific targeting and optical imaging of the GRP receptor over-expressing cancer cells. Absorption spectrum has been measured and showed absorption peaks at 690nm, 720nm and 735nm. Fluorescent band is located at 755nm. In vitro and in vivo investigations have demonstrated the effectiveness of the new conjugates to specifically target human cancer cells overexpressing GRP receptors and tumor xenografts in severely compromised immunodeficient mouse model.

  6. Sensitive force technique to probe molecular adhesion and structural linkages at biological interfaces.

    PubMed

    Evans, E; Ritchie, K; Merkel, R

    1995-06-01

    Adhesion and cytoskeletal structure are intimately related in biological cell function. Even with the vast amount of biological and biochemical data that exist, little is known at the molecular level about physical mechanisms involved in attachments between cells or about consequences of adhesion on the material structure. To expose physical actions at soft biological interfaces, we have combined an ultrasensitive transducer and reflection interference microscopy to image submicroscopic displacements of probe contact with a test surface under minuscule forces. The transducer is a cell-size membrane capsule pressurized by micropipette suction where displacement normal to the membrane under tension is proportional to the applied force. Pressure control of the tension tunes the sensitivity in operation over four orders of magnitude through a range of force from 0.01 pN up to the strength of covalent bonds (approximately 1000 pN)! As the surface probe, a microscopic bead is biochemically glued to the transducer with a densely-bound ligand that is indifferent to the test surface. Movements of the probe under applied force are resolved down to an accuracy of approximately 5 nm from the interference fringe pattern created by light reflected from the bead. With this arrangement, we show that local mechanical compliance of a cell surface can be measured at a displacement resolution set by structural fluctuations. When desired, a second ligand is bound sparsely to the probe for focal adhesion to specific receptors in the test surface. We demonstrate that monitoring fluctuations in probe position at low transducer stiffness enhances detection of molecular adhesion and activation of cytoskeletal structure. Subsequent loading of an attachment tests mechanical response of the receptor-substrate linkage throughout the force-driven process of detachment.

  7. Construction of specific magnetic resonance imaging/optical dual-modality molecular probe used for imaging angiogenesis of gastric cancer.

    PubMed

    Yan, Xuejie; Song, Xiaoyan; Wang, Zhenbo

    2017-05-01

    The purpose of the study was to construct specific magnetic resonance imaging (MRI)/optical dual-modality molecular probe. Tumor-bearing animal models were established. MRI/optical dual-modality molecular probe was construed by coupling polyethylene glycol (PEG)-modified nano-Fe3O4 with specific targeted cyclopeptide GX1 and near-infrared fluorescent dyes Cy5.5. MRI/optical imaging effects of the probe were observed and the feasibility of in vivo double-modality imaging was discussed. It was found that, the double-modality probe was of high stability; tumor signal of the experimental group tended to be weak after injection of the probe, but rose to a level which was close to the previous level after 18 h (p > 0.05). We successively completed the construction of an ideal MRI/optical dual-modality molecular probe. MRI/optical dual-modality molecular probe which can selectively gather in gastric cancer is expected to be a novel probe used for diagnosing gastric cancer in the early stage.

  8. Effect of nuclear motion on molecular high order harmonic pump probe spectroscopy.

    PubMed

    Bredtmann, Timm; Chelkowski, Szczepan; Bandrauk, André D

    2012-11-26

    We study pump-probe schemes for the real time observation of electronic motion on attosecond time scale in the molecular ion H(2)(+) and its heavier isotope T(2)(+) while these molecules dissociate on femtosecond time scale by solving numerically the non-Born-Oppenheimer time-dependent Schrödinger equation. The UV pump laser pulse prepares a coherent superposition of the three lowest lying quantum states and the time-delayed mid-infrared, intense few-femtosecond probe pulse subsequently generates molecular high-order harmonics (MHOHG) from this coherent electron-nuclear wavepacket (CENWP). Varying the pump-probe time delay by a few hundreds of attoseconds, the MHOHG signal intensity is shown to vary by orders of magnitude. Due to nuclear movement, the coherence of these two upper states and the ground state is lost after a few femtoseconds and the MHOHG intensity variations as function of pump-probe delay time are shown to be equal to the period of electron oscillation in the coherent superposition of the two upper dissociative quantum states. Although this electron oscillation period and hence the periodicity of the harmonic spectra are quite constant over a wide range of internuclear distances, a strong signature of nuclear motion is seen in the actual shapes and ways in which these spectra change as a function of pump-probe delay time, which is illustrated by comparison of the MHOHG spectra generated by the two isotopes H(2)(+) and T(2)(+). Two different regimes corresponding roughly to internuclear distances R < 4a(0) and R > 4a(0) are identified: For R < 4a(0), the intensity of a whole range of frequencies in the plateau region is decreased by orders of magnitude when the delay time is changed by a few hundred attoseconds whereas in the cutoff region the peaks in the MHOHG spectra are red-shifted with increasing pump-probe time delay. For R > 4a(0), on the other hand, the peaks both in the cutoff and plateau region are red-shifted with increasing delay times

  9. Nonadiabatic molecular alignment of linear molecules probed by strong-field ionization yields of photoelectrons

    NASA Astrophysics Data System (ADS)

    Kaya, G.; Kaya, N.; Strohaber, J.; Hart, N. A.; Kolomenskii, A. A.; Schuessler, H. A.

    2016-12-01

    The dynamics of rotational wave packets of laser-aligned linear molecules were studied with femtosecond laser-driven strong-field ionization (SFI). The dynamics were observed as a function of the delay between a femtosecond probe pulse and a linearly polarized aligning pump pulse. The induced nonadiabatic molecular alignment was directly monitored by the total SFI yield. The measured revival signatures were compared to the calculated degree of molecular alignment taking into account the effects of electronic structure and symmetry of the molecules. By fitting the calculated alignment parameter to the measured experimental data, we also determined the molecular rotational constants of N2, CO, O2, and C2H2 gas molecules.

  10. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

    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.

  12. 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

  13. Charge carrier mobility in organic molecular materials probed by electromagnetic waves.

    PubMed

    Seki, Shu; Saeki, Akinori; Sakurai, Tsuneaki; Sakamaki, Daisuke

    2014-06-21

    Charge carrier mobility is an essential parameter providing control over the performance of semiconductor devices fabricated using a variety of organic molecular materials. Recent design strategies toward molecular materials have been directed at the substitution of amorphous silicon-based semiconductors; accordingly, numerous measurement techniques have been designed and developed to probe the electronic conducting nature of organic materials bearing extremely wide structural variations in comparison with inorganic and/or metal-oxide semiconductor materials. The present perspective highlights the evaluation methodologies of charge carrier mobility in organic materials, as well as the merits and demerits of techniques examining the feasibility of organic molecules, crystals, and supramolecular assemblies in semiconductor applications. Beyond the simple substitution of amorphous silicon, we have attempted to address in this perspective the systematic use of measurement techniques for future development of organic molecular semiconductors.

  14. Molecular Structure and Dynamics Probed by Photoionization Out of Rydberg States

    NASA Astrophysics Data System (ADS)

    Rudakov, Fedor

    2017-06-01

    Probing the structure of a molecule as a chemical reaction unfolds has been a long standing goal in chemical physics. Most spectroscopic and diffraction techniques work well when the molecules are cold and thus vibrational motion is minimized. Yet, the very ability of a molecule to undergo structural changes implies that a significant amount of energy resides within the molecule. In order to probe structures of even medium sized molecules on an ultrafast time scale a technique that is sensitive to the molecular structure, yet insensitive to the vibrational motion is required. In our research we demonstrated that Rydberg electrons are remarkably sensitive to the molecular structure. Photoionization of a molecule out of Rydberg states reveals a purely electronic spectrum which is largely insensitive to vibrational motion. The talk illustrates how Rydberg electrons can serve as a probe for ultrafast structural dynamics in polyatomic molecules. The talk also demonstrates that photoionization through Rydberg states can be utilized for non-intrusive detection of polyatomic combustion intermediates in flames.

  15. 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.

  16. Evaluation of alpha-tubulin as an antigenic and molecular probe to detect Giardia lamblia.

    PubMed

    Kim, Juri; Shin, Myeong Heon; Song, Kyoung-Ju; Park, Soon-Jung

    2009-09-01

    The alpha/beta-tubulin heterodimer is the basic subunit of microtubules in eukaryotes. Polyclonal antibodies specific to recombinant alpha-tubulin of Giardia lamblia were made, and found effective as a probe to specifically detect G. lamblia by immunofluorescence assays. Nucleotide sequences of alpha-tubulin genes were compared between G. lamblia WB and GS strains, prototypes of assemblage A and assemblage B, respectively. A set of primers was designed and used to amplify a portion of the alpha-tubulin gene from G. lamblia. PCR-RFLP analysis of this alpha-tubulin PCR product successfully differentiated G. lamblia into 2 distinct groups, assemblages A and B. The results indicate that alpha-tubulin can be used as a molecular probe to detect G. lamblia.

  17. Micro-CT molecular imaging of tumor angiogenesis using a magnetite nano-cluster probe.

    PubMed

    Liu, Ping; Li, Jing; Zhang, Chunfu; Xu, Lisa X

    2013-06-01

    Due to its high resolution, micro-CT is desirable for molecular imaging of tumor angiogenesis. However, the sensitivity of micro-CT to contrast agents is relatively low. Therefore, the purpose of this study is to develop high micro-CT sensitive molecular imaging probes for direct visualization and dynamic monitoring of tumor angiogenesis. To this end, Arg-Gly-Asp (RGD) peptides conjugated magnetite nano clusters (RGD-MNCs) were developed by assembling individual magnetite nano particles into clusters with amphiphilic (maleimide) methoxypoly(ethylene glycol)-b-poly(lactic acid) ((Mal)mPEG-PLA) copolymer and subsequently encoding RGD peptides onto the clusters for specific targeting alpha(v)beta3 integrin. The hydrodynamic size of RGD-MNCs was about 85 nm. To test its specificity, alpha(v)beta3 positive cells (H1299) were incubated with magnetite nano clusters (MNCs), RGD-MNCs or RGD-MNCs competition with free RGD peptides. Prussian Blue staining and inductively coupled plasma optical emission spectrometer (ICP-OES) measurements indicated that the cell uptake of RGD-MNCs was significantly more than that of MNCs, which could be inhibited by free RGD peptides. For detection of tumor angiogenesis, mice bearing H1299 tumors were injected intravenously with RGD-MNCs at the dose of 400 micro mol Fe/kg. Tumor angiogenic hot spots as well as individual angiogenic vessels could be clearly manifested by micro-CT imaging 12 h post injection, which was dynamically monitored with the extension of probe circulation time. Subsequent histological studies of tumor tissues verified that RGD-MNCs registered tumor angiogenic vessels. Our study demonstrated that RGD-MNC probes fabricated in this study could be used to effectively target alpha(v)beta3 integrin. Using high resolution micro-CT in combination with the probes, tumor angiogenesis could be studied dynamically.

  18. Potential charge transfer probe induced conformational changes of model plasma protein human serum albumin: Spectroscopic, molecular docking, and molecular dynamics simulation study.

    PubMed

    Jana, Sankar; Dalapati, Sasanka; Ghosh, Shalini; Guchhait, Nikhil

    2012-10-01

    The nature of binding of specially designed charge transfer (CT) fluorophore at the hydrophobic protein interior of human serum albumin (HSA) has been explored by massive blue-shift (82 nm) of the polarity sensitive probe emission accompanying increase in emission intensity, fluorescence anisotropy, red edge excitation shift, and average fluorescence lifetimes. Thermal unfolding of the intramolecular CT probe bound HSA produces almost opposite spectral changes. The spectral responses of the molecule reveal that it can be used as an extrinsic fluorescent reporter for similar biological systems. Circular dichrosim spectra, molecular docking, and molecular dynamics simulation studies scrutinize this binding process and stability of the protein probe complex more closely.

  19. Slow molecular motion of different spin probes in a model glycerol—water matrix studied by double modulation ESR

    NASA Astrophysics Data System (ADS)

    Valić, S.; Rakvin, B.; Veksli, Z.; Pečar, S.

    1992-11-01

    The slow molecular motion of several deuterated and undeuterated spin probes differing in size and shape, embedded in a model glycerol—water matrix, have been studied by double-modulated electron spin resonance (DMESR). The DMESR spectra as a function of temperature reveal two motional regions. From the experimental linewidths of both deuterated and undeuterated spin probes in the lower temperature region and simulated data based on the variation of T1 relaxation, two different dynamics of the -CH 3 groups attached to piperidine ring were resolved. Our results indicate that the onset of the whole spin probe motion depends on the type of probe and the matrix density.

  20. Core-Hole Molecular Frame X-Ray Photoelectron Angular Distributions as Molecular Geometry Probes

    NASA Astrophysics Data System (ADS)

    Trevisan, Cynthia; Williams, Joshua; Menssen, Adrian; Weber, Thorsten; Rescigno, Thomas; McCurdy, Clyde; Landers, Allen

    2014-05-01

    We present experimental and theoretical results for the angular dependence of electrons ejected from the core orbitals of ethane (C2H6) and tetrafluoromethane (CF4) in an effort to understand the origin of the imaging effect by which the molecular frame photoelectron angular distributions (MFPADs) for removing an electron from a 1s orbital effectively image the geometry of a class of molecules. At low energies, our calculations predict the same imaging effect in X2H6 previously found in CH4, H2O and NH3. By contrast, in experiment and calculations CF4 displays an anti-imaging effect, whereby the electron ejected by core photoionization has the tendency to avoid molecular bonds, if averaged over directions of polarization of the incident X-ray beam. Our measurements employ the COLTRIMS method and the calculations were performed with the Complex Kohn Variational method.

  1. Probing molecular interactions on carbon nanotube surfaces using surface plasmon resonance sensors

    NASA Astrophysics Data System (ADS)

    Kakenov, Nurbek; Balci, Osman; Balci, Sinan; Kocabas, Coskun

    2012-11-01

    In this work, we present a method to probe molecular interactions on single-walled carbon nanotube (SWNT) surfaces using a surface plasmon sensor. SWNT networks were synthesized by chemical vapor deposition and transfer-printed on gold surfaces. We studied the excitation of surface plasmon-polaritons on nanotube coated gold surfaces with sub-monolayer, monolayer, and multilayer surface coverage. Integrating the fabricated sensor with a microfluidic device, we were able to obtain binding dynamics of a bovine serum albumin (BSA) protein on SWNT networks with various tube densities. The results reveal the kinetic parameters for nonspecific binding of BSA on SWNT coated surfaces having various tube densities.

  2. Introduction: feature issue on optical molecular probes, imaging, and drug delivery.

    PubMed

    Campagnola, Paul; French, Paul M W; Georgakoudi, Irene; Mycek, Mary-Ann

    2014-02-01

    The editors introduce the Biomedical Optics Express feature issue "Optical Molecular Probes, Imaging, and Drug Delivery," which is associated with a Topical Meeting of the same name held at the 2013 Optical Society of America (OSA) Optics in the Life Sciences Congress in Waikoloa Beach, Hawaii, April 14-18, 2013. The international meeting focused on the convergence of optical physics, photonics technology, nanoscience, and photochemistry with drug discovery and clinical medicine. Papers in this feature issue are representative of meeting topics, including advances in microscopy, nanotechnology, and optics in cancer research.

  3. Light propagation analysis for fluorescence measurements of a molecular probe in the brain

    NASA Astrophysics Data System (ADS)

    Asai, Kota; Togashi, Takuya; Okada, Eiji

    2017-04-01

    Light propagation in the slab head model that consists of five types of tissues was calculated to estimate the fluorescent intensity emerged from a molecular probe in the brain by a Monte Carlo simulation. The thickness of the scalp, skull and cerebrospinal fluid layer was varied to analyze the influence of the thickness of the superficial tissues on the fluorescent intensity detected on the scalp surface. The fluorescent intensity is exponentially reduced with increasing the depth of the brain surface. The thickness of the cerebrospinal fluid layer more significantly affects the fluorescent intensity than that of the scalp and skull.

  4. Targeted Capture and High-Throughput Sequencing Using Molecular Inversion Probes (MIPs).

    PubMed

    Cantsilieris, Stuart; Stessman, Holly A; Shendure, Jay; Eichler, Evan E

    2017-01-01

    Molecular inversion probes (MIPs) in combination with massively parallel DNA sequencing represent a versatile, yet economical tool for targeted sequencing of genomic DNA. Several thousand genomic targets can be selectively captured using long oligonucleotides containing unique targeting arms and universal linkers. The ability to append sequencing adaptors and sample-specific barcodes allows large-scale pooling and subsequent high-throughput sequencing at relatively low cost per sample. Here, we describe a "wet bench" protocol detailing the capture and subsequent sequencing of >2000 genomic targets from 192 samples, representative of a single lane on the Illumina HiSeq 2000 platform.

  5. 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.

  6. NGC 7027: Probing the kinematics and excitation conditions of the warm molecular gas

    NASA Astrophysics Data System (ADS)

    Santander-García, Miguel; Bujarrabal, Valentín; Alcolea, Javier

    2012-08-01

    Tracking the mass-loss history of planetary nebulae (PNe) by means of molecular emission lines (mainly mm and sub-mm ranges) is fundamental to gain insight into the mechanism of nebular shaping. This is particularly important in cases such as NGC 7027, where most of the nebula is constituted by molecular gas (85% of a total of 1.4 M⊙, see Fong et al. 2001). To this aim, Herschel/HIFI provides an invaluable tool to probe warm molecular gas (~50-1000 K). It produces 1-D, high resolution spectra of the whole nebula (convolved with the telescope beam) in high-excitation molecular transitions (e.g. CO J=6-5, 10-9 and 16-15). Although the morphological information is therefore lost, the kinematics and the excitation conditions can be studied with unprecedented detail (see (see Bujarrabal et al. 2011).). We have developed a code, shapemol, which, used along the existing SHAPE software (Steffen et al. 2010), implements spatiokinematical modeling with accurate non-LTE calculations of line excitation and radiative transfer in molecular species. The high quality of the data, together with this code, have allowed us to study, for the first time, the kinematics and excitation conditions of the warm gas of a PN with such a high-excitation.

  7. 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.

  8. Probing the molecular hydrogen fraction in diffuse molecular clouds with observations of HCl+

    NASA Astrophysics Data System (ADS)

    Neufeld, David

    Using the GREAT instrument, we will observe the Doublet Pi 3/2 J = 5/2 - 3/2 transitions of the H-37Cl+ and (where not already observed in Cycle 4) the H-35Cl+ molecular ions at 1.442 and 1.444 THz, in absorption, toward the bright continuum sources Sgr B2 (M), W31C (G10.6-0.4), W49N, and W51. The observations will yield robust estimates of the HCl+ column densities in diffuse clouds lying along the sight-lines to those sources. Because HCl+ reacts rapidly and exothermically with H2 to yield H2Cl+, the abundance ratio HCl+/H2Cl+ is sensitive to the H2 abundance in the interstellar gas; combining the HCl+ measurements with ones already available for H2Cl+ will thus permit independent estimates of the molecular hydrogen fraction along the proposed sight-lines. This proposal follows up on a successful detection of HCl+ obtained in a pilot program performed in Cycle 4.

  9. Molecular engineering of two-photon fluorescent probes for bioimaging applications

    NASA Astrophysics Data System (ADS)

    Liu, Hong-Wen; Liu, Yongchao; Wang, Peng; Zhang, Xiao-Bing

    2017-03-01

    During the past two decades, two-photon microscopy (TPM), which utilizes two near-infrared photons as the excitation source, has emerged as a novel, attractive imaging tool for biological research. Compared with one-photon microscopy, TPM offers several advantages, such as lowering background fluorescence in living cells and tissues, reducing photodamage to biosamples, and a photobleaching phenomenon, offering better 3D spatial localization, and increasing penetration depth. Small-molecule-based two-photon fluorescent probes have been well developed for the detection and imaging of various analytes in biological systems. In this review, we will give a general introduction of molecular engineering of two-photon fluorescent probes based on different fluorescence response mechanisms for bioimaging applications during the past decade. Inspired by the desired advantages of small-molecule two-photon fluorescent probes in biological imaging applications, we expect that more attention will be devoted to the development of new two-photon fluorophores and applications of TPM in areas of bioanalysis and disease diagnosis.

  10. Molecular engineering of two-photon fluorescent probes for bioimaging applications.

    PubMed

    Liu, Hong-Wen; Liu, Yongchao; Wang, Peng; Zhang, Xiao-Bing

    2017-03-22

    During the past two decades, two-photon microscopy (TPM), which utilizes two near-infrared photons as the excitation source, has emerged as a novel, attractive imaging tool for biological research. Compared with one-photon microscopy, TPM offers several advantages, such as lowering background fluorescence in living cells and tissues, reducing photodamage to biosamples, and a photobleaching phenomenon, offering better 3D spatial localization, and increasing penetration depth. Small-molecule-based two-photon fluorescent probes have been well developed for the detection and imaging of various analytes in biological systems. In this review, we will give a general introduction of molecular engineering of two-photon fluorescent probes based on different fluorescence response mechanisms for bioimaging applications during the past decade. Inspired by the desired advantages of small-molecule two-photon fluorescent probes in biological imaging applications, we expect that more attention will be devoted to the development of new two-photon fluorophores and applications of TPM in areas of bioanalysis and disease diagnosis.

  11. Molecular dynamics in rod-like liquid crystals probed by muon spin resonance spectroscopy.

    PubMed

    McKenzie, Iain; Scheuermann, Robert; Sedlak, Kamil; Stoykov, Alexey

    2011-08-04

    Muoniated spin probes were produced by the addition of muonium (Mu) to two rod-like liquid crystals: N-(4-methoxybenzylidene)-4'-n-butylaniline (MBBA) and cholesteryl nonanoate (CN). Avoided level crossing muon spin resonance spectroscopy was used to characterize the muoniated spin probes and to probe dynamics at the molecular level. In MBBA Mu adds predominantly to the carbon of the bridging imine group and the muon and methylene proton hyperfine coupling constants (hfccs) of the resulting radical shift in the nematic phase due to the dipolar hyperfine coupling, the ordering of the molecules along the applied magnetic field and fluctuations about the local director. The amplitude of these fluctuations in in the nematic phase of MBBA is determined from the temperature dependence of the methylene proton hfcc. Mu adds to the double bond of the steroidal ring system of CN and the temperature dependence of the Δ(1) line width provides information about the amplitude of the fluctuations about the local director in the chiral nematic phase and the slow isotropic reorientation in the isotropic phase.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Study of fluorescence quenching in aluminum-doped ceria nanoparticles: potential molecular probe for dissolved oxygen.

    PubMed

    Shehata, N; Meehan, K; Leber, D

    2013-05-01

    This work investigates a novel usage of aluminum-doped ceria nanoparticles (ADC-NPs), as the molecular probe in optical fluorescence quenching for sensing the dissolved oxygen (DO). Cerium oxide (ceria) nanoparticles can be considered one of the most unique nanomaterials that are being studied today due to the diffusion and reactivity of oxygen vacancies in ceria, which contributes to its high oxygen storage capability. Aluminum can be considered a promising dopant to increase the oxygen ionic conductivity in ceria nanoparticles which can improve the sensitivity of ceria nanoparticles to DO. The fluorescence intensity of ADC-NPs, synthesized via chemical precipitation, is found to have a strong inverse relationship with the DO concentration in aqueous solutions. Stern-Volmer constant of ADC-NPs at room temperature is determined to be 454.6 M(-1), which indicates that ADC-NPs have a promising sensitivity to dissolved oxygen, compared to many presently used fluorophores. In addition, Stern-Volmer constant is found to have a relatively small dependence on temperature between 25 °C to 50 °C, which shows excellent thermal stability of ADC-NPs sensitivity. Our work suggests that ADC-NPs, at 6 nm, are the smallest diameter DO molecular probes between the currently used optical DO sensors composed of different nanostructures. This investigation can improve the performance of fluorescence-quenching DO sensors for industrial and environmental applications.

  20. [Research on the Tomato Metacaspase Protein Interactions with Ca2+ by Spectroscopy and Molecular Probe].

    PubMed

    Wen, Shuai; Ma, Ying-xuan; Wu, Kun-sheng; Cui, Jin-tian; Luo, Yun-bo; Qu, Gui-qin

    2015-06-01

    Metacaspases are cysteine-dependent proteases found in protozoa, fungi and plants and are distantly related to metazoan caspases. Most of MCPs activation are the calcium dependent, but the mechanisms are still unknown. Based on the techniques of CD spectroscopy, fluorescence spectroscopy, and Terbium Stains-all probe, we selected three purified recombinant proteins from key residues mutated in tomato metacaspase (LeMCA1), including conserved catalytic site (C139A) mutant, N-sequenced cleaved site (K223G) mutant and the predicted Ca2+ binding sites (D116A/D117A) mutant, to explore the interaction mechanism of LeMCA1 and Ca2+. CD spectroscopy and Stains-all probe results suggested that the intense binding does not exist between LeMCA1 and Ca2+ as well as Ca2+ has little effect on the secondary structure of LeMCA1. However, fluorescence spectroscopy and Tb3+ probe results showed that Ca(2+)-induced the changes occur in the tertiary structure of LeMCA1, which contributes to the activation of zymogen. In addition, predicted Ca2+ binding residues, Asp-116 and Asp117, are the key sites resporisible for the Ca2+ interaction with LeMCA1, and the loss of these two residues resulted in decreased interaction. Our data firstly provided insight on the mechanism of the interaction between Ca2+ and recombinant purified Solanaceae type II metacaspase by spectroscopy and molecular probe techniques. Combined the results we got before from sequence-alignment and sites-mutation, the key residues Asp-116 and Asp117 affect the Ca(2+)-induced the changes of LeMCA1 tertiary structure. Our data provided information for the further biochemical and crystal assays of LeMCA1.

  1. 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.

  2. 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

  3. Selenium- and tellurium-containing fluorescent molecular probes for the detection of biologically important analytes.

    PubMed

    Manjare, Sudesh T; Kim, Youngsam; Churchill, David G

    2014-10-21

    As scientists in recent decades have discovered, selenium is an important trace element in life. The element is now known to play an important role in biology as an enzymatic antioxidant. In this case, it sits at the active site and converts biological hydrogen peroxides to water. Mimicking this reaction, chemists have synthesized several organoselenium compounds that undergo redox transformations. As such, these types of compounds are important in the future of both medicinal and materials chemistry. One main challenge for organochalcogen chemists has been to synthesize molecular probes that are soluble in water where a selenium or tellurium center can best modify electronics of the molecule based on a chemical oxidation or reduction event. In this Account, we discuss chemists' recent efforts to create chalcogen-based chemosensors through synthetic means and current photophysical understanding. Our work has focused on small chromophoric or fluorophoric molecules, in which we incorporate discrete organochalcogen atoms (e.g., R-Se-R, R-Te-R) in predesigned sites. These synthetic molecules, involving rational synthetic pathways, allow us to chemoselectively oxidize compounds and to study the level of analyte selectivity by way of their optical responses. All the reports we discussed here deal with well-defined and small synthetic molecular systems. With a large number of reports published over the last few years, many have notably originated from the laboratory of K. Han (P. R. China). This growing body of research has given chemists new ideas for the previously untenable reversible reactive oxygen species detection. While reversibility of the probe is technically important from the stand-point of the chalcogen center, facile regenerability of the probe using a secondary analyte to recover the initial probe is a very promising avenue. This is because (bio)chalcogen chemistry is extremely rich and bioinspired and continues to yield important developments across many

  4. 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

  5. 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.

  6. Nanoparticle imaging probes for molecular imaging with computed tomography and application to cancer imaging

    NASA Astrophysics Data System (ADS)

    Roeder, Ryan K.; Curtis, Tyler E.; Nallathamby, Prakash D.; Irimata, Lisa E.; McGinnity, Tracie L.; Cole, Lisa E.; Vargo-Gogola, Tracy; Cowden Dahl, Karen D.

    2017-03-01

    Precision imaging is needed to realize precision medicine in cancer detection and treatment. Molecular imaging offers the ability to target and identify tumors, associated abnormalities, and specific cell populations with overexpressed receptors. Nuclear imaging and radionuclide probes provide high sensitivity but subject the patient to a high radiation dose and provide limited spatiotemporal information, requiring combined computed tomography (CT) for anatomic imaging. Therefore, nanoparticle contrast agents have been designed to enable molecular imaging and improve detection in CT alone. Core-shell nanoparticles provide a powerful platform for designing tailored imaging probes. The composition of the core is chosen for enabling strong X-ray contrast, multi-agent imaging with photon-counting spectral CT, and multimodal imaging. A silica shell is used for protective, biocompatible encapsulation of the core composition, volume-loading fluorophores or radionuclides for multimodal imaging, and facile surface functionalization with antibodies or small molecules for targeted delivery. Multi-agent (k-edge) imaging and quantitative molecular imaging with spectral CT was demonstrated using current clinical agents (iodine and BaSO4) and a proposed spectral library of contrast agents (Gd2O3, HfO2, and Au). Bisphosphonate-functionalized Au nanoparticles were demonstrated to enhance sensitivity and specificity for the detection of breast microcalcifications by conventional radiography and CT in both normal and dense mammary tissue using murine models. Moreover, photon-counting spectral CT enabled quantitative material decomposition of the Au and calcium signals. Immunoconjugated Au@SiO2 nanoparticles enabled highly-specific targeting of CD133+ ovarian cancer stem cells for contrast-enhanced detection in model tumors.

  7. 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

  8. 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.

  9. Ultrasensitive broadband probing of molecular vibrational modes with multifrequency optical antennas.

    PubMed

    Aouani, Heykel; Šípová, Hana; Rahmani, Mohsen; Navarro-Cia, Miguel; Hegnerová, Kateřina; Homola, Jiří; Hong, Minghui; Maier, Stefan A

    2013-01-22

    Optical antennas represent an enabling technology for enhancing the detection of molecular vibrational signatures at low concentrations and probing the chemical composition of a sample in order to identify target molecules. However, efficiently detecting different vibrational modes to determine the presence (or the absence) of a molecular species requires a multispectral interrogation in a window of several micrometers, as many molecules present informative fingerprint spectra in the mid-infrared between 2.5 and 10 μm. As most nanoantennas exhibit a narrow-band response because of their dipolar nature, they are not suitable for such applications. Here, we propose the use of multifrequency optical antennas designed for operating with a bandwidth of several octaves. We demonstrate that surface-enhanced infrared absorption gains in the order of 10(5) can be easily obtained in a spectral window of 3 μm with attomolar concentrations of molecules, providing new opportunities for ultrasensitive broadband detection of molecular species via vibrational spectroscopy techniques.

  10. 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; hide

    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.

  11. Probing the surface profile and friction behavior of heterogeneous polymers: a molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Dai, L.; Sorkin, V.; Zhang, Y. W.

    2017-04-01

    We perform molecular dynamics simulations to investigate molecular structure alternation and friction behavior of heterogeneous polymer (perfluoropolyether) surfaces using a nanoscale probing tip (tetrahedral amorphous carbon). It is found that depending on the magnitude of the applied normal force, three regimes exist: the shallow depth-sensing (SDS), deep depth-sensing (DDS), and transitional depth-sensing (TDS) regimes; TDS is between SDS and DDS. In SDS, the tip is floating on the polymer surface and there is insignificant permanent alternation in the polymer structure due to largely recoverable atomic deformations, and the surface roughness profile can be accurately measured. In DDS, the tip is plowing through the polymer surface and there is significant permanent alternation in the molecular structure. In this regime, the lateral friction force rises sharply and fluctuates violently when overcoming surface pile-ups. In SDS, the friction can be described by a modified Amonton’s law including the adhesion effect; meanwhile, in DDS, the adhesion effect is negligible but the friction coefficient is significantly higher. The underlying reason for the difference in these regimes rests upon different contributions by the repulsion and attraction forces between the tip and polymer surfaces to the friction force. Our findings here reveal important insights into lateral depth-sensing on heterogeneous polymer surfaces and may help improve the precision of depth-sensing devices.

  12. Probing molecular adsorption and mechanics at the atomic scale: The Nanocar family of molecules

    NASA Astrophysics Data System (ADS)

    Osgood, Andrew J.

    Molecular machines, typically thought to be only the fanciful imaginings of speculative fiction, have taken great strides in recent years towards real-world viability and usefulness. Under variable temperature scanning tunneling microscopy, (STM) one family of these nascent devices is characterized with atomic resolution, and probed and manipulated with sub-angstrom precision, adding to the growing body of knowledge of how molecular devices behave and react at nanometer scales. Evidence of temperature-dependent rolling of wheel-like fullerene constituents on the Nanocar is discussed in light of newly developed image analysis techniques. Additionally, charge-transfer mediated behavior at step edges, both static and dynamic, is investigated on a Au(111) surface for a more complete understanding of translation and surface diffusion. Molecular flexibility is thought to aid in this three-dimensional atomic-step-crossing diffusion, and is explored and discussed across many species in the Nanocar family of molecules. In all, many similar molecules have been characterized and explored via STM with an eye towards their dynamic capabilities and surface behaviors, in the hopes that future, more complex versions can build on the nascent knowledge base beginning to be established here.

  13. Probing the permeability of polyelectrolyte multilayer capsules via a molecular beacon approach.

    PubMed

    Angelatos, Alexandra S; Johnston, Angus P R; Wang, Yajun; Caruso, Frank

    2007-04-10

    Application of polyelectrolyte multilayer (PEM) capsules as vehicles for the controlled delivery of substances, such as drugs, genes, pesticides, cosmetics, and foodstuffs, requires a sound understanding of the permeability of the capsules. We report the results of a detailed investigation into probing capsule permeability via a molecular beacon (MB) approach. This method involves preparing MB-functionalized bimodal mesoporous silica (BMSMB) particles, encapsulating the BMSMB particles within the PEM film to be probed, and then incubating the encapsulated BMSMB particles with DNA target sequences of different lengths. Permeation of the DNA targets through the capsule shell causes the immobilized MBs to open due to hybridization of the DNA targets with the complementary loop region of the MBs, resulting in an increase in the MB fluorescence. The assay conditions (BMSMB particle concentration, MB loading within the BMS particles, DNA target concentration, DNA target size, pH, sodium chloride concentration) where the MB-DNA sensing process is effective were first examined. The permeability of DNA through poly(sodium 4-styrenesulfonate) (PSS)/poly(allylamine hydrochloride) (PAH) multilayer films, with and without a poly(ethyleneimine) (PEI) precursor layer, was then investigated. The permeation of the DNA targets decreases considerably as the thickness of the PEM film encapsulating the BMSMB particles increases. Furthermore, the presence of a PEI precursor layer gives rise to less permeable PSS/PAH multilayers. The diffusion coefficients calculated for the DNA targets through the PEM capsules range from 10-19 to 10-18 m2 s-1. This investigation demonstrates that the MB approach to measuring permeability is an important new tool for the characterization of PEM capsules and is expected to be applicable for probing the permeability of other systems, such as membranes, liposomes, and emulsions.

  14. 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

  15. 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.

  16. Scanning probe microscopy studies on the adsorption of selected molecular dyes on titania.

    PubMed

    Prauzner-Bechcicki, Jakub S; Zajac, Lukasz; Olszowski, Piotr; Jöhr, Res; Hinaut, Antoine; Glatzel, Thilo; Such, Bartosz; Meyer, Ernst; Szymonski, Marek

    2016-01-01

    Titanium dioxide, or titania, sensitized with organic dyes is a very attractive platform for photovoltaic applications. In this context, the knowledge of properties of the titania-sensitizer junction is essential for designing efficient devices. Consequently, studies on the adsorption of organic dyes on titania surfaces and on the influence of the adsorption geometry on the energy level alignment between the substrate and an organic adsorbate are necessary. The method of choice for investigating the local environment of a single dye molecule is high-resolution scanning probe microscopy. Microscopic results combined with the outcome of common spectroscopic methods provide a better understanding of the mechanism taking place at the titania-sensitizer interface. In the following paper, we review the recent scanning probe microscopic research of a certain group of molecular assemblies on rutile titania surfaces as it pertains to dye-sensitized solar cell applications. We focus on experiments on adsorption of three types of prototypical dye molecules, i.e., perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA), phtalocyanines and porphyrins. Two interesting heteromolecular systems comprising molecules that are aligned with the given review are discussed as well.

  17. The Biophysical Probes 2-fluorohistidine and 4-fluorohistidine: Spectroscopic Signatures and Molecular Properties

    NASA Astrophysics Data System (ADS)

    Kasireddy, Chandana; Ellis, Jonathan M.; Bann, James G.; Mitchell-Koch, Katie R.

    2017-02-01

    Fluorinated amino acids serve as valuable biological probes, by reporting on local protein structure and dynamics through 19F NMR chemical shifts. 2-fluorohistidine and 4-fluorohistidine, studied here with DFT methods, have even more capabilities for biophysical studies, as their altered pKa values, relative to histidine, allow for studies of the role of proton transfer and tautomeric state in enzymatic mechanisms. Considering the two tautomeric forms of histidine, it was found that 2-fluorohistidine primarily forms the common (for histidine) τ-tautomer at neutral pH, while 4-fluorohistidine exclusively forms the less common π-tautomer. This suggests the two isomers of fluorohistidine can also serve as probes of tautomeric form within biomolecules, both by monitoring NMR chemical shifts and by potential perturbation of the tautomeric equilibrium within biomolecules. Fluorine also enables assignment of tautomeric states in crystal structures. The differences in experimental pKa values between the isomers was found to arise from solvation effects, providing insight into the polarization and molecular properties of each isomer. Results also encompass 13C and 19F NMR chemical shifts, from both tautomers of 2-fluorohistidine and 4-fluorohistidine in a number of different environments. This work can serve as a guide for interpretation of spectroscopic results in biophysical studies employing 2-fluorohistidine and 4-fluorohistidine.

  18. Fluorescent molecular probes based on excited state prototropism in lipid bilayer membrane

    NASA Astrophysics Data System (ADS)

    Mohapatra, Monalisa; Mishra, Ashok K.

    2012-03-01

    Excited state prototropism (ESPT) is observed in molecules having one or more ionizable protons, whose proton transfer efficiency is different in ground and excited states. The interaction of various ESPT molecules like naphthols and intramolecular ESPT (ESIPT) molecules like hydroxyflavones etc. with different microheterogeneous media have been studied in detail and excited state prototropism as a probe concept has been gaining ground. The fluorescence of different prototropic forms of such molecules, on partitioning to an organized medium like lipid bilayer membrane, often show sensitive response to the local environment with respect to the local structure, physical properties and dynamics. Our recent work using 1-naphthol as an ESPT fluorescent molecular probe has shown that the incorporation of monomeric bile salt molecules into lipid bilayer membranes composed from dipalmitoylphosphatidylcholine (DPPC, a lung surfactant) and dimyristoylphosphatidylcholine (DMPC), in solid gel and liquid crystalline phases, induce appreciable wetting of the bilayer up to the hydrocarbon core region, even at very low (<= 1 mM) concentrations of the bile salts. The incorporation and location of fisetin, an ESIPT molecule having antioxidant properties, in lipid bilayer membrane has been sensitively monitored from its intrinsic fluorescence behaviour.

  19. Scanning probe microscopy studies on the adsorption of selected molecular dyes on titania

    PubMed Central

    Zajac, Lukasz; Olszowski, Piotr; Jöhr, Res; Hinaut, Antoine; Glatzel, Thilo; Such, Bartosz; Meyer, Ernst; Szymonski, Marek

    2016-01-01

    Titanium dioxide, or titania, sensitized with organic dyes is a very attractive platform for photovoltaic applications. In this context, the knowledge of properties of the titania–sensitizer junction is essential for designing efficient devices. Consequently, studies on the adsorption of organic dyes on titania surfaces and on the influence of the adsorption geometry on the energy level alignment between the substrate and an organic adsorbate are necessary. The method of choice for investigating the local environment of a single dye molecule is high-resolution scanning probe microscopy. Microscopic results combined with the outcome of common spectroscopic methods provide a better understanding of the mechanism taking place at the titania–sensitizer interface. In the following paper, we review the recent scanning probe microscopic research of a certain group of molecular assemblies on rutile titania surfaces as it pertains to dye-sensitized solar cell applications. We focus on experiments on adsorption of three types of prototypical dye molecules, i.e., perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA), phtalocyanines and porphyrins. Two interesting heteromolecular systems comprising molecules that are aligned with the given review are discussed as well. PMID:28144513

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

    PubMed Central

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

    2015-01-01

    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

  1. The Biophysical Probes 2-fluorohistidine and 4-fluorohistidine: Spectroscopic Signatures and Molecular Properties

    PubMed Central

    Kasireddy, Chandana; Ellis, Jonathan M.; Bann, James G.; Mitchell-Koch, Katie R.

    2017-01-01

    Fluorinated amino acids serve as valuable biological probes, by reporting on local protein structure and dynamics through 19F NMR chemical shifts. 2-fluorohistidine and 4-fluorohistidine, studied here with DFT methods, have even more capabilities for biophysical studies, as their altered pKa values, relative to histidine, allow for studies of the role of proton transfer and tautomeric state in enzymatic mechanisms. Considering the two tautomeric forms of histidine, it was found that 2-fluorohistidine primarily forms the common (for histidine) τ-tautomer at neutral pH, while 4-fluorohistidine exclusively forms the less common π-tautomer. This suggests the two isomers of fluorohistidine can also serve as probes of tautomeric form within biomolecules, both by monitoring NMR chemical shifts and by potential perturbation of the tautomeric equilibrium within biomolecules. Fluorine also enables assignment of tautomeric states in crystal structures. The differences in experimental pKa values between the isomers was found to arise from solvation effects, providing insight into the polarization and molecular properties of each isomer. Results also encompass 13C and 19F NMR chemical shifts, from both tautomers of 2-fluorohistidine and 4-fluorohistidine in a number of different environments. This work can serve as a guide for interpretation of spectroscopic results in biophysical studies employing 2-fluorohistidine and 4-fluorohistidine. PMID:28198426

  2. MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing.

    PubMed

    Boyle, Evan A; O'Roak, Brian J; Martin, Beth K; Kumar, Akash; Shendure, Jay

    2014-09-15

    Molecular inversion probes (MIPs) enable cost-effective multiplex targeted gene resequencing in large cohorts. However, the design of individual MIPs is a critical parameter governing the performance of this technology with respect to capture uniformity and specificity. MIPgen is a user-friendly package that simplifies the process of designing custom MIP assays to arbitrary targets. New logistic and SVM-derived models enable in silico predictions of assay success, and assay redesign exhibits improved coverage uniformity relative to previous methods, which in turn improves the utility of MIPs for cost-effective targeted sequencing for candidate gene validation and for diagnostic sequencing in a clinical setting. MIPgen is implemented in C++. Source code and accompanying Python scripts are available at http://shendurelab.github.io/MIPGEN/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  3. 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

  4. Synthesis and Bioconjugation of Gold Nanoparticles as Potential Molecular Probes for Light-Based Imaging Techniques

    PubMed Central

    Rayavarapu, Raja Gopal; Petersen, Wilma; Ungureanu, Constantin; Post, Janine N.; van Leeuwen, Ton G.; Manohar, Srirang

    2007-01-01

    We have synthesized and characterized gold nanoparticles (spheres and rods) with optical extinction bands within the “optical imaging window.” The intense plasmon resonant driven absorption and scattering peaks of these nanoparticles make them suitable as contrast agents for optical imaging techniques. Further, we have conjugated these gold nanoparticles to a mouse monoclonal antibody specific to HER2 overexpressing SKBR3 breast carcinoma cells. The bioconjugation protocol uses noncovalent modes of binding based on a combination of electrostatic and hydrophobic interactions of the antibody and the gold surface. We discuss various aspects of the synthesis and bioconjugation protocols and the characterization results of the functionalized nanoparticles. Some proposed applications of these potential molecular probes in the field of biomedical imaging are also discussed. PMID:18354723

  5. 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

  6. Aptamer/Graphene Oxide Nanocomplex for In Situ Molecular Probing in Living Cells

    SciTech Connect

    Wang, Ying; Li, Zhaohui; Hu, Dehong; Lin, Chiann Tso; Li, Jinghong; Lin, Yuehe

    2010-06-21

    In this communication, we report the illustration of cellular delivering and in situ molecular probing in living cells by using graphene oxide nanosheets (GO-nS) as DNA cargo and sensing platform. Due to the particular interaction between GO and DNA molecules, aptamer/GO-nS nanocomplex was designed and employed to demonstrate the dramatic DNA delivering, enzymatic cleavage protecting and biosensing capabilities of GO-nS in living cells. The results show that GO-nS could successfully transfer DNA aptamer into living cells, efficiently protect oligonucleotides from enzymatic cleavage during the delivery as well as selectively monitoring intra-cellular target in situ. The as-shown advantages of graphene oxide will enable it to be an robust candidate for many biological fields, such as DNA and protein analyzing, gene and drug delivering, intracellular tracking, and in vivo monitoring, etc..

  7. 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.

  8. A visualization method for probing grain boundaries of single layer graphene via molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Zhan, Linjie; Wan, Wen; Zhu, Zhenwei; Zhao, Zhijuan; Zhang, Zhenhan; Shih, Tien-Mo; Cai, Weiwei

    2017-07-01

    Graphene, a member of layered two-dimensional (2D) materials, possesses high carrier mobility, mechanical flexibility, and optical transparency, as well as enjoying a wide range of promising applications in electronics. Adopting the chemical vaporization deposition method, the majority of investigators have ubiquitously grown single layer graphene (SLG), which inevitably involves polycrystalline properties. Here we demonstrate a simple method for the direct visualization of arbitrarily large-size SLG domains by synthesizing one-hundred-nm-scale MoS2 single crystals via a high-vacuum molecular beam epitaxy process. The present study based on epitaxial growth provides a guide for probing the grain boundaries of various 2D materials and implements higher potentials for the next-generation electronic devices.

  9. Characterization of TCP-1 probes for molecular imaging of colon cancer.

    PubMed

    Liu, Zhonglin; Gray, Brian D; Barber, Christy; Bernas, Michael; Cai, Minying; Furenlid, Lars R; Rouse, Andrew; Patel, Charmi; Banerjee, Bhaskar; Liang, Rongguang; Gmitro, Arthur F; Witte, Marlys H; Pak, Koon Y; Woolfenden, James M

    2016-10-10

    Molecular probes capable of detecting colorectal cancer (CRC) are needed for early CRC diagnosis. The objective of this study was to characterize c[CTPSPFSHC]OH (TCP-1), a small peptide derived from phage display selection, for targeting human CRC xenografts using technetium-99m ((99m)Tc)-labeled TCP-1 and fluorescent cyanine-7 (Cy7)-labeled form of the peptide (Cy7-TCP-1). (99m)Tc-TCP-1 was generated by modifying TCP-1 with succinimidyl-6-hydrazino-nicotinamide (S-HYNIC) followed by radiolabeling. In vitro saturation binding experiments were performed for (99m)Tc-TCP-1 in human HCT116 colon cancer cells. SCID mice with human HCT116 cancer xenografts were imaged with (99m)Tc-TCP-1 or control peptide using a small-animal SPECT imager: Group I (n=5) received no blockade; Group II (n=5) received a blocking dose of non-radiolabeled TCP-1. Group III (n=5) were imaged with (99m)Tc-labeled control peptide (inactive peptide). SCID mice with human PC3 prostate cancer xenografts (Group IV, n=5) were also imaged with (99m)Tc-TCP-1. Eight additional SCID mice bearing HCT116 xenografts in dorsal skinfold window chambers (DSWC) were imaged by direct positron imaging of (18)F-fluorodeoxyglucose ((18)F-FDG) and fluorescence microscopy of Cy7-TCP-1. In vitro(99m)Tc-HYNIC-TCP-1 binding assays on HCT 116 cells indicated a mean Kd of 3.04±0.52nM. In cancer xenografts, (99m)Tc-TCP-1 radioactivity (%ID/g) was 1.01±0.15 in the absence of blockade and was reduced to 0.26±0.04 (P<0.01) with blockade. No radioactive uptake was observed in the PC3 tumors with (99m)Tc-TCP-1 or HCT116 tumors with inactive peptide. Cy7-TCP-1 activity localized not only in metabolically active tumors, as defined by (18)F-FDG imaging, but also in peritumoral microvasculature. In conclusion, TCP-1 probes may have a distinct targeting mechanism with high selectivity for CRC and tumor-associated vasculature. Molecular imaging with TCP-1 probes appears promising to detect malignant colorectal lesions.

  10. Multiplex detection of microRNAs by combining molecular beacon probes with T7 exonuclease-assisted cyclic amplification reaction.

    PubMed

    Liu, Yacui; Zhang, Jiangyan; Tian, Jingxiao; Fan, Xiaofei; Geng, Hao; Cheng, Yongqiang

    2017-01-01

    A simple, highly sensitive, and specific assay was developed for the homogeneous and multiplex detection of microRNAs (miRNAs) by combining molecular beacon (MB) probes and T7 exonuclease-assisted cyclic amplification. An MB probe with five base pairs in the stem region without special modification can effectively prevent the digestion by T7 exonuclease. Only in the presence of target miRNA is the MB probe hybridized with the target miRNA, and then digested by T7 exonuclease in the 5' to 3' direction. At the same time, the target miRNA is released and subsequently initiates the nuclease-assisted cyclic digestion process, generating enhanced fluorescence signal significantly. The results show that the combination of T7 exonuclease-assisted cyclic amplification reaction and MB probe possesses higher sensitivity for miRNA detection. Moreover, multiplex detection of miRNAs was successfully achieved by designing two MB probes labeled with FAM and Cy3, respectively. As a result, the method opens a new pathway for the sensitive and multiplex detection of miRNAs as well as clinical diagnosis. Graphical Abstract A simple, highly sensitive, and specific assay was developed for the detection of microRNAs by combining molecular beacon probes with T7 exonuclease-assisted cyclic amplification reaction.

  11. 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

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

    SciTech Connect

    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 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. 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.

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

    DOE PAGES

    Robinson, Joshua W.; Zhou, Yan; Bhattacharya, Priyanka; ...

    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

  14. Fluorescence detection of adenosine triphosphate through an aptamer-molecular beacon multiple probe.

    PubMed

    Zeng, Xiaodan; Zhang, Xiaoling; Yang, Wen; Jia, Hongying; Li, Yamin

    2012-05-01

    An aptamer-molecular beacon (MB) multiple fluorescent probe for adenosine triphosphate (ATP) assay is proposed in this article. The ATP aptamer was used as a molecular recognition part, and an oligonucleotide (short strand, SS) partially complementary with the aptamer and an MB was used as the other part. In the presence of ATP, the aptamer bound with it, accompanied by the hybridization of MB and SS and the fluorescence recovering. Wherever there is only very weak fluorescence can be measured in the absence of ATP. Based on the relationship of recovering fluorescence and the concentration of ATP, a method for quantifying ATP has been developed. The fluorescence intensity was proportional to the concentration of ATP in the range of 10 to 500 nM with a detection limit of 0.1 nM. Moreover, this method was able to detect ATP with high selectivity in the presence of guanosine triphosphate (GTP), cytidine triphosphate (CTP), and uridine triphosphate (UTP). This method is proved to be simple with high sensitivity, selectivity, and specificity.

  15. Isolation of molecular probes associated with the chromosome 15 instability in the Prader-Willi syndrome.

    PubMed Central

    Donlon, T A; Lalande, M; Wyman, A; Bruns, G; Latt, S A

    1986-01-01

    Flow cytometry and recombinant DNA techniques have been used to obtain reagents for a molecular analysis of the Prader-Willi syndrome (PWS). HindIII total-digest libraries were prepared in lambda phage Charon 21A from flow-sorted inverted duplicated no. 15 human chromosomes and propagated on recombination-proficient (LE392) and recBC-, sbcB- (DB1257) bacteria. Twelve distinct chromosome 15-specific probes have been isolated. Eight localized to the region 15q11----13. Four of these eight sublocalized to band 15q11.2 and are shown to be deleted in DNA of one of two patients examined with the PWS. Heteroduplex analysis of two of these clones, which grew on DB1257 but not on LE392, revealed stem-loop structures in the inserts, indicative of inverted, repeated DNA elements. Such DNA repeats might account for some of the cloning instability of DNA segments from proximal 15q. Analysis of the genetic and physical instability associated with the repeated sequences we have isolated from band 15q11.2 may elucidate the molecular basis for the instability of this chromosomal region in patients with the PWS or other diseases associated with chromosomal abnormalities in the proximal long arm of human chromosome 15. Images PMID:3012567

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

    NASA Technical Reports Server (NTRS)

    Smith, D. A.; Allen, R. J.; Bohlin, R. C.; Nicholson, N.; Stecher, T. P.

    1999-01-01

    Studies of nearby spiral galaxies suggest that photodissociation regions (PDRs) are capable of producing the observed large--scale distribution of HI (Allen et al.- 1997, and references therein). The column density of HI in a PDR is fundamentally linked to the amount of far--ultraviolet (FUV) emission produced by nearby young stars and the local molecular gas volume density. Measurements of the HI column density and the FUV emission associated with PDRs thus provide a new probe of the molecular gas distribution in nearby galaxies. Advantages of this method include its insensitivity to assumptions about the CO/{\\rm H2} conversion factor or the gas temperature. We discuss the application of this method to M101. The HI column density and FUV emission have been measured for 35 PDRs from VLA data (Braun 1997) and Ultraviolet Imaging Telescope data (Waller et al.-1997). We derive volume densities ranging from n-100 {\\rm cm(exp -3)} in the central HI--poor regions of M101 to n -3000 {\\rm cm(exp -3)} in the HI--rich periphery of the galaxy.

  18. Characterization of molecular mobility in seed tissues: an electron paramagnetic resonance spin probe study.

    PubMed Central

    Buitink, J; Hemminga, M A; Hoekstra, F A

    1999-01-01

    The relationship between molecular mobility (tauR) of the polar spin probe 3-carboxy-proxyl and water content and temperature was established in pea axes by electron paramagnetic resonance (EPR) and saturation transfer EPR. At room temperature, tauR increased during drying from 10(-11) s at 2.0 g water/g dry weight to 10(-4) s in the dry state. At water contents below 0.07 g water/g dry weight, tauR remained constant upon further drying. At the glass transition temperature, tauR was constant at approximately 10(-4) s for all water contents studied. Above Tg, isomobility lines were found that were approximately parallel to the Tg curve. The temperature dependence of tauR at all water contents studied followed Arrhenius behavior, with a break at Tg. Above Tg the activation energy for rotational motion was approximately 25 kJ/mol compared to 10 kJ/mol below Tg. The temperature dependence of tauR could also be described by the WLF equation, using constants deviating considerably from the universal constants. The temperature effect on tauR above Tg was much smaller in pea axes, as found previously for sugar and polymer glasses. Thus, although glasses are present in seeds, the melting of the glass by raising the temperature will cause only a moderate increase in molecular mobility in the cytoplasm as compared to a huge increase in amorphous sugars. PMID:10354457

  19. Characterization of molecular mobility in seed tissues: an electron paramagnetic resonance spin probe study.

    PubMed

    Buitink, J; Hemminga, M A; Hoekstra, F A

    1999-06-01

    The relationship between molecular mobility (tauR) of the polar spin probe 3-carboxy-proxyl and water content and temperature was established in pea axes by electron paramagnetic resonance (EPR) and saturation transfer EPR. At room temperature, tauR increased during drying from 10(-11) s at 2.0 g water/g dry weight to 10(-4) s in the dry state. At water contents below 0.07 g water/g dry weight, tauR remained constant upon further drying. At the glass transition temperature, tauR was constant at approximately 10(-4) s for all water contents studied. Above Tg, isomobility lines were found that were approximately parallel to the Tg curve. The temperature dependence of tauR at all water contents studied followed Arrhenius behavior, with a break at Tg. Above Tg the activation energy for rotational motion was approximately 25 kJ/mol compared to 10 kJ/mol below Tg. The temperature dependence of tauR could also be described by the WLF equation, using constants deviating considerably from the universal constants. The temperature effect on tauR above Tg was much smaller in pea axes, as found previously for sugar and polymer glasses. Thus, although glasses are present in seeds, the melting of the glass by raising the temperature will cause only a moderate increase in molecular mobility in the cytoplasm as compared to a huge increase in amorphous sugars.

  20. 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

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

    PubMed

    Kobayashi, Hisataka; Longmire, Michelle R; Ogawa, Mikako; Choyke, Peter L

    2011-09-01

    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).

  2. 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.

  3. A Zn2+-specific fluorescent molecular probe for the selective detection of endogenous cyanide in biorelevant samples.

    PubMed

    Divya, Kizhumuri P; Sreejith, Sivaramapanicker; Balakrishna, Bugga; Jayamurthy, Purushothaman; Anees, Palappuravan; Ajayaghosh, Ayyappanpillai

    2010-09-07

    A Zn(2+)-specific molecular probe 3 was developed for the selective detection of CN(-) under aqueous conditions. The fluorescent Zn(2+) complex of 3 upon CN(-) addition generates a bright blue fluorescence that allows the detection of the latter and is useful for the screening of natural products with and without endogenous cyanide content.

  4. Molecular cloning of verrucosidin-producing Penicillium polonicum genes by differential screening to obtain a DNA probe.

    PubMed

    Aranda, E; Rodríguez, M; Benito, M J; Asensio, M A; Córdoba, J J

    2002-06-05

    A differential molecular screening procedure was developed to obtain DNA clones enriched for verrucosidin-related genes that could be used as DNA probes to detect verrucosidin-producing Penicillium polonicum. Permissive and nonpermissive conditions for verrucosidin production were selected to obtain differentiated poly (A)+ RNA for the cloning strategy. P. polonicum yielded the highest amount of verrucosidin when cultured in malt extract broth at 25 degrees C without shaking. These conditions were selected as verrucosidin permissive conditions. When shaking was applied to the verrucosidin permissive conditions, verrucosidin was not detected. Approximately 5000 transformants were obtained for the library of DNA fragments from verrucosidin-producing P. polonicum and hybridized with cDNA probes obtained from poly (A)+ RNA of permissive and nonpermissive conditions. A total of 120 clones hybridized only with the permissive cDNA probes. From these, eight representative DNA inserts selected on the basis of size and labelled with fluorescein-dUTP were assayed as DNA probes in the second differential screening by Northern hybridization. Probe SVr1 gave a strong hybridization signal selectively with poly (A)+ RNAs from high verrucosidin production. When this probe was assayed by dot blot hybridization with DNA of different moulds species, hybridization was detected only with DNA from the verrucosidin-producing strain. The strategy used in this work has proved to be useful to detect unknown genes related to mycotoxins. In addition, the DNA probe obtained should be considered for the detection of verrucosidin-producing moulds.

  5. 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.

  6. Two-Dimensional Analysis of Cross-Junctional Molecular Interaction by Force Probes.

    PubMed

    Ju, Lining; Chen, Yunfeng; Rushdi, Muaz Nik; Chen, Wei; Zhu, Cheng

    2017-01-01

    Upon engagement with a specific ligand, a cell surface receptor transduces intracellular signals to activate various cellular functions. This chapter describes a set of biomechanical methods for analyzing the characteristics of cross-junctional receptor-ligand interactions at the surface of living cells. These methods combine the characterization of kinetics of receptor-ligand binding with real-time imaging of intracellular calcium fluxes, which allow researchers to assess how the signal initiated from single receptor-ligand engagement is transduced across the cell membrane. A major application of these methods is the analysis of antigen recognition by triggering of the T cell receptor (TCR). Three related methods are described in this chapter: (1) the micropipette adhesion assay, (2) the biomembrane force probe (BFP) assay, and (3) combining BFP with fluorescence microscopy (fBFP). In all cases, an ultrasoft human red blood cell (RBC) is used as an ultrasensitive mechanical force probe. The micropipette assay detects binding events visually. The BFP uses a high-speed camera and real-time image tracking techniques to measure mechanical variables on a single molecular bond with up to ~1 pN (10(-12) Newton), ~3 nm (10(-9) m), and ~0.5 ms (10(-3) s) in force, spatial, and temporal resolution, respectively. As an upgrade to the BFP, the fBFP simultaneously images binding-triggered intracellular calcium signals on a single live cell. These technologies can be widely used to study other membrane receptor-ligand interactions and signaling under mechanical regulation.

  7. 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

  8. 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.

  9. Library Synthesis, Screening, and Discovery of Modified Zinc(II)-Bis(dipicolylamine) Probe for Enhanced Molecular Imaging of Cell Death

    PubMed Central

    2015-01-01

    Zinc(II)-bis(dipicolylamine) (Zn-BDPA) coordination complexes selectively target the surfaces of dead and dying mammalian cells, and they have promise as molecular probes for imaging cell death. A necessary step toward eventual clinical imaging applications is the development of next-generation Zn-BDPA complexes with enhanced affinity for the cell death membrane biomarker, phosphatidylserine (PS). This study employed an iterative cycle of library synthesis and screening, using a novel rapid equilibrium dialysis assay, to discover a modified Zn-BDPA structure with high and selective affinity for vesicles containing PS. The lead structure was converted into a deep-red fluorescent probe and its targeting and imaging performance was compared with an unmodified control Zn-BDPA probe. The evaluation process included a series of FRET-based vesicle titration studies, cell microscopy experiments, and rat tumor biodistribution measurements. In all cases, the modified probe exhibited comparatively higher affinity and selectivity for the target membranes of dead and dying cells. The results show that this next-generation deep-red fluorescent Zn-BDPA probe is well suited for preclinical molecular imaging of cell death in cell cultures and animal models. Furthermore, it should be possible to substitute the deep-red fluorophore with alternative reporter groups that enable clinically useful, deep-tissue imaging modalities, such as MRI and nuclear imaging. PMID:24575875

  10. A Flexible Nanoarray Approach for the Assembly and Probing of Molecular Complexes

    PubMed Central

    Krasnoslobodtsev, Alexey V.; Zhang, Yuliang; Viazovkina, Ekaterina; Gall, Alexander; Bertagni, Chad; Lyubchenko, Yuri L.

    2015-01-01

    Immobilization is a key step involved in probing molecular interactions using single-molecule force spectroscopy methods, including atomic force microscopy (AFM). To our knowledge, we describe a novel approach termed flexible nanoarray (FNA) in which the interaction between the two internally immobilized amyloid β peptides is measured by pulling of the tether. The FNA tether was synthesized with nonnucleotide phosphoramidite monomers using the DNA synthesis chemistry. The two anchoring points for immobilization of the peptides inside the tether were incorporated at defined distances between them and from the ends of the polymer. Decamers of amyloid β peptide capable of dimer formation were selected as a test system. The formation of the peptide dimers was verified by AFM force spectroscopy by pulling the tether at the ends. In these experiments, the thiolated end of the FNA tether was covalently immobilized on the AFM substrate functionalized with maleimide. The other end of the FNA tether was functionalized with biotin to form a noncovalent link with the streptavidin functionalized AFM tip during the approach stage. The dimers’ rupture fingerprint was unambiguously identified on the force curves by its position and the force value. The FNA design allowed reversible experiments in which the monomers were allowed to associate after the rupture of the dimers by performing the approach stage before the rupture of the biotin-streptavidin link. This suggests that the FNA technique is capable of analyzing multiple intermolecular interactions in the same molecular complex. The computational analysis showed that the tethered peptides assemble into the same dimer structure as that formed by nontethered peptides, suggesting that the FNA tether has the necessary flexibility to enable assembly of the dimer even during the course of the force spectroscopy experiment. PMID:25954890

  11. Molecular Structure of P2Y Receptors: Mutagenesis, Modeling, and Chemical Probes

    PubMed Central

    Jayasekara, M.P. Suresh; Costanzi, Stefano

    2012-01-01

    There are eight subtypes of P2Y receptors (P2YRs) that are activated, and in some cases inhibited, by a range of extracellular nucleotides. These nucleotides are ubiquitous, but their extracellular concentration can rise dramatically in response to hypoxia, ischemia, or mechanical stress, injury, and release through channels and from vesicles. Two subclasses of P2YRs were defined based on clustering of sequences, second messengers, and receptor sequence analysis. The numbering system for P2YR subtypes is discontinuous; i.e., P2Y1–14Rs have been defined, but six of the intermediate-numbered cloned receptor sequences (e.g., P2y3, P2y5, P2y7–10) are not functional mammalian nucleotide receptors. Of these two clusters, the P2Y12–14 subtypes couple via Gαi to inhibit adenylate cyclase, while the remaining subtypes couple through Gαq to activate phospholipase C. Collectively, the P2YRs respond to both purine and pyrimidine nucleotides, in the form of 5′-mono- and dinucleotides and nucleoside-5′-diphosphosugars. In recent years, the medicinal chemistry of P2Y receptors has advanced significantly, to provide selective agonists and antagonists for many but not all of the subtypes. Ligand design has been aided by insights from structural probing using molecular modelling and mutagenesis. Currently, the molecular modelling of the receptors is effectively based on the X-ray structure of the CXCR4 receptor, which is the closest to the P2Y receptors among all the currently crystallized receptors in terms of sequence similarity. It is now a challenge to develop novel and selective P2YR ligands for disease treatment (although antagonists of the P2Y12R are already widely used as antithrombotics). PMID:23336097

  12. Superior sensitivity of novel molecular imaging probe: simultaneously targeting two types of endothelial injury markers

    PubMed Central

    Sun, Dawei; Nakao, Shintaro; Xie, Fang; Zandi, Souska; Schering, Alexander; Hafezi-Moghadam, Ali

    2010-01-01

    The need remains great for early diagnosis of diseases. The special structure of the eye provides a unique opportunity for noninvasive light-based imaging of fundus vasculature. To detect endothelial injury at the early and reversible stage of adhesion molecule up-regulation, we generated novel imaging agents that target two distinct types of endothelial molecules, a mediator of rolling, P-selectin, and one that mediates firm adhesion, ICAM-1. Interactions of these double-conjugated fluorescent microspheres (MSs) in retinal or choroidal microvasculature were visualized in live animals by scanning laser ophthalmoscopy. The new imaging agents showed significantly higher sensitivity for detection of endothelial injury than singly conjugated MSs (rPSGL-1- or α-ICAM-1-conjugated), both in terms of rolling (P<0.01) and firm adhesion (P<0.01). The rolling flux of α-ICAM-1-conjugated MSs did not differ in EIU animals, whereas double-conjugated MSs showed significantly higher rolling flux (P<0.01), revealing that ICAM-1 in vivo supports rolling, once MS interaction with the endothelium is initiated. Double-conjugated MSs specifically detected firmly adhering leukocytes (P<0.01), allowing in vivo quantification of immune response. Antiinflammatory treatment with dexamethasone led to reduced leukocyte accumulation (P<0.01) as well as MS interaction (P<0.01), which suggests that treatment success and resolution of inflammation is quantitatively reflected with this molecular imaging approach. This work introduces novel imaging agents for noninvasive detection of endothelial injury in vivo. Our approach may be developed further to diagnose human disease at a much earlier stage than currently possible.—Sun, D., Nakao, S., Xie, F., Zandi, S., Schering, A., Hafezi-Moghadam, A. Superior sensitivity of novel molecular imaging probe: simultaneously targeting two types of endothelial injury markers. PMID:20103715

  13. Molecular imaging of endogenous and exogenous chromophores using ground state recovery pump-probe optical coherence tomography.

    PubMed

    Applegate, Brian E; Izatt, Joseph A

    2006-10-02

    We present a novel molecular imaging technique which combines the 3-D tomographic imaging capability of optical coherence tomography with the molecular sensitivity of pump-probe spectroscopy. This technique, based on transient absorption, is sensitive to any molecular chromophore. It is particularly promising for the many important biomarkers, such as hemoglobin, which are poor fluorophores and therefore difficult to image with current optical techniques without chemical labeling. Previous implementations of pump-probe optical coherence tomography have suffered from inefficient pump-probe schemes which hurt the sensitivity and applicability of the technique. Here we optimize the efficiency of the pump-probe approach by avoiding the steady-state kinetics and spontaneous processes exploited in the past in favor of measuring the transient absorption of fully allowed electronic transitions on very short time scales before a steady-state is achieved. In this article, we detail the optimization and characterization of the prototype system, comparing experimental results for the system sensitivity to theoretical predictions. We demonstrate in situ imaging of tissue samples with two different chromophores; the transfectable protein dsRed and the protein hemoglobin. We also demonstrate, with a simple sample vessel and a mixture of human whole blood and rhodamine 6G, the potential to use ground state recovery time to separate the contributions of multiple chromophores to the ground state recovery signal.

  14. Molecular imaging of endogenous and exogenous chromophores using ground state recovery pump-probe optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Applegate, Brian E.; Izatt, Joseph A.

    2006-10-01

    We present a novel molecular imaging technique which combines the 3-D tomographic imaging capability of optical coherence tomography with the molecular sensitivity of pump-probe spectroscopy. This technique, based on transient absorption, is sensitive to any molecular chromophore. It is particularly promising for the many important biomarkers, such as hemoglobin, which are poor fluorophores and therefore difficult to image with current optical techniques without chemical labeling. Previous implementations of pump-probe optical coherence tomography have suffered from inefficient pump-probe schemes which hurt the sensitivity and applicability of the technique. Here we optimize the efficiency of the pump-probe approach by avoiding the steady-state kinetics and spontaneous processes exploited in the past in favor of measuring the transient absorption of fully allowed electronic transitions on very short time scales before a steady-state is achieved. In this article, we detail the optimization and characterization of the prototype system, comparing experimental results for the system sensitivity to theoretical predictions. We demonstrate in situ imaging of tissue samples with two different chromophores; the transfectable protein dsRed and the protein hemoglobin. We also demonstrate, with a simple sample vessel and a mixture of human whole blood and rhodamine 6G, the potential to use ground state recovery time to separate the contributions of multiple chromophores to the ground state recovery signal.

  15. Molecular engineering of a TBET-based two-photon fluorescent probe for ratiometric imaging of living cells and tissues.

    PubMed

    Zhou, Liyi; Zhang, Xiaobing; Wang, Qianqian; Lv, Yifan; Mao, Guojiang; Luo, Aili; Wu, Yongxiang; Wu, Yuan; Zhang, Jing; Tan, Weihong

    2014-07-16

    In contrast to one-photon microscopy, two-photon probe-based fluorescent imaging can provide improved three-dimensional spatial localization and increased imaging depth. Consequently, it has become one of the most attractive techniques for studying biological events in living cells and tissues. However, the quantitation of these probes is primarily based on single-emission intensity change, which tends to be affected by a variety of environmental factors. Ratiometric probes, on the other hand, can eliminate these interferences by the built-in correction of the dual emission bands, resulting in a more favorable system for imaging living cells and tissues. Herein, for the first time, we adopted a through-bond energy transfer (TBET) strategy to design and synthesize a small molecular ratiometric two-photon fluorescent probe for imaging living cells and tissues in real time. Specifically, a two-photon fluorophore (D-π-A-structured naphthalene derivative) and a rhodamine B fluorophore are directly connected by electronically conjugated bond to form a TBET probe, or Np-Rh, which shows a target-modulated ratiometric two-photon fluorescence response with highly efficient energy transfer (93.7%) and two well-resolved emission peaks separated by 100 nm. This novel probe was then applied for two-photon imaging of living cells and tissues and showed high ratiometric imaging resolution and deep-tissue imaging depth of 180 μm, thus demonstrating its practical application in biological systems.

  16. A screen of approved drugs and molecular probes identifies therapeutics with anti-Ebola virus activity.

    PubMed

    Johansen, Lisa M; DeWald, Lisa Evans; Shoemaker, Charles J; Hoffstrom, Benjamin G; Lear-Rooney, Calli M; Stossel, Andrea; Nelson, Elizabeth; Delos, Sue E; Simmons, James A; Grenier, Jill M; Pierce, Laura T; Pajouhesh, Hassan; Lehár, Joseph; Hensley, Lisa E; Glass, Pamela J; White, Judith M; Olinger, Gene G

    2015-06-03

    Currently, no approved therapeutics exist to treat or prevent infections induced by Ebola viruses, and recent events have demonstrated an urgent need for rapid discovery of new treatments. Repurposing approved drugs for emerging infections remains a critical resource for potential antiviral therapies. We tested ~2600 approved drugs and molecular probes in an in vitro infection assay using the type species, Zaire ebolavirus. Selective antiviral activity was found for 80 U.S. Food and Drug Administration-approved drugs spanning multiple mechanistic classes, including selective estrogen receptor modulators, antihistamines, calcium channel blockers, and antidepressants. Results using an in vivo murine Ebola virus infection model confirmed the protective ability of several drugs, such as bepridil and sertraline. Viral entry assays indicated that most of these antiviral drugs block a late stage of viral entry. By nature of their approved status, these drugs have the potential to be rapidly advanced to clinical settings and used as therapeutic countermeasures for Ebola virus infections. Copyright © 2015, American Association for the Advancement of Science.

  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. An in silico pan-genomic probe for the molecular traits behind Lactobacillus ruminis gut autochthony.

    PubMed

    Kant, Ravi; Palva, Airi; von Ossowski, Ingemar

    2017-01-01

    As an ecological niche, the mammalian intestine provides the ideal habitat for a variety of bacterial microorganisms. Purportedly, some commensal genera and species offer a beneficial mix of metabolic, protective, and structural processes that help sustain the natural digestive health of the host. Among these sort of gut inhabitants is the Gram-positive lactic acid bacterium Lactobacillus ruminis, a strict anaerobe with both pili and flagella on its cell surface, but also known for being autochthonous (indigenous) to the intestinal environment. Given that the molecular basis of gut autochthony for this species is largely unexplored and unknown, we undertook a study at the genome level to pinpoint some of the adaptive traits behind its colonization behavior. In our pan-genomic probe of L. ruminis, the genomes of nine different strains isolated from human, bovine, porcine, and equine host guts were compiled and compared for in silico analysis. For this, we conducted a geno-phenotypic assessment of protein-coding genes, with an emphasis on those products involved with cell-surface morphology and anaerobic fermentation and respiration. We also categorized and examined the core and accessory genes that define the L. ruminis species and its strains. Here, we made an attempt to identify those genes having ecologically relevant phenotypes that might support or bring about intestinal indigenousness.

  19. 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.

  20. 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

  1. Molecular analysis of 53 fragile X families with the probe StB12.3

    SciTech Connect

    Puissant, H.; Malinge, M.C.; Larget-Piet, A.; Larget-Piet, L.; Martin, D.; Chauveau, P.; Odent, S.; Lemarec, B.; Plessis, G.; Parent, Ph.

    1994-12-01

    Fifty-three pedigrees with the fragile X syndrome have been studied for amplification of the CGG repeat sequence adjacent to the CpG island in the FMR1 gene. Probe StB12.3 allowed direct detection of affected males, carrier females, normal transmitting males, as well as prenatal diagnosis. Comparison of our molecular data with our previous linkage data from 38 families indicates the effectiveness of direct DNA analysis. A total of 325 individuals were studied and no new mutation was found. All daughters of males with a premutation had a premutation. When the mother had a full mutation no children had a premutation. In premutated mothers, the size of the premutation seems to be a determining factor for the transition to the full mutation. All affected males had a full mutation or mosaicism and only 42% of the females with a full mutation were mentally impaired. Analysis of large families over 3 generations illustrated clearly the Sherman paradox. Furthermore, the analysis of these families is in reasonable agreement with the multiallelic model of Morton and Macpherson. Mosaic cases in the offspring of the mothers with a full mutation suggest a maternal germinal mosaicism. Then an abnormal methylation and a somatic heterogeneity established in very early steps of embryogenesis could explain these cases. 17 refs.

  2. Molecular inversion probe: a new tool for highly specific detection of plant pathogens.

    PubMed

    Lau, Han Yih; Palanisamy, Ramkumar; Trau, Matt; Botella, Jose R

    2014-01-01

    Highly specific detection methods, capable of reliably identifying plant pathogens are crucial in plant disease management strategies to reduce losses in agriculture by preventing the spread of diseases. We describe a novel molecular inversion probe (MIP) assay that can be potentially developed into a robust multiplex platform to detect and identify plant pathogens. A MIP has been designed for the plant pathogenic fungus Fusarium oxysporum f.sp. conglutinans and the proof of concept for the efficiency of this technology is provided. We demonstrate that this methodology can detect as little as 2.5 ng of pathogen DNA and is highly specific, being able to accurately differentiate Fusarium oxysporum f.sp. conglutinans from other fungal pathogens such as Botrytis cinerea and even pathogens of the same species such as Fusarium oxysporum f.sp. lycopersici. The MIP assay was able to detect the presence of the pathogen in infected Arabidopsis thaliana plants as soon as the tissues contained minimal amounts of pathogen. MIP methods are intrinsically highly multiplexable and future development of specific MIPs could lead to the establishment of a diagnostic method that could potentially screen infected plants for hundreds of pathogens in a single assay.

  3. An in silico pan-genomic probe for the molecular traits behind Lactobacillus ruminis gut autochthony

    PubMed Central

    Kant, Ravi; Palva, Airi

    2017-01-01

    As an ecological niche, the mammalian intestine provides the ideal habitat for a variety of bacterial microorganisms. Purportedly, some commensal genera and species offer a beneficial mix of metabolic, protective, and structural processes that help sustain the natural digestive health of the host. Among these sort of gut inhabitants is the Gram-positive lactic acid bacterium Lactobacillus ruminis, a strict anaerobe with both pili and flagella on its cell surface, but also known for being autochthonous (indigenous) to the intestinal environment. Given that the molecular basis of gut autochthony for this species is largely unexplored and unknown, we undertook a study at the genome level to pinpoint some of the adaptive traits behind its colonization behavior. In our pan-genomic probe of L. ruminis, the genomes of nine different strains isolated from human, bovine, porcine, and equine host guts were compiled and compared for in silico analysis. For this, we conducted a geno-phenotypic assessment of protein-coding genes, with an emphasis on those products involved with cell-surface morphology and anaerobic fermentation and respiration. We also categorized and examined the core and accessory genes that define the L. ruminis species and its strains. Here, we made an attempt to identify those genes having ecologically relevant phenotypes that might support or bring about intestinal indigenousness. PMID:28414739

  4. Preparation and Characterization of a Magnetic and Optical Dual-Modality Molecular Probe

    PubMed Central

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

    2010-01-01

    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 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. PMID:20368682

  5. The Use of Luminescent Molecular Probes for Pressure Measurement -Pressure Sensitive Paint

    NASA Astrophysics Data System (ADS)

    Sullivan, John

    1998-04-01

    Traditionally, pressure taps have been used to obtain surface pressure distributions on wind tunnel models, flight vehicles and other fluid flow rigs. This technique can be very labor-intensive and model preparation costs are high when detailed maps of pressure are desired. Further, the spatial resolution is limited by the number of instrumentation locations chosen. By comparison, the pressure sensitive paint (PSP) technique provides a way to obtain simple, inexpensive, full-field measurements of pressure with much higher spatial resolution. Luminescent molecular probes are imbedded in a binder to form a pressure sensitive paint. On excitation by light of the proper wavelength, the luminescence, which is quenched by oxygen, is detected by a camera or photodetector. From the detected luminescent intensity or time decay and a calibration curve, pressure can be determined. The basic photophysics, calibration, accuracy and time response of luminescent paints will be described followed by applications in low speed, transonic, supersonic and cryogenic wind tunnels and in rotating machinery.

  6. Using vibrational branching ratios to probe shape resonances in molecular photoionization

    NASA Astrophysics Data System (ADS)

    Lucchese, Robert; Das, Aloke; Poliakoff, Erwin; Bozek, John

    2009-05-01

    The measurement of vibrational branching ratios in molecular photoionization can be used as a probe of the nature of resonant states, since such states are often sensitive to the geometry of the molecule. Recent computed results for BF3 and C6F6 will be presented. In C6F6, we consider the excitation of the two symmetric stretching modes in the photoionization leading to the C ^3B2u state of the ion. Two prominent shape resonances at photon energies between 18 and 20 eV respond quite differently to the excitation of the symmetric ring-breathing mode and to the symmetric C-F stretching mode. In BF3, the excitation of both the symmetric stretching and the degenerate asymmetric stretching modes are considered in the photoionization leading to the E ^2A1' state of the ion. The symmetric stretching mode shows a relatively weak resonant enhancement in the branching ratio, whereas the asymmetric stretching mode has a much more prominent feature.

  7. Molecular platform for design and synthesis of targeted dual-modality imaging probes.

    PubMed

    Kumar, Amit; Zhang, Shanrong; Hao, Guiyang; Hassan, Gedaa; Ramezani, Saleh; Sagiyama, Koji; Lo, Su-Tang; Takahashi, Masaya; Sherry, A Dean; Öz, Orhan K; Kovacs, Zoltan; Sun, Xiankai

    2015-03-18

    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 (68/67)Ga(3+) and Gd(3+), 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 (67)Ga. 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.

  8. A dynamic molecular probe to investigate catalytic effects and Joule heating in enantioselective MEKC.

    PubMed

    Trapp, Oliver

    2007-02-01

    Enantiomerization of ferroin [tris(1,10-phenanthroline)-iron(II)-complex] was investigated by enantioselective dynamic micellar EKC. The enantiomer separation was performed in an aqueous 50 mM sodium borate/sodium dihydrogenphosphate buffer at pH 8.0 in the presence of the chiral surfactant sodium cholate. The unified equation of dynamic chromatography was employed to determine reaction rate constants from the electropherograms featured with distinct plateau formation. Activation parameters DeltaH( not equal) = 124.0 +/- 0.5 kJ/mol and DeltaS( not equal) = 121 +/- 1 J.K(-1)mol(-1) were calculated from temperature-dependent measurements between 10.0 and 27.5 degrees C in 2.5 K steps. Considering the data obtained by polarimetry of enantiomeric pure ferroin in water, it was found that enantiomerization rate in the micelle is accelerated by a factor of 12. Because of the highly positive activation entropy DeltaS( not equal), ferroin was used as a temperature-sensitive dynamic molecular probe to determine temperature deviations caused by Joule heating.

  9. Effect of solvent model when probing protein dynamics with molecular dynamics.

    PubMed

    Genheden, Samuel

    2017-01-01

    We probe the dynamics of the Bpti and Galectin-3 proteins using molecular dynamics simulations employing three water models at different levels of resolution, viz. the atomistic TIP4P-Ewald, the coarse-grained Elba and an implicit generalised Born model. The dynamics are quantified indirectly by model-free order parameters, S(2) of the backbone NH and selected side-chain bond vectors, which also have been determined experimentally through NMR relaxation measurements. For the backbone, the order parameters produced with the three solvent models agree to a large extent with experiments, giving average unsigned deviations between 0.03 and 0.06. For the side-chains, for which the experimental data is incomplete, the deviations are considerably larger with mean deviations between 0.13 and 0.17. However, for both backbone and side-chains, it is difficult to pick a winner, as all models perform equally well overall. For a more complete set of side-chain vectors, we resort to analysing the variation among the estimates from different solvent models. Unfortunately, the variations are found to be sizeable with mean deviations between 0.11 and 0.15. Implications for computational assessment of protein dynamics are discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Determination of bismuth in pharmaceutical products using phosphoric acid as molecular probe by resonance light scattering.

    PubMed

    Yun, Yanru; Cui, Fengling; Geng, Shaoguang; Jin, Jianhua

    2012-01-01

    A novel method for the sensitive determination of bismuth(III) in pharmaceutical products using phosphoric acid as a molecular probe by resonance light scattering (RLS) is discussed. In 0.5 mol/L phosphoric acid (H3 PO4) medium, bismuth(III) reacted with PO4 (3-) to form an ion association compound, which resulted in the significant enhancement of RLS intensity and the appearance of the corresponding RLS spectral characteristics. The maximum scattering peak of the system existed at 364 nm. Under optimal conditions, there was linear relationship between the relative intensity of RLS and concentration of bismuth(III) in the range of 0.06-10.0 µg/mL for the system. A low detection limit for bismuth(III) of 3.22 ng/mL was achieved. The relative standard deviations (RSD) for the determination of 0.40 and 0.80 µg/mL bismuth(III) were 2.1% and 1.1%, respectively, for five determinations. Based on this fact, a simple, rapid, and sensitive method was developed for the determination of bismuth(III) at nanogram level by RLS technique with a common spectrofluorimeter. This analytical system was successfully applied to determine the trace amounts of bismuth(III) in pharmaceutical products, which was in good agreement with the results obtained by atomic absorption spectrometry (AAS).

  11. 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

  12. Quantum dots coated with molecularly imprinted polymer as fluorescence probe for detection of cyphenothrin.

    PubMed

    Ren, Xiaohui; Chen, Ligang

    2015-02-15

    A newly designed molecularly imprinted polymer (MIP) material was fabricated and successfully utilized as recognition element to develop a quantum dots (QDs) based MIP-coated composite for selective recognition of the template cyphenothrin. The MIP-coated QDs were characterized by fluorescence spectrophotometer, Fourier transform infrared spectroscopy, transmission electron microscope, dynamic light scattering and X-ray powder diffraction. The fluorescence of the coated QDs is quenched on loading the MIP with cyphenothrin, and the effect is much stronger for the MIP than for the non-imprinted polymer, which indicates the MIP could as a recognition template composite. This method can detect down to 9.0 nmol L(-1) of cyphenothrin in water, and a linear relationship has been obtained covering the concentration range of 0.1-80.0 μmol L(-1). The method has been used in the determination of cyphenothrin in water samples and gave recoveries in the range from 88.5% to 97.1% with relative standard deviations in the range of 3.1-6.2%. The present study provides a new and general strategy to fabricate inorganic-organic MIP-coated QDs with highly selective recognition ability in aqueous media and is desirable for chemical probe application.

  13. 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.

  14. Creating and virtually screening databases of fluorescently-labelled compounds for the discovery of target-specific molecular probes

    NASA Astrophysics Data System (ADS)

    Kamstra, Rhiannon L.; Dadgar, Saedeh; Wigg, John; Chowdhury, Morshed A.; Phenix, Christopher P.; Floriano, Wely B.

    2014-11-01

    Our group has recently demonstrated that virtual screening is a useful technique for the identification of target-specific molecular probes. In this paper, we discuss some of our proof-of-concept results involving two biologically relevant target proteins, and report the development of a computational script to generate large databases of fluorescence-labelled compounds for computer-assisted molecular design. The virtual screening of a small library of 1,153 fluorescently-labelled compounds against two targets, and the experimental testing of selected hits reveal that this approach is efficient at identifying molecular probes, and that the screening of a labelled library is preferred over the screening of base compounds followed by conjugation of confirmed hits. The automated script for library generation explores the known reactivity of commercially available dyes, such as NHS-esters, to create large virtual databases of fluorescence-tagged small molecules that can be easily synthesized in a laboratory. A database of 14,862 compounds, each tagged with the ATTO680 fluorophore was generated with the automated script reported here. This library is available for downloading and it is suitable for virtual ligand screening aiming at the identification of target-specific fluorescent molecular probes.

  15. Complementary optical and nuclear imaging of caspase-3 activity using combined activatable and radiolabeled multimodality molecular probe

    PubMed Central

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

    2010-01-01

    Based on the capability of modulating fluorescence intensity by specific molecular events, we have developed a new multimodal optical-nuclear molecular probe with complementary reporting strategies. The molecular probe (LS498) consists of DOTA for chelating a radionuclide, a near infrared fluorescent dye, and an efficient quencher dye. The two dyes were separated by a cleavable peptide substrate for caspase-3, a diagnostic enzyme that is upregulated in dying cells. LS498 was radiolabeled with 64Cu, a radionuclide used in positron emission tomography. In the native form, LS498 fluorescence was quenched until caspase-3 cleavage of the peptide substrate. Enzyme kinetics assay showed that LS498 was 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 was 10-fold less than control. Using radiolabeled 64Cu-LS498 in a controlled and localized in vivo model of caspase-3 activation, a time-dependent 5-fold NIR fluorescence enhancement was observed but radioactivity was the same 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. PMID:19725712

  16. Real-space imaging of molecular structure and chemical bonding by single-molecule inelastic tunneling probe.

    PubMed

    Chiang, Chi-lun; Xu, Chen; Han, Zhumin; Ho, W

    2014-05-23

    The arrangement of atoms and bonds in a molecule influences its physical and chemical properties. The scanning tunneling microscope can provide electronic and vibrational signatures of single molecules. However, these signatures do not relate simply to the molecular structure and bonding. We constructed an inelastic tunneling probe based on the scanning tunneling microscope to sense the local potential energy landscape of an adsorbed molecule with a carbon monoxide (CO)-terminated tip. The skeletal structure and bonding of the molecule are revealed from imaging the spatial variations of a CO vibration as the CO-terminated tip probes the core of the interactions between adjacent atoms. An application of the inelastic tunneling probe reveals the sharing of hydrogen atoms among multiple centers in intramolecular and extramolecular bonding.

  17. 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".

  18. Molecular imaging probes spy on the body's inner workings: miniaturized microscopes, microbubbles, 7- and 15-T scanners, diffusion-tensor MRI, and other molecular-imaging technologies are pushing molecular imaging into the future.

    PubMed

    Mertz, Leslie

    2013-01-01

    Molecular imaging is one of the hot-button areas within medical imaging. This technology employs imaging techniques in concert with molecular probes, or biomarkers, that together noninvasively spy on cellular function and molecular processes. In some cases, this technology may be able to detect the very earliest stages of diseases and eliminate them on the spot. This paper discusses how miniaturized microscopes, microbubbles, 7T and 15T scanners, diffusion-tensor MRI and other molecular imaging technologies are pushing molecular imaging into the future.

  19. 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

  20. 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.

  1. 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

  2. Cooling dynamics of an optically excited molecular probe in solution from femtosecond broadband transient absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Kovalenko, S. A.; Schanz, R.; Hennig, H.; Ernsting, N. P.

    2001-08-01

    The cooling of p-nitroaniline (PNA), dimethylamino-p-nitroaniline (DPNA) and trans-stilbene (t-stilbene) in solution is studied experimentally and theoretically. Using the pump-supercontinuum probe (PSCP) technique we observed the complete spectral evolution of hot absorption induced by femtosecond optical pumping. In t-stilbene the hot S1 state results from Sn→S1 internal conversion with 50 fs characteristic time. The time constant of intramolecular thermalization or intramolecular vibrational redistribution (IVR) in S1 is estimated as τIVR≪100 fs. In PNA and DPNA the hot ground state is prepared by S1→S0 relaxation with characteristic time 0.3-1.0 ps. The initial molecular temperature is 1300 K for PNA and 860 K for t-stilbene. The subsequent cooling dynamics (vibrational cooling) is deduced from the transient spectra by assuming: (i) a Gaussian shape for the hot absorption band, (ii) a linear dependence of its peak frequency νm and width square Γ2 on molecular temperature T. Within this framework we derive analytic expressions for the differential absorption signal ΔOD(T(t),ν). After calibration with stationary absorption spectra in a low temperature range, the solute temperature T(t) may be evaluated from a transient absorption experiment. For highly polar PNA and DPNA, T(t) is well described by a biexponential decay which reflects local heating effects, while for nonpolar t-stilbene the local heating is negligible and the cooling proceeds monoexponentially. To rationalize this behavior, an analytic model is developed, which considers energy flow from the hot solute to a first solvent shell and then to the bulk solvent. Fastest cooling is found for PNA in water: a time constant of 0.64 ps (68%) corresponds to solute-solvent energy transfer while 2.0 ps (32%) characterizes the cooling of the first shell. In aprotic solvents cooling is slower than in alcohols and slows down further with decreasing solvent polarity. This contrasts with nonpolar t

  3. Intravital imaging of mouse colonic adenoma using MMP-based molecular probes with multi-channel fluorescence endoscopy.

    PubMed

    Oh, Gyungseok; Yoo, Su Woong; Jung, Yebin; Ryu, Yeon-Mi; Park, Youngrong; Kim, Sang-Yeob; Kim, Ki Hean; Kim, Sungjee; Myung, Seung-Jae; Chung, Euiheon

    2014-05-01

    Intravital imaging has provided molecular, cellular and anatomical insight into the study of tumor. Early detection and treatment of gastrointestinal (GI) diseases can be enhanced with specific molecular markers and endoscopic imaging modalities. We present a wide-field multi-channel fluorescence endoscope to screen GI tract for colon cancer using multiple molecular probes targeting matrix metalloproteinases (MMP) conjugated with quantum dots (QD) in AOM/DSS mouse model. MMP9 and MMP14 antibody (Ab)-QD conjugates demonstrate specific binding to colonic adenoma. The average target-to-background (T/B) ratios are 2.10 ± 0.28 and 1.78 ± 0.18 for MMP14 Ab-QD and MMP9 Ab-QD, respectively. The overlap between the two molecular probes is 67.7 ± 8.4%. The presence of false negative indicates that even more number of targeting could increase the sensitivity of overall detection given heterogeneous molecular expression in tumors. Our approach indicates potential for the screening of small or flat lesions that are precancerous.

  4. Intravital imaging of mouse colonic adenoma using MMP-based molecular probes with multi-channel fluorescence endoscopy

    PubMed Central

    Oh, Gyungseok; Yoo, Su Woong; Jung, Yebin; Ryu, Yeon-Mi; Park, Youngrong; Kim, Sang-Yeob; Kim, Ki Hean; Kim, Sungjee; Myung, Seung-Jae; Chung, Euiheon

    2014-01-01

    Intravital imaging has provided molecular, cellular and anatomical insight into the study of tumor. Early detection and treatment of gastrointestinal (GI) diseases can be enhanced with specific molecular markers and endoscopic imaging modalities. We present a wide-field multi-channel fluorescence endoscope to screen GI tract for colon cancer using multiple molecular probes targeting matrix metalloproteinases (MMP) conjugated with quantum dots (QD) in AOM/DSS mouse model. MMP9 and MMP14 antibody (Ab)-QD conjugates demonstrate specific binding to colonic adenoma. The average target-to-background (T/B) ratios are 2.10 ± 0.28 and 1.78 ± 0.18 for MMP14 Ab-QD and MMP9 Ab-QD, respectively. The overlap between the two molecular probes is 67.7 ± 8.4%. The presence of false negative indicates that even more number of targeting could increase the sensitivity of overall detection given heterogeneous molecular expression in tumors. Our approach indicates potential for the screening of small or flat lesions that are precancerous. PMID:24877024

  5. Functional molecular lumino-materials to probe serum albumins: solid phase selective staining through noncovalent fluorescent labeling.

    PubMed

    Dey, Gourab; Gupta, Abhishek; Mukherjee, Trinetra; Gaur, Pankaj; Chaudhary, Abhishek; Mukhopadhyay, Subhra Kanti; Nandi, Chayan K; Ghosh, Subrata

    2014-07-09

    Selective staining of human serum albumin protein in gel electrophoresis over wide range of other protein(s) is extremely important because it contains more than 60% volume of serum fluid in human body. Given the nonexistence of suitable dye materials for selective staining of serum albumins in gel electrophoresis, we report a new class of easy synthesizable and low molecular weight staining agents based on 3-amino-N-alkyl-carbazole scaffold for selective staining of serum albumins in solid phase. A detailed structure-efficiency relationship (SER) study enabled us to develop two such potent functional molecular probes which stain both human and bovine serum albumin selectively in gel electrophoresis in the presence of other proteins and enzymes. The present gel staining process was found to be very simple and less time-consuming as compared to the conventional coomassie blue staining which in turn makes these probes a new class of serum albumin-specific staining materials in proteome research. Moreover, these molecular lumino-materials can detect serum albumins at subnanomolar level in the presence of broad spectrum of other proteins/enzymes in aqueous buffer (99.9% water, pH = 7.3) keeping the protein secondary structure intact. Our experimental and the docking simulation results show that these probes bind preferentially at 'binding site I' of both the serum proteins.

  6. Self-assembled gold nanoparticle molecular probes for detecting proteolytic activity in vivo

    PubMed Central

    Mu, C. Jenny; LaVan, David A.; Langer, Robert S.; Zetter, Bruce R.

    2010-01-01

    Target-activatable fluorogenic probes based on gold nanoparticles (AuNPs) functionalized with self-assembled heterogeneous monolayers of dye-labeled peptides and poly(ethylene glycol) have been developed to visualize proteolytic activity in vivo. A one-step synthesis strategy that allows simple generation of surface defined AuNP probe libraries is presented as a means of tailoring and evaluating probe characteristics for maximal fluorescence enhancement after protease activation. Optimal AuNP probes targeted to trypsin and urokinase-type plasminogen activator required the incorporation of a dark quencher to achieve 5 to 8-fold signal amplification. These probes exhibited extended circulation time in vivo and high image contrast in a mouse tumor model. PMID:20146506

  7. 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.

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

    PubMed

    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.

  9. Probing Conditions at Ionized/Molecular Gas Interfaces With High Resolution Near-Infrared Spectroscopy

    NASA Astrophysics Data System (ADS)

    Kaplan, Kyle Franklin

    2017-08-01

    Regions of star formation and star death in our Galaxy trace the cycle of gas and dust in the interstellar medium (ISM). Gas in dense molecular clouds collapses to form stars, and stars at the end of their lives return the gas that made up their outer layers back out into the Galaxy. Hot stars generate copious amounts of ultraviolet photons which interact with the surrounding medium and dominate the energetics, ionization state, and chemistry of the gas. The interface where molecular gas is being dissociated into neutral atomic gas by far-UV photons from a nearby hot source is called a photodissociation or photon-dominated region (PDR). PDRs are found primarily in star forming regions where O and B stars serve as the source of UV photons, and in planetary nebulae where the hot core of the dying star acts as the UV source. The main target of this dissertation is molecular hydrogen (H2), the most abundant molecule in the Universe, made from hydrogen formed during the Big Bang. H2 makes up the overwhelming majority of molecules found in the ISM and in PDRs. Far-UV radiation absorbed by H2 will excite an electron in the molecule. The molecule then either dissociates ( 10% of the time; Field et al. 1966) or decays into excited rotational and vibrational ("rovibrational") levels of the electronic ground state. These excited rovibrational levels then decay via a radiative cascade to the ground rovibrational state (v = 0, J = 0), giving rise to a large number of transitions observable in emission from the mid-IR to the optical (Black & van Dishoeck, 1987). These transitions provide an excellent probe of the excitation and conditions within the gas. These transitions are also observed in warm H2, such as in shocks, where collisions excite H2 to higher rovibrational levels. High resolution near-infrared spectroscopy, with its ability to see through dust, and avoid telluric absorption and emission, serves as an effective tool to detect emission from ions, atoms, and molecules

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

    PubMed Central

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

    2008-01-01

    Background 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 100 kb, careful probe selection and characterization are of paramount importance. Results 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 ~6 kb plasmid onto an unusually small, ~55 kb circular P1 molecule and the determination of the extent of overlap between P1 molecules homologous to the human NF-κB2 locus. Conclusion 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. PMID:19108707

  11. 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.

  12. 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.

  13. Origin and molecular organization of supernumerary chromosomes of Prochilodus lineatus (characiformes, prochilodontidae) obtained by DNA probes.

    PubMed

    Voltolin, Tatiana Aparecida; Laudicina, Alejandro; Senhorini, José Augusto; Bortolozzi, Jehud; Oliveira, Cláudio; Foresti, Fausto; Porto-Foresti, Fábio

    2010-12-01

    In Prochilodus lineatus B-chromosomes are visualized as reduced size extra elements identified as microchromosomes and are variable in morphology and number. We describe the specific total probe (B-chromosome probe) in P. lineatus obtained by chromosome microdissection and a whole genomic probe (genomic probe) from an individual without B-chromosome. The specific B-chromosome was scraped and processed to obtain DNA with amplification by DOP-PCR, and so did the genomic probe DNA. Fluorescence in situ hybridization using the B-chromosome probe labeled with dUTP-Tetramethyl-rhodamine and the genomic probe labeled with digoxigenin-FITC permitted to establish that in this species supernumerary chromosomes with varying number and morphology had different structure of chromatin when compared to that of the regular chromosomes or A complement, since only these extra elements were labeled in the metaphases. The present findings suggest that modifications in the chromatin structure of B-chromosomes to differentiate them from the A chromosomes could occur along their dispersion in the individuals of the population.

  14. Molecular basis of glucagon-like peptide 1 docking to its intact receptor studied with carboxyl-terminal photolabile probes.

    PubMed

    Chen, Quan; Pinon, Delia I; Miller, Laurence J; Dong, Maoqing

    2009-12-04

    The glucagon-like peptide 1 (GLP1) receptor is a member of Family B G protein-coupled receptors and represents an important drug target for type 2 diabetes. Despite recent solution of the structure of the amino-terminal domain of this receptor and that of several close family members, understanding of the molecular basis of natural ligand GLP1 binding to its intact receptor remains limited. The goal of this study was to explore spatial approximations between specific receptor residues within the carboxyl terminus of GLP1 and its receptor as normally docked. Therefore, we developed and characterized two high affinity, full-agonist photolabile GLP1 probes having sites for covalent attachment in positions 24 and 35. Both probes labeled the receptor specifically and saturably. Subsequent peptide mapping using chemical and proteinase cleavages of purified wild-type and mutant GLP1 receptor identified that the Arg(131)-Lys(136) segment at the juxtamembrane region of the receptor amino terminus contained the site of labeling for the position 24 probe, and the specific receptor residue labeled by this probe was identified as Glu(133) by radiochemical sequencing. Similarly, nearby residue Glu(125) within the same region of the receptor amino-terminal domain was identified as the site of labeling by the position 35 probe. These data represent the first direct demonstration of spatial approximation between GLP1 and its intact receptor as docked, providing two important constraints for the modeling of this interaction. This should expand our understanding of the molecular basis of natural agonist ligand binding to the GLP1 receptor and may be relevant to other family members.

  15. High Resolution PET Imaging Probe for the Detection, Molecular Characterization, and Treatment Monitoring of Prostate cancer

    DTIC Science & Technology

    2011-07-01

    4,5] extended with a probe as described in the following text. Within the MADEIRA collaboration a probe detector prototype was developed with a single...Acknowledgments The work was carried out within the Collaborative Project ‘‘ MADEIRA ’’ (www.madeira-project.eu), co-funded by the Eur- opean Commission through...VWWZ=!E𔄀,+@-=! %6-’&@,=!G2O;!! 3204 2010 IEEE Nuclear Science Symposium Conference Record M18-174 Report on the MADEIRA PET Probe Andrej Studen, Enrico

  16. 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

  17. Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes.

    PubMed

    Marras, Salvatore A E; Tyagi, Sanjay; Kramer, Fred Russell

    2006-01-01

    A number of formats for nucleic acid hybridization have been developed to identify DNA and RNA sequences that are involved in cellular processes and that aid in the diagnosis of genetic and infectious diseases. The introduction of hybridization probes with interactive fluorophore pairs has enabled the development of homogeneous hybridization assays for the direct identification of nucleic acids. A change in the fluorescence of these probes indicates the presence of a target nucleic acid, and there is no need to separate unbound probes from hybridized probes. The advantages of homogeneous hybridization assays are their speed and simplicity. In addition, homogeneous assays can be combined with nucleic acid amplification, enabling the detection of rare target nucleic acids. These assays can be followed in real time, providing quantitative determination of target nucleic acids over a broad range of concentrations.

  18. 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

  19. High Resolution PET Imaging Probe for the Detection, Molecular Characterization and Treatment Monitoring of Prostate Cancer

    DTIC Science & Technology

    2012-07-01

    Performance of the MADEIRA PET probe prototype. 2009 Nuclear Science Symposium Conference Record. p. 3111– 3115, 2009. 4. Cochran E, Clinthorne NH, Chesi E...Zontar D: Report on the MADEIRA PET probe. IEEE Nuclear Science Symposium Conference Record, p. 1755–1758, 2010. 11. Lacasta C, Clinthorne NH, Llosa...submillimeter regime at high detection efficiencies.ll rights reserved. e US DHHS NIH Grant R01 -1-0413, and the European 100 ( MADEIRA ). e). , et al

  20. Dansyl-naphthalimide dyads as molecular probes: effect of spacer group on metal ion binding properties.

    PubMed

    Shankar, Balaraman H; Ramaiah, Danaboyina

    2011-11-17

    Interaction of a few dansyl-naphthalimide conjugates 1a-e linked through polymethylene spacer groups with various metal ions was investigated through absorption, fluorescence, NMR, isothermal calorimetric (ITC), and laser flash photolysis techniques. The characteristic feature of these dyads is that they exhibit competing singlet-singlet energy transfer (SSET) and photoinduced electron transfer (PET) processes, both of which decrease with the increase in spacer length. Depending on the spacer group, these dyads interact selectively with divalent Cu(2+) and Zn(2+) ions, as compared to other mono- and divalent metal ions. Jobs plot analysis showed that these dyads form 2:3 complexes with Cu(2+) ions, while 1:1 complexes were observed with Zn(2+) ions. The association constants for the Zn(2+) and Cu(2+) complexes were determined and are found to be in the order 10(3)-10(5) M(-1). Irrespective of the length of the spacer group, these dyads interestingly act as fluorescence ratiometric molecular probes for Cu(2+) ions by altering the emission intensity of both dansyl and naphthalimide chromophores. In contrast, only the fluorescence intensity of the naphthalimide chromophore of the lower homologues (n = 1-3) was altered by Zn(2+) ions. (1)H NMR and ITC measurements confirmed the involvement of both sulfonamide and dimethylamine groups in the complexation with Cu(2+) ions, while only the latter group was involved with Zn(2+) ions. Laser excitation of the dyads 1a-e showed formation of a transient absorption which can be attributed to the radical cation of the naphthalimide chromophore, whereas only the triplet excited state of the dyads 1a-e was observed in the presence of Cu(2+) ions. Uniquely, the complexation of 1a-e with Cu(2+) ions affects both PET and SSET processes, while only the PET process was partially inhibited by Zn(2+) ions in the lower homologues (n = 1-3) and the higher homologues exhibited negligible changes in their emission properties. Our results

  1. 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.

  2. Ficoll and dextran vs. globular proteins as probes for testing glomerular permselectivity: effects of molecular size, shape, charge, and deformability.

    PubMed

    Venturoli, Daniele; Rippe, Bengt

    2005-04-01

    Polydisperse mixtures of dextran or Ficoll have been frequently used as molecular probes for studies of glomerular permselectivity because they are largely inert and not processed (reabsorbed) by the proximal tubules. However, dextrans are linear, flexible molecules, which apparently are hyperpermeable across the glomerular barrier. By contrast, the Ficoll molecule is almost spherical. Still, there is ample evidence that Ficoll fractional clearances (sieving coefficients) across the glomerular capillary wall (GCW) are markedly higher than those for neutral globular proteins of an equivalent in vitro Stokes-Einstein (SE) radius. Physical data, obtained by "crowding" experiments or measurements of intrinsic viscosity, suggest that the Ficoll molecule exhibits a rather open, deformable structure and thus deviates from an ideally hard sphere. This is also indicated from the relationship between (log) in vitro SE radius and (log) molecular weight (MW). Whereas globular proteins seem to behave in a way similar to hydrated hard spheres, polydisperse dextran and Ficoll exhibit in vitro SE radii that are much larger than those for compact spherical molecules of equivalent MW. For dextran, this can be partially explained by a high-molecular-size asymmetry. However, for Ficoll the explanation may be that the Ficoll molecule is more flexible (deformable) than are globular proteins. An increased compressibility of Ficoll and an increased deformability and size asymmetry for dextran may be the explanation for the fact that the permeability of the GCW is significantly higher when assessed using polysaccharides such as Ficoll or dextran compared with that obtained using globular proteins as molecular size probes. We suggest that molecular deformability, besides molecular size, shape, and charge, plays a crucial role in determining the glomerular permeability to molecules of different species.

  3. 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

  4. In silico evaluation of molecular probes for detection and identification of Ralstonia solanacearum and Clavibacter michiganensis subsp. sepedonicus.

    PubMed

    Arahal, David R; Llop, Pablo; Alonso, Manuel Pérez; López, María M

    2004-09-01

    Ralstonia solanacerum and Clavibacter michiganensis subsp. sepedonicus are the two most relevant bacterial pathogens of potato for which a large number of molecular diagnostic methods using specific DNA sequences have been developed. About one hundred oligonucleotides have been described and thoroughly tested experimentally. After having compiled and evaluated all these primers and probes in silico to check their specificity, many discrepancies were found. A detailed analysis permitted the recognition of different possible reasons for such discrepancies: sequencing errors in public sequences, wrong supposed specificity (sometimes due to more recent sequences than the oligonucleotides being evaluated) or even typing errors in the oligonucleotides. Although this study is an exercise about in silico evaluation using two potato bacterial pathogens as a model, the conclusions reflect not only information useful for phytopathologists but, in a broader scope, draw the main situations that can be found during an evaluation of probes, which can be surely found in other scenarios.

  5. 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.

  6. Built-in fields in nanodimensional organic ferroelectric-semiconductor heterostructures: The principal role of molecular probes

    NASA Astrophysics Data System (ADS)

    Lazarev, V. V.; Blinov, L. M.; Yudin, S. G.; Palto, S. P.

    2014-10-01

    The external and internal (built-in) macroscopic fields in a nanodimensional heterostructure consisting of organic ferroelectric and organic semiconductor layers between transparent (indium tin oxide) and semitransparent (aluminum) electrodes have been studied. The fields were measured using optical probe molecules in both the semiconductor layer (copper phthalocyanine, CuPc, with intrinsic specific features of the absorption spectrum) and the ferroelectric layer (poly(vinylidene fluoride)-trifluoroethylene copolymer) in which a molecular probe was introduced as a dopant (palladium tetraphenylporphyrin) possessing a characteristic spectrum. Local fields were measured using electroabsorption, followed by a recalculation in the macroscopic fields. It is established that the amplitude and direction of a macroscopic built-in field in the semiconductor can be controlled by changing the polarization of the heterostructure using pulses of external voltage applied to the heterostructure. This effect can be useful for increasing the efficiency of organic converters of solar radiation energy into electricity.

  7. 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

    2013-08-02

    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.

  8. 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

  9. Molecular dynamics simulations and Kelvin probe force microscopy to study of cholesterol-induced electrostatic nanodomains in complex lipid mixtures.

    PubMed

    Drolle, E; Bennett, W F D; Hammond, K; Lyman, E; Karttunen, M; Leonenko, Z

    2017-01-04

    The molecular arrangement of lipids and proteins within biomembranes and monolayers gives rise to complex film morphologies as well as regions of distinct electrical surface potential, topographical and electrostatic nanoscale domains. To probe these nanodomains in soft matter is a challenging task both experimentally and theoretically. This work addresses the effects of cholesterol, lipid composition, lipid charge, and lipid phase on the monolayer structure and the electrical surface potential distribution. Atomic force microscopy (AFM) was used to resolve topographical nanodomains and Kelvin probe force microscopy (KPFM) to resolve electrical surface potential of these nanodomains in lipid monolayers. Model monolayers composed of dipalmitoylphosphatidylcholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2-dioleoyl-sn-glycero-3-[phospho-rac-(3-lysyl(1-glycerol))] (DOPG), and cholesterol were studied. It is shown that cholesterol changes nanoscale domain formation, affecting both topography and electrical surface potential. The molecular basis for differences in electrical surface potential was addressed with atomistic molecular dynamics (MD). MD simulations are compared the experimental results, with 100 s of mV difference in electrostatic potential between liquid-disordered bilayer (Ld, less cholesterol and lower chain order) and a liquid-ordered bilayer (Lo, more cholesterol and higher chain order). Importantly, the difference in electrostatic properties between Lo and Ld phases suggests a new mechanism by which membrane composition couples to membrane function.

  10. Molecular dynamics simulations and Kelvin probe force microscopy to study of cholesterol-induced electrostatic nanodomains in complex lipid mixtures

    NASA Astrophysics Data System (ADS)

    Drolle, E.; Bennett, W. F. D.; Hammond, K.; Lyman, E.; Karttunen, M.; Leonenko, Z.

    The molecular arrangement of lipids and proteins within biomembranes and monolayers gives rise to complex film morphologies as well as regions of distinct electrical surface potential, topographical and electrostatic nanoscale domains. To probe these nanodomains in soft matter is a challenging task both experimentally and theoretically. This work addresses the effects of cholesterol, lipid composition, lipid charge, and lipid phase on the monolayer structure and the electrical surface potential distribution. Atomic Force Microscopy (AFM) was used to resolve topographical nanodomains and Kelvin Probe Force Microscopy (KPFM) to resolve electrical surface potential of these nanodomains in lipid monolayers. Model monolayers composed of dipalmitoylphosphatidylcholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2-dioleoyl-sn-glycero-3-[phospho-rac-(3-lysyl(1-glycerol))] (DOPG), sphingomyelin, and cholesterol were studied. It is shown that cholesterol changes nanoscale domain formation, affecting both topography and electrical surface potential. The molecular basis for differences in electrical surface potential was addressed with atomistic molecular dynamics (MD). MD simulations qualitatively match the experimental results, with 100s of mV difference in electrostatic potential between liquid-disordered bilayer (Ld, less cholesterol and lower chain order) and a liquid-ordered bilayer (Lo, more cholesterol and higher chain order). Importantly, the difference in electrostatic properties between Lo and Ld phases suggests a new mechanism by which membrane composition couples to membrane function.

  11. Direct probing of the surface ultrastructure and molecular interactions of dormant and germinating spores of Phanerochaete chrysosporium.

    PubMed

    Dufrêne, Y F; Boonaert, C J; Gerin, P A; Asther, M; Rouxhet, P G

    1999-09-01

    Atomic force microscopy (AFM) has been used to probe, under physiological conditions, the surface ultrastructure and molecular interactions of spores of the filamentous fungus Phanerochaete chrysosporium. High-resolution images revealed that the surface of dormant spores was uniformly covered with rodlets having a periodicity of 10 +/- 1 nm, which is in agreement with earlier freeze-etching measurements. In contrast, germinating spores had a very smooth surface partially covered with rough granular structures. Force-distance curve measurements demonstrated that the changes in spore surface ultrastructure during germination are correlated with profound modifications of molecular interactions: while dormant spores showed no adhesion with the AFM probe, germinating spores exhibited strong adhesion forces, of 9 +/- 2 nN magnitude. These forces are attributed to polysaccharide binding and suggested to be responsible for spore aggregation. This study represents the first direct characterization of the surface ultrastructure and molecular interactions of living fungal spores at the nanometer scale and offers new prospects for mapping microbial cell surface properties under native conditions.

  12. Photoinduced molecular chirality probed by ultrafast resonant X-ray spectroscopy

    DOE PAGES

    Rouxel, Jérémy R.; Kowalewski, Markus; Mukamel, Shaul

    2017-07-01

    Recently developed circularly polarized X-ray light sources can probe the ultrafast chiral electronic and nuclear dynamics through spatially localized resonant core transitions. Here, we present simulations of time-resolved circular dichroism signals given by the difference of left and right circularly polarized X-ray probe transmission following an excitation by a circularly polarized optical pump with the variable time delay. Application is made to formamide which is achiral in the ground state and assumes two chiral geometries upon optical excitation to the first valence excited state. Probes resonant with various K-edges (C, N, and O) provide different local windows onto the paritymore » breaking geometry change thus revealing the enantiomer asymmetry.« less

  13. DNA probes for monitoring dynamic and transient molecular encounters on live cell membranes

    NASA Astrophysics Data System (ADS)

    You, Mingxu; Lyu, Yifan; Han, Da; Qiu, Liping; Liu, Qiaoling; Chen, Tao; Sam Wu, Cuichen; Peng, Lu; Zhang, Liqin; Bao, Gang; Tan, Weihong

    2017-05-01

    Cells interact with the extracellular environment through molecules expressed on the membrane. Disruption of these membrane-bound interactions (or encounters) can result in disease progression. Advances in super-resolution microscopy have allowed membrane encounters to be examined, however, these methods cannot image entire membranes and cannot provide information on the dynamic interactions between membrane-bound molecules. Here, we show a novel DNA probe that can transduce transient membrane encounter events into readable cumulative fluorescence signals. The probe, which translocates from one anchor site to another, mimicking motor proteins, is realized through a toehold-mediated DNA strand displacement reaction. Using this probe, we successfully monitored rapid encounter events of membrane lipid domains using flow cytometry and fluorescence microscopy. Our results show a preference for encounters within the same lipid domains.

  14. Photoinduced molecular chirality probed by ultrafast resonant X-ray spectroscopy

    PubMed Central

    Rouxel, Jérémy R.; Kowalewski, Markus; Mukamel, Shaul

    2017-01-01

    Recently developed circularly polarized X-ray light sources can probe the ultrafast chiral electronic and nuclear dynamics through spatially localized resonant core transitions. We present simulations of time-resolved circular dichroism signals given by the difference of left and right circularly polarized X-ray probe transmission following an excitation by a circularly polarized optical pump with the variable time delay. Application is made to formamide which is achiral in the ground state and assumes two chiral geometries upon optical excitation to the first valence excited state. Probes resonant with various K-edges (C, N, and O) provide different local windows onto the parity breaking geometry change thus revealing the enantiomer asymmetry. PMID:28191484

  15. Modulating molecular level space proximity: a simple and efficient strategy to design structured DNA probes.

    PubMed

    Zheng, Jing; Li, Jishan; Gao, Xiaoxia; Jin, Jianyu; Wang, Kemin; Tan, Weihong; Yang, Ronghua

    2010-05-01

    To construct efficient oligonucleotide probes, specific nucleic acid is designed as a conformationally constrained form based on the formation of a Watson-Crick-based duplex. However, instability of Watson-Crick hydrogen bonds in a complex biological environment usually leads to high background signal from the probe itself and false positive signal caused by nonspecific binding. To solve this problem, we propose a way to restrict the labeled-dyes in a hydrophobic cavity of cyclodextrin. This bounding, which acts like extra base pairs to form the Watson-Crick duplex, achieves variation of level of space proximity of the two labels and thus the degree of conformational constraint. To demonstrate the feasibility of the design, a stem-containing oligonucleotide probe (P1) for DNA hybridization assay and a stemless one (P2) for protein detection were examined as models. Both oligonucleotides were doubly labeled with pyrene at the 5'- and 3'- ends, respectively. It is the cyclodextrin/pyrene inclusion interaction that allows modulating the degree of conformational constraints of P1 and P2 and thus their background signals and selectivity. Under the optimal conditions, the ratio of signal-to-background of P1/gamma-CD induced by 1.0 equiv target DNA is near 174, which is 4-fold higher than that in the absence of gamma-CD. In addition, the usage of gamma-CD shifts the melting temperature of P1 from 57 to 68 degrees C, which is reasonable for improving target-binding selectivity. This approach is simple in design, avoiding any variation of the stem's length and sequences. Furthermore, the strategy is generalizable which is suited for not only the stem-containing probe but also the linear probe with comparable sensitivity and selectivity to conventional structured DNA probes.

  16. Dual-Modality Activity-Based Probes as Molecular Imaging Agents for Vascular Inflammation.

    PubMed

    Withana, Nimali P; Saito, Toshinobu; Ma, Xiaowei; Garland, Megan; Liu, Changhao; Kosuge, Hisanori; Amsallem, Myriam; Verdoes, Martijn; Ofori, Leslie O; Fischbein, Michael; Arakawa, Mamoru; Cheng, Zhen; McConnell, Michael V; Bogyo, Matthew

    2016-10-01

    Macrophages are cellular mediators of vascular inflammation and are involved in the formation of atherosclerotic plaques. These immune cells secrete proteases such as matrix metalloproteinases and cathepsins that contribute to disease formation and progression. Here, we demonstrate that activity-based probes (ABPs) targeting cysteine cathepsins can be used in murine models of atherosclerosis to noninvasively image activated macrophage populations using both optical and PET/CT methods. The probes can also be used to topically label human carotid plaques demonstrating similar specific labeling of activated macrophage populations.

  17. Pump-Probe Fragmentation Action Spectroscopy: A Powerful Tool to Unravel Light-Induced Processes in Molecular Photocatalysts.

    PubMed

    Imanbaew, Dimitri; Lang, Johannes; Gelin, Maxim F; Kaufhold, Simon; Pfeffer, Michael G; Rau, Sven; Riehn, Christoph

    2017-05-08

    We present a proof of concept that ultrafast dynamics combined with photochemical stability information of molecular photocatalysts can be acquired by electrospray ionization mass spectrometry combined with time-resolved femtosecond laser spectroscopy in an ion trap. This pump-probe "fragmentation action spectroscopy" gives straightforward access to information that usually requires high purity compounds and great experimental efforts. Results of gas-phase studies on the electronic dynamics of two supramolecular photocatalysts compare well to previous findings in solution and give further evidence for a directed electron transfer, a key process for photocatalytic hydrogen generation. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Noninvasive depth estimation using tissue optical properties and a dual-wavelength fluorescent molecular probe in vivo

    PubMed Central

    Miller, Jessica P.; Maji, Dolonchampa; Lam, Jesse; Tromberg, Bruce J.; Achilefu, Samuel

    2017-01-01

    Translation of fluorescence imaging using molecularly targeted imaging agents for real-time assessment of surgical margins in the operating room requires a fast and reliable method to predict tumor depth from planar optical imaging. Here, we developed a dual-wavelength fluorescent molecular probe with distinct visible and near-infrared excitation and emission spectra for depth estimation in mice and a method to predict the optical properties of the imaging medium such that the technique is applicable to a range of medium types. Imaging was conducted at two wavelengths in a simulated blood vessel and an in vivo tumor model. Although the depth estimation method was insensitive to changes in the molecular probe concentration, it was responsive to the optical parameters of the medium. Results of the intra-tumor fluorescent probe injection showed that the average measured tumor sub-surface depths were 1.31 ± 0.442 mm, 1.07 ± 0.187 mm, and 1.42 ± 0.182 mm, and the average estimated sub-surface depths were 0.97 ± 0.308 mm, 1.11 ± 0.428 mm, 1.21 ± 0.492 mm, respectively. Intravenous injection of the molecular probe allowed for selective tumor accumulation, with measured tumor sub-surface depths of 1.28 ± 0.168 mm, and 1.50 ± 0.394 mm, and the estimated depths were 1.46 ± 0.314 mm, and 1.60 ± 0.409 mm, respectively. Expansion of our technique by using material optical properties and mouse skin optical parameters to estimate the sub-surface depth of a tumor demonstrated an agreement between measured and estimated depth within 0.38 mm and 0.63 mm for intra-tumor and intravenous dye injections, respectively. Our results demonstrate the feasibility of dual-wavelength imaging for determining the depth of blood vessels and characterizing the sub-surface depth of tumors in vivo. PMID:28663929

  19. 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.

  20. Detection of conformational changes in immunoglobulin G using isothermal titration calorimetry with low-molecular-weight probes.

    PubMed

    Rispens, Theo; Lakemond, Catriona M M; Derksen, Ninotska I L; Aalberse, Rob C

    2008-09-15

    Proteins for therapeutic use may contain small amounts of partially misfolded monomeric precursors to postproduction aggregation. To detect these misfolded proteins in the presence of an excess of properly folded protein, fluorescent probes such as 8-anilino-1-naphthalene sulfonate (ANS) are commonly used. We investigated the possibility of using isothermal titration calorimetry (ITC) to improve the detection of this type of conformational change using hydrophobic probes. As a case study, conformational changes in human polyclonal immunoglobulin G (IgG) were monitored by measuring the enthalpies of binding of ANS using ITC. Results were compared with those using fluorescence spectroscopy. IgG heated at 63 degrees C was used as a model system for "damaged" IgG. Heat-treated IgG can be detected already at levels below 5% with both ITC and fluorescence. However, ITC allows a much wider molar probe-to-protein ratio to be sampled. In particular, using reverse titration experiments (allowing high probe-to-protein ratios not available to fluorescence spectroscopy), an increase in the number of binding sites with a K(d)>10 mM was observed for heat-treated IgG, reflecting subtle changes in structure. Both ITC and fluorescence spectroscopy showed low background signals for native IgG. The nature of the background signals was not clear from the fluorescence measurements. However, further analysis of the ITC background signals shows that a fraction (8%) binds ANS with a dissociation constant of approximately 0.2 mM. Measurements were also carried out at pH 4.5. Precipitation of IgG was induced by ANS at concentrations above 0.5 mM, interfering with the ITC measurements. Instead, with the nonfluorescent probes 4-amino-1-naphthalene sulfonate and 1-naphthalene sulfonate, no precipitation is observed. These probes yield differences in the enthalpies of binding to heated and nonheated IgG similar to ANS. The data illustrate that ITC with low-molecular-weight probes is a versatile

  1. Use of molecular probes to detect parasites and retrotransposons in gypsy moths

    Treesearch

    John H. Werren; Thomas O' Dell

    1991-01-01

    Retrotransposon screen: Gypsy moth families containing straggling and nonstraggling individuals were divided into categories of straggling, medium, and nonstraggling individuals, from which DNA was extracted. Four families were tested by southern hybridization and probing with ribosomal sequences designed to detect R1 and R2 retrotransposon insertions. Results showed...

  2. Molecular probe dynamics reveals suppression of ice-like regions in strongly confined supercooled water.

    PubMed

    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.

  3. 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

  4. Simulation of field-induced molecular dissociation in atom-probe tomography: Identification of a neutral emission channel

    NASA Astrophysics Data System (ADS)

    Zanuttini, David; Blum, Ivan; Rigutti, Lorenzo; Vurpillot, François; Douady, Julie; Jacquet, Emmanuelle; Anglade, Pierre-Matthieu; Gervais, Benoit

    2017-06-01

    We investigate the dynamics of dicationic metal-oxide molecules under large electric-field conditions, on the basis of ab initio calculations coupled to molecular dynamics. Applied to the case of ZnO2 + in the field of atom probe tomography (APT), our simulation reveals the dissociation into three distinct exit channels. The proportions of these channels depend critically on the field strength and on the initial molecular orientation with respect to the field. For typical field strength used in APT experiments, an efficient dissociation channel leads to emission of neutral oxygen atoms, which escape detection. The calculated composition biases and their dependence on the field strength show remarkable consistency with recent APT experiments on ZnO crystals. Our work shows that bond breaking in strong static fields may lead to significant neutral atom production, and therefore to severe elemental composition biases in measurements.

  5. Synthesis and Properties of Molecular Probes for the Rescue Site on Mutant Cystic Fibrosis Transmembrane Conductance Regulator

    PubMed Central

    2011-01-01

    Cystic fibrosis is a genetic disease caused by mutations in the gene for the cystic fibrosis transmembrane conductance regulator (CFTR) protein. In vitro experiments have demonstrated that 4-methyl-2-(5-phenyl-1H-pyrazol-3-yl)phenol (VRT-532, 1) is able to partially restore the function of mutant CFTR proteins. To help elucidate the nature of the interactions between 1 and mutant CFTR, molecular probes based on the structure of 1 have been prepared. These include a photoreactive aryl azide derivative 11 and a fluorescent dansyl sulfonamide 15. Additionally, a method for hydrogen isotope exchange on 1 has been developed, which could be used for the incorporation of radioactive tritium. Using iodide efflux assays, the probe molecules have been demonstrated to modulate the activity of mutant CFTR in the same manner as 1. These probe molecules enable a number of biochemical experiments aimed at understanding how 1 rescues the function of mutant CFTR. This understanding can in turn aid in the design and development of more efficacious compounds which may serve as therapeutic agents in the treatment of cystic fibrosis. PMID:22074181

  6. Determination of mutated genes in the presence of wild-type DNA by using molecular beacons as probe

    NASA Astrophysics Data System (ADS)

    Zhang, Yonghua; Ai, Junjie; Gu, Qiaorong; Gao, Qiang; Qi, Honglan; Zhang, Chengxiao

    2017-03-01

    Low-abundance mutations in the presence of wild-type DNA can be determined using molecular beacon (MB) as probe. A MB is generally used as DNA probe because it can distinguish single-base mismatched target DNA from fully matched target DNA. However, the probe can not determine low-abundance mutations in the presence of wild-type DNA. In this study, this limitation is addressed by enhancing the stability of unpaired base-containing dsDNA with a hydrogen-bonding ligand, which was added after hybridization of the MB to the target DNA. The ligand formed hydrogen bonds with unpaired bases and stabilized the unpaired base-containing dsDNA if target DNA is mutated one. As a result, more MBs were opened by the mutant genes in the presence of the ligand and a further increase in the fluorescence intensity was obtained. By contrast, fluorescence intensity did not change if target DNA is wild-type one. Consequent increase in the fluorescence intensity of the MB was regarded as a signal derived from mutant genes. The proposed method was applied in synthetic template systems to determine point mutation in DNA obtained from PCR analysis. The method also allows rapid and simple discrimination of a signal if it is originated in the presence of mutant gene or alternatively by a lower concentration of wild gene.

  7. Molecular probes for the detection and identification of ichthyotoxic marine microalgae of the genus Pseudochattonella (Dictyochophyceae, Ochrophyta).

    PubMed

    Dittami, Simon M; Riisberg, Ingvild; Edvardsen, Bente

    2013-10-01

    Phytoflagellates of the genus Pseudochattonella (Dictyochophyceae, Ochrophyta) form blooms in marine coastal waters in northern Europe, Japan, and New Zealand that at times cause fish kills with severe losses for the aquaculture industry. The aim of this study was to develop molecular probes for the detection and identification of Pseudochattonella at the genus and species level. A variety of probes were developed and applied to either dot blot hybridization, (q)PCR, or microarray format. In the dot blot hybridization assay, five different oligonucleotide probes targeting the small subunit (SSU) rDNA were tested against DNA from 18 microalgal strains and shown to be specific to the genus Pseudochattonella. A genus-specific PCR assay was developed by identifying an appropriate primer pair in the SSU-internal transcribed spacer 1 (ITS1) rDNA region. Its specificity was tested by screening against both target and non-target strains, and the assay was used to confirm the presence or absence of Pseudochattonella species in environmental samples. In order to distinguish between the two species of the genus, two PCR primer pairs each biased towards one of the species were designed in the large subunit (LSU) rDNA D1 domain and used for quantitative real-time PCR. Five selected probes (three SSU and two LSU rDNA) were adapted for the use on microarrays and included on a prototype multi-species microarray for the detection of harmful algae ( http://www.midtal.com ). Finally, microarrays and qPCR were used for the monthly monitoring of a sampling site in outer Oslofjorden during a 1-year period. Members of Pseudochattonella are difficult to identify by light microscopy in Lugol's preserved samples, and the two species Pseudochattonella verruculosa and Pseudochattonella farcimen can be morphologically distinguished only by transmission electron microscopy. The molecular probes designed in this study will be a valuable asset to microscopical detection methods in the monitoring

  8. Turbulence in molecular clouds - A new diagnostic tool to probe their origin

    NASA Technical Reports Server (NTRS)

    Canuto, V. M.; Battaglia, A.

    1985-01-01

    A method is presented to uncover the instability responsible for the type of turbulence observed in molecular clouds and the value of the physical parameters of the 'placental medium' from which turbulence originated. The method utilizes the observational relation between velocities and sizes of molecular clouds, together with a recent model for large-scale turbulence (constructed by Canuto and Goldman, 1985).

  9. 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

  10. Detection of DNA damage by using hairpin molecular beacon probes and graphene oxide.

    PubMed

    Zhou, Jie; Lu, Qian; Tong, Ying; Wei, Wei; Liu, Songqin

    2012-09-15

    A hairpin molecular beacon tagged with carboxyfluorescein in combination with graphene oxide as a quencher reagent was used to detect the DNA damage by chemical reagents. The fluorescence of molecular beacon was quenched sharply by graphene oxide; while in the presence of its complementary DNA the quenching efficiency decreased because their hybridization prevented the strong adsorbability of molecular beacon on graphene oxide. If the complementary DNA was damaged by a chemical reagent and could not form intact duplex structure with molecular beacon, more molecular beacon would adsorb on graphene oxide increasing the quenching efficiency. Thus, damaged DNA could be detected based on different quenching efficiencies afforded by damaged and intact complementary DNA. The damage effects of chlorpyrifos-methyl and three metabolites of styrene such as mandelieaeids, phenylglyoxylieaeids and epoxystyrene on DNA were studied as models. The method for detection of DNA damage was reliable, rapid and simple compared to the biological methods. Copyright © 2012 Elsevier B.V. All rights reserved.

  11. Lithium naphthalocyanine as a new molecular radical probe for electron paramagnetic resonance oximetry

    NASA Astrophysics Data System (ADS)

    Manivannan, Ayyakkannu; Yanagi, Hisao; Ilangovan, Govindasamy; Kuppusamy, Periannan

    2001-08-01

    A new lithium naphthalocyanine dye aggregate [Li 2Nc][LiNc] is reported as a potential electron paramagnetic resonance (EPR) oximetry probe for accurate measurement of oxygen concentration in biological systems. The Li 2Nc is diamagnetic; however, the LiNc molecule has an unpaired electron and hence is paramagnetic. The aggregate shows a strong and single line EPR signal that is non-saturating at normal EPR power levels. An oxygen-dependent peak-to-peak EPR spectral width ranging from 0.51 G (at pO 2: 0 mmHg) to 26.2 G (at pO 2: 760 mmHg) has been observed. The application of this probe has been demonstrated in the measurement of arterial and venous oxygen tensions in a rat.

  12. 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

  13. 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.

  14. Design, development, and use of molecular primers and probes for the detection of Gluconacetobacter species in the pink sugarcane mealybug.

    PubMed

    Franke-Whittle, Ingrid H; O'Shea, Michael G; Leonard, Graham J; Sly, Lindsay I

    2005-07-01

    Molecular tools for the species-specific detection of Gluconacetobacter sacchari, Gluconacetobacter diazotrophicus, and Gluconacetobacter liquefaciens from the pink sugarcane mealybug (PSMB) Saccharicoccus sacchari Cockerell (Homiptera: Pseudococcidae) were developed and used in polymerase chain reactions (PCR) and in fluorescence in situ hybridizations (FISH) to better understand the microbial diversity and the numerical significance of the acetic acid bacteria in the PSMB microenvironment. The presence of these species in the PSMB occurred over a wide range of sites, but not in all sites in sugarcane-growing areas of Queensland, Australia, and was variable over time. Molecular probes for use in FISH were also designed for the three acetic acid bacterial species, and shown to be specific only for the target species. Use of these probes in FISH of "squashed" whole mealybugs indicated that these acetic acid bacteria species represent only a small proportion of the microbial population of the PSMB. Despite the detection of Glac. sacchari, Glac. diazotrophicus, and Glac. liquefaciens by PCR from different mealybugs isolated at various times and from various sugarcane-growing areas in Queensland, Australia, these bacteria do not appear to be significant commensals in the PSMB environment.

  15. Specific Recognition and Detection of MRSA Based on Molecular Probes Comprised of Lytic Phage and Antibody

    DTIC Science & Technology

    2011-03-29

    For this purpose we use a newly isolated Saureus bacteriophage with a wide spectrum of hosts (including MRSA strains) together with monoclonal...with two parallel channels. One channel will have a Saureus bacteriophage monolayer as a sensor probe, while the sensor of another channel will be...covered with PBP 2a specific antibodies. Consequently, one channel will identify Saureus bacteria, while another one will be sensitive to the

  16. Specific tracking of xylan using fluorescent-tagged carbohydrate-binding module 15 as molecular probe.

    PubMed

    Khatri, Vinay; Hébert-Ouellet, Yannick; Meddeb-Mouelhi, Fatma; Beauregard, Marc

    2016-01-01

    Xylan has been identified as a physical barrier which limits cellulose accessibility by covering the outer surface of fibers and interfibrillar space. Therefore, tracking xylan is a prerequisite for understanding and optimizing lignocellulosic biomass processes. In this study, we developed a novel xylan tracking approach using a two-domain probe called OC15 which consists of a fusion of Cellvibrio japonicus carbohydrate-binding domain 15 with the fluorescent protein mOrange2. The new probe specifically binds to xylan with an affinity similar to that of CBM15. The sensitivity of the OC15-xylan detection approach was compared to that of standard methods such as X-ray photoelectron spectroscopy (XPS) and chemical composition analysis (NREL/TP-510-42618). All three approaches were used to analyze the variations of xylan content of kraft pulp fibers. XPS, which allows for surface analysis of fibers, did not clearly indicate changes in xylan content. Chemical composition analysis responded to the changes in xylan content, but did not give any specific information related to the fibers surface. Interestingly, only the OC15 probe enabled the highly sensitive detection of xylan variations at the surface of kraft pulp fibers. At variance with the other methods, the OC15 probe can be used in a high throughput format. We developed a rapid and high throughput approach for the detection of changes in xylan exposure at the surface of paper fibers. The introduction of this method into the lignocellulosic biomass-based industries should revolutionize the understanding and optimization of most wood biomass processes.

  17. 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.

  18. Molecular Probes for Imaging the Sigma-2 Receptor: In Vitro and In Vivo Imaging Studies.

    PubMed

    Zeng, Chenbo; McDonald, Elizabeth S; Mach, Robert H

    2017-02-08

    The sigma-2 (σ2) receptor has been validated as a biomarker of the proliferative status of solid tumors. Therefore, radiotracers having a high affinity and high selectivity for σ2 receptors have the potential to assess the proliferative status of human tumors using noninvasive imaging techniques such as Positron Emission Tomography (PET). Since the σ2 receptor has not been cloned, the current knowledge of this receptor has relied on receptor binding studies with the radiolabeled probes and investigation of the effects of the σ2 receptor ligands on tumor cells. The development of the σ2 selective fluorescent probes has proven to be useful for studying subcellular localization and biological functions of the σ2 receptor, for revealing pharmacological properties of the σ2 receptor ligands, and for imaging cell proliferation. Preliminary clinical imaging studies with [(18)F]ISO-1, a σ2 receptor probe, have shown promising results in cancer patients. However, the full utility of imaging the σ2 receptor status of solid tumors in the diagnosis and prediction of cancer therapeutic response will rely on elucidation of the functional role of this protein in normal and tumor cell biology.

  19. Molecular beacon probes-base multiplex NASBA Real-time for detection of HIV-1 and HCV.

    PubMed

    Mohammadi-Yeganeh, S; Paryan, M; Mirab Samiee, S; Kia, V; Rezvan, H

    2012-06-01

    Developed in 1991, nucleic acid sequence-based amplification (NASBA) has been introduced as a rapid molecular diagnostic technique, where it has been shown to give quicker results than PCR, and it can also be more sensitive. This paper describes the development of a molecular beacon-based multiplex NASBA assay for simultaneous detection of HIV-1 and HCV in plasma samples. A well-conserved region in the HIV-1 pol gene and 5'-NCR of HCV genome were used for primers and molecular beacon design. The performance features of HCV/HIV-1 multiplex NASBA assay including analytical sensitivity and specificity, clinical sensitivity and clinical specificity were evaluated. The analysis of scalar concentrations of the samples indicated that the limit of quantification of the assay was <1000 copies/ml for HIV-1 and <500 copies/ml for HCV with 95% confidence interval. Multiplex NASBA assay showed a 98% sensitivity and 100% specificity. The analytical specificity study with BLAST software demonstrated that the primers do not attach to any other sequences except for that of HIV-1 or HCV. The primers and molecular beacon probes detected all HCV genotypes and all major variants of HIV-1. This method may represent a relatively inexpensive isothermal method for detection of HIV-1/HCV co-infection in monitoring of patients.

  20. Freezing of Molecular Motions Probed by Cryogenic Magic Angle Spinning NMR.

    PubMed

    Concistrè, Maria; Carignani, Elisa; Borsacchi, Silvia; Johannessen, Ole G; Mennucci, Benedetta; Yang, Yifeng; Geppi, Marco; Levitt, Malcolm H

    2014-02-06

    Cryogenic magic angle spinning makes it possible to obtain the NMR spectra of solids at temperatures low enough to freeze out most molecular motions. We have applied cryogenic magic angle spinning NMR to a crystalline small-molecule solid (ibuprofen sodium salt), which displays a variety of molecular dynamics. Magic angle (13)C NMR spectra are shown for a wide range of temperatures, including in the cryogenic regime down to 20 K. The hydrophobic and hydrophilic regions of the molecular structure display different behavior in the cryogenic regime, with the hydrophilic region remaining well-structured, while the hydrophobic region exhibits a broad frozen conformational distribution.

  1. 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.

  2. Measurement of molecular binding using the Brownian motion of magnetic nanoparticle probes

    NASA Astrophysics Data System (ADS)

    Rauwerdink, Adam M.; Weaver, John B.

    2010-01-01

    Molecular binding is important in many venues including antibody binding for diagnostic and therapeutic agents and pharmaceutical function. We demonstrate that a method of measuring nanoparticle Brownian motion, termed magnetic spectroscopy of nanoparticle Brownian motion (MSB), can be used to monitor molecular binding and the bound fraction. It is plausible that MSB can be used to measure binding in vivo because the same signal has been used to image nanoparticles in nanogram quantities in vivo.

  3. Probing Molecular Mechanisms of the Hsp90 Chaperone: Biophysical Modeling Identifies Key Regulators of Functional Dynamics

    PubMed Central

    Dixit, Anshuman; Verkhivker, Gennady M.

    2012-01-01

    Deciphering functional mechanisms of the Hsp90 chaperone machinery is an important objective in cancer biology aiming to facilitate discovery of targeted anti-cancer therapies. Despite significant advances in understanding structure and function of molecular chaperones, organizing molecular principles that control the relationship between conformational diversity and functional mechanisms of the Hsp90 activity lack a sufficient quantitative characterization. We combined molecular dynamics simulations, principal component analysis, the energy landscape model and structure-functional analysis of Hsp90 regulatory interactions to systematically investigate functional dynamics of the molecular chaperone. This approach has identified a network of conserved regions common to the Hsp90 chaperones that could play a universal role in coordinating functional dynamics, principal collective motions and allosteric signaling of Hsp90. We have found that these functional motifs may be utilized by the molecular chaperone machinery to act collectively as central regulators of Hsp90 dynamics and activity, including the inter-domain communications, control of ATP hydrolysis, and protein client binding. These findings have provided support to a long-standing assertion that allosteric regulation and catalysis may have emerged via common evolutionary routes. The interaction networks regulating functional motions of Hsp90 may be determined by the inherent structural architecture of the molecular chaperone. At the same time, the thermodynamics-based “conformational selection” of functional states is likely to be activated based on the nature of the binding partner. This mechanistic model of Hsp90 dynamics and function is consistent with the notion that allosteric networks orchestrating cooperative protein motions can be formed by evolutionary conserved and sparsely connected residue clusters. Hence, allosteric signaling through a small network of distantly connected residue clusters

  4. Ultrafast laser-probing spectroscopy for studying molecular structure of protein aggregates.

    PubMed

    Jung, Huihun; Szwejkowski, Chester J; Pena-Francesch, Abdon; Tomko, John A; Allen, Benjamin; Özdemir, Şahin Kaya; Hopkins, Patrick; Demirel, Melik C

    2017-03-09

    We report the development of a new technique to screen protein aggregation based on laser-probing spectroscopy with sub-picosecond resolution. Protein aggregation is an important topic for materials science, fundamental biology as well as clinical studies in neurodegenerative diseases and translation studies in biomaterials engineering. However, techniques to study protein aggregation and assembly are limited to infrared spectroscopy, fluorescent assays, immunostaining, or functional assays among others. Here, we report a new technique to characterize protein structure-property relationship based on ultrafast laser-probing spectroscopy. First, we show theoretically that the temperature dependence of the refractive index of a protein is correlated to its crystallinity. Then, we performed time-domain thermo-transmission experiments on purified semi-crystalline proteins, both native and recombinant (i.e., silk and squid ring teeth), and also on intact E. coli cells bearing overexpressed recombinant protein. Our results demonstrate, for the first time, relative quantification of crystallinity in real time for protein aggregates. Our approach can potentially be used for screening an ultra-large number of proteins in vivo. Using this technique, we could answer many fundamental questions in structural protein research, such as the underlying sequence-structure relationship for protein assembly and aggregation.

  5. Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study.

    PubMed

    do Canto, António M T M; Robalo, João R; Santos, Patrícia D; Carvalho, Alfredo J Palace; Ramalho, J P Prates; Loura, Luís M S

    2016-11-01

    Fluorescence spectroscopy and microscopy have been utilized as tools in membrane biophysics for decades now. Because phospholipids are non-fluorescent, the use of extrinsic membrane probes in this context is commonplace. Among the latter, 1,6-diphenylhexatriene (DPH) and its trimethylammonium derivative (TMA-DPH) have been extensively used. It is widely believed that, owing to its additional charged group, TMA-DPH is anchored at the lipid/water interface and reports on a bilayer region that is distinct from that of the hydrophobic DPH. In this study, we employ atomistic MD simulations to characterize the behavior of DPH and TMA-DPH in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and POPC/cholesterol (4:1) bilayers. We show that although the dynamics of TMA-DPH in these membranes is noticeably more hindered than that of DPH, the location of the average fluorophore of TMA-DPH is only ~3-4Å more shallow than that of DPH. The hindrance observed in the translational and rotational motions of TMA-DPH compared to DPH is mainly not due to significant differences in depth, but to the favorable electrostatic interactions of the former with electronegative lipid atoms instead. By revealing detailed insights on the behavior of these two probes, our results are useful both in the interpretation of past work and in the planning of future experiments using them as membrane reporters. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Probing the molecular interaction of triazole fungicides with human serum albumin by multispectroscopic techniques and molecular modeling.

    PubMed

    Zhang, Jing; Zhuang, Shulin; Tong, Changlun; Liu, Weiping

    2013-07-31

    Triazole fungicides, one category of broad-spectrum fungicides, are widely applied in agriculture and medicine. The extensive use leads to many residues and casts potential detrimental effects on aquatic ecosystems and human health. After exposure of the human body, triazole fungicides may penetrate into the bloodstream and interact with plasma proteins. Whether they could have an impact on the structure and function of proteins is still poorly understood. By using multispectroscopic techniques and molecular modeling, the interaction of several typical triazole fungicides with human serum albumin (HSA), the major plasma protein, was investigated. The steady-state and time-resolved fluorescence spectra manifested that static type, due to complex formation, was the dominant mechanism for fluorescence quenching. Structurally related binding modes speculated by thermodynamic parameters agreed with the prediction of molecular modeling. For triadimefon, hydrogen bonding with Arg-218 and Arg-222 played an important role, whereas for imazalil, myclobutanil, and penconazole, the binding process was mainly contributed by hydrophobic and electrostatic interactions. Via alterations in three-dimensional fluorescence and circular dichroism spectral properties, it was concluded that triazoles could induce slight conformational and some microenvironmental changes of HSA. It is anticipated that these data can provide some information for possible toxicity risk of triazole fungicides to human health and be helpful in reinforcing the supervision of food safety.

  7. Probing the Molecular Ordering and Thermal Stability of Azopolymer Layer-by-Layer Films by Second-Harmonic Generation.

    PubMed

    Silva, Heurison S; Miranda, Paulo B

    2016-10-04

    Polyelectrolyte layer-by-layer (LbL) films have many applications, but several parameters and procedures during film fabrication determine their morphology and molecular arrangement, with important practical consequences. Here we have used optical second-harmonic generation (SHG) to investigate the molecular ordering of LbL films containing the anionic azopolymer PS-119 and the cationic polyelectrolyte PAH. We show that spontaneous drying leads to laterally homogeneous and isotropic films, while the opposite occurs for nitrogen-flow drying. The effect of film thickness and pH of the assembling/rinsing solutions on the molecular ordering was also investigated. The optical nonlinearity tends to significantly decrease for thicker films (∼10 bilayers), and a slight alternation of SHG intensity for films with odd or even number of layers (complete vs incomplete bilayers) was also observed, which results from the reorientation of azopolymer groups in the last layer after adsorption of an additional PAH layer. We propose a qualitative electrostatic model to explain the pH dependence of film growth and azopolymer orientation, which is based on changes of the charge density of the substrate and PAH and on different ionic screening of electrostatic interactions at various pH values. We also found that the nonlinear response presents a gradual and significant reduction upon heating, which is inconsistent with a glass transition temperature for these ultrathin LbL films. The thermal stability is improved with a combination of low ionic strength and higher charge density of the polyelectrolytes and substrate, which promotes better interlayer complexation. The SHG signal is recovered upon cooling, although for some conditions the molecular arrangement became anisotropic after a heating/cooling cycle. Such detailed information about the structural order of thin nonlinear optical azopolymer LbL films demonstrates that SHG is a powerful technique to probe the film structure at

  8. Probing structure-nanoaggregation relations of polyaromatic surfactants: a molecular dynamics simulation and dynamic light scattering study.

    PubMed

    Teklebrhan, Robel B; Ge, Lingling; Bhattacharjee, Subir; Xu, Zhenghe; Sjöblom, Johan

    2012-05-24

    Four synthetic perylene bisimide-based polyaromatic (PA) surfactants with a structural or functional group difference in their attached hydrophilic/hydrophobic substituent side chains were used to probe structure-nanoaggregation relations in organic media by molecular dynamics simulations and dynamic light scattering. The results from the simulated radial distribution functions and light scattering experiments indicate that variation in the structure of side chains and polarity of functional groups leads to significant variations in molecular association, dynamics of molecular nanoaggregation and structure of nanoaggregates. The aggregates of PA surfactant molecules grow to much larger sizes in heptane than in toluene. The aromatic solvent is shown to hinder molecular association by weakening π-π stacking, demonstrating the control of molecular aggregation by tuning solvent properties. In aliphatic solvent, the aggregates formed from PA surfactants of aliphatic alkyl groups and phenylalanine derivatives as a side chain usually have a higher solvent accessible surface area to accessible volume ratio (SASA:AV) than that of tryptophan derivatives in their side chains. PA surfactants with an aliphatic functional group in both side chains does not form polyaromatic π-π stacking (T-stacking) due to its strong steric hindrance in both solvents. Depending on the nature of the side chains attached, various stacking distributions, aggregation sizes, and SASA:AV ratios were obtained. In PA surfactant nanoaggregates, all of the solvent molecules were found to be excluded from the interstices of the stacked polyaromatic cores, regardless of whether the solvent molecules are aliphatic or aromatic. Although the change in the structure of side chain substituent in polyaromatic surfactants has a negligible impact on their self-diffusivity, it can strongly influence their intermolecular interactions, leading to different aggregate diffusion coefficients.

  9. Spitzer spectral line mapping of interstellar shock waves: probing the physics and chemistry of shocked molecular clouds

    NASA Astrophysics Data System (ADS)

    Neufeld, David; Banhidi, Zita; Bergin, Ted; Giannini, Teresa; Guesten, Rolf; Kaufman, Michael; Liseau, Rene; Melnick, Gary; Nisini, Brunella; Philipp, Sabine; Tolls, Volker

    2007-05-01

    We propose to carry out a comprehensive, spectroscopic imaging study of interstellar shock waves in molecular clouds, in which the IRS instrument will be used to obtain spectral line maps with complete wavelength coverage over the 5.2 to 37 micron spectral region and at the highest spectral resolution achievable with IRS. By observing, in their entirety, five protostellar outflows with diverse properties, and two shocked molecular clumps within the supernova remnant IC433, we will probe the physics and chemistry of interstellar shock waves in a wide variety of environments. All the sources that we propose to observe are also be targeted for spectroscopic observations in Guaranteed Time Key Projects of the Herschel Space Observatory, providing an important synergy between the mid-IR spectroscopy that is possible with Spitzer and the far-IR and submillimeter spectroscopy to be carried out by Herschel. The wavelength range covered by Spitzer/IRS provides access to 15 fine structure transitions of NeII, NeIII, SiII, PII, SI, SII, ClII, FeII, and FeIII; the S(0) through S(7) pure rotational lines of molecular hydrogen; the R(3) and R(4) transitions hydrogen deuteride (HD); several rotational transitions of water vapor; and the 6.2, 7.7, 8.6 and 11.3 micron PAH emission bands; all which have been detected in one or more sources that we have observed previously. Analysis of the resultant data will provide a wealth of information that will constitute an important legacy to interstellar medium science, probing - among other things - (1) the H2 ortho-to-para ratio, a valuable probe of the thermal history of the gas; (2) the HD abundance, from which the gas-phase D/H ratio can be determined ; (3) the water abundance, a key parameter that determines thermal balance in the shocked material; (4) the relative distribution of gas that has been heated by fast dissociative shocks and by slower non-dissociative shocks.

  10. Dynamical transition in molecular glasses and proteins observed by spin relaxation of nitroxide spin probes and labels

    NASA Astrophysics Data System (ADS)

    Golysheva, Elena A.; Shevelev, Georgiy Yu.; Dzuba, Sergei A.

    2017-08-01

    In glassy substances and biological media, dynamical transitions are observed in neutron scattering that manifests itself as deviations of the translational mean-squared displacement, , of hydrogen atoms from harmonic dynamics. In biological media, the deviation occurs at two temperature intervals, at ˜100-150 K and at ˜170-230 K, and it is attributed to the motion of methyl groups in the former case and to the transition from harmonic to anharmonic or diffusive motions in the latter case. In this work, electron spin echo (ESE) spectroscopy—a pulsed version of electron paramagnetic resonance—is applied to study the spin relaxation of nitroxide spin probes and labels introduced in molecular glass former o-terphenyl and in protein lysozyme. The anisotropic contribution to the rate of the two-pulse ESE decay, ΔW, is induced by spin relaxation appearing because of restricted orientational stochastic molecular motion; it is proportional to <α2>τc, where <α2> is the mean-squared angle of reorientation of the nitroxide molecule around the equilibrium position and τc is the correlation time of reorientation. The ESE time window allows us to study motions with τc < 10-7 s. For glassy o-terphenyl, the <α2>τc temperature dependence shows a transition near 240 K, which is in agreement with the literature data on . For spin probes of essentially different size, the obtained data were found to be close, which evidences that motion is cooperative, involving a nanocluster of several neighboring molecules. For the dry lysozyme, the <α2>τc values below 260 K were found to linearly depend on the temperature in the same way as it was observed in neutron scattering for . As spin relaxation is influenced only by stochastic motion, the harmonic motions seen in ESE must be overdamped. In the hydrated lysozyme, ESE data show transitions near 130 K for all nitroxides, near 160 K for the probe located in the hydration layer, and near 180 K for the label in the

  11. Probes of turbulent driving mechanisms in molecular clouds from fluctuations in synchrotron intensity

    NASA Astrophysics Data System (ADS)

    Herron, C. A.; Federrath, C.; Gaensler, B. M.; Lewis, G. F.; McClure-Griffiths, N. M.; Burkhart, Blakesley

    2017-04-01

    Previous studies have shown that star formation depends on the driving of molecular cloud turbulence, and differences in the driving can produce an order of magnitude difference in the star formation rate. The turbulent driving is characterized by the parameter ζ, with ζ = 0 for compressive, curl-free driving (e.g. accretion or supernova explosions), and ζ = 1 for solenoidal, divergence-free driving (e.g. Galactic shear). Here we develop a new method to measure ζ from observations of synchrotron emission from molecular clouds. We calculate statistics of mock synchrotron intensity images produced from magnetohydrodynamic simulations of molecular clouds, in which the driving was controlled to produce different values of ζ. We find that the mean and standard deviation of the log-normalized synchrotron intensity are sensitive to ζ, for values of ζ between 0 (curl-free driving) and 0.5 (naturally mixed driving). We quantify the dependence of zeta on the direction of the magnetic field relative to the line of sight. We provide best-fitting formulae for ζ in terms of the log-normalized mean and standard deviation of synchrotron intensity, with which ζ can be determined for molecular clouds that have similar Alfvénic Mach number to our simulations. These formulae are independent of the sonic Mach number. Signal-to-noise ratios larger than 5, and angular resolutions smaller than 5 per cent of the cloud diameter, are required to apply these formulae. Although there are no firm detections of synchrotron emission from molecular clouds, by combining Green Bank Telescope and Very Large Array observations it should be possible to detect synchrotron emission from molecular clouds, thereby constraining the value of ζ.

  12. A differential ICT based molecular probe for multi-ions and multifunction logic circuits.

    PubMed

    Luxami, Vijay; Kumar, Subodh

    2012-04-21

    This paper presents anthraquinone and benzimidazole based hybrid molecular architect as the state of the art for multifunctional molecular logic circuits. The moleculator exhibits differential output behavior towards F(-), Zn(2+) and Cu(2+) ions to provide opportunities for elaboration of XOR, INHIBIT, XNOR, AND, OR, NOR, logic functions and their integrated logic functions half-adder, half-subtractor and comparator within a single molecule. These integral logic functions can be reprogrammed by self-annihilation or by another additional input in the same cell. This single molecule behaves uniquely where different logic functions can be operated and reset by using different inputs and outputs.

  13. Carbon-fiber tips for scanning probe microscopes and molecular electronics experiments.

    PubMed

    Rubio-Bollinger, Gabino; Castellanos-Gomez, Andres; Bilan, Stefan; Zotti, Linda A; Arroyo, Carlos R; Agraït, Nicolás; Cuevas, Juan Carlos

    2012-05-15

    We fabricate and characterize carbon-fiber tips for their use in combined scanning tunneling and force microscopy based on piezoelectric quartz tuning fork force sensors. An electrochemical fabrication procedure to etch the tips is used to yield reproducible sub-100-nm apex. We also study electron transport through single-molecule junctions formed by a single octanethiol molecule bonded by the thiol anchoring group to a gold electrode and linked to a carbon tip by the methyl group. We observe the presence of conductance plateaus during the stretching of the molecular bridge, which is the signature of the formation of a molecular junction.

  14. Carbon-fiber tips for scanning probe microscopes and molecular electronics experiments

    PubMed Central

    2012-01-01

    We fabricate and characterize carbon-fiber tips for their use in combined scanning tunneling and force microscopy based on piezoelectric quartz tuning fork force sensors. An electrochemical fabrication procedure to etch the tips is used to yield reproducible sub-100-nm apex. We also study electron transport through single-molecule junctions formed by a single octanethiol molecule bonded by the thiol anchoring group to a gold electrode and linked to a carbon tip by the methyl group. We observe the presence of conductance plateaus during the stretching of the molecular bridge, which is the signature of the formation of a molecular junction. PMID:22587692

  15. 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.

  16. The accumulation mechanism of the hypoxia imaging probe "FMISO" by imaging mass spectrometry: possible involvement of low-molecular metabolites.

    PubMed

    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

    2015-11-19

    (18)F-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.

  17. Influence of molecular order on the local work function of nanographene architectures: a Kelvin-probe force microscopy study.

    PubMed

    Palermo, Vincenzo; Palma, Matteo; Tomović, Zeljko; Watson, Mark D; Friedlein, Rainer; Müllen, Klaus; Samorì, Paolo

    2005-11-11

    We report a Kelvin-probe force microscopy (KPFM) investigation on the structural and electronic properties of different submicron-scale supramolecular architectures of a synthetic nanographene, including extended layers, percolated networks and broken patterns grown from solutions at surfaces. This study made it possible to determine the local work function (WF) of the different pi-conjugated nanostructures adsorbed on mica with a resolution below 10 nm and 0.05 eV. It revealed that the WF strongly depends on the local molecular order at the surface, in particular on the delocalization of electrons in the pi-states, on the molecular orientation at surfaces, on the molecular packing density, on the presence of defects in the film and on the different conformations of the aliphatic peripheral chains that might cover the conjugated core. These results were confirmed by comparing the KPFM-estimated local WF of layers supported on mica, where the molecules are preferentially packed edge-on on the substrate, with the ultraviolet photoelectron spectroscopy microscopically measured WF of layers adsorbed on graphite, where the molecules should tend to assemble face-on at the surface. It appears that local WF studies are of paramount importance for understanding the electronic properties of active organic nanostructures, being therefore fundamental for the building of high-performance organic electronic devices, including field-effect transistors, light-emitting diodes and solar cells.

  18. Tracing few-femtosecond photodissociation dynamics on molecular oxygen with a single-color pump-probe scheme in the VUV

    NASA Astrophysics Data System (ADS)

    Schepp, Oliver; Baumann, Arne; Rompotis, Dimitrios; Gebert, Thomas; Azima, Armin; Wieland, Marek; Drescher, Markus

    2016-09-01

    Molecular wave-packet dynamics in oxygen are studied in the time domain, using a single-color VUV-pump-VUV-probe scheme. 17-fs VUV pulses, centered at 161 nm are generated via high-order harmonic generation driven by an intense 800-nm pulse leading to VUV pulse energies that reach 1.1 μ J per pulse. An all-reflective interferometric pump-probe scheme is used for studying the delay dependence of the molecular oxygen ion signal with simultaneous nonresonant photoionization of krypton as a precise timing-reference. Access to the excited dissociative state lifetime is provided by the resulting delay-dependent O2 + signal, ultimately limited by the molecular ionization window. The ability to use a two-photon VUV probe provides the delay-dependent detection of O+ as an additional observable, extending the dissociation observation window.

  19. 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

  20. Genetic engineered molecular imaging probes for applications in cell therapy: emphasis on MRI approach.

    PubMed

    Cho, In K; Wang, Silun; Mao, Hui; Chan, Anthony Ws

    2016-01-01

    Recent advances in stem cell-based regenerative medicine, cell replacement therapy, and genome editing technologies (i.e. CRISPR-Cas 9) have sparked great interest in in vivo cell monitoring. Molecular imaging promises a unique approach to noninvasively monitor cellular and molecular phenomena, including cell survival, migration, proliferation, and even differentiation at the whole organismal level. Several imaging modalities and strategies have been explored for monitoring cell grafts in vivo. We begin this review with an introduction describing the progress in stem cell technology, with a perspective toward cell replacement therapy. The importance of molecular imaging in reporting and assessing the status of cell grafts and their relation to the local microenvironment is highlighted since the current knowledge gap is one of the major obstacles in clinical translation of stem cell therapy. Based on currently available imaging techniques, we provide a brief discussion on the pros and cons of each imaging modality used for monitoring cell grafts with particular emphasis on magnetic resonance imaging (MRI) and the reporter gene approach. Finally, we conclude with a comprehensive discussion of future directions of applying molecular imaging in regenerative medicine to emphasize further the importance of correlating cell graft conditions and clinical outcomes to advance regenerative medicine.

  1. Probing Gelation and Rheological Behavior of a Self-Assembled Molecular Gel.

    PubMed

    Hashemnejad, Seyed Meysam; Kundu, Santanu

    2017-08-08

    Molecular gels have been investigated over the last few decades; however, mechanical behavior of these self-assembled gels is not well understood, particularly how these materials fail at large strain. Here, we report the gelation and rheological behavior of a molecular gel formed by self-assembly of a low molecular weight gelator (LMWG), di-Fmoc-l-lysine, in 1-propanol/water mixture. Gels were prepared by solvent-triggered technique, and gelation was tracked using Fourier transform infrared (FTIR) spectroscopy and shear rheology. FTIR spectroscopy captures the formation of hydrogen bonding between the gelator molecules, and the change in IR spectra during the gelation process correlates with the gelation kinetics results captured by rheology. Self-assembly of gelator molecules leads to a fiber-like structure, and these long fibers topologically interact to form a gel-like material. Stretched-exponential function can capture the stress-relaxation data. Stress-relaxation time for these gels have been found to be long owing to long fiber dimensions, and the stretching exponent value of 1/3 indicates polydispersity in fiber dimensions. Cavitation rheology captures fracture-like behavior of these gels, and critical energy release rate has been estimated to be of the order 0.1 J/m(2). Our results provide new understanding of the rheological behavior of molecular gels and their structural origin.

  2. Genetic engineered molecular imaging probes for applications in cell therapy: emphasis on MRI approach

    PubMed Central

    Cho, In K; Wang, Silun; Mao, Hui; Chan, Anthony WS

    2016-01-01

    Recent advances in stem cell-based regenerative medicine, cell replacement therapy, and genome editing technologies (i.e. CRISPR-Cas 9) have sparked great interest in in vivo cell monitoring. Molecular imaging promises a unique approach to noninvasively monitor cellular and molecular phenomena, including cell survival, migration, proliferation, and even differentiation at the whole organismal level. Several imaging modalities and strategies have been explored for monitoring cell grafts in vivo. We begin this review with an introduction describing the progress in stem cell technology, with a perspective toward cell replacement therapy. The importance of molecular imaging in reporting and assessing the status of cell grafts and their relation to the local microenvironment is highlighted since the current knowledge gap is one of the major obstacles in clinical translation of stem cell therapy. Based on currently available imaging techniques, we provide a brief discussion on the pros and cons of each imaging modality used for monitoring cell grafts with particular emphasis on magnetic resonance imaging (MRI) and the reporter gene approach. Finally, we conclude with a comprehensive discussion of future directions of applying molecular imaging in regenerative medicine to emphasize further the importance of correlating cell graft conditions and clinical outcomes to advance regenerative medicine. PMID:27766183

  3. Human skin penetration of hyaluronic acid of different molecular weights as probed by Raman spectroscopy.

    PubMed

    Essendoubi, M; Gobinet, C; Reynaud, R; Angiboust, J F; Manfait, M; Piot, O

    2016-02-01

    Topical delivery of molecules into the human skin is one of the main issues in dermatology and cosmetology. Several techniques were developed to study molecules penetration into the human skin. Although widely accepted, the conventional methods such as Franz diffusion cells are unable to provide the accurate localization of actives in the skin layers. A different approach based on Raman spectroscopy has been proposed to follow-up the permeation of actives. It presents a high molecular specificity to distinguish exogenous molecules from skin constituents. Raman micro-imaging was applied to monitor the skin penetration of hyaluronic acids (HA) of different molecular weights. The first step, was the spectral characterization of these HA. After, we have determined spectral features of HA by which they can be detected in the skin. In the second part, transverse skin sections were realized and spectral images were recorded. Our results show a difference of skin permeation of the three HA. Indeed, HA with low molecular weight (20-300 kDa) passes through the stratum corneum in contrast of the impermeability of high molecular weight HA (1000-1400 kDa). Raman spectroscopy represents an analytical, non-destructive, and dynamic method to evaluate the permeation of actives in the skin layers. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  4. A probe to study the toxic interaction of tartrazine with bovine hemoglobin at the molecular level.

    PubMed

    Li, Yating; Wei, Haoran; Liu, Rutao

    2014-03-01

    Tartrazine is an artificial azo dye commonly used in food products, but tartrazine in the environment is potentially harmful. The toxic interaction between tartrazine and bovine hemoglobin (BHb) was investigated using fluorescence, synchronous fluorescence, UV-vis absorption, circular dichroism (CD) and molecular modeling techniques under simulated physiological conditions. The fluorescence data showed that tartrazine can bind with BHb to form a complex. The binding process was a spontaneous molecular interaction, in which van der Waals' forces and hydrogen bonds played major roles. Molecular docking results showed that the hydrogen bonds exist between the oxygen atoms at position 31 of tartrazine and the nitrogen atom NZ7 on Lys99, and also between the oxygen atoms at position 15 of tartrazine and the nitrogen atom NZ7 on Lys104, Lys105. The results of UV-vis and CD spectra revealed that tartrazine led to conformational changes in BHb, including loosening of the skeleton structure and decreasing α helix in the secondary structure. The synchronous fluorescence experiment revealed that tartrazine binds into the hemoglobin central cavity, and this was verified using a molecular modeling study.

  5. Franck—Condon breakdown as a probe of continuum coupling in molecular photoionization

    NASA Astrophysics Data System (ADS)

    Kakar, Sandeep; Choi, Heung Cheun; Poliakoff, E. D.

    1992-03-01

    We have measured vibrational branching ratios for 4σ -1 photoionization of CO in order to characterize continuum channel coupling. The results indicate that the shape resonance in the 5σ→ɛσ channel influences vibrational branching ratios of the 4σ -1 channel via continuum coupling, and the data illustrate how continuum channel coupling affects molecular photoionization dynamics.

  6. Genetically encoded molecular probes to visualize and perturb signaling dynamics in living biological systems

    PubMed Central

    Sample, Vedangi; Mehta, Sohum; Zhang, Jin

    2014-01-01

    ABSTRACT In this Commentary, we discuss two sets of genetically encoded molecular tools that have significantly enhanced our ability to observe and manipulate complex biochemical processes in their native context and that have been essential in deepening our molecular understanding of how intracellular signaling networks function. In particular, genetically encoded biosensors are widely used to directly visualize signaling events in living cells, and we highlight several examples of basic biosensor designs that have enabled researchers to capture the spatial and temporal dynamics of numerous signaling molecules, including second messengers and signaling enzymes, with remarkable detail. Similarly, we discuss a number of genetically encoded biochemical perturbation techniques that are being used to manipulate the activity of various signaling molecules with far greater spatial and temporal selectivity than can be achieved using standard pharmacological or genetic techniques, focusing specifically on examples of chemically driven and light-inducible perturbation strategies. We then describe recent efforts to combine these diverse and powerful molecular tools into a unified platform that can be used to elucidate the molecular details of biological processes that may potentially extend well beyond the realm of signal transduction. PMID:24634506

  7. Probing Silica-Biomolecule Interactions by Solid-State NMR and Molecular Dynamics Simulations.

    PubMed

    Brückner, Stephan Ingmar; Donets, Sergii; Dianat, Arezoo; Bobeth, Manfred; Gutiérrez, Rafael; Cuniberti, Gianaurelio; Brunner, Eike

    2016-11-08

    Understanding the molecular interactions between inorganic phases such as silica and organic material is fundamental for chromatographic applications, for tailoring silica-enzyme interactions, and for elucidating the mechanisms of biomineralization. The formation, structure, and properties of the organic/inorganic interface is crucial in this context. Here, we investigate the interaction of selectively (13)C-labeled choline with (29)Si-labeled monosilicic acid/silica at the molecular level. Silica/choline nanocomposites were analyzed by solid-state NMR spectroscopy in combination with extended molecular dynamics (MD) simulations to understand the silica/organic interface. Cross-polarization magic angle spinning (CP MAS)-based NMR experiments like (1)H-(13)C CP-REDOR (rotational-echo double resonance), (1)H-(13)C HETCOR (heteronuclear correlation), and (1)H-(29)Si-(1)H double CP are employed to determine spatial parameters. The measurement of (29)Si-(13)C internuclear distances for selectively (13)C-labeled choline provides an experimental parameter that allows the direct verification of MD simulations. Atomistic modeling using classical MD methodologies is performed using the INTERFACE force field. The modeling results are in excellent agreement with the experimental data and reveal the relevant molecular conformations as well as the nature and interplay of the interactions between the choline cation and the silica surface. Electrostatic interactions and hydrogen bonding are both important and depend strongly on the hydration level as well as the charge state of the silica surface.

  8. 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.

    2016-05-01

    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.

  9. Electrochemical reverse engineering: A systems-level tool to probe the redox-based molecular communication of biology.

    PubMed

    Li, Jinyang; Liu, Yi; Kim, Eunkyoung; March, John C; Bentley, William E; Payne, Gregory F

    2016-12-29

    The intestine is the site of digestion and forms a critical interface between the host and the outside world. This interface is composed of host epithelium and a complex microbiota which is "connected" through an extensive web of chemical and biological interactions that determine the balance between health and disease for the host. This biology and the associated chemical dialogues occur within a context of a steep oxygen gradient that provides the driving force for a variety of reduction and oxidation (redox) reactions. While some redox couples (e.g., catecholics) can spontaneously exchange electrons, many others are kinetically "insulated" (e.g., biothiols) allowing the biology to set and control their redox states far from equilibrium. It is well known that within cells, such non-equilibrated redox couples are poised to transfer electrons to perform reactions essential to immune defense (e.g., transfer from NADH to O2 for reactive oxygen species, ROS, generation) and protection from such oxidative stresses (e.g., glutathione-based reduction of ROS). More recently, it has been recognized that some of these redox-active species (e.g., H2O2) cross membranes and diffuse into the extracellular environment including lumen to transmit redox information that is received by atomically-specific receptors (e.g., cysteine-based sulfur switches) that regulate biological functions. Thus, redox has emerged as an important modality in the chemical signaling that occurs in the intestine and there have been emerging efforts to develop the experimental tools needed to probe this modality. We suggest that electrochemistry provides a unique tool to experimentally probe redox interactions at a systems level. Importantly, electrochemistry offers the potential to enlist the extensive theories established in signal processing in an effort to "reverse engineer" the molecular communication occurring in this complex biological system. Here, we review our efforts to develop this

  10. Probing the evolution of molecular cloud structure. II. From chaos to confinement

    NASA Astrophysics Data System (ADS)

    Kainulainen, J.; Beuther, H.; Banerjee, R.; Federrath, C.; Henning, T.

    2011-06-01

    We present an analysis of the large-scale molecular cloud structure and of the stability of clumpy structures in nearby molecular clouds. In our recent work, we identified a structural transition in molecular clouds by studying the probability distributions of their gas column densities. In this paper, we further examine the nature of this transition. The transition takes place at the visual extinction of A_V^tail = 2{-4} mag, or equivalently, at Σtail ≈ 40-80 M⊙ pc-2. The clumps identified above this limit have wide ranges of masses and sizes, but a remarkably constant mean volume density of overline{n ≈ 10^3} cm-3. This is 5-10 times higher than the density of the medium surrounding the clumps. By examining the stability of the clumps, we show that they are gravitationally unbound entities, and that the external pressure from the parental molecular cloud is a significant source of confining pressure for them. Then, the structural transition at A_V^tail may be linked to a transition between this population and the surrounding medium. The star-formation rates in the clouds correlate strongly with the total mass in the clumps, i.e., with the mass above A_V^tail, and drops abruptly below that threshold. These results imply that the formation of pressure-confined clumps introduces a prerequisite for star formation. Furthermore, they give a physically motivated explanation for the recently reported relation between the star-formation rates and the amount of dense material in molecular clouds. Likewise, they give rise to a natural threshold for star formation at A_V^tail.

  11. Molecular probing of TNF: From identification of therapeutic target to guidance of therapy in inflammatory diseases.

    PubMed

    Chu, Cong-Qiu

    2016-09-12

    Therapy by blocking tumor necrosis factor (TNF) activity is highly efficacious and profoundly changed the paradigm of several inflammatory diseases. However, a significant proportion of patients with inflammatory diseases do not respond to TNF inhibitors (TNFi). Prediction of therapeutic response is required for TNFi therapy. Isotope labeled anti-TNF antibodies or TNF receptor have been investigated to localize TNF production at inflammatory tissue in animal models and in patients with inflammatory diseases. The in vivo detection of TNF has been associated with treatment response. Recently, fluorophore labeled anti-TNF antibody in combination with confocal laser endomicroscopy in patients with Crohn's disease yielded more accurate and quantitative in vivo detection of TNF in the diseased mucosa. More importantly, this method demonstrated high therapeutic predication value. Fluorophore labeled TNF binding aptamers in combination with modern imaging technology offers additional tools for in vivo TNF probing.

  12. Probing electronic properties of molecular engineered zinc oxide nanowires with photoelectron spectroscopy.

    PubMed

    Aguilar, Carlos A; Haight, Richard; Mavrokefalos, Anastassios; Korgel, Brian A; Chen, Shaochen

    2009-10-27

    ZnO nanowires (NWs) are emerging as key elements for new lasing, photovoltaic and sensing applications but elucidation of their fundamental electronic properties has been hampered by a dearth of characterization tools capable of probing single nanowires. Herein, ZnO NWs were synthesized in solution and integrated into a low energy photoelectron spectroscopy system, where quantitative optical measurements of the NW work function and Fermi level location within the band gap were collected. Next, the NWs were decorated with several dipolar self-assembled monolayers (SAMs) and control over the electronic properties is demonstrated, yielding a completely tunable hybrid electronic material. Using this new metrology approach, a host of other extraordinary interfacial phenomena could be explored on nanowires such as spatial dopant profiling or heterostructures.

  13. Use of molecular probes to assess geographic distribution of Pfiesteria species.

    PubMed

    Rublee, P A; Kempton, J W; Schaefer, E F; Allen, C; Harris, J; Oldach, D W; Bowers, H; Tengs, T; Burkholder, J M; Glasgow, H B

    2001-10-01

    We have developed multiple polymerase chain reaction (PCR)-based methods for the detection of Pfiesteria sp. in cultures and environmental samples. More than 2,100 water and sediment samples from estuarine sites of the U.S. Atlantic and gulf coasts were assayed for the presence of Pfiesteria piscicida Steidinger & Burkholder and Pfiesteria shumwayae Glasgow & Burkholder by PCR probing of extracted DNA. Positive results were found in about 3% of samples derived from routine monitoring of coastal waters and about 8% of sediments. The geographic range of both species was the same, ranging from New York to Texas. Pfiesteria spp. are likely common and generally benign inhabitants of coastal areas, but their presence maintains a potential for fish and human health problems.

  14. Molecular requirements for inhibition of the chemokine receptor CCR8 – probe-dependent allosteric interactions

    PubMed Central

    Rummel, PC; Arfelt, KN; Baumann, L; Jenkins, TJ; Thiele, S; Lüttichau, HR; Johnsen, A; Pease, J; Ghosh, S; Kolbeck, R; Rosenkilde, MM

    2012-01-01

    BACKGROUND AND PURPOSE Here we present a novel series of CCR8 antagonists based on a naphthalene-sulfonamide structure. This structure differs from the predominant pharmacophore for most small-molecule CC-chemokine receptor antagonists, which in fact activate CCR8, suggesting that CCR8 inhibition requires alternative structural probes. EXPERIMENTAL APPROACH The compounds were tested as inverse agonists and as antagonists against CCL1-induced activity in Gαi signalling and chemotaxis. Furthermore, they were assessed by heterologous competition binding against two radiolabelled receptor ligands: the endogenous agonist CCL1 and the virus-encoded antagonist MC148. KEY RESULTS All compounds were highly potent inverse agonists with EC50 values from 1.7 to 23 nM. Their potencies as antagonists were more widely spread (EC50 values from 5.9 to 1572 nM). Some compounds were balanced antagonists/inverse agonists whereas others were predominantly inverse agonists with >100-fold lower potency as antagonists. A correspondingly broad range of affinities, which followed the antagonist potencies, was disclosed by competition with [125I]-CCL1 (Ki 3.4–842 nM), whereas the affinities measured against [125I]-MC148 were less widely spread (Ki 0.37–27 nM), and matched the inverse agonist potencies. CONCLUSION AND IMPLICATIONS Despite highly potent and direct effects as inverse agonists, competition-binding experiments against radiolabelled agonist and tests for antagonism revealed a probe-dependent allosteric effect of these compounds. Thus, minor chemical changes affected the ability to modify chemokine binding and action, and divided the compounds into two groups: predominantly inverse agonists and balanced antagonists/inverse agonists. These studies have important implications for the design of new inverse agonists with or without antagonist properties. PMID:22708643

  15. Mono-dispersed high magnetic resonance sensitive magnetite nanocluster probe for detection of nascent tumors by magnetic resonance molecular imaging.

    PubMed

    Zhang, Chunfu; Xie, Xuan; Liang, Sheng; Li, Mingli; Liu, Yajie; Gu, Hongchen

    2012-08-01

    Sensitive molecular imaging and detection of tumors or their supporting neovascularity require high-avidity, target-specific probes, which produce robust signal amplification compatible with a sensitive high-resolution imaging modality. In this context, we fabricated a high magnetic resonance (MR)-sensitive magnetite nanocluster (MNC) probe specific for tumor angiogenesis by assembly of hydrophobic superparamagnetic iron oxide nanoparticles (SPIONs) with (Mal)mPEG-PLA copolymer into cluster and subsequent encoding c(RGDyC) peptide on the cluster (RGD-MNC) for detection of nascent tumors. We found that RGD-MNC is highly sensitive (r(2) = 464.94 s(-1)mM(-1)) and specific for αvβ3-positive cells. Both nascent (35 ± 6.6 mm(3)) and large tumors (256 ± 22.3 mm(3)) can be registered by RGD-MNC and detected by MR imaging (MRI), with the nascent tumors demonstrating more pronounced MR contrast. Immunohistochemical studies revealed that MR signal decrease was closely correlated with histological characteristics of tumors (microvessel density and αvβ3 expression levels) at different growth stages.

  16. Molecular contrast optical coherence tomography: A pump-probe scheme using indocyanine green as a contrast agent.

    PubMed

    Yaqoob, Zahid; McDowell, Emily; Wu, Jigang; Heng, Xin; Fingler, Jeff; Yang, Changhuei

    2006-01-01

    The use of indocyanine green (ICG), a U.S. Food and Drug Administration approved dye, in a pump-probe scheme for molecular contrast optical coherence tomography (MCOCT) is proposed and demonstrated for the first time. In the proposed pump-probe scheme, an optical coherence tomography (OCT) scan of the sample containing ICG is first acquired. High fluence illumination (approximately 190 kJ/cm2) is then used to permanently photobleach the ICG molecules--resulting in a permanent alteration of the overall absorption of the ICG. A second OCT scan is next acquired. The difference of the two OCT scans is used to determine the depth resolved distribution of ICG within a sample. To characterize the extent of photobleaching in different ICG solutions, we determine the cumulative probability of photobleaching, phi(B,cum), defined as the ratio of the total photobleached ICG molecules to the total photons absorbed by the ground state molecules. An empirical study of ICG photobleaching dynamics shows that phi(B,cum) decreases with fluence as well as with increasing dye concentration. The quantity phi(B,cum) is useful for estimating the extent of photobleaching in an ICG sample (MCOCT contrast) for a given fluence of the pump illumination. The paper also demonstrates ICG-based MCOCT imaging in tissue phantoms as well as within stage 54 Xenopus laevis.

  17. Design and synthesis of molecular probes for the determination of the target of the anthelmintic drug praziquantel.

    PubMed

    Sharma, Lalit Kumar; Cupit, Pauline M; Goronga, Tino; Webb, Thomas R; Cunningham, Charles

    2014-06-01

    Schistosomiasis is a highly prevalent neglected tropical disease caused by blood-dwelling helminths of the genus Schistosoma. Praziquantel (PZQ) is the only drug available widely for the treatment of this disease and is administered in racemic form, even though only the (R)-isomer has significant anthelmintic activity. Progress towards the development of a second generation of anthelmintics is hampered by a lack of understanding of the mechanism of action of PZQ. In this Letter, we report an efficient protocol for the small-scale separation of enantiomers of 2 (hydrolyzed PZQ) using supercritical fluid chromatography (SFC). The enantiopure 2 was then used to develop several molecular probes, which can potentially be used to help identify the protein target of PZQ and study its mode of action.

  18. 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.

  19. Deuteration of a molecular probe for DNP hyperpolarization--a new approach and validation for choline chloride.

    PubMed

    Allouche-Arnon, Hyla; Lerche, Mathilde H; Karlsson, Magnus; Lenkinski, Robert E; Katz-Brull, Rachel

    2011-01-01

    The promising dynamic nuclear polarization (DNP) for hyperpolarized (13)C-MRI/MRS of real-time metabolism in vivo is challenged by the limited number of agents with the required physical and biological properties. The physical requirement of a liquid-state T(1) of tens of seconds is mostly found for (13)C-carbons in small molecules that have no direct protons attached, i.e. carbonyl, carboxyl and certain quaternary carbons. Unfortunately, such carbon positions do not exist in a large number of metabolic agents, and chemical shift dispersion often limits detection of their chemical evolution. We have previously shown that direct deuteration of protonated carbon positions significantly prolongs the (13)C T(1) in the liquid state and provides potential (13)C-labeled agents with differential chemical shift with respect to metabolism. The Choline Molecular Probe [1,1,2,2-D(4), 2-(13)C]choline chloride (CMP2) has recently been introduced as a means of studying choline metabolism in a hyperpolarized state. Here, the biophysical properties of CMP2 were characterized and compared with those of [1-(13)C]pyruvate to evaluate the impact of molecular probe deuteration. The CMP2 solid-state polarization build-up time constant (30 min) and polarization level (24%) were comparable to those of [1-(13)C]pyruvate. Both compounds' liquid state T(1) increased with temperature. The high-field T(1) of CMP2 compared favorably with [1-(13)C]pyruvate. Thus, a deuterated agent demonstrated physical properties comparable to a hyperpolarized compound of already proven value, whereas both showed chemical shift dispersion that allowed monitoring of their metabolism. It is expected that the use of deuterated carbon-13 positions as reporting hyperpolarized nuclei will substantially expand the library of agents for DNP-MR.

  20. 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

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

    SciTech Connect

    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 the 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

    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.

  3. 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

  4. Can we trust CO emission as a probe of the densities and temperatures of molecular clouds?

    NASA Astrophysics Data System (ADS)

    Molina, F.; Glover, S.; Federrath, C.

    2011-05-01

    We have analyzed the distributions of CO and temperature in a large suite of simulated molecular clouds, in order to help us understand how to interpret CO line emission from real molecular clouds. The simulations were performed using a fully dynamical 3D model of magnetized turbulence coupled to a chemical network simplified to follow the dominant pathways for CO formation and destruction. We find that most of the CO is located at densities over 10^3 cm^-3 where the temperature is roughly 10-40 K independently of the mean density, metallicity and UV field strength. Although most of the volume is in warmer and less dense regions, CO photodisociation is more efficient there making the CO abundance small. It follows that CO observations alone give a misleading view of the physical conditions in the clouds.

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

    DOE PAGES

    Yoo, Brian; Jing, Benxin; Jones, Stuart E.; ...

    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

  6. 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.

  7. Experimental and Theoretical Probing of Molecular Dynamics at Catalytic and Ionic Liquid Interfaces

    DTIC Science & Technology

    2014-04-01

    Yang, G. A. Voth, Spectroscopy and Molecular Dynamics Simulations of Nonpolar and Polar Molecules in Ionic Liquids. In Ionic Liquids: Science and...nanoparticle surface. A method to vastly increase the two photon fluorescence yield of metallic nanoparticles, based on bonding of thiol molecules to the...fluorescence yield of metallic nanoparticles, based on bonding of thiol molecules to the particle, has been discovered, a process that has implications

  8. Fluorescent Resonance Energy Transfer: A Tool for Probing Molecular Cell-Biomaterial Interactions in Three Dimensions

    PubMed Central

    Huebsch, Nathaniel D.; Mooney, David J.

    2007-01-01

    The current paradigm in designing biomaterials is to optimize material chemical and physical parameters based on correlations between these parameters and downstream biological responses, whether in vitro or in vivo. Extensive developments in molecular design of biomaterials have facilitated identification of several biophysical and biochemical variables (e.g. adhesion peptide density, substrate elastic modulus) as being critical to cell response. However, these empirical observations do not indicate whether different parameters elicit cell responses by modulating redundant variables of the cell-material interface (e.g. number of cell-material bonds, cell-matrix mechanics). Recently, a molecular fluorescence technique, Fluorescence Resonance Energy Transfer (FRET) has been applied to quantitatively analyze parameters of the cell-material interface for both two and three-dimensional adhesion substrates. Tools based on FRET have been utilized to quantify several parameters of the cell-material interface relevant to cell response, including molecular changes in matrix proteins induced by interactions both with surfaces and cells, the number of bonds between integrins and their adhesion ligands, and changes in the crosslink density of hydrogel synthetic extracellular matrix analogs. As such techniques allow both dynamic and 3D analyses they will be useful to quantitatively relate downstream cellular responses (e.g. gene expression) to the composition of this interface. Such understanding will allow bioengineers to fully exploit the potential of biomaterials engineered on the molecular scale, by optimizing material chemical and physical properties to a measurable set of interfacial parameters known to elicit a predictable response in a specific cell population. This will facilitate the rational design of complex, multi-functional biomaterials used as model systems for studying diseases or for clinical applications. PMID:17270268

  9. 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.

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

    DOE PAGES

    Ade, P. A. R.; Aghanim, N.; Alves, M. I. R.; ...

    2016-02-09

    Within ten nearby (d < 450 pc) Gould belt molecular clouds we evaluate in this paper 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 frommore » 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. Finally, 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.« less

  11. Ultrafast NMR T1 relaxation measurements: probing molecular properties in real time.

    PubMed

    Smith, Pieter E S; Donovan, Kevin J; Szekely, Or; Baias, Maria; Frydman, Lucio

    2013-09-16

    The longitudinal relaxation properties of NMR active nuclei carry useful information about the site-specific chemical environments and about the mobility of molecular fragments. Molecular mobility is in turn a key parameter reporting both on stable properties, such as size, as well as on dynamic ones, such as transient interactions and irreversible aggregation. In order to fully investigate the latter, a fast sampling of the relaxation parameters of transiently formed molecular species may be needed. Nevertheless, the acquisition of longitudinal relaxation data is typically slow, being limited by the requirement that the time for which the nucleus relaxes be varied incrementally until a complete build-up curve is generated. Recently, a number of single-shot-inversion-recovery methods have been developed capable of alleviating this need; still, these may be challenged by either spectral resolution restrictions or when coping with very fast relaxing nuclei. Here, we present a new experiment to measure the T1s of multiple nuclear spins that experience fast longitudinal relaxation, while retaining full high-resolution chemical shift information. Good agreement is observed between T1s measured with conventional means and T1s measured using the new technique. The method is applied to the real-time investigation of the reaction between D-xylose and sodium borate, which is in turn elucidated with the aid of ancillary ultrafast and conventional 2D TOCSY measurements. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    DOE PAGES

    Fan, Quli; Cheng, Kai; Hu, Xiang; ...

    2014-10-07

    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 alsomore » 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. As a result, the multimodal properties of MNPs demonstrate the high potential of endogenous materials with multifunctions as nanoplatforms for molecular theranostics and clinical translation.« less

  13. 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

  14. Detection and identification of fungal pathogens in blood by using molecular probes.

    PubMed Central

    Einsele, H; Hebart, H; Roller, G; Löffler, J; Rothenhofer, I; Müller, C A; Bowden, R A; van Burik, J; Engelhard, D; Kanz, L; Schumacher, U

    1997-01-01

    A PCR assay was developed for the detection and identification of Candida and Aspergillus species. The design of the oligonucleotide primer pair as well as the species-specific probes used for species identification was derived from a comparison of the sequences of the 18S rRNA genes of various fungal pathogens. The primers targeted a consensus sequence for a variety of fungal pathogens. The assay was tested for sensitivity and specificity with 134 fungal and 85 nonfungal isolates. To assess clinical applicability, 601 blood samples from four defined groups were tested: group A (n = 35), controls; groups B to D (n = 86), patients with febrile neutropenia, without fungal colonization (group B; n = 29) and with fungal colonization (group C; n = 36); and patients with documented invasive fungal infection (IFI) (group D; n = 21). The assay detected and, by species-specific hybridization, identified most of the clinically relevant Candida and Aspergillus species at 1 CFU/ml of blood. Amplification was 100% sensitive for all molds and yeasts tested, with Histoplasma capsulatum being the only non-Aspergillus species hybridizing with the Aspergillus spp. probe. None of 35 group A patients and only 3 of 65 group B and C patients were PCR positive. The sensitivity of the assay for specimens from patients with IFI (21 patients in group D) was 100% if two specimens were tested. For specificity, 3 of 189 specimens from patients at risk but with negative cultures were positive by the assay, for a specificity of 98%. PCR preceded radiological signs by a median of 4 days (range, 4 to 7 days) for 12 of 17 patients with hepatosplenic candidiasis or pulmonary aspergillosis. For the 10 patients with IFI responding to antifungal therapy, PCR assays became persistently negative after 14 days of treatment, in contrast to the case for 11 patients, who remained PCR positive while not responding to antifungal therapy. Thus, the described PCR assay allows for the highly sensitive and

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Bulky melamine-based Zn-porphyrin tweezer as a CD probe of molecular chirality.

    PubMed

    Petrovic, Ana G; Vantomme, Ghislaine; Negrón-Abril, Yashira L; Lubian, Elisa; Saielli, Giacomo; Menegazzo, Ileana; Cordero, Roselynn; Proni, Gloria; Nakanishi, Koji; Carofiglio, Tommaso; Berova, Nina

    2011-10-01

    The transfer of chirality from a guest molecule to an achiral host is the subject of significant interest especially when, upon chiral induction, the chiroptical response of the host/guest complex can effectively report the absolute configuration (AC) of the guest. For more than a decade, dimeric metalloporphyrin hosts (tweezers) have been successfully applied as chirality probes for determination of the AC for a wide variety of chiral synthetic compounds and natural products. The objective of this study is to investigate the utility of a new class of melamine-bridged Zn-porphyrin tweezers as sensitive AC reporters. A combined approach based on an experimental CD analysis and a theoretical prediction of the prevailing interporphyrin helicity demonstrates that these tweezers display favorable properties for chiral recognition. Herein, we discuss the application of the melamine-bridged tweezer to the chiral recognition of a diverse set of chiral guests, such as 1,2-diamines, α-amino-esters and amides, secondary alcohols, and 1,2-amino-alcohols. The bulky periphery and the presence of a rigid porphyrin linkage lead, in some cases, to a more enhanced CD sensitivity than that reported earlier with other tweezers.

  1. Design and synthesis of tricyclic JAK3 inhibitors with picomolar affinities as novel molecular probes.

    PubMed

    Gehringer, Matthias; Pfaffenrot, Ellen; Bauer, Silke; Laufer, Stefan A

    2014-02-01

    The Janus kinase (JAK) signaling pathway is of particular importance in the pathology of inflammatory diseases and oncological disorders, and the inhibition of Janus kinase 3 (JAK3) with small molecules has proven to provide therapeutic immunosuppression. A novel class of tricyclic JAK inhibitors derived from the 3-methyl-1,6-dihydrodipyrrolo[2,3-b:2',3'-d]pyridine scaffold was designed based on the tofacitinib-JAK3 crystal structure by applying a rigidization approach. A convenient synthetic strategy to access the scaffold via an intramolecular Heck reaction was developed, and a small library of inhibitors was prepared and characterized using in vitro biochemical as well as cellular assays. IC50 values as low as 220 pM could be achieved with selectivity for JAK3 over other JAK family members. Both activity and selectivity were confirmed in a cellular STAT phosphorylation assay, providing also first-time data for tofacitinib. Our novel inhibitors may serve as tool compounds and useful probes to explore the role of JAK3 inhibition in pharmacodynamics studies.

  2. Probing a Structural Model of the Nuclear Pore Complex Channel through Molecular Dynamics

    PubMed Central

    Miao, Lingling; Schulten, Klaus

    2010-01-01

    Abstract The central pore of a nuclear pore complex (NPC) is filled with unstructured proteins that contain many FG-repeats separated by hydrophilic regions. An example of such protein is nsp1. By simulating an array of nsp1 segments, we identified, in an earlier study, a spontaneously formed brushlike structure that promises to explain selective transport in the NPC channel. Here we report four (350,000 atom, 200 ns) simulations probing this structure via its interaction with transport receptor NTF2 as well as with an inert protein. NTF2 dimers are observed to gradually enter the brush, but the inert protein is not. Both NTF2 and the inert protein are found to bind to FG-repeats, but binding periods lasted more briefly for the inert protein. A simulation also investigated the behavior of a brush made of mutant nsp1 that is known to be less effective in NPC-selective transport, finding that this brush does not attract NTF2. PMID:20409487

  3. Molecular probes of phylogeny and biogeography in toads of the widespread genus Bufo.

    PubMed

    Maxson, L R

    1984-07-01

    Genetic relationships among 25 species of Central and South American Bufo and among representative North, Central, and South American, Asian, and African Bufo were probed, using the quantitative immunological technique of microcomplement fixation (MC'F) which indicated a clear separation of North, Central, and South American lineages of Bufo. The South American lineage likely diverged from the Central and North American lineages in the Eocene; the latter two lineages diverged later, probably in the mid-Oligocene. Some species groups of South American toads, defined on the basis of traditional morphological studies, are genetically quite similar within groups, whereas others are genetically divergent. The amount of albumin evolution does not appear to parallel the amount of karyotypic, morphological, ecological, or behavioral evolution documented. Comparisons suggest that the African lineages separated from the American and Asian lineages in the late Cretaceous, corresponding to the time of the final separation of Gondwanaland, the southern supercontinent including the modern continents of South America, Africa, Australia, Antarctica, and India. The Asian lineages diverged from the lineage giving rise to all of the American species in the early Paleocene.

  4. Molecular motions of nitroxyl radical spin probes in X-zeolites. Dependence on zeolite cation and spin probe chemical functional group

    NASA Astrophysics Data System (ADS)

    Doetschman, David C.; Thomas, Gregory D.

    1998-03-01

    The nitroxyl radical spin probes, 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO), 4-oxo-TEMPO (TEMPONE) and 4-amino-TEMPO (TEMPAMINE) were examined by continuous wave (CW) electron paramagnetic resonance (EPR) in a series of cation-exchanged X-type faujasite zeolite supercages. The spectra in Li-X, Na-X and K-X between 10 and 300 K were fitted by varying the rotational correlation constants, the homogeneous linewidth, and the principal nitrogen nuclear hyperfine coupling matrix element ( Azz) for the axis near the C-N-C plane normal. The TEMPONE activation energies for rotation, 12.1-3.1 kJ mol -1, decrease monotonically with cation size, suggesting an attractive interaction with the cation that depends on cation Lewis activity. TEMPO and TEMPAMINE have activation energies for rotation, 6.7-12.8 and 2.8-10.0 kJ mol -1, respectively, that increase with cation size, suggesting non-bonded repulsion of the molecules by the cations. We propose that the attraction of the cation to TEMPONE is via its carbonyl π electrons, an interaction found for the larger phenalenyl π systems in previous work (D.C. Doetschman, D.W. Dwyer, J.D. Fox, C.K. Frederick, S. Scull, G.D. Thomas, S.G. Utterback, J. Wei, Chem. Phys. 185 (1994) 343). In contrast, the amino group of TEMPAMINE is sp 3 hybridized and has essentially no π character. It is well known from X-ray diffraction studies, in which the NO group is found to project out of the C-N-C plane, and from the magnitude of the Azz nuclear hyperfine coupling element that the NO group has relatively little π character. The activation energies of the TEMPO rotation are consistently larger than those of TEMPAMINE. We propose that the volume of TEMPO is effectively larger than that of TEMPAMINE because TEMPO is undergoing rapid piperidine ring inversion which does not occur in TEMPAMINE. Preliminary pulsed EPR results for TEMPO are presented that appear to indicate a second type of molecular motion associated with the motion with the

  5. Vibrational frequency fluctuations of ionic vibrational probe in water: Theoretical study with molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Okuda, Masaki; Higashi, Masahiro; Ohta, Kaoru; Saito, Shinji; Tominaga, Keisuke

    2017-09-01

    The vibrational dynamics of SCN- in H2O are theoretically investigated by molecular dynamics simulations. Based on the vibrational solvatochromism theory, we calculate the frequency-frequency time correlation function of the SCN anti-symmetric stretching mode, which is characterized by time constants of 0.13 and 1.41 ps. We find that the frequency fluctuation is almost determined by the electrostatic interaction from the water molecules in the first-hydration shell. The collective dynamics of the water molecules in the first-hydration shell is found to be similar to that of bulk water, though the hydrogen bond between the ion and water molecule is very strong.

  6. Probing molecular frame photoelectron angular distributions via high-order harmonic generation from aligned molecules

    NASA Astrophysics Data System (ADS)

    Lin, C. D.; Jin, Cheng; Le, Anh-Thu; Lucchese, R. R.

    2012-10-01

    We analyse the theory of single photoionization (PI) and high-order harmonic generation (HHG) by intense lasers from aligned molecules. We show that molecular-frame photoelectron angular distributions can be extracted from these measurements. We also show that, under favourable conditions, the phase of PI transition dipole matrix elements can be extracted from the HHG spectra. Furthermore, by varying the polarization axis of the HHG generating laser with respect to the polarization axis of the aligning laser, it is possible to extract angle-dependent tunnelling ionization rates for different subshells of the molecules.

  7. Kinematics and properties of the central molecular zone as probed with [C ii

    NASA Astrophysics Data System (ADS)

    Langer, W. D.; Velusamy, T.; Morris, M. R.; Goldsmith, P. F.; Pineda, J. L.

    2017-03-01

    Context. The Galactic central molecular zone (CMZ) is a region containing massive and dense molecular clouds, with dynamics driven by a variety of energy sources including a massive black hole. It is thus the nearest template for understanding physical processes in extragalactic nuclei. The CMZ's neutral interstellar gas has been mapped spectrally in many neutral atomic and molecular gas tracers, but the ionized and CO-dark H2 regions are less well traced spectroscopically. Aims: We identify features of the UV irradiated neutral gas, photon dominated regions (PDRs) and CO-dark H2, and highly ionized gas in the CMZ as traced by the fine structure line of C+ at 158 μm, [C ii], and characterize their properties. Methods: We observed the [C ii] 158 μm fine structure line with high spectral resolution using Herschel HIFI with two perpendicular on-the-fly strip scans, along l = -0.8° to +0.8° and b = -0.8° to +0.8°, both centered on (l, b) = (0°, 0°). We analyze the spatial-velocity distribution of the [C ii] data, compare them to those of [C i] and CO, and to dust continuum maps, in order to determine the properties and distribution of the ionized and neutral gas and its dynamics within the CMZ. Results: The longitude- and latitude-velocity maps of [C ii] trace portions of the orbiting open gas streams of dense molecular clouds, the cloud G0.253+0.016, also known as the Brick, the arched filaments, the ionized gas within several pc of Sgr A and Sgr B2, and the warm dust bubble. We use the [C ii] data to determine the physical and dynamical properties of these CMZ features. Conclusions: The bright far-IR 158 μm C+ line, [C ii], when observed with high spatial and spectral resolution, traces a wide range of emission features in the CMZ. The [C ii] emission arises primarily from dense PDRs and highly ionized gas, and is an important tracer of the kinematics and physical conditions of this gas.

  8. Evaluating Atmospheric pressure Solids Analysis Probe (ASAP) mass spectrometry for the analysis of low molecular weight synthetic polymers.

    PubMed

    Smith, Michael J P; Cameron, Neil R; Mosely, Jackie A

    2012-10-07

    Atmospheric pressure Solids Analysis Probe (ASAP) mass spectrometry has facilitated the ionisation of oligomers from low molecular weight synthetic polymers, poly(ethylene glycol) (PEG: M(n) = 1430) and poly(styrene) (PS: M(n) = 1770), directly from solids, providing a fast and efficient method of identification. Ion source conditions were evaluated and it was found that the key instrument parameter was the ion source desolvation temperature which, when set to 600 °C was sufficient to vapourise the heavier oligomers for ionisation. PS, a non-polar polymer that is very challenging to analyse by MALDI or ESI without the aid of metal salts to promote cationisation, was ionised promptly by ASAP resulting in the production of radical cations. A small degree of in-source dissociation could be eliminated by control of the instrument ion source voltages. The fragmentation observed through in-source dissociation could be duplicated in a controlled manner through Collision-Induced Dissociation (CID) of the radical cations. PEG, which preferentially ionises through adduction with alkali metal cations in MALDI and ESI, was observed as a protonated molecular ion by ASAP. In-source dissociation could not be eliminated entirely and the fragmentation observed resulted from cleavage of the C-C and C-O backbone bonds, as opposed to only C-O bond cleavage observed from tandem mass spectrometry.

  9. Pushing the Limits of a Molecular Mechanics Force Field To Probe Weak CH···π Interactions in Proteins.

    PubMed

    Barman, Arghya; Batiste, Bruce; Hamelberg, Donald

    2015-04-14

    The relationship among biomolecular structure, dynamics, and function is far from being understood, and the role of subtle, weak interactions in stabilizing different conformational states is even less well-known. The cumulative effect of these interactions has broad implications for biomolecular stability and recognition and determines the equilibrium distribution of the ensemble of conformations that are critical for function. Here, we accurately capture the stabilizing effects of weak CH···π interaction using an empirical molecular mechanics force field in excellent agreement with experiments. We show that the side chain of flanking C-terminal aromatic residues preferentially stabilize the cis isomer of the peptidyl-prolyl bond of the protein backbone through this weak interaction. Cis-trans isomerization of peptidyl-prolyl protein bond plays a pivotal role in many cellular processes, including signal transduction, substrate recognition, and many diseases. Although the cis isomer is relatively less stable than the trans isomer, aromatic side chains of neighboring residues can play a significant role in stabilizing the cis relative to the trans isomer. We carry out extensive regular and accelerated molecular dynamics simulations and establish an approach to simulate the pH profile of the cis/trans ratio in order to probe the stabilizing role of the CH···π interaction. The results agree very well with NMR experiments, provide detailed atomistic description of this crucial biomolecular interaction, and underscore the importance of weak stabilizing interactions in protein function.

  10. Diffuse gamma-ray emission from nearby molecular clouds as a probe of cosmic ray density variations

    NASA Astrophysics Data System (ADS)

    Abrahams, Ryan Douglas

    We analyze gamma-ray emission from nearby, interstellar molecular clouds in order to calibrate current tracers of the interstellar medium and to probe local cosmic ray gradients. Gamma-rays detected by the Fermi Gamma-ray Space Telescope are created when cosmic rays collide with atomic nuclei in the interstellar medium, and thus provide a unique, unbiased view of the distribution of gas. The gamma-ray flux per proton in the interstellar medium, also known as the gamma-ray emissivity, contains information about the density of high energy cosmic rays. These cosmic rays are born in supernovae shock waves and diffuse throughout the Galaxy. The cosmic ray density therefore traces star formation. Previous models of cosmic ray propagation predict small density gradients in the Solar neighborhood. We analyze the gamma-ray emission from 93 nearby molecular clouds. We find no evidence for a local cosmic ray density gradient, and that the variance in the emissivity is larger than previously reported by the Fermi science team. Nor do we find a gradient in Xco = N(H 2)/WCO, which is predicted to increase with Galactocentric radius. Finally, we suggest future work which may finally detect a local cosmic ray density gradient. A significant result would constrain the population of cosmic ray sources, thus revealing the distribution of star formation close to the Solar System.

  11. 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.

  12. PROBING THE PRE-REIONIZATION EPOCH WITH MOLECULAR HYDROGEN INTENSITY MAPPING

    SciTech Connect

    Gong Yan; Cooray, Asantha; Santos, Mario G.

    2013-05-10

    Molecular hydrogen is now understood to be the main coolant of the primordial gas clouds leading to the formation of the very first stars and galaxies. The line emissions associated with molecular hydrogen should then be a good tracer of the matter distribution at the onset of the reionization of the universe. Here, we propose intensity mapping of H{sub 2} line emission in rest-frame mid-infrared wavelengths to map out the spatial distribution of gas at redshifts z > 10. We calculate the expected mean intensity and clustering power spectrum for several H{sub 2} lines. We find that the 0-0S(3) rotational line at a rest wavelength of 9.66 {mu}m is the brightest line over the redshift range of 10-30 with an intensity of about 5-10 Jy sr{sup -1} at z {approx} 15. To reduce astrophysical and instrumental systematics, we propose the cross-correlation between multiple lines of the H{sub 2} rotational and vibrational line emission spectrum. Our estimates of the intensity can be used as guidance in planning instruments for future mid-IR spectroscopy missions such as SPICA.

  13. 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.

  14. Using dSTORM to probe the molecular architecture of filopodia

    NASA Astrophysics Data System (ADS)

    Ahmed, Sohail; Chou, Amy; Sem, K. P.; Thankiah, Sudaharan; Wright, Graham; Lim, John; Hariharan, Srivats

    2014-03-01

    IRSp53 is a Cdc42 effector and a member of the Inverse-Bin-Amphiphysins-Rvs (I-BAR) domain family which can induce negative membrane curvature. IRSp53 generates filopodia by coupling membrane protrusion (I-BAR domain) with actin dynamics through its SH3 domain binding partners. Dynamin 1 (Dyn1), a large GTPase associated with endocytosis, is a novel interacting partner of IRSp53 that localises to filopodia. Using rapid time-lapse TIRF microscopy we have shown that Dyn1 localized to a subcellular region just behind Mena at the leading edge, or in filopodial tip complexes when co-expressed with IRSp53. Dyn1-GFP was strongly localized in the filopodial shaft during the early phase of elongation, after which it moved rearward, suggestive of a role in early filopodia assembly. Mena and Eps8, accumulate at the tip complex in sequence and are involved in filopodial extension and retraction, respectively (Chou at al, 2014 submitted). Here we describe the use of dSTORM to investigate the molecular architecture of filopodia and in particular the size of the F-actin bundle in these structures. The data suggest that direct Stochastic Optical Reconstruction Microscopy (dSTORM) in combination with other techniques will allow the molecular architecture of

  15. Approaches for probing the sequence space of substrates recognized by molecular chaperones

    PubMed Central

    Kota, Pradeep; Dokholyan, Nikolay V.

    2011-01-01

    Neurodegeneration, the progressive loss of function in neurons that eventually leads to their death, is the cause of many neurodegenerative disorders including Alzheimer’s, Parkinson’s, and Huntington’s diseases. Protein aggregation is a hallmark of most neurodegenerative diseases, where unfolded proteins form intranuclear, cytosolic, and extracellular insoluble aggregates in neurons. Mounting evidence from studies in neurodegenerative disease models shows that molecular chaperones, key regulators of protein aggregation and degradation, play critical roles in the progression of neurodegeneration. Although chaperones exhibit promiscuity in their substrate specificity, specific molecular features are required for substrate recognition. Understanding the basis for substrate recognition by chaperones will aid in the development of therapeutic strategies that regulate chaperone expression levels in order to combat neurodegeneration. Many experimental techniques, including alanine scanning mutagenesis and phage display library screening, have been developed and applied to understand the basis of substrate recognition by chaperones. Here, we present computational algorithms that can be applied to rapidly screen the sequence space of potential substrates to determine the sequence and structural requirements for substrate recognition by chaperones. PMID:21195183

  16. Approaches for probing the sequence space of substrates recognized by molecular chaperones.

    PubMed

    Kota, Pradeep; Dokholyan, Nikolay V

    2011-03-01

    Neurodegeneration, the progressive loss of function in neurons that eventually leads to their death, is the cause of many neurodegenerative disorders including Alzheimer's, Parkinson's, and Huntington's diseases. Protein aggregation is a hallmark of most neurodegenerative diseases, where unfolded proteins form intranuclear, cytosolic, and extracellular insoluble aggregates in neurons. Mounting evidence from studies in neurodegenerative disease models shows that molecular chaperones, key regulators of protein aggregation and degradation, play critical roles in the progression of neurodegeneration. Although chaperones exhibit promiscuity in their substrate specificity, specific molecular features are required for substrate recognition. Understanding the basis for substrate recognition by chaperones will aid in the development of therapeutic strategies that regulate chaperone expression levels in order to combat neurodegeneration. Many experimental techniques, including alanine scanning mutagenesis and phage display library screening, have been developed and applied to understand the basis of substrate recognition by chaperones. Here, we present computational algorithms that can be applied to rapidly screen the sequence space of potential substrates to determine the sequence and structural requirements for substrate recognition by chaperones. Copyright © 2010 Elsevier Inc. All rights reserved.

  17. Ultrafast probing of ejection dynamics of Rydberg atoms and molecular fragments from electronically excited helium nanodroplets.

    PubMed

    Bünermann, Oliver; Kornilov, Oleg; Haxton, Daniel J; Leone, Stephen R; Neumark, Daniel M; Gessner, Oliver

    2012-12-07

    The ejection dynamics of Rydberg atoms and molecular fragments from electronically excited helium nanodroplets are studied with time-resolved extreme ultraviolet ion imaging spectroscopy. At excitation energies of 23.6 ± 0.2 eV, Rydberg atoms in n = 3 and n = 4 states are ejected on different time scales and with significantly different kinetic energy distributions. Specifically, n = 3 Rydberg atoms are ejected with kinetic energies as high as 0.85 eV, but their appearance is delayed by approximately 200 fs. In contrast, n = 4 Rydberg atoms appear within the time resolution of the experiment with considerably lower kinetic energies. Major features in the Rydberg atom kinetic energy distributions for both principal quantum numbers can be described within a simple elastic scattering model of localized perturbed atomic Rydberg atoms that are expelled from the droplet due to their repulsive interaction with the surrounding helium bath. Time-dependent kinetic energy distributions of He(2) (+) and He(3) (+) ions are presented that support the formation of molecular ions in an indirect droplet ionization process and the ejection of neutral Rydberg dimers on a similar time scale as the n = 3 Rydberg atoms.

  18. Probing irradiation induced DNA damage mechanisms using excited state Car-Parrinello molecular dynamics

    NASA Astrophysics Data System (ADS)

    Markwick, Phineus R. L.; Doltsinis, Nikos L.; Schlitter, Jürgen

    2007-01-01

    Photoinduced proton transfer in the Watson-Crick guanine (G)-cytosine (C) base pair has been studied using Car-Parrinello molecular dynamics (CP-MD). A flexible mechanical constraint acting on all three hydrogen bonds in an unbiased fashion has been devised to explore the free energy profile along the proton transfer coordinate. The lowest barrier has been found for proton transfer from G to C along the central hydrogen bond. The resulting charge transfer excited state lies energetically close to the electronic ground state suggesting the possibility of efficient radiationless decay. It is found that dynamic, finite temperature fluctuations significantly reduce the energy gap between the ground and excited states for this charge transfer product, promoting the internal conversion process. A detailed analysis of the internal degrees of freedom reveals that the energy gap is considerably reduced by out-of-plane molecular vibrations, in particular. Consequently, it appears that considering only the minimum energy path provides an upper-bound estimate of the associated energy gap compared to the full-dimension dynamical reaction coordinate. Furthermore, the first CP-MD simulations of the G-C base pair in liquid water are presented, and the effects of solvation on its electronic structure are analyzed.

  19. Carotenoid radical cations as a probe for the molecular mechanism of nonphotochemical quenching in oxygenic photosynthesis.

    PubMed

    Amarie, Sergiu; Standfuss, Jörg; Barros, Tiago; Kühlbrandt, Werner; Dreuw, Andreas; Wachtveitl, Josef

    2007-04-05

    Nonphotochemical quenching (NPQ) is a fundamental mechanism in photosynthesis which protects plants against excess excitation energy and is of crucial importance for their survival and fitness. Recently, carotenoid radical cation (Car*+) formation has been discovered to be a key step for the feedback deexcitation quenching mechanism (qE), a component of NPQ, of which the molecular mechanism and location is still unknown. We have generated and characterized carotenoid radical cations by means of resonant two color, two photon ionization (R2C2PI) spectroscopy. The Car*+ bands have maxima located at 830 nm (violaxanthin), 880 nm (lutein), 900 nm (zeaxanthin), and 920 nm (beta-carotene). The positions of these maxima depend strongly on solution conditions, the number of conjugated C=C bonds, and molecular structure. Furthermore, R2C2PI measurements on the light-harvesting complex of photosystem II (LHC II) samples with or without zeaxanthin (Zea) reveal the violaxanthin (Vio) radical cation (Vio*+) band at 909 nm and the Zea*+ band at 983 nm. The replacement of Vio by Zea in the light-harvesting complex II (LHC II) has no influence on the Chl excitation lifetime, and by exciting the Chls lowest excited state, no additional rise and decay corresponding to the Car*+ signal observed previously during qE was detected in the spectral range investigated (800-1050 nm). On the basis of our findings, the mechanism of qE involving the simple replacement of Vio with Zea in LHC II needs to be reconsidered.

  20. Probing the flexibility of tropomyosin and its binding to filamentous actin using molecular dynamics simulations.

    PubMed

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

    2013-10-15

    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.

  1. Combined spectroscopic and molecular docking approach to probing binding interactions between lovastatin and calf thymus DNA.

    PubMed

    Chen, C-B; Chen, J; Wang, J; Zhu, Y-Y; Shi, J-H

    2015-11-01

    The binding interaction of lovastatin with calf thymus DNA (ct-DNA) was studied using UV/Vis absorption spectroscopy, fluorescence emission spectroscopy, circular dichroism (CD), viscosity measurement and molecular docking methods. The experimental results showed that there was an obvious binding interaction of lovastatin with ct-DNA and the binding constant (Kb ) was 5.60 × 10(3) M(-1) at 298 K. In the binding process of lovastatin with ct-DNA, the enthalpy change (ΔH(0)) and entropy change (ΔS(0)) were -24.9 kJ/mol and -12.0 J/mol/K, respectively, indicating that the main binding interaction forces were van der Waal's force and hydrogen bonding. The molecular docking results suggested that lovastatin preferred to bind on the minor groove of different B-DNA fragments and the conformation change of lovastatin in the lovastatin-DNA complex was obviously observed, implying that the flexibility of lovastatin molecule plays an important role in the formation of the stable lovastatin-ct-DNA complex. Copyright © 2015 John Wiley & Sons, Ltd.

  2. Probing irradiation induced DNA damage mechanisms using excited state Car-Parrinello molecular dynamics.

    PubMed

    Markwick, Phineus R L; Doltsinis, Nikos L; Schlitter, Jürgen

    2007-01-28

    Photoinduced proton transfer in the Watson-Crick guanine (G)-cytosine (C) base pair has been studied using Car-Parrinello molecular dynamics (CP-MD). A flexible mechanical constraint acting on all three hydrogen bonds in an unbiased fashion has been devised to explore the free energy profile along the proton transfer coordinate. The lowest barrier has been found for proton transfer from G to C along the central hydrogen bond. The resulting charge transfer excited state lies energetically close to the electronic ground state suggesting the possibility of efficient radiationless decay. It is found that dynamic, finite temperature fluctuations significantly reduce the energy gap between the ground and excited states for this charge transfer product, promoting the internal conversion process. A detailed analysis of the internal degrees of freedom reveals that the energy gap is considerably reduced by out-of-plane molecular vibrations, in particular. Consequently, it appears that considering only the minimum energy path provides an upper-bound estimate of the associated energy gap compared to the full-dimension dynamical reaction coordinate. Furthermore, the first CP-MD simulations of the G-C base pair in liquid water are presented, and the effects of solvation on its electronic structure are analyzed.

  3. Can we accurately quantify nanoparticle associated proteins when constructing high-affinity MRI molecular imaging probes?

    PubMed

    Rimkus, Gabriella; Bremer-Streck, Sibylle; Grüttner, Cordula; Kaiser, Werner Alois; Hilger, Ingrid

    2011-01-01

    Targeted magnetic resonance contrast agents (e.g. iron oxide nanoparticles) have the potential to become highly selective imaging tools. In this context, quantification of the coupled amount of protein is essential for the design of antibody- or antibody fragment-conjugated nanoparticles. Nevertheless, the presence of magnetic iron oxide nanoparticles is still an unsolved problem for this task. The aim of the present work was to clarify whether proteins can be reliably quantified directly in the presence of magnetic iron oxide nanoparticles without the use of fluorescence or radioactivity. Protein quantification via Bradford was not influenced by the presence of magnetic iron oxide nanoparticles (0-17.2 mmol Fe l(-1) ). Instead, bicinchoninic acid based assay was, indeed, distinctly affected by the presence of nanoparticle-iron in suspension (0.1-17.2 mmol Fe l(-1) ), although the influence was linear. This observation allowed for adequate mathematical corrections with known iron content of a given nanoparticle. The applicability of our approach was demonstrated by the determination of bovine serum albumin (BSA) content coupled to dextrane-coated magnetic nanoparticles, which was found with the QuantiPro Bicinchoninic acid assay to be of 1.5 ± 0.2 µg BSA per 1 mg nanoparticle. Both Bradford and bicinchoninic acid assay protein assays allow for direct quantification of proteins in the presence of iron oxide containing magnetic nanoparticles, without the need for the introduction of radioactivity or fluorescence modules. Thus in future it should be possible to make more precise estimations about the coupled protein amount in high-affinity targeted MRI probes for the identification of specific molecules in living organisms, an aspect which is lacking in corresponding works published so far. Additionally, the present protein coupling procedures can be drastically improved by our proposed protein quantification method.

  4. Insulin-Insulin-like Growth Factors Hybrids as Molecular Probes of Hormone:Receptor Binding Specificity.

    PubMed

    Křížková, Květoslava; Chrudinová, Martina; Povalová, Anna; Selicharová, Irena; Collinsová, Michaela; Vaněk, Václav; Brzozowski, Andrzej M; Jiráček, Jiří; Žáková, Lenka

    2016-05-31

    Insulin, insulin-like growth factors 1 and 2 (IGF-1 and -2, respectively), and their receptors (IR and IGF-1R) are the key elements of a complex hormonal system that is essential for the development and functioning of humans. The C and D domains of IGFs (absent in insulin) likely play important roles in the differential binding of IGF-1 and -2 to IGF-1R and to the isoforms of IR (IR-A and IR-B) and specific activation of these receptors. Here, we attempted to probe the impact of IGF-1 and IGF-2 D domains (DI and DII, respectively) and the IGF-2 C domain (CII) on the receptor specificity of these hormones. For this, we made two types of insulin hybrid analogues: (i) with the C-terminus of the insulin A chain extended by the amino acids from the DI and DII domains and (ii) with the C-terminus of the insulin B chain extended by some amino acids derived from the CII domain. The receptor binding affinities of these analogues and their receptor autophosphorylation potentials were characterized. Our results indicate that the DI domain has a more negative impact than the DII domain does on binding to IR, and that the DI domain Pro-Leu-Lys residues are important factors for a different IR-A versus IR-B binding affinity of IGF-1. We also showed that the additions of amino acids that partially "mimic" the CII domain, to the C-terminus of the insulin B chain, change the binding and autophosphorylation specificity of insulin in favor of the "metabolic" IR-B isoform. This opens new venues for rational enhancement of insulin IR-B specificity by modifications beyond the C-terminus of its B chain.

  5. Ultra-Broadband Two-Dimensional Electronic Spectroscopy and Pump-Probe Microscopy of Molecular Systems

    NASA Astrophysics Data System (ADS)

    Spokoyny, Boris M.

    Ultrafast spectroscopy offers an unprecedented view on the dynamic nature of chemical reactions. From charge transfer in semiconductors to folding and isomerization of proteins, these all important processes can now be monitored and in some instances even controlled on real, physical timescales. One of the biggest challenges of ultrafast science is the incredible energetic complexity of most systems. It is not uncommon to encounter macromolecules or materials with absorption spectra spanning significant portions of the visible spectrum. Monitoring a multitude of electronic and vibrational transitions, all dynamically interacting with each other on femtosecond timescales poses a truly daunting experimental task. The first part of this thesis deals with the development of a novel Two-Dimensional Electronic Spectroscopy (2DES) and its associated, advanced detection methodologies. Owing to its ultra-broadband implementation, this technique enables us to monitor femtosecond chemical dynamics that span the energetic landscape of the entire visible spectrum. In order to demonstrate the utility of our method, we apply it to two laser dye molecules, IR-144 and Cresyl Violet. Variation of photophysical properties on a microscopic scale in either man-made or naturally occurring systems can have profound implications on how we understand their macroscopic properties. Recently, inorganic hybrid perovskites have been tapped as the next generation solar energy harvesting materials. Their remarkable properties include low exciton binding energy, low exciton recombination rates and long carrier diffusion lengths. Nevertheless, considerable variability in device properties made with nearly identical preparation methods has puzzled the community. In the second part of this thesis we use non-linear pump probe microscopy to study the heterogeneous nature of femtosecond carrier dynamics in thin film perovskites. We show that the local morphology of the perovskite thin films has a

  6. Probing the structure and function of biopolymer-carbon nanotube hybrids with molecular dynamics

    NASA Astrophysics Data System (ADS)

    Johnson, Robert R.

    2009-12-01

    Nanoscience deals with the characterization and manipulation of matter on the atomic/molecular size scale in order to deepen our understanding of condensed matter and develop revolutionary technology. Meeting the demands of the rapidly advancing nanotechnological frontier requires novel, multifunctional nanoscale materials. Among the most promising nanomaterials to fulfill this need are biopolymer-carbon nanotube hybrids (Bio-CNT). Bio-CNT consists of a single-walled carbon nanotube (CNT) coated with a self-assembled layer of biopolymers such as DNA or protein. Experiments have demonstrated that these nanomaterials possess a wide range of technologically useful properties with applications in nanoelectronics, medicine, homeland security, environmental safety and microbiology. However, a fundamental understanding of the self-assembly mechanics, structure and energetics of Bio-CNT is lacking. The objective of this thesis is to address this deficiency through molecular dynamics (MD) simulation, which provides an atomic-scale window into the behavior of this unique nanomaterial. MD shows that Bio-CNT composed of single-stranded DNA (ssDNA) self-assembles via the formation of high affinity contacts between DNA bases and the CNT sidewall. Calculation of the base-CNT binding free energy by thermodynamic integration reveals that these contacts result from the attractive pi--pi stacking interaction. Binding affinities follow the trend G > A > T > C. MD reveals that long ssDNA sequences are driven into a helical wrapping about CNT with a sub-10 nm pitch by electrostatic and torsional interactions in the backbone. A large-scale replica exchange molecular dynamics simulation reveals that ssDNA-CNT hybrids are disordered. At room temperature, ssDNA can reside in several low-energy conformations that contain a sequence-specific arrangement of bases detached from CNT surface. MD demonstrates that protein-CNT hybrids composed of the Coxsackie-adenovirus receptor are biologically

  7. Probing the molecular structures of plasma-damaged and surface-repaired low-k dielectrics.

    PubMed

    Zhang, Xiaoxian; Myers, John N; Lin, Qinghuang; Bielefeld, Jeffery D; Chen, Zhan

    2015-10-21

    Fully understanding the effect and the molecular mechanisms of plasma damage and silylation repair on low dielectric constant (low-k) materials is essential to the design of low-k dielectrics with defined properties and the integration of low-k dielectrics into advanced interconnects of modern electronics. Here, analytical techniques including sum frequency generation vibrational spectroscopy (SFG), Fourier transform infrared spectroscopy (FTIR), contact angle goniometry (CA) and X-ray photoelectron spectroscopy (XPS) have been employed to provide a comprehensive characterization of the surface and bulk structure changes of poly(methyl)silsesquioxane (PMSQ) low-k thin films before and after O2 plasma treatment and silylation repair. O2 plasma treatment altered drastically both the molecular structures and water structures at the surfaces of the PMSQ film while no bulk structural change was detected. For example, ∼34% Si-CH3 groups were removed from the PMSQ surface, and the Si-CH3 groups at the film surface tilted toward the surface after the O2 plasma treatment. The oxidation by the O2 plasma made the PMSQ film surface more hydrophilic and thus enhanced the water adsorption at the film surface. Both strongly and weakly hydrogen bonded water were detected at the plasma-damaged film surface during exposure to water with the former being the dominate component. It is postulated that this enhancement of both chemisorbed and physisorbed water after the O2 plasma treatment leads to the degradation of low-k properties and reliability. The degradation of the PMSQ low-k film can be recovered by repairing the plasma-damaged surface using a silylation reaction. The silylation method, however, cannot fully recover the plasma induced damage at the PMSQ film surface as evidenced by the existence of hydrophilic groups, including C-O/C[double bond, length as m-dash]O and residual Si-OH groups. This work provides a molecular level picture on the surface structural changes of low

  8. 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

  9. 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

  10. Circularly Polarized X Rays: Another Probe of Ultrafast Molecular Decay Dynamics

    SciTech Connect

    Travnikova, Oksana; Lindblad, Andreas; Nicolas, Christophe; Soederstroem, Johan; Kimberg, Victor; Miron, Catalin; Liu Jicai; Gel'mukhanov, Faris

    2010-12-03

    Dissociative nuclear motion in core-excited molecular states leads to a splitting of the fragment Auger lines: the Auger-Doppler effect. We present here for the first time experimental evidence for an Auger-Doppler effect following F1s{yields}a{sub 1g}* inner-shell excitation by circularly polarized x rays in SF{sub 6}. In spite of a uniform distribution of the dissociating S-F bonds near the polarization plane of the light, the intersection between the subpopulation of molecules selected by the core excitation with the cone of dissociation induces a strong anisotropy in the distribution of the S-F bonds that contributes to the scattering profile measured in the polarization plane.

  11. 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.

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

    PubMed

    Bian, Xue-Bin; Bandrauk, André D

    2014-11-07

    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.

  13. Accelerating ab initio Molecular Dynamics and Probing the Weak Dispersive Forces in Dense Liquid Hydrogen

    NASA Astrophysics Data System (ADS)

    Mazzola, Guglielmo; Sorella, Sandro

    2017-01-01

    We propose an ab initio molecular dynamics method, capable of dramatically reducing the autocorrelation time required for the simulation of classical and quantum particles at finite temperatures. The method is based on an efficient implementation of a first order Langevin dynamics modified by means of a suitable, position dependent acceleration matrix S . Here, we apply this technique to both Lennard-Jones models, to demonstrate the accuracy and speeding-up of the sampling, and within a quantum Monte Carlo based wave function approach, for determining the phase diagram of high-pressure hydrogen with simulations much longer than the autocorrelation time. With the proposed method, we are able to equilibrate in a few hundred steps even close to the liquid-liquid phase transition (LLT). Within our approach, we find that the LLT transition is consistent with recent density functionals predicting a much larger transition pressure when the long range dispersive forces are taken into account.

  14. Probing diameter-selective solubilisation of carbon nanotubes by reversible cyclic peptides using molecular dynamics simulations.

    PubMed

    Friling, S R; Notman, R; Walsh, T R

    2010-01-01

    Molecular dynamics simulations are used to explore the encapsulation behaviour of reversible cyclic peptides when adsorbed onto single-walled carbon nanotubes (CNTs) in aqueous solution. Our findings suggest that CNT encapsulation via cyclisation of a single peptide chain is relatively less likely, compared with encapsulation via two-chain complexes. These two-chain complexes comprise pairings of the motifs identified for single-chain adsorption. Our simulation data are compared with existing experimental findings [A. Ortiz-Acevedo et al., J. Am. Chem. Soc., 2005, 127, 9512], for relevant CNT diameters, and are found to be consistent with the experimental results. Our data help to explain the limited diameter selectivity reported by Ortiz-Acevedo et al. These findings should help in the optimisation and future design of peptides capable of enhanced selectivity for specific CNT diameters.

  15. 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.

  16. A modified staining technique for arbuscular mycorrhiza compatible with molecular probes.

    PubMed

    Pitet, M; Camprubí, A; Calvet, C; Estaún, V

    2009-02-01

    The effects of the different steps of the root staining on the arbuscular mycorrhizal (AM) fungal rDNA extraction and amplification have been assessed. The results obtained using molecular techniques are compared with those obtained from fresh, non-stained leek roots. A modified staining procedure that eliminates heating, the use of hydrochloric acid and trypan blue, has been proved to be the most adequate to observe the AM colonisation in different plant species with/without lignified roots allowing at the same time the subsequent rDNA extraction and amplification from the stained roots. The staining technique decreased the sensitivity of the process and a higher number of roots had to be used to obtain enough material for a positive amplification. The extraction and amplification process was reliable up to 3 days after staining. A week after staining, the amplification was not dependable and after 2 weeks there was no amplification from stained material.

  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. Simple fluorescence-based detection of protein kinase A activity using a molecular beacon probe.

    PubMed

    Ma, Changbei; Lv, Xiaoyuan; Wang, Kemin; Jin, Shunxin; Liu, Haisheng; Wu, Kefeng; Zeng, Weimin

    2017-06-08

    Protein kinase A was detected by quantifying the amount of ATP used after a protein kinase reaction. The ATP assay was performed using the T4 DNA ligase and a molecular beacon (MB). In the presence of ATP, DNA ligase catalyzed the ligation of short DNA. The ligation product then hybridized to MB, resulting in a fluorescence enhancement of the MB. This assay was capable of determining protein kinase A in the range of 12.5∼150 nM, with a detection limit of 1.25 nM. Furthermore, this assay could also be used to investigate the effect of genistein on protein kinase A. It was a universal, non-radioisotopic, and homogeneous method for assaying protein kinase A.

  19. Mechanism of Interaction between the General Anesthetic Halothane and a Model Ion Channel Protein, III: Molecular Dynamics Simulation Incorporating a Cyanophenylalanine Spectroscopic Probe

    PubMed Central

    Zou, Hongling; Liu, Jing; Blasie, J. Kent

    2009-01-01

    A nitrile-derived amino acid, PheCN, has been used as an internal spectroscopic probe to study the binding of an inhalational anesthetic to a model membrane protein. The infrared spectra from experiment showed a blue-shift of the nitrile vibrational frequency in the presence of the anesthetic halothane. To interpret the infrared results and explore the nature of the interaction between halothane and the model protein, all-atom molecular dynamics (MD) simulations have been used to probe the structural and dynamic properties of the protein in the presence and absence of one halothane molecule. The frequency shift analyzed from MD simulations agrees well with the experimental infrared results. Decomposition of the forces acting on the nitrile probes demonstrates an indirect impact on the probes from halothane, namely a change of the protein's electrostatic local environment around the probes induced by halothane. Although the halothane remains localized within the designed hydrophobic binding cavity, it undergoes a significant amount of translational and rotational motion, modulated by the interaction of the trifluorine end of halothane with backbone hydrogens of the residues forming the cavity. This dominant interaction between halothane and backbone hydrogens outweighs the direct interaction between halothane and the nitrile groups, making it a good “spectator” probe of the halothane-protein interaction. These MD simulations provide insight into action of anesthetic molecules on the model membrane protein, and also support the further development of nitrile-labeled amino acids as spectroscopic probes within the designed binding cavity. PMID:19450489

  20. Dynamic structure of retinylidene ligand of rhodopsin probed by molecular simulations.

    PubMed

    Lau, Pick-Wei; Grossfield, Alan; Feller, Scott E; Pitman, Michael C; Brown, Michael F

    2007-09-28

    Rhodopsin is currently the only available atomic-resolution template for understanding biological functions of the G protein-coupled receptor (GPCR) family. The structural basis for the phenomenal dark state stability of 11-cis-retinal bound to rhodopsin and its ultrafast photoreaction are active topics of research. In particular, the beta-ionone ring of the retinylidene inverse agonist is crucial for the activation mechanism. We analyzed a total of 23 independent, 100 ns all-atom molecular dynamics simulations of rhodopsin embedded in a lipid bilayer in the microcanonical (N,V,E) ensemble. Analysis of intramolecular fluctuations predicts hydrogen-out-of-plane (HOOP) wagging modes of retinal consistent with those found in Raman vibrational spectroscopy. We show that sampling and ergodicity of the ensemble of simulations are crucial for determining the distribution of conformers of retinal bound to rhodopsin. The polyene chain is rigidly locked into a single, twisted conformation, consistent with the function of retinal as an inverse agonist in the dark state. Most surprisingly, the beta-ionone ring is mobile within its binding pocket; interactions are non-specific and the cavity is sufficiently large to enable structural heterogeneity. We find that retinal occupies two distinct conformations in the dark state, contrary to most previous assumptions. The beta-ionone ring can rotate relative to the polyene chain, thereby populating both positively and negatively twisted 6-s-cis enantiomers. This result, while unexpected, strongly agrees with experimental solid-state (2)H NMR spectra. Correlation analysis identifies the residues most critical to controlling mobility of retinal; we find that Trp265 moves away from the ionone ring prior to any conformational transition. Our findings reinforce how molecular dynamics simulations can challenge conventional assumptions for interpreting experimental data, especially where existing models neglect conformational fluctuations.

  1. Probing the importance of lipid diversity in cell membranes via molecular simulation.

    PubMed

    Khakbaz, Pouyan; Klauda, Jeffery B

    2015-11-01

    Lipid membranes in prokaryotes and eukaryotes have a wide array of lipids that are necessary for proper membrane structure and function. In this paper, an introduction to lipid diversity in biology and a mini-review on how molecular simulations have been used to model biological membranes (primarily limited to one to three lipid types in most simulation-based models) is provided, which motivates the use of all-atom molecular dynamics (MD) simulations to study the effect of lipid diversity on properties of realistic membrane models of prokaryotes and eukaryotes. As an example, cytoplasmic membrane models of Escherichia coli were developed at different stages of the colony growth cycle (early-log, mid-log, stationary and overnight). The main difference between lipid compositions at each stage was the concentration of a cyclopropane-containing moiety on the sn-2 lipid acyl chain (cyC17:0). Triplicate MD simulations for each stage were run for 300 ns to study the influence of lipid diversity on the surface area per lipid, area compressibility modulus, deuterium order parameters, and electron density profiles. The overnight stage (also known as the death stage) had the highest average surface area per lipid, highest rigidity, and lowest bilayer thickness compare to other stages of E. coli cytoplasmic membrane. Although bilayer thickness did depend on the growth stage, the changes between these were small suggesting that the hydrophobic core of transmembrane proteins fit well with the membrane in all growth stages. Although it is still common practise in MD simulations of membrane proteins to use simple one- or two-component membranes, it can be important to use diverse lipid model membranes when membrane protein structure and function are influenced by changes in lipid membrane composition.

  2. 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.

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

    PubMed

    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: R (2) Tr = 0.9576 and RMSETr = 0.0958 for the training set; Q (2) CV = 0.9239 and RMSECV = 0.1304 for the LOO-CV set as well as Q (2) Ext = 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.

  4. Probing diameter-selective solubilisation of carbon nanotubes by reversible cyclic peptides using molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Friling, S. R.; Notman, R.; Walsh, T. R.

    2010-01-01

    Molecular dynamics simulations are used to explore the encapsulation behaviour of reversible cyclic peptides when adsorbed onto single-walled carbon nanotubes (CNTs) in aqueous solution. Our findings suggest that CNT encapsulation via cyclisation of a single peptide chain is relatively less likely, compared with encapsulation via two-chain complexes. These two-chain complexes comprise pairings of the motifs identified for single-chain adsorption. Our simulation data are compared with existing experimental findings [A. Ortiz-Acevedo et al., J. Am. Chem. Soc., 2005, 127, 9512], for relevant CNT diameters, and are found to be consistent with the experimental results. Our data help to explain the limited diameter selectivity reported by Ortiz-Acevedo et al. These findings should help in the optimisation and future design of peptides capable of enhanced selectivity for specific CNT diameters.Molecular dynamics simulations are used to explore the encapsulation behaviour of reversible cyclic peptides when adsorbed onto single-walled carbon nanotubes (CNTs) in aqueous solution. Our findings suggest that CNT encapsulation via cyclisation of a single peptide chain is relatively less likely, compared with encapsulation via two-chain complexes. These two-chain complexes comprise pairings of the motifs identified for single-chain adsorption. Our simulation data are compared with existing experimental findings [A. Ortiz-Acevedo et al., J. Am. Chem. Soc., 2005, 127, 9512], for relevant CNT diameters, and are found to be consistent with the experimental results. Our data help to explain the limited diameter selectivity reported by Ortiz-Acevedo et al. These findings should help in the optimisation and future design of peptides capable of enhanced selectivity for specific CNT diameters. Electronic supplementary information (ESI) available: Table S1 and Figs. S2-S7. See DOI: 10.1039/b9nr00226j

  5. Lipidic Carbo-benzenes: Molecular Probes of Magnetic Anisotropy and Stacking Properties of α-Graphyne.

    PubMed

    Zhu, Chongwei; Rives, Arnaud; Duhayon, Carine; Maraval, Valérie; Chauvin, Remi

    2017-01-20

    Solubilization of the C18 fundamental circuit of α-graphyne has been envisaged by decoration with aliphatic chains R = n-CnH2n+1. The synthesis and characterization of p-dialkyl-tetraphenyl-carbo-benzenes (n = 2, 8, 14, 20) are thus presented and compared to the monoalkyl series produced concomitantly. In both series, a dramatic enhancement of solubility in organic solvents (CH2Cl2, CHCl3) is observed for n ≥ 8, and in the dialkyl series, the melting-decomposition temperature of the solid products is shown to decrease linearly from 208 °C for n = 2 to 149 °C for n = 20. Fluoroalkyl analogues with R = n-C8H4F13 are also described. The products display classical UV-vis electronic spectra of carbo-benzenes in solution (λmax = 445.5 ± 1 nm, ε ≈ 200 000 L·mol(-1)·cm(-1)). They are also characterized by UV-vis absorption in the solid state, which is found to be correlated with the color and crystal packing. The methylene groups of R provide an experimental probe of the magnetic anisotropy and aromaticity of the C18 ring through the progressive NMR shielding of the (1)H nuclei from ca. 4.70 to 1.25 ppm going away from the border of the ring (as far as 8 Å away). All alkyl-carbo-benzenes were also found to be highly crystalline. Seven of them have been characterized by X-ray diffraction analysis and the C18 columnar packing compared in a systematic manner. Crystals of the diethyl and bistetradecyl derivatives, containing no solvent molecule, provided the first examples of direct π-stacking of carbo-benzene rings, with inter-ring distances very close to calculated interlayer distances in AB and ABC α-graphityne (3.255 and 3.206 Å vs 3.266 and 3.201 Å, respectively).

  6. Detection of pulmonary metastases with the novel radiolabeled molecular probe, 99mTc-RRL

    PubMed Central

    Yao, Ning; Yan, Ping; Wang, Rong-Fu; Zhang, Chun-Li; Ma, Chao; Chen, Xue-Qi; Zhao, Qian; Hao, Pan

    2015-01-01

    Background: To improve the detection of pulmonary metastases, experimental blood-borne pulmonary metastasis mouse models were established using three intravenously administered cell lines. In a previous study we demonstrated that 99mTc-radiolabeled arginine-arginine-leucine (RRL) could be used to non-invasively image malignant tumors. Methods: 99mTc-RRL was prepared and injected intravenously in mice with pulmonary metastases that arose from the intravenous injection of HepG2, B16, and Hela cells. The bio-distribution and imaging of 99mTc-RRL were determined in different pulmonary metastases mouse models and in normal mice. Results: 99mTc-RRL exhibited higher uptake values in the lungs of pulmonary metastatic mice compared to normal mice (P<0.05; 3.92±0.48% ID/g 2 h post-injection and 3.89±0.36% ID/g 4 h post-injection in metastatic hepatic carcinoma [HepG2]-bearing lungs; 5.49±0.84% ID/g 2 h post-injection and 5.11±0.75% ID/g 4 h post-injection in metastatic melanoma [B16]-bearing lungs; 3.72±0.52% ID/g 2 h post-injection and 3.51±0.35% ID/g 4 h post-injection in metastatic cervical carcinoma [Hela]-bearing lungs; 2.38±0.20% ID/g 2 h post-injection and 2.11±0.24% ID/g 4 h post-injection in normal lungs). The pulmonary metastatic lesions were clearly visualized using 99mTc-RRL. Conclusions: 99mTc-RRL exhibited favorable metastatic tumor targeting and imaging properties, thus highlighting its potential as an effective imaging probe for detection of pulmonary metastases. 99mTc-RRL can be used as a reasonable supplement to 18F-FDG imaging in the non-invasive imaging of tumor angiogenesis. PMID:25932101

  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

    2011-10-04

    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 ion-molecule structure and dynamics in isolated molecular clusters and proteins

    NASA Astrophysics Data System (ADS)

    Abate, Yohannes

    Ion-molecule interactions in isolated molecular clusters and proteins are studied in this work using experimental and theoretical methods. Photodissociation spectroscopy and chemical dynamics of several metal ion-molecule clusters are studied. The experimental tool used for these studies is an Angular Reflectron Time Of Flight Mass Spectrometer (ARTOFMS). The experimental work is supported by ab initio electronic structure calculations on the Gaussian and GAMESS platforms. This work also describes a computational study of the interaction of protonated histidine with other aromatic residues in proteins. We have studied the photodissociation spectroscopy of weakly bound Zn +(H2O) and Zn+(D2O) bimolecular complexes. We assign two molecular absorption bands in the near UV correlating to Zn+ (4s-4p)-metal centered transitions, and identify vibrational progressions associated with both intermolecular and intramolecular vibrational modes of the cluster. Partially resolved rotational structure is consistent with a C2 V equilibrium complex geometry. The photodissociation spectroscopy and chemical dynamics of Zn +-formaldehyde and Zn+-acetaldehyde clusters are investigated in the near UV spectral range. The work is also supported by ab initio electronic structure calculations to study the ground-state bonding and interactions in the low-lying doublet excited states. We identify absorption bands corresponding to photoinduced charge transfer, Zn+(4s-4p)-based transitions, and aldehyde-based excitations. We propose a reaction mechanism for the reactive dissociation that proceeds via H-atom abstraction on the charge-transfer surface. This work shows important differences with results from earlier experiments on Mg+- and Ca+-aldehyde complexes despite the similar valence character for these metal ions. In the study of Mg+-acetic acid we observe three distinct absorption bands, two red-shifted and one blue-shifted from the Mg +(3s ← 3p) resonance at 280 nm (35714 cm-1). We

  9. VCD spectroscopy as a novel probe for chirality transfer in molecular interactions.

    PubMed

    Sadlej, Joanna; Dobrowolski, Jan Cz; Rode, Joanna E

    2010-05-01

    Most of the research in contemporary physical chemistry is devoted to the development of methods that extend our understanding, interpretation, and capacity to predict structural properties and dynamic behavior of molecules. The optical and magnetic spectroscopies, as well as diffraction techniques, are the principal methods for studying properties of molecules, biomolecules, and biopolymers of which the vast majority are chiral. On the other hand, information on molecular configuration can be obtained mainly from optical spectroscopies because other well-established spectroscopic techniques used for structural investigations, such as crystallographic, ESR, and NMR methods, do not allow for registration of signals from an individual conformer owing to intrinsic slow response to structural changes. This is the reason why the optical spectroscopy methods, based on natural chiroptical phenomena, have become so important and their renaissance in the last decade is noticed. Vibrational circular dichroism (VCD) spectroscopy is one such chiroptical technique that sheds new light on many important phenomena studied intensively. We provide an overview of recent theoretical predictions and innovative VCD observations of chirality transfer (called by other authors "induced chirality") from a chiral molecule to an achiral one as a result of hydrogen bond interactions between them. In this tutorial review we search for answers as to whether we can obtain further information about intermolecular interactions using the VCD technique. In our opinion this technique has opened new horizons for both understanding and monitoring intermolecular interactions and it could be used as a relatively new and powerful physicochemical method.

  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. Probing the interaction of anthraquinone with DNA by spectroscopy, molecular modeling and cancer cell imaging technique.

    PubMed

    Yang, Lei; Fu, Zheng; Niu, Xiaoqing; Zhang, Guisheng; Cui, Fengling; Zhou, Chunwu

    2015-05-25

    A new anthraquinone derivative, (E)-2-(1-(4,5-dihydroxy-6-(hydroxymethyl)-tetrahydro-2H-pyran-2-yloxyimino)ethyl)-1,4-dihydroxyanthracene-9,10-dione (AODGlc), was synthesized and its binding properties towards DNA were explored under physiological conditions by fluorescence spectroscopy, DNA melting as well as docking techniques. The experimental results revealed that AODGlc could bind to calf thymus DNA (ctDNA) through intercalation between DNA base pairs. The values of thermodynamic parameters at different temperatures including ΔG, ΔH, and ΔS and the molecular modeling study implied that hydrophobic interactions and hydrogen bonds were the main interactions in the AODGlc-ctDNA system. Cervical cancer cells (HepG2 cells) were used in cell viability assay and cell imaging experiment. AODGlc could interact with HepG2 cells and kill HepG2 cells under high concentration with nice curative effect, indicating its potential bioapplication in the future. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  12. Surface transport mechanisms in molecular glasses probed by the exposure of nano-particles

    NASA Astrophysics Data System (ADS)

    Ruan, Shigang; Musumeci, Daniele; Zhang, Wei; Gujral, Ankit; Ediger, M. D.; Yu, Lian

    2017-05-01

    For a glass-forming liquid, the mechanism by which its surface contour evolves can change from bulk viscous flow at high temperatures to surface diffusion at low temperatures. We show that this mechanistic change can be conveniently detected by the exposure of nano-particles native in the material. Despite its high chemical purity, the often-studied molecular glass indomethacin contains low-concentration particles approximately 100 nm in size and 0.3% in volume fraction. Similar particles are present in polystyrene, another often-used model. In the surface-diffusion regime, particles are gradually exposed in regions vacated by host molecules, for example, the peak of a surface grating and the depletion zone near a surface crystal. In the viscous-flow regime, particle exposure is not observed. The surface contour around an exposed particle widens over time in a self-similar manner as 3 (Bt)1/4, where B is a surface mobility constant and the same constant obtained by surface grating decay. This work suggests that in a binary system composed of slow- and fast-diffusing molecules, slow-diffusing molecules can be stranded in surface regions vacated by fast-diffusing molecules, effectively leading to phase separation.

  13. Hydrogen-bonding molecular ruler surfactants as probes of specific solvation at liquid/liquid interfaces.

    PubMed

    Siler, A Renee; Brindza, Michael R; Walker, Robert A

    2009-10-01

    Resonance-enhanced, second harmonic generation (SHG) is used to measure the electronic structure of solutes sensitive to specific solvation adsorbed to liquid/liquid and liquid/solid interfaces. Here, specific solvation refers to solvent-solute interactions that are directional and localized. N-methyl-p-methoxyaniline (NMMA) is a solute whose first allowed electronic transition wavelength remains almost constant (approximately 315 nm) in non-hydrogen-bonding solvents regardless of solvent polarity. However, in hydrogen-bond-accepting solvents such as dimethylsulfoxide, NMMA's absorbance shifts to longer wavelengths (320 nm), whereas in hydrogen-bond-donating solvents (e.g., water), the absorbance shifts to shorter wavelengths (approximately 300 nm). SHG experiments show that at alkane/silica interfaces, surface silanol groups serve as moderately strong hydrogen-bond donors as evidenced by NMMA's absorbance of 307 nm. At the carbon tetrachloride/water interface, NMMA absorbance also shifts to slightly shorter wavelengths (298 nm) implying that water molecules at this liquid/liquid interface are donating strong hydrogen bonds to the adsorbed NMMA solutes. In contrast, experiments using newly developed molecular ruler surfactants with NMMA as a model hydrophobic solute and a hydrophilic, cationic headgroup imply that, as NMMA migrates across an aqueous/alkane interface, it carries with it water that functions as a hydrogen-bond-accepting partner.

  14. C-5-disubstituted barbiturates as potential molecular probes for noninvasive matrix metalloproteinase imaging.

    PubMed

    Breyholz, Hans-Jörg; Schäfers, Michael; Wagner, Stefan; Höltke, Carsten; Faust, Andreas; Rabeneck, Helmut; Levkau, Bodo; Schober, Otmar; Kopka, Klaus

    2005-05-05

    Studies have demonstrated a positive correlation between inflammation, metastasis, or atherosclerosis and the unbalanced or culminated expression of matrix metalloproteinases (MMPs). The molecular imaging of locally upregulated MMP activity in vivo is a clinical challenge. Actually, radioligands based on nonpeptidyl MMP inhibitors (MMPIs) are currently in development as putative radiopharmaceutical agents for the noninvasive in vivo assessment of activated MMPs. Nonpeptidyl MMPIs bind to the zinc active site of the activated enzyme via mono- (e.g. carboxylate) or bidentate (e.g. hydroxamate) complexation thereby exhibiting a broad-spectrum MMP binding potency. Thus, these mentioned endopeptidase inhibitors should be useable lead compounds for the redevelopment as diagnostic MMPI radiotracers. Recently, the non-hydroxamate C-5-disubstituted pyrimidine-2,4,6-triones were disclosed as subgroup-selective MMP inhibitors. We here describe a set of fine-tuned barbiturates as a new class of MMPI radiotracers for the noninvasive in vivo visualization of activated MMPs using scintigraphic techniques such as SPECT or PET.

  15. MOLECULAR CLOUDS AS A PROBE OF COSMIC-RAY ACCELERATION IN A SUPERNOVA REMNANT

    SciTech Connect

    Fujita, Yutaka; Ohira, Yutaka; Tanaka, Shuta J.; Takahara, Fumio

    2009-12-20

    We study cosmic-ray acceleration in a supernova remnant (SNR) and the escape from it. We model nonthermal particle and photon spectra for the hidden SNR in the open cluster Westerlund 2, and the old-age mixed-morphology SNR W 28. We assume that the SNR shock propagates in a low-density cavity, which is created and heated through the activities of the progenitor stars and/or previous supernova explosions. We indicate that the diffusion coefficient for cosmic rays around the SNRs is less than approx1% of that away from them. We compare our predictions with the gamma-ray spectra of molecular clouds illuminated by the cosmic rays (Fermi and H.E.S.S.). We found that the spectral indices of the particles are approx2.3. This may be because the particles were accelerated at the end of the Sedov phase, and because energy-dependent escape and propagation of particles did not much affect the spectrum.

  16. Probing the Disordered Domain of the Nuclear Pore Complex through Coarse-Grained Molecular Dynamics Simulations

    PubMed Central

    Ghavami, Ali; Veenhoff, Liesbeth M.; van der Giessen, Erik; Onck, Patrick R.

    2014-01-01

    The distribution of disordered proteins (FG-nups) that line the transport channel of the nuclear pore complex (NPC) is investigated by means of coarse-grained molecular dynamics simulations. A one-bead-per-amino-acid model is presented that accounts for the hydrophobic/hydrophilic and electrostatic interactions between different amino acids, polarity of the solvent, and screening of free ions. The results indicate that the interaction of the FG-nups forms a high-density, doughnut-like distribution inside the NPC, which is rich in FG-repeats. We show that the obtained distribution is encoded in the amino-acid sequence of the FG-nups and is driven by both electrostatic and hydrophobic interactions. To explore the relation between structure and function, we have systematically removed different combinations of FG-nups from the pore to simulate inviable and viable NPCs that were previously studied experimentally. The obtained density distributions show that the maximum density of the FG-nups inside the pore does not exceed 185 mg/mL in the inviable NPCs, whereas for the wild-type and viable NPCs, this value increases to 300 mg/mL. Interestingly, this maximum density is not correlated to the total mass of the FG-nups, but depends sensitively on the specific combination of essential Nups located in the central plane of the NPC. PMID:25229147

  17. 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

  18. Probing the binding and spatial arrangement of molecular hydrogen in porous hosts via neutron Compton scattering.

    PubMed

    Krzystyniak, Maciej; Adams, Mark A; Lovell, Arthur; Skipper, Neal T; Bennington, Stephen M; Mayers, Jerry; Fernandez-Alonso, Felix

    2011-01-01

    The adsorption of molecular hydrogen (H2) in the alkali-graphite intercalate KC24 has been studied using simultaneous neutron diffraction and Compton scattering. Neutron Compton scattering data for the (H2)xKC24 system (x = 0-2.5) were measured at T = 1.5 K as a function of the relative orientation between the neutron beam and the intercalate c-axis. Synchronous with the above proton-recoil measurements, high-resolution diffraction patterns were measured in backscattering geometry. From these diffraction measurements, the intrinsic mosaicity of the Papyex-based intercalate was determined to be approximately 15 degrees half-width-at-half-maximum, in good agreement with previous studies [Finkelstein et al., Physica B, 2000, 291, 213]. Hydrogen uptake by the intercalate leads to a distinct and readily detectable broadening of the isotropic Compton profile compared to bulk H2, indicative of an enhanced interaction of the H2 molecule with the surrounding solid-state environment. Total proton-recoil intensities also scale linearly with the amount of adsorbed hydrogen. Taking as our starting point previous experimental and theoretical results, the isotropic widths of the proton momentum distributions can be explained on the basis of three energy scales, namely, intramolecular H-H vibrations, followed by H-H librations and H2 centre-of-mass translations. From the coverage dependence of these neutron data, we also establish an upper bound of approximately 10 meV for intermolecular hydrogen-hydrogen interactions. Finally, we observe a weak anisotropy of the width of the proton momentum distributions. Comparison of these experimental data with first-principles predictions indicates that subtle quantum mechanical effects associated with particle delocalisation and exchange lie at the heart of the observed behaviour. Overall, these results demonstrate the suitability and largely untapped potential of neutron Compton scattering to explore H2 uptake by solid-state hosts.

  19. Probing molecular conformations in momentum space: The case of n-pentane

    NASA Astrophysics Data System (ADS)

    Knippenberg, S.; Huang, Y. R.; Hajgató, B.; François, J.-P.; Deng, J. K.; Deleuze, M. S.

    2007-11-01

    A comprehensive study, throughout the valence region, of the electronic structure and electron momentum density distributions of the four conformational isomers of n-pentane is presented. Theoretical (e,2e) valence ionization spectra at high electron impact energies (1200eV+electron binding energy) and at azimuthal angles ranging from 0° to 10° in a noncoplanar symmetric kinematical setup are generated according to the results of large scale one-particle Green's function calculations of Dyson orbitals and related electron binding energies, using the third-order algebraic-diagrammatic construction [ADC(3)] scheme. The results of a focal point analysis (FPA) of relative conformer energies [A. Salam and M. S. Deleuze, J. Chem. Phys. 116, 1296 (2002)] and improved thermodynamical calculations accounting for hindered rotations are also employed in order to quantitatively evaluate the abundance of each conformer in the gas phase at room temperature and reliably predict the outcome of experiments on n-pentane employing high resolution electron momentum spectroscopy. Comparison with available photoelectron measurements confirms the suggestion that, due to entropy effects, the trans-gauche (tg) conformer strongly dominates the conformational mixture characterizing n-pentane at room temperature. Our simulations demonstrate therefore that experimental measurements of (e,2e) valence ionization spectra and electron momentum distributions would very consistently and straightforwardly image the topological changes and energy variations that molecular orbitals undergo due to torsion of the carbon backbone. The strongest fingerprints for the most stable conformer (tt) are found for the electron momentum distributions associated with ionization channels at the top of the inner-valence region, which sensitively image the development of methylenic hyperconjugation in all-staggered n-alkane chains.

  20. Use of molecular modelling to probe the mechanism of the nucleoside transporter NupG.

    PubMed

    Vaziri, Hamidreza; Baldwin, Stephen A; Baldwin, Jocelyn M; Adams, David G; Young, James D; Postis, Vincent L G

    2013-03-01

    Nucleosides play key roles in biology as precursors for salvage pathways of nucleotide synthesis. Prokaryotes import nucleosides across the cytoplasmic membrane by proton- or sodium-driven transporters belonging to the Concentrative Nucleoside Transporter (CNT) family or the Nucleoside:H(+) Symporter (NHS) family of the Major Facilitator Superfamily. The high resolution structure of a CNT from Vibrio cholerae has recently been determined, but no similar structural information is available for the NHS family. To gain a better understanding of the molecular mechanism of nucleoside transport, in the present study the structures of two conformations of the archetypical NHS transporter NupG from Escherichia coli were modelled on the inward- and outward-facing conformations of the lactose transporter LacY from E. coli, a member of the Oligosaccharide:H(+) Symporter (OHS) family. Sequence alignment of these distantly related proteins (∼ 10% sequence identity), was facilitated by comparison of the patterns of residue conservation within the NHS and OHS families. Despite the low sequence similarity, the accessibilities of endogenous and introduced cysteine residues to thiol reagents were found to be consistent with the predictions of the models, supporting their validity. For example C358, located within the predicted nucleoside binding site, was shown to be responsible for the sensitivity of NupG to inhibition by p-chloromercuribenzene sulphonate. Functional analysis of mutants in residues predicted by the models to be involved in the translocation mechanism, including Q261, E264 and N228, supported the hypothesis that they play important roles, and suggested that the transport mechanisms of NupG and LacY, while different, share common features.

  1. Probing the Chemistry and Dynamics of Hot Molecular Cores Using Highly Excited Cyanopolyynic Transitions

    NASA Astrophysics Data System (ADS)

    Loughnane, Robert John; Lique, François; Singh, Navtej; Kurtz, Stan

    2014-06-01

    A hyperfine line fitting program is presented, which decomposes an observed rotational transition into its individual hyperfine components. The fit is optimized by the use of the Levenberg-Marquardt algorithm (for non-linear fitting) or Caruana's algorithm (linearization of the Gaussian function). From the optimal fit, various parameters from the decomposed components are derived such as the linewidth dispersion, peak brightness temperature and peak position in velocity units. The closeness in frequency units of two neighbouring hyperfine components within a rotational transition spectrum allows the derivation of a more credible estimate of the optical depth for the observed source of emission. Effective smoothing of the data subsequent to the fitting procedure greatly reduces the perceived error in the determination of various physical conditions of the observed region. The technique has been employed in observations of massive hot molecular cores (HMCs), considered to be the birthplace of high mass stars. In particular, observations of the cyanopolyynes HC_3N and HC_5N, each of which include a quadrupole hyperfine structure, as well as methyl cyanide, CH_3CN, have been analysed with this technique and modelled with a radiative transfer code incorporating non-LTE conditions, in order to derive abundances and column densities for a total of 10 HMCs and 5 massive cores. Using these derived parameters for each core, we have been able to test the time-dependent chemical models presented for these species by Chapman et al. (2009) and thus verify the suitability of their usefulness as "chemical clocks" by which to constrain the ages of the observed objects. In addition to this work, a detailed study of the magnetic hyperfine structure of a selection of inversion transitions of NH_3 is presented. As part of the continuing preparatory work for Herschel, SOFIA and, in particular, ALMA - improved rest frequencies for this commonly used kinetic temperature detecting species

  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.

    2012-01-01

    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

  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.

    2012-05-01

    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

  4. Fetal and maternal absorbed dose estimates for positron-emitting molecular imaging probes.

    PubMed

    Xie, Tianwu; Zaidi, Habib

    2014-09-01

    -generation computational models can be used for the assessment of radiation risks to pregnant women and the embryo/fetus undergoing PET/CT imaging procedures. This work also contributes to a better understanding of the absorbed dose distribution in the fetus. © 2014 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

  5. Probing the mechanism of interaction of metoprolol succinate with human serum albumin by spectroscopic and molecular docking analysis.

    PubMed

    Pawar, Suma K; Jaldappagari, Seetharamappa

    2017-09-01

    In the present work, the mechanism of the interaction between a β1 receptor blocker, metoprolol succinate (MS) and human serum albumin (HSA) under physiological conditions was investigated by spectroscopic techniques, namely fluorescence, Fourier transform infra-red spectroscopy (FT-IR), fluorescence lifetime decay and circular dichroism (CD) as well as molecular docking and cyclic voltammetric methods. The fluorescence and lifetime decay results indicated that MS quenched the intrinsic intensity of HSA through a static quenching mechanism. The Stern-Volmer quenching constants and binding constants for the MS-HSA system at 293, 298 and 303 K were obtained from the Stern-Volmer plot. Thermodynamic parameters for the interaction of MS with HSA were evaluated; negative values of entropy change (ΔG°) indicated the spontaneity of the MS and HSA interaction. Thermodynamic parameters such as negative ΔH° and positive ΔS° values revealed that hydrogen bonding and hydrophobic forces played a major role in MS-HSA interaction and stabilized the complex. The binding site for MS in HSA was identified by competitive site probe experiments and molecular docking studies. These results indicated that MS was bound to HSA at Sudlow's site I. The efficiency of energy transfer and the distance between the donor (HSA) and acceptor (MS) was calculated based on the theory of Fosters' resonance energy transfer (FRET). Three-dimensional fluorescence spectra and CD results revealed that the binding of MS to HSA resulted in an obvious change in the conformation of HSA. Cyclic voltammograms of the MS-HSA system also confirmed the interaction between MS and HSA. Furthermore, the effects of metal ions on the binding of MS to HSA were also studied. Copyright © 2017 John Wiley & Sons, Ltd.

  6. Molecular dynamics force probe simulations of antibody/antigen unbinding: entropic control and nonadditivity of unbinding forces.

    PubMed Central

    Heymann, B; Grubmüller, H

    2001-01-01

    Unbinding of a spin-labeled dinitrophenyl (DNP) hapten from the monoclonal antibody AN02 F(ab) fragment has been studied by force probe molecular dynamics (FPMD) simulations. In our nanosecond simulations, unbinding was enforced by pulling the hapten molecule out of the binding pocket. Detailed inspection of the FPMD trajectories revealed a large heterogeneity of enforced unbinding pathways and a correspondingly large flexibility of the binding pocket region, which exhibited induced fit motions. Principal component analyses were used to estimate the resulting entropic contribution of approximately 6 kcal/mol to the AN02/DNP-hapten bond. This large contribution may explain the surprisingly large effect on binding kinetics found for mutation sites that are not directly involved in binding. We propose that such "entropic control" optimizes the binding kinetics of antibodies. Additional FPMD simulations of two point mutants in the light chain, Y33F and I96K, provided further support for a large flexibility of the binding pocket. Unbinding forces were found to be unchanged for these two mutants. Structural analysis of the FPMD simulations suggests that, in contrast to free energies of unbinding, the effect of mutations on unbinding forces is generally nonadditive. PMID:11509346

  7. Electronic and molecular properties of an adsorbed protein monolayer probed by two-color sum-frequency generation spectroscopy.

    PubMed

    Dreesen, L; Humbert, C; Sartenaer, Y; Caudano, Y; Volcke, C; Mani, A A; Peremans, A; Thiry, P A; Hanique, S; Frère, J-M

    2004-08-17

    Two-color sum-frequency generation spectroscopy (2C-SFG) is used to probe the molecular and electronic properties of an adsorbed layer of the green fluorescent protein mutant 2 (GFPmut2) on a platinum (111) substrate. First, the spectroscopic measurements, performed under different polarization combinations, and atomic force microscopy (AFM) show that the GFPmut2 proteins form a fairly ordered monolayer on the platinum surface. Next, the nonlinear spectroscopic data provide evidence of particular coupling phenomena between the GFPmut2 vibrational and electronic properties. This is revealed by the occurrence of two doubly resonant sum-frequency generation processes for molecules having both their Raman and infrared transition moments in a direction perpendicular to the sample plane. Finally, our 2C-SFG analysis reveals two electronic transitions corresponding to the absorption and fluorescence energy levels which are related to two different GFPmut2 conformations: the B (anionic) and I forms, respectively. Their observation and wavelength positions attest the keeping of the GFPmut2 electronic properties upon adsorption on the metallic surface.

  8. 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.

  9. Effect of cholesterol on molecular transport of organic cations across liposome bilayers probed by second harmonic generation.

    PubMed Central

    Yan, E C; Eisenthal, K B

    2000-01-01

    The effect of cholesterol on the molecular transport of an organic cation, malachite green (MG), across large unilamellar dioleolyphosphatidylglycerol (DOPG) liposome bilayers with 0-50 mol% cholesterol was studied by second harmonic generation (SHG). Because SHG is a surface-specific technique, it requires no labeled molecule, quencher, or shifting agent to distinguish the location of the solute molecules. An additional important feature of SHG is that it is sensitive only to the probe molecules bound to the liposome, whereas other methods can only differentiate between molecules that are outside and those inside the liposome. The transport kinetics of MG across the liposome bilayers was observed in real time, and the results show that cholesterol retards the rate of transport of MG across liposome bilayers. The rate was found to decrease by six times for 50 mol% cholesterol content compared with cholesterol-free liposomes. This demonstrates the applicability of SHG to investigation of the effect of liposome composition on the transport kinetics across the liposome bilayers. PMID:10920021

  10. Precise ERBB2 copy number assessment in breast cancer by means of molecular inversion probe array analysis.

    PubMed

    Christgen, Matthias; van Luttikhuizen, Jana L; Raap, Mieke; Braubach, Peter; Schmidt, Lars; Jonigk, Danny; Feuerhake, Friedrich; Lehmann, Ulrich; Schlegelberger, Brigitte; Kreipe, Hans H; Steinemann, Doris

    2016-12-13

    HER2/ERBB2 amplification/overexpression determines the eligibility of breast cancer patients to HER2-targeted therapy. This study evaluates the agreement between ERBB2 copy number assessment by fluorescence in situ hybridization, a standard method recommended by the American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP), and newly available DNA extraction-based methods. A series of n=29 formalin-fixed paraffin-embedded breast cancers were subjected to ERBB2 copy number assessment by fluorescence in situ hybridization (FISH, Vysis, Abbott). Following macrodissection of invasive breast cancer tissue and DNA extraction, ERBB2 copy number was also determined by molecular inversion probe array analysis (MIP, OncoScan, Affymetrix) and next generation sequencing combined with normalized amplicon coverage analysis (NGS/NAC, AmpliSeq, Ion Torrent). ERBB2 copy number values obtained by MIP or NGS/NAC were tightly correlated with ERBB2 copy number values obtained by conventional FISH (rs = 0.940 and rs = 0.894, P < 0.001). Using ASCO/CAP guideline-conform thresholds for categorization of breast cancers as HER2-negative, equivocal or positive, nearly perfect concordance was observed for HER2 classification by FISH and MIP (93% concordant classifications, κ = 0.87). Substantial concordance was observed for FISH and NGS/NAC (83% concordant classifications, κ = 0.62). In conclusion, MIP facilitates precise ERBB2 copy number detection and should be considered as an ancillary method for clinical HER2 testing.

  11. Efficient and Scalable Synthesis of 4-Carboxy-Pennsylvania Green Methyl Ester: A Hydrophobic Building Block for Fluorescent Molecular Probes.

    PubMed

    Woydziak, Zachary R; Fu, Liqiang; Peterson, Blake R

    2014-01-01

    Fluorinated fluorophores are valuable tools for studies of biological systems. However, amine-reactive single-isomer derivatives of these compounds are often very expensive. To provide an inexpensive alternative, we report a practical synthesis of 4-carboxy-Pennsylvania Green methyl ester. Derivatives of this hydrophobic fluorinated fluorophore, a hybrid of the dyes Oregon Green and Tokyo Green, are often cell permeable, enabling labeling of intracellular targets and components. Moreover, the low pKa of Pennsylvania Green (4.8) confers bright fluorescence in acidic cellular compartments such as endosomes, enhancing its utility for chemical biology investigations. To improve access to the key intermediate 2,7-difluoro-3,6-dihydroxyxanthen-9-one, we subjected bis-(2,4,5-trifluorophenyl)methanone to iterative nucleophilic aromatic substitution by hydroxide on scales of > 40 g. This intermediate was used to prepare over 15 grams of pure 4-carboxy-Pennsylvania Green methyl ester in 28% overall yield without requiring chromatography. This compound can be converted into the amine reactive N-hydroxysuccinimidyl ester in essentially quantitative yield for the synthesis of a wide variety of fluorescent molecular probes.

  12. 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.

  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. Tiny Molecular Beacons: LNA/2'-O-methyl RNA Chimeric Probes for Imaging Dynamic mRNA Processes in Living Cells

    PubMed Central

    Catrina, Irina E.; Marras, Salvatore A.E.; Bratu, Diana P.

    2012-01-01

    New approaches for imaging dynamic processes involving RNAs in living cells are continuously being developed and optimized. The use of molecular beacons synthesized from 2'-O-methylribonucleotides (which are resistant to cellular nucleases) is an established approach for visualizing native mRNAs in real time. In order to spatially and temporally resolve dynamic steps involving RNA in cells, molecular beacons need to efficiently hybridize to their RNA targets. To expand the repertoire of target sites accessible to molecular beacons, we decreased the length of their probe sequences and altered their backbone by the inclusion of LNA (locked nucleic acid) nucleotides. We named these new LNA/2'-O-methyl RNA chimera oligonucleotides, “tiny molecular beacons”. We analyzed these tiny molecular beacons and found that the incorporation of just a few LNA nucleotides enables these shorter probes to stably anneal to more structured regions of the RNA than is possible with conventional molecular beacons. The ease of synthesis of tiny molecular beacons, and the flexibility to couple them to a large variety of fluorophores and quenchers, renders them optimal for the detection of less abundant and/or highly structured RNAs. To determine their efficiency to detect endogenous mRNAs in live specimens, we designed tiny molecular beacons that were specific for oskar mRNA and microinjected them into living Drosophila melanogaster oocytes. We then imaged the live oocytes via spinning disc confocal microscopy. The results demonstrate that tiny molecular beacons hybridize to target mRNA at faster rates than classically designed molecular beacons, and are able to access previously inaccessible target regions. PMID:22738327

  15. Systematic discovery of molecular probes targeting multiple non-orthosteric and spatially distinct sites in the botulinum neurotoxin subtype A (BoNT/A).

    PubMed

    Dadgar, Saedeh; Floriano, Wely B

    2015-06-01

    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.

  16. Molecular screening test in familial forms of cerebral cavernous malformation: the impact of the Multiplex Ligation-dependent Probe Amplification approach.

    PubMed

    Penco, Silvana; Ratti, Rachele; Bianchi, Elena; Citterio, Alberto; Patrosso, Maria Cristina; Marocchi, Alessandro; Tassi, Laura; La Camera, Alessandro; Collice, Massimo

    2009-05-01

    Object The purpose of this study was to underline the effectiveness of molecular analysis in cerebral cavernous angioma, with special attention to the familial forms. Methods Multiplex Ligation-dependent Probe Amplification analysis integrates the consecutive sequence analysis of the 3 genes (Krit1/CCM1, MGC4607/CCM2, and PDCD10/CCM3) known to be responsible for cerebral cavernous malformation lesions. Results The Multiplex Ligation-dependent Probe Amplification analysis revealed a new mutation, a heterozygous exon 9/10 deletion of Krit1, in the proband and in all affected family members. Conclusions The identification of the molecular defect allows physicians to screen family members at risk and to identify affected individuals before the onset of clinical symptoms caused by the presence of lesions.

  17. Nanoscopic electrode molecular probes

    DOEpatents

    Krstic, Predrag S [Knoxville, TN; Meunier, Vincent [Knoxville, TN

    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.

  18. Characterization of sorbent properties of soil organic matter and carbonaceous geosorbents using n-alkanes and cycloalkanes as molecular probes.

    PubMed

    Endo, Satoshi; Grathwohl, Peter; Haderlein, Stefan B; Schmidt, Torsten C

    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 n- 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 (Freundlich exponents 0.2-0.7) and strong (Koc values being up to 10(5) 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. Sorption by CGs was generally stronger and more nonlinear for n-octane than for cyclooctane, which suggests a strong dependence of sorption on the 3-D structure of sorbate molecules. The n-octane-to-cyclooctane sorption coefficient ratios (Kn/Kc) for adsorption to CGs were > or = 1, being distinctly different from those for absorption to the OM-rich materials (Kn/Kc < 1). 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

  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. Use of the nitrile oxide cycloaddition (NOC) reaction for molecular probe generation: a new class of enzyme selective histone deacetylase inhibitors (HDACIs) showing picomolar activity at HDAC6.

    PubMed

    Kozikowski, Alan P; Tapadar, Subhasish; Luchini, Doris N; Kim, Ki Hwan; Billadeau, Daniel D

    2008-08-14

    A series of hydroxamate based HDAC inhibitors containing a phenylisoxazole as the CAP group has been synthesized using nitrile oxide cycloaddition chemistry. An HDAC6 selective inhibitor having a potency of approximately 2 picomolar was identified. Some of the compounds were examined for their ability to block pancreatic cancer cell growth and found to be about 10-fold more potent than SAHA. This research provides valuable, new molecular probes for use in exploring HDAC biology.

  1. Water participation in molecular recognition and protein-ligand association: Probing the drug binding site "Sudlow I" in human serum albumin

    NASA Astrophysics Data System (ADS)

    Al-Lawatia, Najla; Steinbrecher, Thomas; Abou-Zied, Osama K.

    2012-03-01

    Human serum albumin (HSA) plays an important role in the transport and disposition of endogenous and exogenous ligands present in blood. Its capacity to reversibly bind a large variety of drugs results in its prevailing role in drug pharmacokinetics and pharmacodynamics. In this work, we used 7-hydroxyquinoline (7HQ) as a probe to study the binding nature of one of the major drug binding sites of HSA (Sudlow I) and to reveal the local environment around the probe in the binding site. The interaction between 7HQ and HSA at a physiological pH of 7.2 was investigated using steady-state and lifetime spectroscopic measurements, molecular docking and molecular dynamics (MD) simulations methods. The fluorescence results indicate a selective interaction between 7HQ and the Trp214 residue. The reduction in both the intensity and lifetime of the Trp214 fluorescence upon probe binding indicates the dominant role of static quenching. Molecular docking and MD simulations show that 7HQ binds in Sudlow site I close to Trp214, confirming the experimental results, and pinpoint the dominant role of hydrophobic interaction in the binding site. Electrostatic interactions were also found to be important in which two water molecules form strong hydrogen bonds with the polar groups of 7HQ. Detection of water in the binding site agrees with the absorption and fluorescence results that show the formation of a zwitterion tautomer of 7HQ. The unique spectral signatures of 7HQ in water make this molecule a potential probe for detecting the presence of water in nanocavities of proteins. Interaction of 7HQ with water in the binding site shows that water molecules can be crucial for molecular recognition and association in protein binding sites.

  2. A new strategy to screen molecular imaging probe uptake in cell culture without radiolabeling using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

    PubMed

    Cheng, Zhen; Winant, Richard C; Gambhir, Sanjiv S

    2005-05-01

    Numerous new molecular targets for diseases are rapidly being identified and validated in the postgenomic era, urging scientists to explore novel techniques for accelerating molecular probe development. In this study, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) was investigated as a potential tool for high-throughput screening and characterization of molecular imaging probes. Specifically, MALDI-TOF-MS was used to screen a small library of phosphonium cations for their ability to accumulate in cells. C6 cells incubated with phosphonium cations at room temperature were collected and lysed for experiments. Calibration curves for the internal standard, methyltriphenyl phosphonium, and for tetraphenylphosphonium bromide (TPP) and other phosphonium cations were first established. The time course of TPP uptake by C6 cells was then quantified using both MALDI-TOF-MS and liquid scintillation counting with (3)H-TPP. In addition, MALDI-TOF-MS was used to screen a library of 8 phosphonium cations and subsequently rank their ability to penetrate membranes and accumulate in cells. Finally, the accumulation of 4-fluorophenyltriphenyl phosphonium (FTPP) in the membrane potential-modulated cells was also measured by MALDI-TOF-MS. MALDI-TOF-MS spectra clearly revealed that TPP was easily identified from cell lysates even as early as 10 min after incubation and that levels as low as 0.11 fmol of TPP per cell could be detected, suggesting the high sensitivity of this technique. The time course of TPP influx determined by both MALDI-TOF-MS and radioactivity counting showed no statistically significant difference (P > 0.05 for all time points). These data validated MALDI-TOF-MS as an alternative approach for accurately measuring uptake of phosphonium cations by cells. TPP and FTPP demonstrated greater accumulation in cells than did the other cations evaluated in this study. Furthermore, uptake profiles suggested that FTPP preserves the

  3. Development of Molecular Probes Based on Iron Oxide Nanoparticles for in Vivo Magnetic Resonance/Photoacoustic Dual Imaging of Target Molecules in Tumors.

    PubMed

    Sano, Kohei

    2017-01-01

    Molecular imaging probes that enable seamless diagnoses of tumors in the preoperative and intraoperative stages could lead to surgical resection of tumors based on highly accurate diagnoses. Because iron oxide nanoparticles (IONPs) have high proton relaxivity and high molar extinction coefficients suitable for magnetic resonance imaging (MRI) and photoacoustic imaging, respectively, we planned to develop molecular imaging probes applicable to the pre- (MRI) and intraoperative (photoacoustic imaging) stages. Human epidermal growth factor receptor 2 (EGFR2; HER2) was selected as a target molecule, and we designed IONPs (20, 50, and 100 nm) conjugated with anti-HER2 moieties [whole IgG (trastuzumab), single-chain fragment variable (scFv), and peptide] for HER2-targeted tumor imaging. Among the probes tested, scFv-conjugated IONPs (scFv-IONPs) (20 nm) exhibited the highest binding affinity to HER2 (Kd=0.01 nM). An in vivo biodistribution study using (111)In-labeled probes demonstrated that more scFv-IONPs (20 nm) accumulated in HER2-positive than in HER2-negative tumors, suggesting that the uptake of scFv-IONPs is HER2 specific. The scFv-IONPs (20 nm) showed high proton relaxivity and a probe concentration-dependent photoacoustic signal. In vivo MR/photoacoustic imaging studies using scFv-IONPs (20 nm) facilitated HER2-specific visualization of tumors. Furthermore, an iron-staining study demonstrated that the uptake of scFv-IONPs was notable only in HER2-positive tumors. These results suggest that scFv-IONPs (20 nm) may be useful for MR/photoacoustic dual imaging, which could achieve seamless diagnoses in the preoperative and intraoperative stages.

  4. Refinement of glucagon-like peptide 1 docking to its intact receptor using mid-region photolabile probes and molecular modeling.

    PubMed

    Miller, Laurence J; Chen, Quan; Lam, Polo C-H; Pinon, Delia I; Sexton, Patrick M; Abagyan, Ruben; Dong, Maoqing

    2011-05-06

    The glucagon-like peptide 1 (GLP1) receptor is an important drug target within the B family of G protein-coupled receptors. Its natural agonist ligand, GLP1, has incretin-like actions and the receptor is a recognized target for management of type 2 diabetes mellitus. Despite recent solution of the structure of the amino terminus of the GLP1 receptor and several close family members, the molecular basis for GLP1 binding to and activation of the intact receptor remains unclear. We previously demonstrated molecular approximations between amino- and carboxyl-terminal residues of GLP1 and its receptor. In this work, we study spatial approximations with the mid-region of this peptide to gain insights into the orientation of the intact receptor and the ligand-receptor complex. We have prepared two new photolabile probes incorporating a p-benzoyl-l-phenylalanine into positions 16 and 20 of GLP1(7-36). Both probes bound to the GLP1 receptor specifically and with high affinity. These were each fully efficacious agonists, stimulating cAMP accumulation in receptor-bearing CHO cells in a concentration-dependent manner. Each probe specifically labeled a single receptor site. Protease cleavage and radiochemical sequencing identified receptor residue Leu(141) above transmembrane segment one as its site of labeling for the position 16 probe, whereas the position 20 probe labeled receptor residue Trp(297) within the second extracellular loop. Establishing ligand residue approximation with this loop region is unique among family members and may help to orient the receptor amino-terminal domain relative to its helical bundle region.

  5. A Novel 99mTc-Labeled Molecular Probe for Tumor Angiogenesis Imaging in Hepatoma Xenografts Model: A Pilot Study

    PubMed Central

    Zhao, Qian; Yan, Ping; Wang, Rong Fu; Zhang, Chun Li; Li, Ling; Yin, Lei

    2013-01-01

    Introduction Visualization of tumor angiogenesis using radionuclide targeting provides important diagnostic information. In previous study, we proved that an arginine-arginine-leucine (RRL) peptide should be a tumor endothelial cell specific binding sequence. The overall aim of this study was to evaluate whether 99mTc-radiolabeled RRL could be noninvasively used for imaging of malignant tumors in vivo, and act as a new molecular probe targeting tumor angiogenesis. Methods The RRL peptide was designed and radiosynthesized with 99mTc by a one-step method. The radiolabeling efficiency and radiochemical purity were then characterized in vitro. 99mTc-RRL was injected intravenously in HepG2 xenograft-bearing BALB/c nude mice. Biodistribution and in vivo imaging were performed periodically. The relationship between tumor size and %ID uptake of 99mTc-RRL was also explored. Results The labeling efficiencies of 99mTc-RRL reached 76.9%±4.5% (n = 6) within 30–60 min at room temperature, and the radiochemical purity exceeded 96% after purification. In vitro stability experiment revealed the radiolabeled peptide was stable. Biodistribution data showed that 99mTc-RRL rapidly cleared from the blood and predominantly accumulated in the kidneys and tumor. The specific uptake of 99mTc-RRL in tumor was significantly higher than that of unlabeled RRL blocking and free pertechnetate control test after injection (p<0.05). The ratio of the tumor-to-muscle exceeded 6.5, tumor-to-liver reached 1.98 and tumor-to-blood reached 1.95. In planar gamma imaging study, the tumors were imaged clearly at 2–6 h after injection of 99mTc-RRL, whereas the tumor was not imaged clearly in blocking group. The tumor-to-muscle ratio of images with 99mTc-RRL was comparable with that of 18F-FDG PET images. Immunohistochemical analysis verified the excessive vasculature of tumor. There was a linear relationship between the tumor size and uptake of 99mTc-RRL with R2 = 0.821. Conclusion 99mTc-RRL can

  6. Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear genome using molecular beacon probes

    PubMed Central

    Ni, Yanxiang; Cao, Bo; Ma, Tszshan; Niu, Gang; Huo, Yingdong; Huang, Jiandong; Chen, Danni; Liu, Yi; Yu, Bin; Zhang, Michael Q; Niu, Hanben

    2017-01-01

    High-resolution visualization of short non-repetitive DNA in situ in the nuclear genome is essential for studying looping interactions and chromatin organization in single cells. Recent advances in fluorescence in situ hybridization (FISH) using Oligopaint probes have enabled super-resolution imaging of genomic domains with a resolution limit of 4.9 kb. To target shorter elements, we developed a simple FISH method that uses molecular beacon (MB) probes to facilitate the probe-target binding, while minimizing non-specific fluorescence. We used three-dimensional stochastic optical reconstruction microscopy (3D-STORM) with optimized imaging conditions to efficiently distinguish sparsely distributed Alexa-647 from background cellular autofluorescence. Utilizing 3D-STORM and only 29–34 individual MB probes, we observed 3D fine-scale nanostructures of 2.5 kb integrated or endogenous unique DNA in situ in human or mouse genome, respectively. We demonstrated our MB-based FISH method was capable of visualizing the so far shortest non-repetitive genomic sequence in 3D at super-resolution. DOI: http://dx.doi.org/10.7554/eLife.21660.001 PMID:28485713

  7. Development of new PTK7-targeting aptamer-fluorescent and -radiolabelled probes for evaluation as molecular imaging agents: Lymphoma and melanoma in vivo proof of concept.

    PubMed

    Calzada, Victoria; Moreno, María; Newton, Jessica; González, Joel; Fernández, Marcelo; Gambini, Juan Pablo; Ibarra, Manuel; Chabalgoity, Alejandro; Deutscher, Susan; Quinn, Thomas; Cabral, Pablo; Cerecetto, Hugo

    2017-02-01

    Aptamers are single-stranded oligonucleotides that recognize molecular targets with high affinity and specificity. Aptamer that selectively bind to the protein tyrosine kinase-7 (PTK7) receptor, overexpressed on many cancers, has been labelled as probes for molecular imaging of cancer. Two new PTK7-targeting aptamer probes were developed by coupling frameworks from the fluorescent dye AlexaFluor647 or the 6-hydrazinonicotinamide (HYNIC) chelator-labelled to (99m)Tc. The derivatizations via a 5'-aminohexyl terminal linker were done at room temperature and under mild buffer conditions. Physicochemical and biological controls for both imaging agents were performed verifying the integrity of the aptamer-conjugates by HPLC. Recognition of melanoma (B16F1) and lymphoma (A20) mouse cell lines by the aptamer was studied using cell binding, flow cytometry and confocal microscopy. Finally, in vivo imaging studies in tumour-bearing mice were performed. The new probes were able to bind to melanoma and lymphoma cell lines in vitro, the in vivo imaging in tumour-bearing mice showed different uptake behaviours showing for the fluorescent conjugate good uptake by B cell lymphoma while the radiolabelled conjugate did not display tumour uptake due to its high extravascular distribution, and both showed rapid clearance properties in tumour-bearing mice.

  8. 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.

  9. A concise review of magnetic resonance molecular imaging of tumor angiogenesis by targeting integrin αvβ3 with magnetic probes.

    PubMed

    Liu, Yajie; Yang, Yi; Zhang, Chunfu

    2013-01-01

    Angiogenesis is an essential step for the growth and spread of malignant tumors. Accurate detection and quantification of tumor angiogenesis is important for early diagnosis of cancers as well as post therapy assessment of antiangiogenic drugs. The cell adhesion molecule integrin αvβ3 is a specific marker of angiogenesis, which is highly expressed on activated and proliferating endothelial cells, but generally not on quiescent endothelial cells. Therefore, in recent years, many different approaches have been developed for imaging αvβ3 expression, for the detection and characterization of tumor angiogenesis. The present review provides an overview of the current status of magnetic resonance molecular imaging of integrin αvβ3, including the new development of high sensitive contrast agents and strategies for improving the specificity of targeting probes and the biological effects of imaging probes on αvβ3 positive cells.

  10. Magnetic/upconversion fluorescent NaGdF4:Yb,Er nanoparticle-based dual-modal molecular probes for imaging tiny tumors in vivo.

    PubMed

    Liu, Chunyan; Gao, Zhenyu; Zeng, Jianfeng; Hou, Yi; Fang, Fang; Li, Yilin; Qiao, Ruirui; Shen, Lin; Lei, Hao; Yang, Wensheng; Gao, Mingyuan

    2013-08-27

    Detection of early malignant tumors remains clinically difficult; developing ultrasensitive imaging agents is therefore highly demanded. Owing to the unusual magnetic and optical properties associated with f-electrons, rare-earth elements are very suitable for creating functional materials potentially useful for tumor imaging. Nanometer-sized particles offer such a platform with which versatile unique properties of the rare-earth elements can be integrated. Yet the development of rare-earth nanoparticle-based tumor probes suitable for imaging tiny tumors in vivo remains difficult, which challenges not only the physical properties of the nanoparticles but also the rationality of the probe design. Here we report new approaches for size control synthesis of magnetic/upconversion fluorescent NaGdF4:Yb,Er nanocrystals and their applications for imaging tiny tumors in vivo. By independently varying F(-):Ln(3+) and Na(+):Ln(3+) ratios, the size and shape regulation mechanisms were investigated. By replacing the oleic acid ligand with PEG2000 bearing a maleimide group at one end and two phosphate groups at the other end, PEGylated NaGdF4:Yb,Er nanoparticles with optimized size and upconversion fluorescence were obtained. Accordingly, a dual-modality molecular tumor probe was prepared, as a proof of concept, by covalently attaching antitumor antibody to PEGylated NaGdF4:Yb,Er nanoparticles through a "click" reaction. Systematic investigations on tumor detections, through magnetic resonance imaging and upconversion fluorescence imaging, were carried out to image intraperitoneal tumors and subcutaneous tumors in vivo. Owing to the excellent properties of the molecular probes, tumors smaller than 2 mm was successfully imaged in vivo. In addition, pharmacokinetic studies on differently sized particles were performed to disclose the particle size dependent biodistributions and elimination pathways.

  11. Probing the emitter site of Renilla luciferase using small organic molecules; an attempt to understand the molecular architecture of the emitter site.

    PubMed

    Salehi, Farajollah; Emamzadeh, Rahman; Nazari, Mahboobeh; Rasa, Seyed Mohammad Mahdi

    2016-12-01

    Renilla luciferase is a sensitive enzyme and has wide applications in biotechnology such as drug screening. Previous studies have tried to show the catalytic residues, nevertheless, the accurate architecture and molecular behavior of its emitter site remains uncharacterized. In this study, the activity of Renilla luciferase, in the presence of two small organic molecules including dimethyl sulfoxide (DMSO) and isopropanol was considered and the structure was studied by circular dichroism (CD) and fluorescence spectroscopy. Moreover, the interaction of small organic molecules with the Renilla luciferase was studied using molecular dynamics simulations. Kinetics studies showed that at low concentration of DMSO (16.6-66mM) and isopropanol (19.3-76mM) the Km changed and a competitive inhibition pattern was observed. Moreover, spectroscopy studies reveled that the changes of activity of Renilla luciferase in the presence of low concentrations of small organic molecules was not associated with structural collapse or severe changes in the enzyme conformation. Molecular dynamics simulations indicated that DMSO and isopropanol, as probing molecules, were both able to bind to the emitter site and remained with the residues of the emitter site. Based on the probing data, the architecture of the emitter site in the "non-binding" model was proposed.

  12. Premutation for the Martin-Bell syndrome analyzed in a large Sardinian family: III. Molecular analysis with the StB12.3 probe

    SciTech Connect

    Grasso, M.; Perroni, L.; Dagna-Bricarelli, F.

    1996-08-09

    This report complements a series of clinical, cytogenetical, and psychological studies previously reported on a large Sardinian pedigree segregating for premutations and full mutations associated with the Martin-Bell syndrome (MBS). Using the StB12.3 probe, we report now the molecular classification of all of the critical members of the pedigree. These molecular findings are evaluated against the variable phenotypic manifestations of the disease in the course of a six-generation segregation of an MBS premutation allegedly present in a common female progenitor of 14 MBS male patients and 9 female MBS heterozygotes seen in the last two generations. The nature and stepwise progression of MBS-premutations toward the fully manifested Martin-Bell syndrome and the possibility of reverse mutational events toward the normal allele are discussed with respect to the application of the presently available diagnostic tools in genetic counseling. 12 refs., 1 fig.

  13. 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

  14. 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.

  15. Molecular imaging of human tumor cells that naturally overexpress type 2 cannabinoid receptors using a quinolone-based near-infrared fluorescent probe.

    PubMed

    Wu, Zhiyuan; Shao, Pin; Zhang, Shaojuan; Ling, Xiaoxi; Bai, Mingfeng

    2014-01-01

    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 CB2R 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 CB2R-targeted molecular imaging probe and evaluate the specificity of the probe using human tumor cells that naturally overexpress CB2R. To synthesize the CB2R-targeted probe (NIR760-Q), a conjugable CB2R 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 CB2R positive cancers and elucidating the role of CB2R in the regulation of disease progression.

  16. 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

  17. Binding hotspots on K-ras: consensus ligand binding sites and other reactive regions from probe-based molecular dynamics analysis.

    PubMed

    Prakash, Priyanka; Hancock, John F; Gorfe, Alemayehu A

    2015-05-01

    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 nonpocket-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.

  18. 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

    Yoshihara, Toshitada; Murayama, Saori; Tobita, Seiji

    2015-06-09

    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 (R(I) = (I(p)/I(f))) between the phosphorescence (I(p)) and fluorescence (I(f)) intensities showed excellent oxygen responses; the ratio of R(I) under degassed and aerated conditions ( R(I)(0) 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 R(I)) 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.

  19. 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

  20. The molecular underpinnings of a solute-pump/solvent-probe spectroscopy: the theory of polarizability response spectra and an application to preferential solvation.

    PubMed

    Sun, Xiang; Stratt, Richard M

    2012-05-14

    Recent ultrafast experiments on liquids have made clear that it is possible to go beyond light scattering techniques such as optical Kerr spectroscopy that look at the dynamics of a liquid as a whole. It is now possible to measure something far more conceptually manageable: how that liquid dynamics (and that light scattering) can be modified by electronically exciting a solute. Resonant-pump polarizability-response spectra (RP-PORS) in particular, seem to show that different solvents respond in noticeably distinct ways to such solute perturbations. This paper is a theoretical attempt at understanding the kinds of molecular information that can be revealed by experiments of this sort. After developing the general classical statistical mechanical linear response theory for these spectra, we show that the experimentally interesting limit of long solute-pump/solvent-probe delays corresponds to measuring the differences in 4-wave-mixing spectra between solutions with equilibrated ground- and excited-state solutes-meaning that the spectra are essentially probes of how changing liquid structure affects intermolecular liquid vibrations and librations. We examine the spectra in this limit for the special case of an atomic solute dissolved in an atomic-liquid mixture, a preferential solvation problem, and show that, as with the experimental spectra, different solvents can lead to spectra with different magnitudes and even different signs. Our molecular-level analysis of these results points out that solvents can also differ in how local a portion of the solvent dynamics is accessed by this spectroscopy.

  1. Matrix-assisted laser desorption/ionization mass spectrometry imaging: a powerful tool for probing the molecular topology of plant cutin polymer.

    PubMed

    Veličković, Dušan; Herdier, Hélène; Philippe, Glenn; Marion, Didier; Rogniaux, Hélène; Bakan, Bénédicte

    2014-12-01

    The cutin polymers of different fruit cuticles (tomato, apple, nectarine) were examined using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) after in situ release of the lipid monomers by alkaline hydrolysis. The mass spectra were acquired from each coordinate with a lateral spatial resolution of approximately 100 μm. Specific monomers were released at their original location in the tissue, suggesting that post-hydrolysis diffusion can be neglected. Relative quantification of the species was achieved by introducing an internal standard, and the collection of data was subjected to non-supervised and supervised statistical treatments. The molecular images obtained showed a specific distribution of ions that could unambiguously be ascribed to cutinized and suberized regions observed at the surface of fruit cuticles, thus demonstrating that the method is able to probe some structural changes that affect hydrophobic cuticle polymers. Subsequent chemical assignment of the differentiating ions was performed, and all of these ions could be matched to cutin and suberin molecular markers. Therefore, this MALDI-MSI procedure provides a powerful tool for probing the surface heterogeneity of plant lipid polymers. This method should facilitate rapid investigation of the relationships between cuticle phenotypes and the structure of cutin within a large population of mutants.

  2. Molecular diagnosis of African Swine Fever by a new real-time PCR using universal probe library.

    PubMed

    Fernández-Pinero, J; Gallardo, C; Elizalde, M; Robles, A; Gómez, C; Bishop, R; Heath, L; Couacy-Hymann, E; Fasina, F O; Pelayo, V; Soler, A; Arias, M

    2013-02-01

    A highly sensitive and specific real-time PCR method was developed for the reliable and rapid detection of African swine fever virus (ASFV). The method uses a commercial Universal Probe Library (UPL) probe combined with a specifically designed primer set to amplify an ASFV DNA fragment within the VP72 coding genome region. The detection range of the optimized UPL PCR technique was confirmed by analysis of a large panel (n = 46) of ASFV isolates, belonging to 19 of the 22 viral p72 genotypes described. No amplification signal was observed when closely clinically related viruses, such as classical swine fever, or other porcine pathogens were tested by this assay. The detection limit of the UPL PCR method was established below 18 DNA copies. Validation experiments using an extensive collection of field porcine and tick samples (n = 260), coming from Eastern and Western African regions affected by ASF, demonstrated that the UPL PCR technique was able to detect over 10% more positive samples than the real-time TaqMan PCR test recommended in the OIE manual, confirming its superior diagnostic sensitivity. Clinical material collected during experimental infections with different ASFV p72 genotypes was useful for assuring both the capacity of the UPL PCR for an early viral DNA detection and the competence of the technique to be applied in any ASF diagnostic target sample. The reliability and robustness of the UPL PCR was finally verified with a panel of ASFV-infected clinical samples which was repeatedly tested at different times. Additionally, an internal control PCR assay was also developed and standardized using UPL probes within the endogenous β-actin gene. Finally, the complete study offers a new validated real-time PCR technique, by means of a standardized commercial probe, providing a simple, rapid and affordable test, which is ready for application in the routine diagnosis of ASF.

  3. Molecularly imprinted probe for solid-phase extraction of hippuric and 4-methylhippuric acids directly from human urine samples followed by MEKC analysis.

    PubMed

    Boscari, Carolina Nasser; Mazzuia, Giovanna Rodrigues; Wisniewski, Célio; Borges, Keyller Bastos; Figueiredo, Eduardo Costa

    2017-04-01

    Hippuric acid (HA) and 4-methylhippuric acid (4-MHA) are metabolites as well as biological indicators for toluene and xylenes, respectively, and their determination in urine samples is very important, in order to monitor the occupational exposition to these solvents, ensuring a safe working environment. Thus, this paper describes the synthesis and characterization of a probe impregnated with molecularly imprinted polymers (MIPs) for the solid-phase extraction of HA and 4-MHA directly from untreated urine samples followed by micellar electrokinetic chromatography (MEKC) analyses. The MIP probe selectivity was compared to the non-imprinted polymer probe. The MEKC separations were carried out in 50 mmol/L sodium tetraborate pH 10.0/0.5 mmol/L cetyltrimethylammonium bromide aqueous solution, with a constant voltage of -15 kV. The system variables were optimized to provide ideal conditions for the extraction and desorption of the analytes, as well as for the MEKC analyses. The method was linear from 0.5 to 5.0 g/L for both analytes, with correlation coefficients > 0.994. Precisions and accuracies, expressed as relative standard deviation and relative error, were < 20.0 and within -15.4 to 16.6%, respectively, in accordance with the United States Food and Drug Administration recommendation. The MIP probe has proven to be simple, cheap, resistant, and synthetically reproducible, being successfully used to analyze both HA and 4-MHA from real samples. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Excited state molecular structure determination in disordered media using laser pump/x-ray probe time-domain x-ray absorption spectroscopy.

    SciTech Connect

    Chen, L. X.; Chemistry

    2003-01-01

    Advances in X-ray technologies provide opportunities for solving structures of photoexcited state molecules with short lifetimes. Using X-ray pulses from a modern synchrotron source, the structure of a metal-to-ligand-charge-transfer (MLCT) excited state of CuI(dmp)2+ (dmp 1/4 2,9-dimethyl-1,10-phenanthroline) was investigated by laser pump/X-ray probe X-ray absorption fine structure (LPXP-XAFS) in fluid solution at room temperature on a nanosecond time scale. The experimental requirements for such pump-probe XAFS are described in terms of technical challenges: (1) conversion of optimal excited state population, (2) synchronization of the pump laser pulse and probe Xray pulse, and (3) timing of the detection. Using a laser pump pulse for the photoexcitation, a photoluminescent MLCT excited state of CuI(dmp)2(BArF), (dmp 1/4 2,9-dimethyl-1,10-phenanthroline), BArF 1/4 tetrakis(3,5-bis(trifluoromethylphenyl)borate) with a lifetime of 98{+-}5 ns was created. Probing the structure of this state at its optimal concentration using an X-ray pulse cluster with a total duration of 14.2 ns revealed that (1) a Cu{sup II} center was generated via a whole charge transfer; (2) the copper in the MLCT state bound an additional ligand to form a penta-coordinate complex with a likely trigonal bipyramidal geometry; and (3) the average Cu-N bond length increases in the MLCT excited state by 0.07 . In contrast to previously reported literature, the photoluminescence of this pentacoordinate MLCT state was not quenched upon ligation with the fifth ligand. On the basis of experimental results, we propose that the absorptive and emissive states have distinct geometries. The results represent X-ray characterization of a molecular excited state in fluid solution on a nanosecond time scale.

  5. 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

    Spoz, Aneta; Boron, Alicja; Porycka, Katarzyna; Karolewska, Monika; Ito, Daisuke; Abe, Syuiti; Kirtiklis, Lech; Juchno, Dorota

    2014-01-01

    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.

  6. 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.

  7. 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.

  8. Probing dynamic interference in high-order harmonic generation from long-range molecular ion: Bohmian trajectory investigation

    NASA Astrophysics Data System (ADS)

    Wang, Jun; Wang, Bing-Bing; Guo, Fu-Ming; Li, Su-Yu; Ding, Da-Jun; Chen, Ji-Gen; Zeng, Si-Liang; Yang, Yu-Jun

    2014-05-01

    Using Bohmian trajectory (BT) method, we investigate the dynamic interference in high-order harmonic generation from diatomic molecular ions. It is demonstrated that the main characteristics of the molecular harmonic spectrum can be well reproduced by only two BTs which are located at the two ions. This happens because these two localized trajectories can receive and store the whole collision information coming from all of the other re-collision trajectories. Therefore, the amplitudes and frequencies of these two trajectories represent the intensity and frequency distribution of the harmonic generation. Moreover, the interference between these two trajectories shows a dip in the harmonic spectrum, which reveals the molecular structure information.

  9. Probing the specificity of polyurethane foam as a 'solid-phase extractant': Extractability-governing molecular attributes of lipophilic phenolic compounds.

    PubMed

    Han, Jie; Cao, Zhi; Qiu, Wei; Gao, Wei; Hu, Jiangyong; Xing, Baoshan

    2017-09-01

    The long-proposed use of open-cell polyurethane foam (PUF) as a convenient 'solid-phase extractant' for aqueous organic compounds has been hindered by a critical lack of understanding on the underlying specificity of its extraction mechanism. In this work, we tasked ourselves to understand the hierarchy of molecular structure, properties, and partitioning characteristics of compounds in PUF and aqueous phase by targeting lipophilic phenolic compounds (LPCs) as a group of primary targets for PUF extraction. Using six structurally related bisphenol analogs as comparative probes, we identified molecular lipophilicity and H-bond acidity as key molecular attributes that governed their extractability by PUF. Molecular modeling study on H-bonding interactions between PUF surrogates, bisphenols, and water molecules elucidated the governing effect of H-bond acidity in the binding affinity of guest molecules onto PUF lone-pair donors. A holistic view must be adopted when assessing the extractability of LPCs with reactive lone-pair donors e.g. bisphenol S which forms multidentate H-bond adducts with water molecules. We validated our theory on two model groups of monofunctional LPCs, alkylphenols and chlorophenols, with the observation that the presence of a second proton-donating moiety dramatically enhanced the extractability of bisphenol molecules. The specificity of PUF rendered it selective towards compounds with correlating molecular attributes against other structural analogs and co-existing matrix organics. For LPCs, the PUF macromolecular structure can be conceptualized as a flexible 'molecular zipper network' that is most affinitive towards nonionic, permeable, and lipophilic guest molecules with multiple reactive proton donors. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. A Fluorescent Molecular Probe for the Detection of Hydrogen Based on Oxidative Addition Reactions with Crabtree-Type Hydrogenation Catalysts.

    PubMed

    Kos, Pavlo; Plenio, Herbert

    2015-11-02

    A Crabtree-type Ir(I) complex tagged with a fluorescent dye (bodipy) was synthesized. The oxidative addition of H2 converts the weakly fluorescent Ir(I) complex (Φ=0.038) into a highly fluorescent Ir(III) species (Φ=0.51). This fluorogenic reaction can be utilized for the detection of H2 and to probe the oxidative addition step in the catalytic hydrogenation of olefins. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. 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