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Sample records for acid photoluminescence probing

  1. Photoluminescent gold nanoclusters as sensing probes for uropathogenic Escherichia coli.

    PubMed

    Chan, Po-Han; Ghosh, Bhaswati; Lai, Hong-Zheng; Peng, Hwei-Ling; Mong, Kwok Kong Tony; Chen, Yu-Chie

    2013-01-01

    Glycan-bound nanoprobes have been demonstrated as suitable sensing probes for bacteria containing glycan binding sites. In this study, we demonstrated a facile approach for generating glycan-bound gold nanoclusters (AuNCs). The generated AuNCs were used as sensing probes for corresponding target bacteria. Mannose-capped AuNCs (AuNCs@Mann) were generated and used as the model sensors for target bacteria. A one-step synthesis approach was employed to generate AuNCs@Mann. In this approach, an aqueous solution of tetrachloroauric acid and mannoside that functionized with a thiol group (Mann-SH) was stirred at room temperature for 48 h. The mannoside functions as reducing and capping agent. The size of the generated AuNCs@Mann is 1.95±0.27 nm, whereas the AuNCs with red photoluminescence have a maximum emission wavelength of ~630 nm (λexcitation = 375 nm). The synthesis of the AuNCs@Mann was accelerated by microwave heating, which enabled the synthesis of the AuNCs@Mann to complete within 1 h. The generated AuNCs@Mann are capable of selectively binding to the urinary tract infection isolate Escherichia coli J96 containing the mannose binding protein FimH expressed on the type 1 pili. On the basis of the naked eye observation, the limit of detection of the sensing approach is as low as ~2×10(6) cells/mL.

  2. Wide-field time-gated photoluminescence microscopy for fast ultrahigh-sensitivity imaging of photoluminescent probes.

    PubMed

    Razali, Wan A W; Sreenivasan, Varun K A; Bradac, Carlo; Connor, Mark; Goldys, Ewa M; Zvyagin, Andrei V

    2016-08-01

    Fluorescence microscopy is a fundamental technique for the life sciences, where biocompatible and photostable photoluminescence probes in combination with fast and sensitive imaging systems are continually transforming this field. A wide-field time-gated photoluminescence microscopy system customised for ultrasensitive imaging of unique nanoruby probes with long photoluminescence lifetime is described. The detection sensitivity derived from the long photoluminescence lifetime of the nanoruby makes it possible to discriminate signals from unwanted autofluorescence background and laser backscatter by employing a time-gated image acquisition mode. This mode enabled several-fold improvement of the photoluminescence imaging contrast of discrete nanorubies dispersed on a coverslip. It enabled recovery of the photoluminescence signal emanating from discrete nanorubies when covered by a layer of an organic fluorescent dye, which were otherwise invisible without the use of spectral filtering approaches. Time-gated imaging also facilitated high sensitivity detection of nanorubies in a biological environment of cultured cells. Finally, we monitor the binding kinetics of nanorubies to a functionalised substrate, which exemplified a real-time assay in biological fluids. 3D-pseudo colour images of nanorubies immersed in a highly fluorescent dye solution. Nanoruby photoluminescence is subdued by that of the dye in continuous excitation/imaging (left), however it can be recovered by time-gated imaging (right). At the bottom is schematic diagram of nanoruby assay in a biological fluid. PMID:27264934

  3. Functionalization of graphene oxide nanostructures improves photoluminescence and facilitates their use as optical probes in preclinical imaging.

    PubMed

    Prabhakar, Neeraj; Näreoja, Tuomas; von Haartman, Eva; Şen Karaman, Didem; Burikov, Sergey A; Dolenko, Tatiana A; Deguchi, Takahiro; Mamaeva, Veronika; Hänninen, Pekka E; Vlasov, Igor I; Shenderova, Olga A; Rosenholm, Jessica M

    2015-06-21

    Recently reported photoluminescent nanographene oxides (nGOs), i.e. nanographene oxidised with a sulfuric/nitric acid mixture (SNOx method), have tuneable photoluminescence and are scalable, simple and fast to produce optical probes. This material belongs to the vast class of photoluminescent carbon nanostructures, including carbon dots, nanodiamonds (NDs), graphene quantum dots (GQDs), all of which demonstrate a variety of properties that are attractive for biomedical imaging such as low toxicity and stable photoluminescence. In this study, the nGOs were organically surface-modified with poly(ethylene glycol)-poly(ethylene imine) (PEG-PEI) copolymers tagged with folic acid as the affinity ligand for cancer cells expressing folate receptors. The functionalization enhanced both the cellular uptake and quantum efficiency of the photoluminescence as compared to non-modified nGOs. The nGOs exhibited an excitation dependent photoluminescence that facilitated their detection with a wide range of microscope configurations. The functionalized nGOs were non-toxic, they were retained in the stained cell population over a period of 8 days and they were distributed equally between daughter cells. We have evaluated their applicability in in vitro and in vivo (chicken embryo CAM) models to visualize and track migratory cancer cells. The good biocompatibility and easy detection of the functionalized nGOs suggest that they could address the limitations faced with quantum dots and organic fluorophores in long-term in vivo biomedical imaging. PMID:25998585

  4. Functionalization of graphene oxide nanostructures improves photoluminescence and facilitates their use as optical probes in preclinical imaging.

    PubMed

    Prabhakar, Neeraj; Näreoja, Tuomas; von Haartman, Eva; Şen Karaman, Didem; Burikov, Sergey A; Dolenko, Tatiana A; Deguchi, Takahiro; Mamaeva, Veronika; Hänninen, Pekka E; Vlasov, Igor I; Shenderova, Olga A; Rosenholm, Jessica M

    2015-06-21

    Recently reported photoluminescent nanographene oxides (nGOs), i.e. nanographene oxidised with a sulfuric/nitric acid mixture (SNOx method), have tuneable photoluminescence and are scalable, simple and fast to produce optical probes. This material belongs to the vast class of photoluminescent carbon nanostructures, including carbon dots, nanodiamonds (NDs), graphene quantum dots (GQDs), all of which demonstrate a variety of properties that are attractive for biomedical imaging such as low toxicity and stable photoluminescence. In this study, the nGOs were organically surface-modified with poly(ethylene glycol)-poly(ethylene imine) (PEG-PEI) copolymers tagged with folic acid as the affinity ligand for cancer cells expressing folate receptors. The functionalization enhanced both the cellular uptake and quantum efficiency of the photoluminescence as compared to non-modified nGOs. The nGOs exhibited an excitation dependent photoluminescence that facilitated their detection with a wide range of microscope configurations. The functionalized nGOs were non-toxic, they were retained in the stained cell population over a period of 8 days and they were distributed equally between daughter cells. We have evaluated their applicability in in vitro and in vivo (chicken embryo CAM) models to visualize and track migratory cancer cells. The good biocompatibility and easy detection of the functionalized nGOs suggest that they could address the limitations faced with quantum dots and organic fluorophores in long-term in vivo biomedical imaging.

  5. Photoluminescence and electrochemiluminescence of a Ru(II)(bpy)3-quencher dual-labeled oligonucleotide probe.

    PubMed

    Wilson, Robert; Johansson, Mary Katherine

    2003-11-01

    A molecular beacon oligonucleotide probe covalently labeled with Ru(II)(bpy)3 and Black Hole Quencher-2 is synthesized, and hybridization assays are performed using photoluminescence and electrochemiluminescence methods of excitation.

  6. Functionalization of graphene oxide nanostructures improves photoluminescence and facilitates their use as optical probes in preclinical imaging

    NASA Astrophysics Data System (ADS)

    Prabhakar, Neeraj; Näreoja, Tuomas; von Haartman, Eva; Şen Karaman, Didem; Burikov, Sergey A.; Dolenko, Tatiana A.; Deguchi, Takahiro; Mamaeva, Veronika; Hänninen, Pekka E.; Vlasov, Igor I.; Shenderova, Olga A.; Rosenholm, Jessica M.

    2015-06-01

    Recently reported photoluminescent nanographene oxides (nGOs), i.e. nanographene oxidised with a sulfuric/nitric acid mixture (SNOx method), have tuneable photoluminescence and are scalable, simple and fast to produce optical probes. This material belongs to the vast class of photoluminescent carbon nanostructures, including carbon dots, nanodiamonds (NDs), graphene quantum dots (GQDs), all of which demonstrate a variety of properties that are attractive for biomedical imaging such as low toxicity and stable photoluminescence. In this study, the nGOs were organically surface-modified with poly(ethylene glycol)-poly(ethylene imine) (PEG-PEI) copolymers tagged with folic acid as the affinity ligand for cancer cells expressing folate receptors. The functionalization enhanced both the cellular uptake and quantum efficiency of the photoluminescence as compared to non-modified nGOs. The nGOs exhibited an excitation dependent photoluminescence that facilitated their detection with a wide range of microscope configurations. The functionalized nGOs were non-toxic, they were retained in the stained cell population over a period of 8 days and they were distributed equally between daughter cells. We have evaluated their applicability in in vitro and in vivo (chicken embryo CAM) models to visualize and track migratory cancer cells. The good biocompatibility and easy detection of the functionalized nGOs suggest that they could address the limitations faced with quantum dots and organic fluorophores in long-term in vivo biomedical imaging.Recently reported photoluminescent nanographene oxides (nGOs), i.e. nanographene oxidised with a sulfuric/nitric acid mixture (SNOx method), have tuneable photoluminescence and are scalable, simple and fast to produce optical probes. This material belongs to the vast class of photoluminescent carbon nanostructures, including carbon dots, nanodiamonds (NDs), graphene quantum dots (GQDs), all of which demonstrate a variety of properties that are

  7. Optimizing the sensitivity of photoluminescent probes using time-resolved spectroscopy: a molecular beacon case study.

    PubMed

    Huang, Kewei; Martí, Angel A

    2012-09-18

    Improving probes so that they can perform more sensitive and accurate detections is at the heart of much fundamental and applied research. Within the past few years a considerable amount of effort has been devoted to the study of photoluminescent probes in combination with time-resolved photoluminescence spectroscopy (TRPS). Although TRPS is a powerful and important technique for improving the sensitivity of long-lived probes, there is a lack of a general methodology that would allow one to unambiguously optimize the parameter affecting this technique. In this manuscript it will be shown how parameters that are probe- and technique-specific can affect the effectiveness of TRPS in improving sensitivity. Furthermore, it will be demonstrated that, when TRPS is used, the sensitivity of the probe is strongly dependent on the time window used to generate the time-resolved emission spectra (TRES). A method will be described that will allow one to remove the uncertainty in the selection of the time window that would yield the optimum improvement in probe performance, as well as the experimental parameters that need to be considered. Molecular beacon probes (MBs) were used to demonstrate these points. These probes show signal-to-background ratios (S/B) of less than 9 when SSPS is used, which can be easily enhanced to 17 using TRPS. The detection limits were also improved when TRPS is used allowing detecting target DNA with concentrations as low as 13.6 nM.

  8. An integrated photoluminescence sensing platform using a single-multi-mode fiber coupler-based probe.

    PubMed

    Long, Feng; Zhu, Anna; Shi, Hanchang

    2014-01-01

    We demonstrate an integrated fiber optic photoluminescence sensing platform using a novel single-multi-mode fiber coupler (SMFC)-based probe with high collection efficiency for fluorescence signals. The SMFC, prepared using fused biconical taper technology, not only transmits excitation light, but also collects and transmits fluorescence. The entire system does not use complex optical components and rarely requires optical alignment. The simple structure of the SMFC considerably improves the light transmission efficiency, signal-to-noise ratio, and sensitivity of the system. Theoretical and experimental results show that the proposed probe increases the collection efficiency by more than eight-fold compared with a bifurcated fiber probe. The performance of the proposed probe was experimentally evaluated by measuring the fluorescence spectra of well-known targets and a fresh Tall Fescue leaf. PMID:24662405

  9. Functional nucleic acid probes and uses thereof

    DOEpatents

    Nilsen-Hamilton, Marit

    2006-10-03

    The present invention provides functional nucleic acid probes, and methods of using functional nucleic acid probes, for binding a target to carry out a desired function. The probes have at least one functional nucleic acid, at least one regulating nucleic acid, and at least one attenuator. The functional nucleic acid is maintained in an inactive state by the attenuator and activated by the regulating nucleic acid only in the presence of a regulating nucleic acid target. In its activated state the functional nucleic acid can bind to its target to carry out a desired function, such as generating a signal, cleaving a nucleic acid, or catalyzing a reaction.

  10. Experimental and theoretical photoluminescence studies in nucleic acid assembled gold-upconverting nanoparticle clusters.

    PubMed

    He, Liangcan; Mao, Chenchen; Cho, Suehyun; Ma, Ke; Xi, Weixian; Bowman, Christopher N; Park, Wounjhang; Cha, Jennifer N

    2015-11-01

    Combinations of rare earth doped upconverting nanoparticles (UCNPs) and gold nanostructures are sought as nanoscale theranostics due to their ability to convert near infrared (NIR) photons into visible light and heat, respectively. However, because the large NIR absorption cross-section of the gold coupled with their thermo-optical properties can significantly hamper the photoluminescence of UCNPs, methods to optimize the ratio of gold nanostructures to UCNPs must be developed and studied. We demonstrate here nucleic acid assembly methods to conjugate spherical gold nanoparticles (AuNPs) and gold nanostars (AuNSs) to silica-coated UCNPs and probe the effect on photoluminescence. These studies showed that while UCNP fluorescence enhancement was observed from the AuNPs conjugated UCNPs, AuNSs tended to quench fluorescence. However, conjugating lower ratios of AuNSs to UCNPs led to reduced quenching. Simulation studies both confirmed the experimental results and demonstrated that the orientation and distance of the UCNP with respect to the core and arms of the gold nanostructures played a significant role in PL. In addition, the AuNS-UCNP assemblies were able to cause rapid gains in temperature of the surrounding medium enabling their potential use as a photoimaging-photodynamic-photothermal agent. PMID:26427014

  11. Experimental and theoretical photoluminescence studies in nucleic acid assembled gold-upconverting nanoparticle clusters.

    PubMed

    He, Liangcan; Mao, Chenchen; Cho, Suehyun; Ma, Ke; Xi, Weixian; Bowman, Christopher N; Park, Wounjhang; Cha, Jennifer N

    2015-11-01

    Combinations of rare earth doped upconverting nanoparticles (UCNPs) and gold nanostructures are sought as nanoscale theranostics due to their ability to convert near infrared (NIR) photons into visible light and heat, respectively. However, because the large NIR absorption cross-section of the gold coupled with their thermo-optical properties can significantly hamper the photoluminescence of UCNPs, methods to optimize the ratio of gold nanostructures to UCNPs must be developed and studied. We demonstrate here nucleic acid assembly methods to conjugate spherical gold nanoparticles (AuNPs) and gold nanostars (AuNSs) to silica-coated UCNPs and probe the effect on photoluminescence. These studies showed that while UCNP fluorescence enhancement was observed from the AuNPs conjugated UCNPs, AuNSs tended to quench fluorescence. However, conjugating lower ratios of AuNSs to UCNPs led to reduced quenching. Simulation studies both confirmed the experimental results and demonstrated that the orientation and distance of the UCNP with respect to the core and arms of the gold nanostructures played a significant role in PL. In addition, the AuNS-UCNP assemblies were able to cause rapid gains in temperature of the surrounding medium enabling their potential use as a photoimaging-photodynamic-photothermal agent.

  12. Probing the photoluminescence properties of gold nanoclusters by fluorescence lifetime correlation spectroscopy

    SciTech Connect

    Yuan, C. T. Lin, T. N.; Shen, J. L.; Lin, C. A.; Chang, W. H.; Cheng, H. W.; Tang, J.

    2013-12-21

    Gold nanoclusters (Au NCs) have attracted much attention for promising applications in biological imaging owing to their tiny sizes and biocompatibility. So far, most efforts have been focused on the strategies for fabricating high-quality Au NCs and then characterized by conventional ensemble measurement. Here, a fusion single-molecule technique combining fluorescence correlation spectroscopy and time-correlated single-photon counting can be successfully applied to probe the photoluminescence (PL) properties for sparse Au NCs. In this case, the triplet-state dynamics and diffusion process can be observed simultaneously and the relevant time constants can be derived. This work provides a complementary insight into the PL mechanism at the molecular levels for Au NCs in solution.

  13. Nucleic acid probes in diagnostic medicine

    NASA Technical Reports Server (NTRS)

    Oberry, Phillip A.

    1991-01-01

    The need for improved diagnostic procedures is outlined and variations in probe technology are briefly reviewed. A discussion of the application of probe technology to the diagnosis of disease in animals and humans is presented. A comparison of probe versus nonprobe diagnostics and isotopic versus nonisotopic probes is made and the current state of sequence amplification is described. The current market status of nucleic acid probes is reviewed with respect to their diagnostic application in human and veterinary medicine. Representative product examples are described and information on probes being developed that offer promise as future products is discussed.

  14. In situ temperature measurements of reaction spaces under microwave irradiation using photoluminescent probes.

    PubMed

    Ano, Taishi; Kishimoto, Fuminao; Sasaki, Ryo; Tsubaki, Shuntaro; Maitani, Masato M; Suzuki, Eiichi; Wada, Yuji

    2016-05-11

    We demonstrate two novel methods for the measurement of the temperatures of reaction spaces locally heated by microwaves, which have been applied here to two example systems, i.e., BaTiO3 particles covered with a SiO2 shell (BaTiO3-SiO2) and layered tungstate particles. Photoluminescent (PL) probes showing the temperature-sensitivity in their PL lifetimes are located in the nanospaces of the above systems. In the case of BaTiO3-SiO2 core-shell particles, rhodamine B is loaded into the mesopores of the SiO2 shell covering the BaTiO3 core, which generates the heat through the dielectric loss of microwaves. The inner nanospace temperature of the SiO2 shell is determined to be 28 °C higher than the bulk temperature under microwave irradiation at 24 W. On the other hand, Eu(3+) is immobilized in the interlayer space of layered tungstate as the PL probe, showing that the nanospace temperature of the interlayer is only 4 °C higher than the bulk temperature. This method for temperature-measurement is powerful for controlling microwave heating and elucidates the ambiguous mechanisms of microwave special effects often observed in chemical reactions, contributing greatly to the practical application of microwaves in chemistry and materials sciences. PMID:27136754

  15. Coupling atom probe tomography and photoluminescence spectroscopy: exploratory results and perspectives.

    PubMed

    Rigutti, Lorenzo; Vella, Angela; Vurpillot, François; Gaillard, Aurore; Sevelin-Radiguet, Nicolas; Houard, Jonathan; Hideur, Ammar; Martel, Gilles; Jacopin, Gwénolé; De Luna Bugallo, Andrés; Deconihout, Bernard

    2013-09-01

    The development of laser-assisted atom probes makes it possible, in principle, to exploit the femtosecond laser pulse not only for triggering ion evaporation from a nanometric field emission tip, but also for generating photons via the radiative recombination of electron-hole pairs in tips made of dielectric materials. In this article we demonstrate a first step towards a correlation of micro-photoluminescence (μ-PL) and laser-assisted tomographic atom probe (LA-TAP) analysis applied separately on the same objects, namely on ZnO microwires. In particular, we assess that the use of the focused ion beam (FIB) tip preparation method significantly degrades the radiative recombination yield of the analyzed microwires. We discuss the strategies to avoid the FIB-induced damage on the optical properties of the sample and how to get beyond the correlated μ-PL and LA-TAP analysis with a coupled approach allowing to perform the two analyses within the same instrument. PMID:23489908

  16. Monitoring of photoluminescence decay by alkali and alkaline earth metal cations using a photoluminescent bolaamphiphile self-assembly as an optical probe.

    PubMed

    Kim, Sunhyung; Kwak, Jinyoung; Lee, Sang-Yup

    2014-05-01

    Photoluminescence (PL) decay induced by the displacement of an ionic fluorescence component, Tb(3+), with alkali and alkaline earth metal cations was investigated using photoluminescent spherical self-assemblies as optical probes. The photoluminescent spherical self-assembly was prepared by the self-organization of a tyrosine-containing bolaamphiphile molecule with a photosensitizer and Tb(3+) ion. The lanthanide ion, Tb(3+), electrically bound to the carboxyl group of the bolaamphiphile molecule, was displaced by alkali and alkaline earth metal cations that had stronger electrophilicity. The PL of the self-assembly decayed remarkably due to the substitution of lanthanide ions with alkali and alkaline earth metal cations. The PL decay showed a positive correlation with cation concentration and was sensitive to the cation valency. Generally, the PL decay was enhanced by the electrophilicity of the cations. However, Ca(2+) showed greater PL decay than Mg(2+) because Ca(2+) could create various complexes with the carboxyl groups of the bolaamphiphile molecule. Microscopic and spectroscopic investigations were conducted to study the photon energy transfer and displacement of Tb(3+) by the cation exchange. This study demonstrated that the PL decay by the displacement of the ionic fluorescent compound was applied to the detection of various cations in aqueous media and is applicable to the development of future optical sensors.

  17. Time-integrated photoluminescence and pump-probe reflection spectroscopy of Si doped InN thin films

    SciTech Connect

    Mohanta, Antaryami; Jang, Der-Jun Wang, Ming-Sung; Tu, L. W.

    2014-01-28

    Temperature and excitation power dependent time-integrated photoluminescence of Si doped InN thin films are investigated. Photoluminescence (PL) spectra at low temperatures are described by single emission peak ensued due to “free-to-bound” recombination; whereas PL spectra at higher temperatures above 150 K are characterized by both “band-to-band” and “free-to-bound” transition. Carrier dynamics of Si doped InN thin films is studied using pump-probe reflection spectroscopy at room temperature. The hot electron cooling process is well described by electron-electron scattering. The dependence of the hot electron cooling rate on total electron density shows sublinear to linear behavior with increase of background electron density. The variation of the carrier recombination lifetime with total electron density implicates the dominance of the defect-related nonradiative recombination channel over other recombination processes.

  18. Structural tuning of photoluminescence in nanoporous anodic alumina by hard anodization in oxalic and malonic acids

    NASA Astrophysics Data System (ADS)

    Santos, Abel; Alba, Maria; Rahman, Mahbubur M.; Formentín, Pilar; Ferré-Borrull, Josep; Pallarès, Josep; Marsal, Lluis F.

    2012-04-01

    We report on an exhaustive and systematic study about the photoluminescent properties of nanoporous anodic alumina membranes fabricated by the one-step anodization process under hard conditions in oxalic and malonic acids. This optical property is analysed as a function of several parameters (i.e. hard anodization voltage, pore diameter, membrane thickness, annealing temperature and acid electrolyte). This analysis makes it possible to tune the photoluminescent behaviour at will simply by modifying the structural characteristics of these membranes. This structural tuning ability is of special interest in such fields as optoelectronics, in which an accurate design of the basic nanostructures (e.g. microcavities, resonators, filters, supports, etc.) yields the control over their optical properties and, thus, upon the performance of the nanodevices derived from them (biosensors, interferometers, selective filters, etc.)

  19. Arrays of nucleic acid probes on biological chips

    DOEpatents

    Chee, Mark; Cronin, Maureen T.; Fodor, Stephen P. A.; Huang, Xiaohua X.; Hubbell, Earl A.; Lipshutz, Robert J.; Lobban, Peter E.; Morris, MacDonald S.; Sheldon, Edward L.

    1998-11-17

    DNA chips containing arrays of oligonucleotide probes can be used to determine whether a target nucleic acid has a nucleotide sequence identical to or different from a specific reference sequence. The array of probes comprises probes exactly complementary to the reference sequence, as well as probes that differ by one or more bases from the exactly complementary probes.

  20. High excitation photoluminescence effects as a probing tool for the growth of Cu(In,Ga)Se2

    NASA Astrophysics Data System (ADS)

    Moret, Matthieu; Briot, Olivier; Gil, Bernard; Lepetit, Thomas; Arzel, Ludovic; Barreau, Nicolas

    2015-03-01

    Copper Indium Gallium deSelenide (Cu(In,Ga)Se2, CIGS) is a promising material for cost-efficient solar cells. Efficiencies above 20% have already been demonstrated in laboratory, and large area CIGS solar panels are already on the market. However, it is still an interesting issue to find efficient characterization techniques that can be used to validate the quality of the different layers at any step of the process, without having to process a complete cell and measure its electrical properties. In this work, we have deposited CIGS onto Mo coated soda lime glass by co-evaporation, using the so-called three step deposition process. Then, photoluminescence (PL) measurements were made on the samples, in the range of 10K to the room temperature, and the excitation intensity was varied in a very large range, in order to reach non-linear regime. We report the first observation of stimulated emission in mechanisms are discussed. The threshold at which sample photoluminescence changes from spontaneous to stimulated is well known to be sensitive to overall sample quality, and we propose to use this measurement as a probing tool for sample quality. This opens an interesting perspective for characterization of CIGS during solar cell processing.

  1. Vibrational Stark Effect Probes for Nucleic Acids

    PubMed Central

    Silverman, Lisa N.; Pitzer, Michael E.; Ankomah, Peter O.; Boxer, Steven G.; Fenlon, Edward E.

    2008-01-01

    The vibrational Stark effect (VSE) has proven to be an effective method for the study of electric fields in proteins via the use of infrared probes. In order to explore the use of VSE in nucleic acids, the Stark spectroscopy of nine structurally diverse nucleosides was investigated. These nucleosides contained nitrile or azide probes in positions that correspond to both the major and minor grooves of DNA. The nitrile probes showed better characteristics and exhibited absorption frequencies over a broad range; i.e., from 2253 cm−1 for 2′-O-cyanoethyl ribonucleosides 8 and 9 to 2102 cm−1 for a 13C-labeled 5-thiocyanatomethyl-2’-deoxyuridine 3c. The largest Stark tuning rate observed was |Δµ| = 1.1 cm−1/(MV/cm) for both 5-cyano-2′-deoxyuridine 1 and N2-nitrile-2′-deoxyguanosine 7. The latter is a particularly attractive probe because of its high extinction coefficient (ε = 412 M−1cm−1) and ease of incorporation into oligomers. PMID:17877390

  2. Electric Field Modulation of Semiconductor Quantum Dot Photoluminescence: Insights Into the Design of Robust Voltage-Sensitive Cellular Imaging Probes.

    PubMed

    Rowland, Clare E; Susumu, Kimihiro; Stewart, Michael H; Oh, Eunkeu; Mäkinen, Antti J; O'Shaughnessy, Thomas J; Kushto, Gary; Wolak, Mason A; Erickson, Jeffrey S; Efros, Alexander L; Huston, Alan L; Delehanty, James B

    2015-10-14

    The intrinsic properties of quantum dots (QDs) and the growing ability to interface them controllably with living cells has far-reaching potential applications in probing cellular processes such as membrane action potential. We demonstrate that an electric field typical of those found in neuronal membranes results in suppression of the QD photoluminescence (PL) and, for the first time, that QD PL is able to track the action potential profile of a firing neuron with millisecond time resolution. This effect is shown to be connected with electric-field-driven QD ionization and consequent QD PL quenching, in contradiction with conventional wisdom that suppression of the QD PL is attributable to the quantum confined Stark effect.

  3. Probing protein stability with unnatural amino acids

    SciTech Connect

    Mendel, D.; Ellman, J.A.; Zhiyuh Chang; Veenstra, D.L.; Kollman, P.A.; Schultz, P.G. )

    1992-06-26

    Unnatural amino acid mutagenesis, in combination with molecular modeling and simulation techniques, was used to probe the effect of side chain structure on protein stability. Specific replacements at position 133 in T4 lysozyme included (1) leucine (wt), norvaline, ethylglycine, and alanine to measure the cost of stepwise removal of methyl groups from the hydrophobic core, (2) norvaline and O-methyl serine to evaluate the effects of side chain solvation, and (3) leucine, S,S-2-amino-4-methylhexanoic acid, and S-2-amino-3-cyclopentylpropanoic acid to measure the influence of packing density and side chain conformational entropy on protein stability. All of these factors (hydrophobicity, packing, conformational entropy, and cavity formation) significantly influence protein stability and must be considered when analyzing any structural change to proteins.

  4. CdSe/CdS/ZnS double shell nanorods with high photoluminescence efficiency and their exploitation as biolabeling probes.

    PubMed

    Deka, Sasanka; Quarta, Alessandra; Lupo, Maria Grazia; Falqui, Andrea; Boninelli, Simona; Giannini, Cinzia; Morello, Giovanni; De Giorgi, Milena; Lanzani, Guglielmo; Spinella, Corrado; Cingolani, Roberto; Pellegrino, Teresa; Manna, Liberato

    2009-03-01

    We report the synthesis, the structural and optical characterization of CdSe/CdS/ZnS "double shell" nanorods and their exploitation in cell labeling experiments. To synthesize such nanorods, first "dot-in-a-rod" CdSe(dot)/CdS(rod) core/shell nanocrystals were prepared. Then a ZnS shell was grown epitaxially over these CdSe/CdS nanorods, which led to a fluorescence quantum yield of the final core-shell-shell nanorods that could be as high as 75%. The quantum efficiency was correlated with the aspect ratio of the nanorods and with the thickness of the ZnS shell around the starting CdSe/CdS rods, which varied from 1 to 4 monolayers (as supported by a combination of X-ray diffraction, elemental analysis with inductively coupled plasma atomic emission spectroscopy and high resolution transmission electron microscopy analysis). Pump-probe and time-resolved photoluminescence measurements confirmed the reduction of trapping at CdS surface due to the presence of the ZnS shell, which resulted in more efficient photoluminescence. These double shell nanorods have potential applications as fluorescent biological labels, as we found that they are brighter in cell imaging as compared to the starting CdSe/CdS nanorods and to the CdSe/ZnS quantum dots, therefore a lower amount of material is required to label the cells. Concerning their cytotoxicity, according to the MTT assay, the double shell nanorods were less toxic than the starting core/shell nanorods and than the CdSe/ZnS quantum dots, although the latter still exhibited a lower intracellular toxicity than both nanorod samples.

  5. Photoluminescence Enhancement and Structure Repairing of Monolayer MoSe2 by Hydrohalic Acid Treatment.

    PubMed

    Han, Hau-Vei; Lu, Ang-Yu; Lu, Li-Syuan; Huang, Jing-Kai; Li, Henan; Hsu, Chang-Lung; Lin, Yung-Chang; Chiu, Ming-Hui; Suenaga, Kazu; Chu, Chih-Wei; Kuo, Hao-Chung; Chang, Wen-Hao; Li, Lain-Jong; Shi, Yumeng

    2016-01-26

    Atomically thin two-dimensional transition-metal dichalcogenides (TMDCs) have attracted much attention recently due to their unique electronic and optical properties for future optoelectronic devices. The chemical vapor deposition (CVD) method is able to generate TMDCs layers with a scalable size and a controllable thickness. However, the TMDC monolayers grown by CVD may incorporate structural defects, and it is fundamentally important to understand the relation between photoluminescence and structural defects. In this report, point defects (Se vacancies) and oxidized Se defects in CVD-grown MoSe2 monolayers are identified by transmission electron microscopy and X-ray photoelectron spectroscopy. These defects can significantly trap free charge carriers and localize excitons, leading to the smearing of free band-to-band exciton emission. Here, we report that the simple hydrohalic acid treatment (such as HBr) is able to efficiently suppress the trap-state emission and promote the neutral exciton and trion emission in defective MoSe2 monolayers through the p-doping process, where the overall photoluminescence intensity at room temperature can be enhanced by a factor of 30. We show that HBr treatment is able to activate distinctive trion and free exciton emissions even from highly defective MoSe2 layers. Our results suggest that the HBr treatment not only reduces the n-doping in MoSe2 but also reduces the structural defects. The results provide further insights of the control and tailoring the exciton emission from CVD-grown monolayer TMDCs. PMID:26716765

  6. Probing the Quenching of Quantum Dot Photoluminescence by Peptide-Labeled Ruthenium(II) Complexes.

    PubMed

    Scott, Amy M; Algar, W Russ; Stewart, Michael H; Trammell, Scott A; Blanco-Canosa, Juan B; Dawson, Philip E; Deschamps, Jeffrey R; Goswami, Ramasis; Oh, Eunkeu; Huston, Alan L; Medintz, Igor L

    2014-05-01

    Charge transfer processes with semiconductor quantum dots (QDs) have generated much interest for potential utility in energy conversion. Such configurations are generally nonbiological; however, recent studies have shown that a redox-active ruthenium(II)-phenanthroline complex (Ru(2+)-phen) is particularly efficient at quenching the photoluminescence (PL) of QDs, and this mechanism demonstrates good potential for application as a generalized biosensing detection modality since it is aqueous compatible. Multiple possibilities for charge transfer and/or energy transfer mechanisms exist within this type of assembly, and there is currently a limited understanding of the underlying photophysical processes in such biocomposite systems where nanomaterials are directly interfaced with biomolecules such as proteins. Here, we utilize redox reactions, steady-state absorption, PL spectroscopy, time-resolved PL spectroscopy, and femtosecond transient absorption spectroscopy (FSTA) to investigate PL quenching in biological assemblies of CdSe/ZnS QDs formed with peptide-linked Ru(2+)-phen. The results reveal that QD quenching requires the Ru(2+) oxidation state and is not consistent with Förster resonance energy transfer, strongly supporting a charge transfer mechanism. Further, two colors of CdSe/ZnS core/shell QDs with similar macroscopic optical properties were found to have very different rates of charge transfer quenching, by Ru(2+)-phen with the key difference between them appearing to be the thickness of their ZnS outer shell. The effect of shell thickness was found to be larger than the effect of increasing distance between the QD and Ru(2+)-phen when using peptides of increasing persistence length. FSTA and time-resolved upconversion PL results further show that exciton quenching is a rather slow process consistent with other QD conjugate materials that undergo hole transfer. An improved understanding of the QD-Ru(2+)-phen system can allow for the design of more

  7. Probing the Quenching of Quantum Dot Photoluminescence by Peptide-Labeled Ruthenium(II) Complexes

    PubMed Central

    2015-01-01

    Charge transfer processes with semiconductor quantum dots (QDs) have generated much interest for potential utility in energy conversion. Such configurations are generally nonbiological; however, recent studies have shown that a redox-active ruthenium(II)–phenanthroline complex (Ru2+-phen) is particularly efficient at quenching the photoluminescence (PL) of QDs, and this mechanism demonstrates good potential for application as a generalized biosensing detection modality since it is aqueous compatible. Multiple possibilities for charge transfer and/or energy transfer mechanisms exist within this type of assembly, and there is currently a limited understanding of the underlying photophysical processes in such biocomposite systems where nanomaterials are directly interfaced with biomolecules such as proteins. Here, we utilize redox reactions, steady-state absorption, PL spectroscopy, time-resolved PL spectroscopy, and femtosecond transient absorption spectroscopy (FSTA) to investigate PL quenching in biological assemblies of CdSe/ZnS QDs formed with peptide-linked Ru2+-phen. The results reveal that QD quenching requires the Ru2+ oxidation state and is not consistent with Förster resonance energy transfer, strongly supporting a charge transfer mechanism. Further, two colors of CdSe/ZnS core/shell QDs with similar macroscopic optical properties were found to have very different rates of charge transfer quenching, by Ru2+-phen with the key difference between them appearing to be the thickness of their ZnS outer shell. The effect of shell thickness was found to be larger than the effect of increasing distance between the QD and Ru2+-phen when using peptides of increasing persistence length. FSTA and time-resolved upconversion PL results further show that exciton quenching is a rather slow process consistent with other QD conjugate materials that undergo hole transfer. An improved understanding of the QD–Ru2+-phen system can allow for the design of more sophisticated

  8. Kit for detecting nucleic acid sequences using competitive hybridization probes

    DOEpatents

    Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

    2001-01-01

    A kit is provided for detecting a target nucleic acid sequence in a sample, the kit comprising: a first hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a first portion of the target sequence, the first hybridization probe including a first complexing agent for forming a binding pair with a second complexing agent; and a second hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a second portion of the target sequence to which the first hybridization probe does not selectively hybridize, the second hybridization probe including a detectable marker; a third hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a first portion of the target sequence, the third hybridization probe including the same detectable marker as the second hybridization probe; and a fourth hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a second portion of the target sequence to which the third hybridization probe does not selectively hybridize, the fourth hybridization probe including the first complexing agent for forming a binding pair with the second complexing agent; wherein the first and second hybridization probes are capable of simultaneously hybridizing to the target sequence and the third and fourth hybridization probes are capable of simultaneously hybridizing to the target sequence, the detectable marker is not present on the first or fourth hybridization probes and the first, second, third, and fourth hybridization probes each include a competitive nucleic acid sequence which is sufficiently complementary to a third portion of the target sequence that the competitive sequences of the first, second, third, and fourth hybridization probes compete with each other to hybridize to the third portion of the

  9. Photoluminescence probing of interface evolution with annealing in InGa(N)As/GaAs single quantum wells

    SciTech Connect

    Shao, Jun Qi, Zhen; Zhu, Liang; Chen, Xiren; Guo, Shaoling; Zhao, H.; Song, Yuxin; Zha, F.-X.; Wang, S. M.

    2015-10-28

    The effects of thermal annealing on the interfaces of InGa(N)As/GaAs single quantum wells (SQWs) are investigated by excitation-, temperature-, and magnetic field-dependent photoluminescence (PL). The annealing at 750 °C results in more significant blueshift and narrowing to the PL peak than that at 600 °C. Each of the PL spectra can be reproduced with two PL components: (i) the low-energy component (LE) keeps energetically unchanged, while the high-energy component (HE) moves up with excitation and shows at higher energy for the In{sub 0.375}Ga{sub 0.625}As/GaAs but crosses over with the LE at a medium excitation power for the In{sub 0.375}Ga{sub 0.625}N{sub 0.012}As{sub 0.988}/GaAs SQWs. The HE is broader than the corresponding LE, the annealing at 750 °C narrows the LE and HE and shrinks their energetic separation; (ii) the PL components are excitonic, and the InGaNAs shows slightly enhanced excitonic effects relative to the InGaAs SQW; (iii) no typical S-shape evolution of PL energy with temperature is detectable, and similar blueshift and narrowing are identified for the same annealing. The phenomena are mainly from the interfacial processes. Annealing improves the intralayer quality, enhances the interfacial In-Ga interdiffusion, and reduces the interfacial fluctuation. The interfacial interdiffusion does not change obviously by the small N content and hence similar PL-component narrowing and blueshift are observed for the SQWs after a nominally identical annealing. Comparison with previous studies is made and the PL measurements under different conditions are shown to be effective for probing the interfacial evolution in QWs.

  10. Zip nucleic acids are potent hydrolysis probes for quantitative PCR

    PubMed Central

    Paris, Clément; Moreau, Valérie; Deglane, Gaëlle; Voirin, Emilie; Erbacher, Patrick; Lenne-Samuel, Nathalie

    2010-01-01

    Zip nucleic acids (ZNAs) are oligonucleotides conjugated with cationic spermine units that increase affinity for their target. ZNAs were recently shown to enable specific and sensitive reactions when used as primers for polymerase chain reaction (PCR) and reverse-transcription. Here, we report their use as quantitative PCR hydrolysis probes. Ultraviolet duplex melting data demonstrate that attachment of cationic residues to the 3′ end of an oligonucleotide does not alter its ability to discriminate nucleotides nor the destabilization pattern relative to mismatch location in the oligonucleotide sequence. The stability increase provided by the cationic charges allows the use of short dual-labeled probes that significantly improve single-nucleotide polymorphism genotyping. Longer ZNA probes were shown to display reduced background fluorescence, therefore, generating greater sensitivity and signal level as compared to standard probes. ZNA probes thus provide broad flexibility in assay design and also represent an effective alternative to minor groove binder- and locked nucleic-acid-containing probes. PMID:20071749

  11. Photoluminescence Enhancement in CdSe/ZnS–DNA linked–Au Nanoparticle Heterodimers Probed by Single Molecule Spectroscopy

    SciTech Connect

    Cotlet, M.; Maye, M.M.; Gang, O.

    2010-07-26

    Photoluminescence enhancement of up to 20 fold is demonstrated at the single molecule level for heterodimers composed of a core/shell CdSe/ZnS semiconductive quantum dot and a gold nanoparticle of 60 nm size separated by a 32 nm-long dsDNA linker when employing optical excitation at wavelengths near the surface plasmon resonance of the gold nanoparticle.

  12. Synthesis of highly photoluminescent carbon dots via citric acid and Tris for iron(III) ions sensors and bioimaging.

    PubMed

    Zhou, Ming; Zhou, Zhulong; Gong, Aihua; Zhang, Yan; Li, Qijun

    2015-10-01

    In this work, high quantum yield and strong photoluminescent carbon quantum dots (C-QDs) are successfully synthesized via a facile and green hydrothermal method using citric acid and Tris as precursors. The as-synthesized C-QDs with a quantum yield (QY) as high as 52% were characterized by UV, FT-IR, TEM, XPS and fluorescence spectroscope. TEM results show that C-QDs are mono-dispersed spherical particles and the diameter distribution of C-QDs is 2.8±1.1 nm. The extraordinary photoluminescent properties and low cytotoxicity of C-QDs were obtained through optical property characterization and cytotoxicity assay. In addition, we found that the as-prepared C-QDs had a high affinity for Fe(3+) ions and the response toward Fe(3+) ions was highly linear (R(2)=0.997) over the concentration range from 2 to 50 μM, which could provide an effective platform for portable detection of Fe(3+) ions. Also, it is demonstrated that the photoluminescent C-QDs display hypotoxicity and are biocompatible for use as biosensors in living cells.

  13. Hybrid molecular probe for nucleic acid analysis in biological samples.

    PubMed

    Yang, Chaoyong James; Martinez, Karen; Lin, Hui; Tan, Weihong

    2006-08-01

    The ability to detect changes in gene expression, especially in real-time and with sensitivity sufficient enough to monitor small variations in a single-cell, will have considerable value in biomedical research and applications. Out of the many available molecular probes for intracellular monitoring of nucleic acids, molecular beacon (MB) is the most frequently used probe with the advantages of high sensitivity and selectivity. However, any processes in which the MB stem-loop structure is broken will result in a restoration of the fluorescence in MB. This brings in a few possibilities for false positive signal such as nuclease degradation, protein binding, thermodynamic fluctuation, solution composition variations (such as pH, salt concentration) and sticky-end pairing. These unwanted processes do exist inside living cells, making nucleic acid monitoring inside living cells difficult. We have designed and synthesized a hybrid molecular probe (HMP) for intracellular nucleic acid monitoring to overcome these problems. HMP has two DNA probes, one labeled with a donor and the other an acceptor. The two DNA probes are linked by a poly(ethylene glycol) (PEG) linker, with each DNA being complementary to adjacent areas of a target sequence. Target binding event brings the donor and acceptor in proximity, resulting in quenching of the donor fluorescence and enhancement of the acceptor emission. The newly designed HMP has high sensitivity, selectivity, and fast hybridization kinetics. The probe is easy to design and synthesize. HMP does not generate any false positive signal upon digestion by nuclease, binding by proteins, forming complexes by sticky-end pairing, or by other molecular interaction processes. HMP is capable of selectively detecting nucleic acid targets from cellular samples.

  14. Facile preparation of Gd3+ doped carbon quantum dots: Photoluminescence materials with magnetic resonance response as magnetic resonance/fluorescence bimodal probes

    NASA Astrophysics Data System (ADS)

    Ren, X. Y.; Yuan, X. X.; Wang, Y. P.; Liu, C. L.; Qin, Y.; Guo, L. P.; Liu, L. H.

    2016-07-01

    There are a few bimodal molecular imaging probes constructed by gadolinium (3+) ions in combination with carbon quantum dots (CQDs), and the reported ones show such obvious drawbacks as low luminous efficiency and weak MRI contrast. In the paper, a kind of CQDs photoluminescence materials with magnetic resonance response was prepared by hydrothermal method and employing gadopentetate monomeglumine (GdPM) as a precusor. Here, the GdPM plays a role of not only carbon source, but also gadolinium (3+) sources. When the GdPM aqueous solution with a concentration of 4 mg mL-1 was pyrolyzed under 220 °C and 2.0 MPa for 8 h, an optimal CQDs was obtained which are doped with gadolinium (3+) ions in both chelates and Gd2O3 (named as Gd3+-CQDs). The average diameter of the Gd3+-CQDs is about 1.6 nm, which show a high photoluminescence quantum yield of 7.1%, as well as high longitudinal relaxivity (r1) of 9.87 mM-1 s-1. And owing to the unconspicuous cell toxicity, the Gd3+-CQDs show big possibility for clinical application in magnetic resonance/fluorescence bimodal molecular imaging.

  15. Correlated high-resolution x-ray diffraction photoluminescence and atom probe tomography analysis of continuous and discontinuous InxGa1-xN quantum wells

    DOE PAGES

    Ren, Xiaochen; Riley, James R.; Koleske, Daniel; Lauhon, Lincoln J.

    2015-07-14

    In this study, atom probe tomography (APT) is used to characterize the influence of hydrogen dosing duringGaN barrier growth on the indium distribution of InxGa1-xN quantum wells, and correlatedmicro-photoluminescence is used to measure changes in the emission spectrum and efficiency. We found that relative to the control growth, hydrogen dosing leads to a 50% increase in emission intensity arising from discontinuous quantum wells that are narrower, of lower indium content, and with more abrupt interfaces. Additionally, simulations of carrier distributions based on APT composition profiles indicate that the greater carrier confinement leads to an increased radiative recombination rate. Furthermore, APTmore » analysis of quantum well profiles enables refinement of x-ray diffractionanalysis for more accurate nondestructive measurements of composition.« less

  16. Designer nucleic acids to probe and program the cell.

    PubMed

    Krishnan, Yamuna; Bathe, Mark

    2012-12-01

    Recent advances in nucleic acid sequencing, structural, and computational technologies have resulted in dramatic progress in our understanding of nucleic acid structure and function in the cell. This knowledge, together with the predictable base-pairing of nucleic acids and powerful synthesis and expression capabilities now offers the unique ability to program nucleic acids to form precise 3D architectures with diverse applications in synthetic and cell biology. The unique modularity of structural motifs that include aptamers, DNAzymes, and ribozymes, together with their well-defined construction rules, enables the synthesis of functional higher-order nucleic acid complexes from these subcomponents. As we illustrate here, these highly programmable, smart complexes are increasingly enabling researchers to probe and program the cell in a sophisticated manner that moves well beyond the use of nucleic acids for conventional genetic manipulation alone.

  17. Luminescent Probes for Ultrasensitive Detection of Nucleic Acids

    PubMed Central

    Krasnoperov, Lev N.; Marras, Salvatore A.E.; Kozlov, Maxim; Wirpsza, Laura; Mustaev, Arkady

    2010-01-01

    Novel amino-reactive derivatives of lanthanide-based luminescent labels of enhanced brightness and metal retention were synthesized and used for the detection of complementary DNA oligonucleotides by molecular beacons. Time-resolved acquisition of the luminescent signal that occurs upon hybridization of the probe to the target enabled the avoidance of short-lived background fluorescence, markedly enhancing the sensitivity of detection, which was less than 1 pM. This value is about 50 to 100 times more sensitive than the level achieved with conventional fluorescence-based molecular beacons, and is 10 to 60 times more sensitive than previously reported for other lanthanide-based hybridization probes. These novel luminescent labels should significantly enhance the sensitivity of all type of nucleic acid hybridization probes, and could dramatically improve the detection limit of other biopolymers and small compounds that are used in a variety of biological applications. PMID:20085336

  18. Non-redox modulated fluorescence strategy for sensitive and selective ascorbic acid detection with highly photoluminescent nitrogen-doped carbon nanoparticles via solid-state synthesis.

    PubMed

    Zhu, Xiaohua; Zhao, Tingbi; Nie, Zhou; Liu, Yang; Yao, Shouzhuo

    2015-08-18

    Highly photoluminescent nitrogen-doped carbon nanoparticles (N-CNPs) were prepared by a simple and green route employing sodium alginate as a carbon source and tryptophan as both a nitrogen source and a functional monomer. The as-synthesized N-CNPs exhibited excellent water solubility and biocompatibility with a fluorescence quantum yield of 47.9%. The fluorescence of the N-CNPs was intensively suppressed by the addition of ascorbic acid (AA). The mechanism of the fluorescence suppression of the N-CNPs was investigated, and the synergistic action of the inner filter effect (IFE) and the static quenching effect (SQE) contributed to the intensive fluorescence suppression, which was different from those reported for the traditional redox-based fluorescent probes. Owing to the spatial effect and hydrogen bond between the AA and the groups on the N-CNP surface, excellent sensitivity and selectivity for AA detecting was obtained in a wide linear relationship from 0.2 μM to 150 μM. The detection limit was as low as 50 nM (signal-to-noise ratio of 3). The proposed sensing systems also represented excellent sensitivity and selectivity for AA analysis in human biological fluids, providing a valuable platform for AA sensing in clinic diagnostic and drug screening. PMID:26202861

  19. Band-gap narrowing in Mn-doped GaAs probed by room-temperature photoluminescence

    NASA Astrophysics Data System (ADS)

    Prucnal, S.; Gao, K.; Skorupa, I.; Rebohle, L.; Vines, L.; Schmidt, H.; Khalid, M.; Wang, Y.; Weschke, E.; Skorupa, W.; Grenzer, J.; Hübner, R.; Helm, M.; Zhou, S.

    2015-12-01

    The electronic band structure of the (Ga,Mn)As system has been one of the most intriguing problems in solid state physics over the past two decades. Determination of the band structure evolution with increasing Mn concentration is a key issue to understand the origin of ferromagnetism. Here, we present room-temperature photoluminescence and ellipsometry measurements of G a100 %-xM nxAs alloy. The upshift of the valence band is proven by the redshift of the room temperature near band-gap emission from the G a100 %-xM nxAs alloy with increasing Mn content. It is shown that even a doping by 0.02% of Mn affects the valence-band edge, and it merges with the impurity band for a Mn concentration as low as 0.6%. Both x-ray diffraction pattern and high-resolution cross-sectional transmission electron microscopy images confirmed full recrystallization of the implanted layer and GaMnAs alloy formation.

  20. Synthesis of kojic acid derivatives as secondary binding site probes of D-amino acid oxidase

    PubMed Central

    Raje, Mithun; Hin, Niyada; Duvall, Bridget; Ferraris, Dana V.; Berry, James F.; Thomas, Ajit G.; Alt, Jesse; Rojas, Camilo; Slusher, Barbara S.; Tsukamoto, Takashi

    2013-01-01

    A series of kojic acid (5-hydroxy-2-hydroxymethyl-4H-pyran-4-one) derivatives were synthesized and tested for their ability to inhibit D-amino acid oxidase (DAAO). Various substituents were incorporated into kojic acid at its 2-hydroxymethyl group. These analogs serve as useful molecular probes to explore the secondary binding site, which can be exploited in designing more potent DAAO inhibitors. PMID:23683589

  1. Composition-dependent trap distributions in CdSe and InP quantum dots probed using photoluminescence blinking dynamics

    NASA Astrophysics Data System (ADS)

    Chung, Heejae; Cho, Kyung-Sang; Koh, Weon-Kyu; Kim, Dongho; Kim, Jiwon

    2016-07-01

    Although Group II-VI quantum dots (QDs) have attracted much attention due to their wide range of applications in QD-based devices, the presence of toxic ions in II-VI QDs raises environmental concerns. To fulfill the demands of nontoxic QDs, synthetic routes for III-V QDs have been developed. However, only a few comparative analyses on optical properties of III-V QDs have been performed. In this study, the composition-related energetic trap distributions have been explored by using three different types of core/multishell QDs: CdSe-CdS (CdSe/CdS/ZnS), InP-ZnSe (InP/ZnSe/ZnS), and InP-GaP (InP/GaP/ZnS). It was shown that CdSe-CdS QDs have much larger trap densities than InP-shell QDs at higher energy states (at least 1Eg (band gap energy) above the lowest conduction band edge) based on probability density plots and Auger ionization efficiencies which are determined by analyses of photoluminescence blinking dynamics. This result suggests that the composition of encapsulated QDs is closely associated with the charge trapping processes, and also provides an insight into the development of more environmentally friendly QD-based devices.Although Group II-VI quantum dots (QDs) have attracted much attention due to their wide range of applications in QD-based devices, the presence of toxic ions in II-VI QDs raises environmental concerns. To fulfill the demands of nontoxic QDs, synthetic routes for III-V QDs have been developed. However, only a few comparative analyses on optical properties of III-V QDs have been performed. In this study, the composition-related energetic trap distributions have been explored by using three different types of core/multishell QDs: CdSe-CdS (CdSe/CdS/ZnS), InP-ZnSe (InP/ZnSe/ZnS), and InP-GaP (InP/GaP/ZnS). It was shown that CdSe-CdS QDs have much larger trap densities than InP-shell QDs at higher energy states (at least 1Eg (band gap energy) above the lowest conduction band edge) based on probability density plots and Auger ionization

  2. Pyrene excimer signaling molecular beacons for probing nucleic acids.

    PubMed

    Conlon, Patrick; Yang, Chaoyong James; Wu, Yanrong; Chen, Yan; Martinez, Karen; Kim, Youngmi; Stevens, Nathan; Marti, Angel A; Jockusch, Steffen; Turro, Nicholas J; Tan, Weihong

    2008-01-01

    Molecular beacon DNA probes, containing 1-4 pyrene monomers on the 5' end and the quencher DABCYL on the 3' end, were engineered and employed for real-time probing of DNA sequences. In the absence of a target sequence, the multiple-pyrene labeled molecular beacons (MBs) assumed a stem-closed conformation resulting in quenching of the pyrene excimer fluorescence. In the presence of target, the beacons switched to a stem-open conformation, which separated the pyrene label from the quencher molecule and generated an excimer emission signal proportional to the target concentration. Steady-state fluorescence assays resulted in a subnanomolar limit of detection in buffer, whereas time-resolved signaling enabled low-nanomolar target detection in cell-growth media. It was found that the excimer emission intensity could be scaled by increasing the number of pyrene monomers conjugated to the 5' terminal. Each additional pyrene monomer resulted in substantial increases in the excimer emission intensities, quantum yields, and excited-state lifetimes of the hybridized MBs. The long fluorescence lifetime ( approximately 40 ns), large Stokes shift (130 nm), and tunable intensity of the excimer make this multiple-pyrene moiety a useful alternative to traditional fluorophore labeling in nucleic acid probes.

  3. Pyrene Excimer Signaling Molecular Beacons for Probing Nucleic Acids

    PubMed Central

    Conlon, Patrick; Yang, Chaoyong James; Wu, Yanrong; Chen, Yan; Martinez, Karen; Kim, Youngmi; Stevens, Nathan; Marti, Angel A.; Jockusch, Steffen

    2008-01-01

    Molecular beacon DNA probes, containing one to four pyrene monomers on the 5′ end and the quencher DABCYL on the 3′ end, were engineered and employed for real-time probing of DNA sequences. In the absence of a target sequence, the multiple-pyrene labeled molecular beacons (MBs) assumed a stem-closed conformation resulting in quenching of the pyrene excimer fluorescence. In the presence of target, the beacons switched to a stem-open conformation which separated the pyrene label from the quencher molecule and generated an excimer emission signal proportional to the target concentration. Steady-state fluorescence assays resulted in a sub-nanomolar limit of detection in buffer, while time-resolved signaling enabled low-nanomolar target detection in cell growth media. It was found that the excimer emission intensity could be scaled by increasing the number of pyrene monomers conjugated to the 5′ terminal. Each additional pyrene monomer resulted in substantial increases in the excimer emission intensities, quantum yields, and excited-state lifetimes of the hybridized MBs. The long fluorescence lifetime (~40 ns), large Stokes shift (130 nm), and tunable intensity of the excimer make this multiple-pyrene moiety a useful alternative to traditional fluorophore labeling in nucleic acid probes. In addition, this excimer complex serves as an efficient FRET donor for red-emitting fluorophores, such as TMR, for further extending the Stokes shift of the fluorescent complex. PMID:18078339

  4. Oligonucleotide-conjugated thiazole orange probes as "light-up" probes for messenger ribonucleic acid molecules in living cells.

    PubMed

    Privat, E; Melvin, T; Asseline, U; Vigny, P

    2001-10-01

    "Light-up" probes, icosa-alpha-thymidylate-thiazole orange conjugates, for the in situ time-resolved detection of messenger ribonucleic acid (mRNA) in living cells are evaluated. Upon annealing with polyA in aqueous solutions, the icosa-alpha-thymidylate-thiazole orange conjugates were shown to be up to 15 times more fluorescent. Microinjection of these probes into adherent fibroblasts resulted in high yields of hybridization and fluorescent signals. Incubation of cells in the presence of these probes resulted in facile internalization of the probe and similar painting of the messenger RNA in the nuclear and cytosolic regions.

  5. Temperature dependence of the energy bandgap of two-dimensional hexagonal boron nitride probed by excitonic photoluminescence

    SciTech Connect

    Du, X. Z.; Lin, J. Y.; Jiang, H. X.; Frye, C. D.; Edgar, J. H.

    2014-02-07

    Hexagonal boron nitride (hBN) is an emerging material for the exploration of new physics in two-dimensional (2D) systems that are complementary to graphene. Nanotubes with a diameter (∼60 nm) that is much larger than the exciton binding energy in hBN have been synthesized and utilized to probe the fundamental optical transitions and the temperature dependence of the energy bandgap of the corresponding 2D hBN sheets. An excitonic transition at 5.901 eV and its longitudinal optical phonon replica at 5.735 eV were observed. The excitonic emission line is blue shifted by about 130 meV with respect to that in hBN bulk crystals due to the effects of reduced dimensionality. The temperature evolution of the excitonic emission line measured from 300 to 800 K revealed that the temperature coefficient of the energy bandgap of hBN nanotubes with large diameters (or equivalently hBN sheets) is about 0.43 meV/{sup 0}K, which is a factor of about 5 times smaller than the theoretically predicted value for the transitions between the π and π* bands in hBN bulk crystals and 6 times smaller than the measured value in AlN epilayers with a comparable energy bandgap. The observed weaker temperature dependence of the bandgap than those in 3D hBN and AlN is a consequence of the effects of reduced dimensionality in layer-structured hBN.

  6. Method for producing labeled single-stranded nucleic acid probes

    DOEpatents

    Dunn, John J.; Quesada, Mark A.; Randesi, Matthew

    1999-10-19

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.

  7. Effect of doping of calcium fluoride nanoparticles on the photoluminescence properties of europium complexes with benzoic acid derivatives as secondary ligands and 2-aminopyridine as primary ligand

    NASA Astrophysics Data System (ADS)

    Sharma, Garima; Narula, Anudeep Kumar

    2015-08-01

    The present article reports the synthesis of three Eu(III) complexes [Eu(BA)3(2-ap)] (1), [Eu(HBA)3(2-ap)] (2) and [Eu(ABA)3(2-ap)] (3) (BA = benzoic acid, HBA = 2-hydroxy benzoic acid, ABA = 2-amino benzoic acid and 2-ap = 2-aminopyridine) carried out in ethanol solution. The complexes were further doped with CaF2 nanoparticles and a change in the photoluminescence properties was observed. The compositions and structural investigation of the complexes were determined by elemental analysis and Fourier transform infrared spectroscopy (FTIR) which suggest the coordination of ligands with the central Eu(III) ion. The optical properties of the complexes were studied by Ultraviolet Visible absorption spectroscopy (UV-Vis) and photoluminescence studies (PL). The relative PL intensity was enhanced in the Eu(III) complexes doped with CaF2 nanoparticles as compared to the pure Eu(III) complexes, however the increase in intensity varied in the order of ligands ABA > HBA > BA. The photoluminescence lifetime decay curves also revealed the longer lifetime (τ) and higher quantum efficiency (η) for europium complexes with ABA ligands suggesting the efficient energy transfer and better sensitizing ability of the ligand to europium ion. The morphology of the synthesized compounds were studied by Scanning Electron Microscopy (SEM) revealing spherical morphology with agglomeration of the nanoparticles.

  8. Probing the Specificity Determinants of Amino Acid Recognition by Arginase

    SciTech Connect

    Shishova, E.; Di Costanzo, L; Emig, F; Ash, D; Christianson, D

    2009-01-01

    Arginase is a binuclear manganese metalloenzyme that serves as a therapeutic target for the treatment of asthma, erectile dysfunction, and atherosclerosis. In order to better understand the molecular basis of inhibitor affinity, we have employed site-directed mutagenesis, enzyme kinetics, and X-ray crystallography to probe the molecular recognition of the amino acid moiety (i.e., the ?-amino and ?-carboxylate groups) of substrate l-arginine and inhibitors in the active site of arginase I. Specifically, we focus on (1) a water-mediated hydrogen bond between the substrate ?-carboxylate and T135, (2) a direct hydrogen bond between the substrate ?-carboxylate and N130, and (3) a direct charged hydrogen bond between the substrate ?-amino group and D183. Amino acid substitutions for T135, N130, and D183 generally compromise substrate affinity as reflected by increased KM values but have less pronounced effects on catalytic function as reflected by minimal variations of kcat. As with substrate KM values, inhibitor Kd values increase for binding to enzyme mutants and suggest that the relative contribution of intermolecular interactions to amino acid affinity in the arginase active site is water-mediated hydrogen bond < direct hydrogen bond < direct charged hydrogen bond. Structural comparisons of arginase with the related binuclear manganese metalloenzymes agmatinase and proclavaminic acid amidinohydrolase suggest that the evolution of substrate recognition in the arginase fold occurs by mutation of residues contained in specificity loops flanking the mouth of the active site (especially loops 4 and 5), thereby allowing diverse guanidinium substrates to be accommodated for catalysis.

  9. Method for analyzing nucleic acids by means of a substrate having a microchannel structure containing immobilized nucleic acid probes

    DOEpatents

    Ramsey, J. Michael; Foote, Robert S.

    2003-12-09

    A method and apparatus for analyzing nucleic acids includes immobilizing nucleic probes at specific sites within a microchannel structure and moving target nucleic acids into proximity to the probes in order to allow hybridization and fluorescence detection of specific target sequences.

  10. Method for analyzing nucleic acids by means of a substrate having a microchannel structure containing immobilized nucleic acid probes

    DOEpatents

    Ramsey, J. Michael; Foote, Robert S.

    2002-01-01

    A method and apparatus for analyzing nucleic acids includes immobilizing nucleic probes at specific sites within a microchannel structure and moving target nucleic acids into proximity to the probes in order to allow hybridization and fluorescence detection of specific target sequences.

  11. Visible photoluminescence from nearly monodispersed Au 12 clusters protected by meso-2,3-dimercaptosuccinic acid

    NASA Astrophysics Data System (ADS)

    Negishi, Yuichi; Tsukuda, Tatsuya

    2004-01-01

    Nearly monodispersed Au 12 clusters protected by monolayers of meso-2,3-dimercaptosuccinic acid (DMSA) exhibited luminescence at 630 nm with a quantum yield of 1 × 10 -6 upon the photoexcitation at 395 nm to the lowest electronic excited state. The visible PL is assigned to phosphorescence originating from a triplet-like excited state based on the large Stokes shift (1.2 eV). The PL quantum yield was enhanced up to ≈0.9%, greater by eight orders of magnitude than that of bulk gold, by thickening the protecting layer and freezing a solvent at 77 K. The emission peak energy is discussed within the context of core-size dependent electronic structures by comparison with those of thiolate-protected gold clusters reported in the literature.

  12. Probing the carrier transfer processes in a self-assembled system with In0.3Ga0.7As/GaAs quantum dots by photoluminescence excitation spectroscopy

    NASA Astrophysics Data System (ADS)

    Podemski, Paweł; Pieczarka, Maciej; Maryński, Aleksander; Misiewicz, Jan; Löffler, Andreas; Höfling, Sven; Reithmaier, Johann Peter; Reitzenstein, Stephan; Sęk, Grzegorz

    2016-05-01

    In this report we present experimental studies on the energy transfer between the wetting layer and single large elongated In0.3Ga0.7As/GaAs quantum dots. We obtain insight into the electronic and optical properties of In0.3Ga0.7As/GaAs quantum dots by probing their confined electronic states via photoluminescence excitation spectroscopy on the single dot level. We demonstrate that the energy separation between the states of a quantum dot and the wetting layer states affects the carrier transfer efficiency - reduced transfer efficiency is observed for smaller dots with higher indium content. We also discuss the effects of the excited states and the trapping of carriers on confinement potential fluctuations of the wetting layer. Eventually, the transfer of charge carriers from localized wetting layer states to a single quantum dot is evidenced in temperature-dependent photoluminescence excitation spectroscopy.

  13. Method for replicating an array of nucleic acid probes

    DOEpatents

    Cantor, Charles R.; Przetakiewicz, Marek; Smith, Cassandra L.; Sano, Takeshi

    1998-01-01

    The invention relates to the replication of probe arrays and methods for replicating arrays of probes which are useful for the large scale manufacture of diagnostic aids used to screen biological samples for specific target sequences. Arrays created using PCR technology may comprise probes with 5'- and/or 3'-overhangs.

  14. Method for replicating an array of nucleic acid probes

    DOEpatents

    Cantor, C.R.; Przetakiewicz, M.; Smith, C.L.; Sano, T.

    1998-08-18

    The invention relates to the replication of probe arrays and methods for replicating arrays of probes which are useful for the large scale manufacture of diagnostic aids used to screen biological samples for specific target sequences. Arrays created using PCR technology may comprise probes with 5{prime}- and/or 3{prime}-overhangs. 16 figs.

  15. Photoluminescence: A probe for short, medium and long-range self-organization order in ZrTiO{sub 4} oxide

    SciTech Connect

    Lucena, Poty R. de . E-mail: poty@liec.ufscar.br; Roberto Leite, Edson; Pontes, Fenelon M.; Longo, Elson; Pizani, Paulo S.; Arana Varela, Jose

    2006-12-15

    Photoluminescent disordered ZrTiO{sub 4} powders were obtained by the polymeric precursor soft-chemical method. This oxide system (ordered and disordered) was characterized by photoluminescence, Raman spectroscopy, X-ray diffraction, differential scanning calorimetry and UV-vis absorption experiments. The UV absorption tail formation in the disordered oxides was related to the diminution of optical band gap. In the disordered phase, this oxide displayed broad band photoluminescence caused by change in coordination number of titanium and zirconium with oxygen atoms. The gap decreased from 3.09eV in crystalline oxide to 2.16 eV in disordered oxide. The crystalline oxide presented an orthorhombic {alpha}-PbO{sub 2}-type structure in which Zr{sup 4+} and Ti{sup 4+} were randomly distributed in octahedral coordination polyhedra with oxygen atoms. The amorphous-crystalline transition occurred at almost 700 deg. C, at which point the photoluminescence vanished. The Raman peak at close to 80-200cm{sup -1} indicated the presence of locally ordered Ti-O{sub n} and Zr-O{sub n} polyhedra in disordered photoluminescent oxides.

  16. Organic acids and protein compounds causing the photoluminescence properties of natural rubber membranes and the quenching phenomena from Au nanoparticle incorporation.

    PubMed

    Cabrera, Flávio C; Agostini, Deuber L S; Dos Santos, Renivaldo J; Guimarães, Francisco E G; Guerrero, Ariel R; Aroca, Ricardo F; Job, Aldo E

    2014-12-01

    Natural rubber membranes were fabricated using latex from Hevea brasiliensis trees (clone RRIM 600) by casting, and controlling the time and temperature of thermal treatment. Three temperatures were used: 65, 80 and 120 °C and the corresponding annealing times of 6, 8, 10 and 12 h. The centrifugation of the latex produces the constituent phases: solid rubber (F1), serum or protein components (F2) and bottom fraction (F3). The photoluminescence properties could be correlated with organic acid components of latex. Natural rubber membranes were used as the active substrate (reducing agent) for the incorporation of colloidal Au nanoparticles synthesized by in situ reduction at different times. The intensity of photoluminescence bands assigned to the natural rubber decreases with the increase in amount of nanoparticles present on the membrane surface. It can be assumed that Au nanoparticles may be formed by reduction of the Au cation reacting with functional groups that are directly related to photoluminescence properties. However, the quenching of fluorescence may be attributed to the formation of a large amount of metal nanostructures on the natural rubber surface.

  17. Light-up probes: thiazole orange-conjugated peptide nucleic acid for detection of target nucleic acid in homogeneous solution.

    PubMed

    Svanvik, N; Westman, G; Wang, D; Kubista, M

    2000-05-15

    We have constructed light-up probes for nucleic acid detection. The light-up probe is a peptide nucleic acid (PNA) oligonucleotide to which the asymmetric cyanine dye thiazole orange (TO) is tethered. It combines the excellent hybridization properties of PNA and the large fluorescence enhancement of TO upon binding to DNA. When the PNA hybridizes to target DNA, the dye binds and becomes fluorescent. Free probes have low fluorescence, which may increase almost 50-fold upon hybridization to complementary nucleic acid. This makes the light-up probes particularly suitable for homogeneous hybridization assays, where separation of the bound and free probe is not necessary. We find that the fluorescence enhancement upon hybridization varies among different probes, which is mainly due to variations in free probe fluorescence. For eight probes studied the fluorescence quantum yield at 25 degrees C in the unbound state ranged from 0.0015 to 0.08 and seemed to depend mainly on the PNA sequence. The binding of the light-up probes to target DNA is highly sequence specific and a single mismatch in a 10-mer target sequence was readily identified.

  18. Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes.

    PubMed

    Junager, Nina P L; Kongsted, Jacob; Astakhova, Kira

    2016-01-01

    Nucleic acid mutations are of tremendous importance in modern clinical work, biotechnology and in fundamental studies of nucleic acids. Therefore, rapid, cost-effective and reliable detection of mutations is an object of extensive research. Today, Förster resonance energy transfer (FRET) probes are among the most often used tools for the detection of nucleic acids and in particular, for the detection of mutations. However, multiple parameters must be taken into account in order to create efficient FRET probes that are sensitive to nucleic acid mutations. In this review; we focus on the design principles for such probes and available computational methods that allow for their rational design. Applications of advanced, rationally designed FRET probes range from new insights into cellular heterogeneity to gaining new knowledge of nucleic acid structures directly in living cells. PMID:27472344

  19. Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes

    PubMed Central

    Junager, Nina P. L.; Kongsted, Jacob; Astakhova, Kira

    2016-01-01

    Nucleic acid mutations are of tremendous importance in modern clinical work, biotechnology and in fundamental studies of nucleic acids. Therefore, rapid, cost-effective and reliable detection of mutations is an object of extensive research. Today, Förster resonance energy transfer (FRET) probes are among the most often used tools for the detection of nucleic acids and in particular, for the detection of mutations. However, multiple parameters must be taken into account in order to create efficient FRET probes that are sensitive to nucleic acid mutations. In this review; we focus on the design principles for such probes and available computational methods that allow for their rational design. Applications of advanced, rationally designed FRET probes range from new insights into cellular heterogeneity to gaining new knowledge of nucleic acid structures directly in living cells. PMID:27472344

  20. Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes.

    PubMed

    Junager, Nina P L; Kongsted, Jacob; Astakhova, Kira

    2016-01-01

    Nucleic acid mutations are of tremendous importance in modern clinical work, biotechnology and in fundamental studies of nucleic acids. Therefore, rapid, cost-effective and reliable detection of mutations is an object of extensive research. Today, Förster resonance energy transfer (FRET) probes are among the most often used tools for the detection of nucleic acids and in particular, for the detection of mutations. However, multiple parameters must be taken into account in order to create efficient FRET probes that are sensitive to nucleic acid mutations. In this review; we focus on the design principles for such probes and available computational methods that allow for their rational design. Applications of advanced, rationally designed FRET probes range from new insights into cellular heterogeneity to gaining new knowledge of nucleic acid structures directly in living cells.

  1. Detection and isolation of nucleic acid sequences using competitive hybridization probes

    DOEpatents

    Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

    1997-01-01

    A method for detecting a target nucleic acid sequence in a sample is provided using hybridization probes which competitively hybridize to a target nucleic acid. According to the method, a target nucleic acid sequence is hybridized to first and second hybridization probes which are complementary to overlapping portions of the target nucleic acid sequence, the first hybridization probe including a first complexing agent capable of forming a binding pair with a second complexing agent and the second hybridization probe including a detectable marker. The first complexing agent attached to the first hybridization probe is contacted with a second complexing agent, the second complexing agent being attached to a solid support such that when the first and second complexing agents are attached, target nucleic acid sequences hybridized to the first hybridization probe become immobilized on to the solid support. The immobilized target nucleic acids are then separated and detected by detecting the detectable marker attached to the second hybridization probe. A kit for performing the method is also provided.

  2. Detection and isolation of nucleic acid sequences using competitive hybridization probes

    DOEpatents

    Lucas, J.N.; Straume, T.; Bogen, K.T.

    1997-04-01

    A method for detecting a target nucleic acid sequence in a sample is provided using hybridization probes which competitively hybridize to a target nucleic acid. According to the method, a target nucleic acid sequence is hybridized to first and second hybridization probes which are complementary to overlapping portions of the target nucleic acid sequence, the first hybridization probe including a first complexing agent capable of forming a binding pair with a second complexing agent and the second hybridization probe including a detectable marker. The first complexing agent attached to the first hybridization probe is contacted with a second complexing agent, the second complexing agent being attached to a solid support such that when the first and second complexing agents are attached, target nucleic acid sequences hybridized to the first hybridization probe become immobilized on to the solid support. The immobilized target nucleic acids are then separated and detected by detecting the detectable marker attached to the second hybridization probe. A kit for performing the method is also provided. 7 figs.

  3. Fluorescence probe for the convenient and sensitive detection of ascorbic acid.

    PubMed

    Matsuoka, Yuta; Yamato, Mayumi; Yamada, Ken-Ichi

    2016-01-01

    Ascorbic acid is an important antioxidant that plays an essential role in the biosynthesis of numerous bioactive substances. The detection of ascorbic acid has traditionally been achieved using high-performance liquid chromatography and absorption spectrophotometry assays. However, the development of fluorescence probes for this purpose is highly desired because they provide a much more convenient and highly sensitive technique for the detection of this material. OFF-ON-type fluorescent probes have been developed for the detection of non-fluorescent compounds. Photo-induced electron transfer and fluorescence resonance energy transfer are the two main fluorescence quenching mechanisms for the detection of ascorbic acid, and several fluorescence probes have been reported based on redox-responsive metals and quantum dots. Profluorescent nitroxide compounds have also been developed as non-metal organic fluorescence probes for ascorbic acid. These nitroxide systems have a stable unpaired electron and can therefore react with ascorbic acid and a strong fluorescence quencher. Furthermore, recent synthetic advances have allowed for the synthesis of α-substituted nitroxides with varying levels of reactivity towards ascorbic acid. In this review, we have discussed the design strategies used for the preparation of fluorescent probes for ascorbic acid, with particular emphasis on profluorescent nitroxides, which are unique radical-based redox-active fluorescent probes.

  4. Fluorescence probe for the convenient and sensitive detection of ascorbic acid

    PubMed Central

    Matsuoka, Yuta; Yamato, Mayumi; Yamada, Ken-ichi

    2016-01-01

    Ascorbic acid is an important antioxidant that plays an essential role in the biosynthesis of numerous bioactive substances. The detection of ascorbic acid has traditionally been achieved using high-performance liquid chromatography and absorption spectrophotometry assays. However, the development of fluorescence probes for this purpose is highly desired because they provide a much more convenient and highly sensitive technique for the detection of this material. OFF-ON-type fluorescent probes have been developed for the detection of non-fluorescent compounds. Photo-induced electron transfer and fluorescence resonance energy transfer are the two main fluorescence quenching mechanisms for the detection of ascorbic acid, and several fluorescence probes have been reported based on redox-responsive metals and quantum dots. Profluorescent nitroxide compounds have also been developed as non-metal organic fluorescence probes for ascorbic acid. These nitroxide systems have a stable unpaired electron and can therefore react with ascorbic acid and a strong fluorescence quencher. Furthermore, recent synthetic advances have allowed for the synthesis of α-substituted nitroxides with varying levels of reactivity towards ascorbic acid. In this review, we have discussed the design strategies used for the preparation of fluorescent probes for ascorbic acid, with particular emphasis on profluorescent nitroxides, which are unique radical-based redox-active fluorescent probes. PMID:26798193

  5. A phosphomolybdic acid anion probe-based label-free, stable and simple electrochemical biosensing platform.

    PubMed

    Wei, Tianxiang; Chen, Yuyun; Tu, Wenwen; Lan, Yaqian; Dai, Zhihui

    2014-08-25

    A versatile label-free, stable, low-cost and simple electrochemical biosensing platform has been developed based on a phosphomolybdic acid anion probe by jointly taking advantages of its native electronegativity, electrochemical activity and chemisorption with graphene oxide.

  6. A rapid microwave synthesis of nitrogen-sulfur co-doped carbon nanodots as highly sensitive and selective fluorescence probes for ascorbic acid.

    PubMed

    Duan, Junxia; Yu, Jie; Feng, Suling; Su, Li

    2016-06-01

    A ultrafast one-step microwave-assisted method was developed for the synthesis of nitrogen-sulfur co-doped carbon nanodots (N,S-CDs) by using ethylenediamine as the carbon source and sulfamic acid as the surface passivation reagent. The morphology and the properties of N,S-CDs were explored by a series of techniques, such as high-resolution transmission electron microscopy, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, UV-vis absorption and fluorescence spectroscopy. The prepared N,S-CDs exhibit bright blue photoluminescence with a high fluorescence quantum yield (FLQY) up to 28%, and high stability and excellent water solubility. A N,S-CDs-based fluorescent probe was developed for sensitive detection ascorbic acid (AA) in the presence of Cu(2+), based on the mechanism that AA reduces Cu(2+) to Cu(+), then Cu(+) quenches the fluorescence of N,S-CDs through electron or energy transfer due to the interaction between Cu(+) and thiol ligand on the N,S-CDs surface. The observed linear response concentration range was from 0.057 to 4.0μM to AA with a detection limit as low as 18nM. The probe exhibited a highly selective response toward AA even in the presence of possible interfering substances, such as uric acid and citric acid. Moreover, these promising features made the sensing system used for the analysis of human serum and urine samples. PMID:27130124

  7. Probe kit for identifying a base in a nucleic acid

    DOEpatents

    Fodor, Stephen P. A.; Lipshutz, Robert J.; Huang, Xiaohua

    2001-01-01

    Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

  8. Detection and isolation of nucleic acid sequences using a bifunctional hybridization probe

    DOEpatents

    Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

    2000-01-01

    A method for detecting and isolating a target sequence in a sample of nucleic acids is provided using a bifunctional hybridization probe capable of hybridizing to the target sequence that includes a detectable marker and a first complexing agent capable of forming a binding pair with a second complexing agent. A kit is also provided for detecting a target sequence in a sample of nucleic acids using a bifunctional hybridization probe according to this method.

  9. Large scale synthesis of graphene quantum dots (GQDs) from waste biomass and their use as an efficient and selective photoluminescence on-off-on probe for Ag(+) ions.

    PubMed

    Suryawanshi, Anil; Biswal, Mandakini; Mhamane, Dattakumar; Gokhale, Rohan; Patil, Shankar; Guin, Debanjan; Ogale, Satishchandra

    2014-10-21

    Graphene quantum dots (GQDs) are synthesized from bio-waste and are further modified to produce amine-terminated GQDs (Am-GQDs) which have higher dispersibility and photoluminescence intensity than those of GQDs. A strong fluorescence quenching of Am-GQDs (switch-off) is observed for a number of metal ions, but only for the Ag(+) ions is the original fluorescence regenerated (switch-on) upon addition of L-cysteine.

  10. Copper(II)-lanthanide(III) coordination polymers constructed from pyridine-2,5-dicarboxylic acid: Preparation, crystal structure and photoluminescence

    SciTech Connect

    Xia Zhengqiang; Wei Qing; Chen Sanping; Feng Xinming; Xie Gang; Qiao Chengfang; Zhang Guochun; Gao Shengli

    2013-01-15

    A series of 3d-4f heterometallic coordination polymers, formulated as {l_brace} [Cu{sub 3}Ln{sub 2}(pydc){sub 6}(H{sub 2}O){sub 12}]{center_dot}4H{sub 2}O{r_brace} {sub n} [Ln=Tb (1), Eu (2), Dy (3), Ho (4), Lu (5)], {l_brace} [CuNd{sub 2}(pydc){sub 4}(H{sub 2}O){sub 3}]{center_dot}H{sub 2}O{r_brace} {sub n} (6) and {l_brace} [Cu{sub 3}Pr{sub 2}(pydc){sub 6}(H{sub 2}O){sub 13}]{center_dot}4H{sub 2}O{r_brace} {sub n} (7) (where H{sub 2}pydc=pyridine-2,5-dicarboxylic acid), have been hydrothermally prepared by reactions of H{sub 2}pydc ligand with lanthanide ions in the presence of Cu(II) ion. X-ray crystal structure analysis reveals that these compounds exhibit rich structural chemistry. 1-5 are isomorphous and present a two-dimensional network constructed from Ln{sub 2}Cu{sub 2}L{sub 2}(H{sub 2}O){sub 2} SBU rings and CuL{sub 2}(H{sub 2}O) building blocks. In 6, two-dimensional ladder-like layers based on Nd(III) belts and CuL{sub 2}O{sub 2} units are assembled by H{sub 2}pydc ligands into a three-dimensional open framework. Polymer 7 displays a two-dimensional wave-like layer structure containing two distinct ring units, in which a new coordination mode of the pydc{sup 2-} ligand is observed. The results indicate that the coordination flexibility of the pydc{sup 2-} ligand and lanthanide contraction effect play cooperative roles in the formation of coordination polymers with different polymeric architectures. Compounds 1-2 exhibit intense green and red luminescence emission characteristics of Tb(III) and Eu(III), respectively. Furthermore, elemental analyses (EA), infrared spectra (IR) and thermogravimetric analyses (TGA) of these compounds were also studied. - Graphical abstract: Seven 3d-4f heterometallic coordination polymers were synthesized by reactions of H{sub 2}pydc with lanthanide metal ions in the presence of Cu{sup 2+}, the effects of Cu{sup 2+} on the structures and photoluminescent properties of Ln-pydc{sup 2-} systems were investigated. Highlights

  11. Synthesis of nucleic acid probes on membrane supports: a procedure for the removal of unincorporated precursors.

    PubMed

    Bhat, S P

    1990-01-01

    We have used DNA bound to small pieces of nylon membrane for the synthesis of radioactive probes. The DNA to be used for generating the probe(s) is first bound to nylon membranes and then introduced into the reaction mix. The labeling reaction takes place on the membrane and therefore allows easy removal of unincorporated precursors by simple washing for 1-2 min. The clean labeled probe is eluted from the membrane in formamide or in water and is ready for use. This DNA-membrane can be stored for reuse. Synthesis of probes on a solid support such as nylon membrane thus circumvents problems associated with chromatographic manipulations needed for the separation of labeled DNA from unicorporated precursors. Probes synthesized in this manner are as efficient in detecting nucleic acid sequences as those synthesized in solution. PMID:2321760

  12. Methods of staining target chromosomal DNA employing high complexity nucleic acid probes

    DOEpatents

    Gray, Joe W.; Pinkel, Daniel; Kallioniemi, Ol'li-Pekka; Kallioniemi, Anne; Sakamoto, Masaru

    2006-10-03

    Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML), retinoblastoma, ovarian and uterine cancers, and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

  13. Bright photoluminescent hybrid mesostructured silica nanoparticles.

    PubMed

    Miletto, Ivana; Bottinelli, Emanuela; Caputo, Giuseppe; Coluccia, Salvatore; Gianotti, Enrica

    2012-07-28

    Bright photoluminescent mesostructured silica nanoparticles were synthesized by the incorporation of fluorescent cyanine dyes into the channels of MCM-41 mesoporous silica. Cyanine molecules were introduced into MCM-41 nanoparticles by physical adsorption and covalent grafting. Several photoluminescent nanoparticles with different organic loadings have been synthesized and characterized by X-ray powder diffraction, high resolution transmission electron microscopy and nitrogen physisorption porosimetry. A detailed photoluminescence study with the analysis of fluorescence lifetimes was carried out to elucidate the cyanine molecules distribution within the pores of MCM-41 nanoparticles and the influence of the encapsulation on the photoemission properties of the guests. The results show that highly stable photoluminescent hybrid materials with interesting potential applications as photoluminescent probes for diagnostics and imaging can be prepared by both methods. PMID:22706523

  14. Acid properties of solid acid catalysts characterized by solid-state 31P NMR of adsorbed phosphorous probe molecules.

    PubMed

    Zheng, Anmin; Huang, Shing-Jong; Liu, Shang-Bin; Deng, Feng

    2011-09-01

    A brief review is presented on acidity characterization of solid acid catalysts by means of solid-state phosphor-31 magic-angle-spinning nuclear magnetic resonance ((31)P MAS NMR) spectroscopy using phosphor-containing molecules as probes. It is emphasized that such a simple approach using (31)P MAS NMR of adsorbed phosphorous probe molecules, namely trimethylphosphine (TMP) and trialkylphosphine oxides (R(3)PO), represents a unique technique in providing detailed qualitative and quantitative features, viz. type, strength, distribution, and concentration of acid sites in solid acid catalysts. In particular, it will be shown that when applied with a proper choice of probe molecules with varied sizes and results obtained from elemental analysis, the amounts and locations (intracrystalline vs. extracrystalline) of different types (Brønsted vs. Lewis) of acid sites may be determined. In addition, by incorporating the NMR results with that obtained from theoretical density functional theory (DFT) calculations, correlations between the (31)P chemical shifts (δ(31)P) and acidic strengths of Brønsted and Lewis acid sites may also be derived, facilitating a suitable acidity scale for solid acid catalysts.

  15. Terbium fluorescence as a sensitive, inexpensive probe for UV-induced damage in nucleic acids.

    PubMed

    El-Yazbi, Amira F; Loppnow, Glen R

    2013-07-01

    Much effort has been focused on developing methods for detecting damaged nucleic acids. However, almost all of the proposed methods consist of multi-step procedures, are limited, require expensive instruments, or suffer from a high level of interferences. In this paper, we present a novel simple, inexpensive, mix-and-read assay that is generally applicable to nucleic acid damage and uses the enhanced luminescence due to energy transfer from nucleic acids to terbium(III) (Tb(3+)). Single-stranded oligonucleotides greatly enhance the Tb(3+) emission, but duplex DNA does not. With the use of a DNA hairpin probe complementary to the oligonucleotide of interest, the Tb(3+)/hairpin probe is applied to detect ultraviolet (UV)-induced DNA damage. The hairpin probe hybridizes only with the undamaged DNA. However, the damaged DNA remains single-stranded and enhances the intrinsic fluorescence of Tb(3+), producing a detectable signal directly proportional to the amount of DNA damage. This allows the Tb(3+)/hairpin probe to be used for sensitive quantification of UV-induced DNA damage. The Tb(3+)/hairpin probe showed superior selectivity to DNA damage compared to conventional molecular beacons probes (MBs) and its sensitivity is more than 2.5 times higher than MBs with a limit of detection of 4.36±1.2 nM. In addition, this probe is easier to synthesize and more than eight times cheaper than MBs, which makes its use recommended for high-throughput, quantitative analysis of DNA damage.

  16. Correlated high-resolution x-ray diffraction photoluminescence and atom probe tomography analysis of continuous and discontinuous InxGa1-xN quantum wells

    SciTech Connect

    Ren, Xiaochen; Riley, James R.; Koleske, Daniel; Lauhon, Lincoln J.

    2015-07-14

    In this study, atom probe tomography (APT) is used to characterize the influence of hydrogen dosing duringGaN barrier growth on the indium distribution of InxGa1-xN quantum wells, and correlatedmicro-photoluminescence is used to measure changes in the emission spectrum and efficiency. We found that relative to the control growth, hydrogen dosing leads to a 50% increase in emission intensity arising from discontinuous quantum wells that are narrower, of lower indium content, and with more abrupt interfaces. Additionally, simulations of carrier distributions based on APT composition profiles indicate that the greater carrier confinement leads to an increased radiative recombination rate. Furthermore, APT analysis of quantum well profiles enables refinement of x-ray diffractionanalysis for more accurate nondestructive measurements of composition.

  17. Correlated high-resolution x-ray diffraction, photoluminescence, and atom probe tomography analysis of continuous and discontinuous In{sub x}Ga{sub 1−x}N quantum wells

    SciTech Connect

    Ren, Xiaochen; Riley, James R.; Lauhon, Lincoln J.; Koleske, Daniel D.

    2015-07-13

    Atom probe tomography (APT) is used to characterize the influence of hydrogen dosing during GaN barrier growth on the indium distribution of In{sub x}Ga{sub 1−x}N quantum wells, and correlated micro-photoluminescence is used to measure changes in the emission spectrum and efficiency. Relative to the control growth, hydrogen dosing leads to a 50% increase in emission intensity arising from discontinuous quantum wells that are narrower, of lower indium content, and with more abrupt interfaces. Simulations of carrier distributions based on APT composition profiles indicate that the greater carrier confinement leads to an increased radiative recombination rate. Furthermore, APT analysis of quantum well profiles enables refinement of x-ray diffraction analysis for more accurate nondestructive measurements of composition.

  18. Auxiliary aromatic-acid effect on the structures of a series of Zn{sup II} coordination polymers: Syntheses, crystal structures, and photoluminescence properties

    SciTech Connect

    Xu Yanhong; Lan Yaqian; Shao Kuizhan; Su Zhongmin; Liao Yi

    2010-04-15

    Five novel Zn{sup II}-(pyridyl)imidazole derivative coordination polymers, [Zn(L){sub 2}] (1), [Zn{sub 2}(mu{sub 3}-OH)L(m-BDC)] (2), [Zn{sub 2}(mu{sub 3}-OH)L(p-BDC)].H{sub 2}O (3), [Zn{sub 2}L(BTC)(H{sub 2}O)].2.5H{sub 2}O (4) and [Zn{sub 3.5}(mu{sub 3}-OH)L{sub 2}(BTEC)(H{sub 2}O)].H{sub 2}O (5) (L=4-((2-(pyridine-2-yl)-1H-imidazol-1-yl)methyl)benzoic acid, p-H{sub 2}BDC=1,4-benzenedicarboxylic acid, m-H{sub 2}BDC=1,3-benzenedicarboxylic acid, H{sub 3}BTC=1,3,5-benzenetricarboxylic acid, H{sub 4}BTEC=1,2,4,5-benzenetetracarboxylic acid), were successfully synthesized under hydrothermal conditions through varying auxiliary aromatic-acid ligands and structurally characterized by X-ray crystallography. Compound 1 exhibits a 1D chain linked via double L bridges. Compound 2 features a well-known pcu topology with bent dicarboxylate ligand (m-H{sub 2}BDC) as an auxiliary ligand, while 3 displays a bcu network with linear dicarboxylate ligand (p-H{sub 2}BDC) as an auxiliary ligand. The structure of compound 4 is a novel 3D (3,5)-connected network with (4.6{sup 2})(4.6{sup 4}.8{sup 2}.10.12{sup 2}) topology. It is interesting that compound 5 shows an intricate (3,4,8)-connected framework with (4.6{sup 2})(4{sup 2}.6{sup 3}.8)(4{sup 2}.6{sup 4})(4{sup 2}.6{sup 18}.7.8{sup 6}.10) topology. In addition, their infrared spectra (IR), X-ray powder diffraction (XPRD) and photoluminescent properties were also investigated in detail. - Graphical abstract: Five novel Zn{sup II}-organic architectures have been hydrothermally synthesized through varying auxiliary aromatic-acid ligands and characterized by X-ray diffraction, the photoluminescence properties of compounds 1-5 were studied.

  19. Molecular-beacon-based tricomponent probe for SNP analysis in folded nucleic acids.

    PubMed

    Nguyen, Camha; Grimes, Jeffrey; Gerasimova, Yulia V; Kolpashchikov, Dmitry M

    2011-11-11

    Hybridization probes are often inefficient in the analysis of single-stranded DNA or RNA that are folded in stable secondary structures. A molecular beacon (MB) probe is a short DNA hairpin with a fluorophore and a quencher attached to opposite sides of the oligonucleotide. The probe is widely used in real-time analysis of specific DNA and RNA sequences. This study demonstrates how a conventional MB probe can be used for the analysis of nucleic acids that form very stable (T(m) > 80 °C) hairpin structures. Here we demonstrate that the MB probe is not efficient in direct analysis of secondary structure-folded analytes, whereas a MB-based tricomponent probe is suitable for these purposes. The tricomponent probe takes advantage of two oligonucleotide adaptor strands f and m. Each adaptor strand contains a fragment complementary to the analyte and a fragment complementary to a MB probe. In the presence of a specific analyte, the two adaptor strands hybridize to the analyte and the MB probe, thus forming a quadripartite complex. DNA strand f binds to the analyte with high affinity and unwinds its secondary structure. Strand m forms a stable complex only with the fully complementary analyte. The MB probe fluorescently reports the formation of the quadripartite associate. It was demonstrated that the DNA analytes folded in hairpin structures with stems containing 5, 6, 7, 8, 9, 11, or 13 base pairs can be detected in real time with the limit of detection (LOD) lying in the nanomolar range. The stability of the stem region in the DNA analyte did not affect the LOD. Analytes containing single base substitutions in the stem or in the loop positions were discriminated from the fully complementary DNA at room temperature. The tricomponent probe promises to simplify nucleic acid analysis at ambient temperatures in such applications as in vivo RNA monitoring, detection of pathogens, and single nucleotide polymorphism (SNP) genotyping by DNA microarrays.

  20. Large scale synthesis of graphene quantum dots (GQDs) from waste biomass and their use as an efficient and selective photoluminescence on-off-on probe for Ag+ ions

    NASA Astrophysics Data System (ADS)

    Suryawanshi, Anil; Biswal, Mandakini; Mhamane, Dattakumar; Gokhale, Rohan; Patil, Shankar; Guin, Debanjan; Ogale, Satishchandra

    2014-09-01

    Graphene quantum dots (GQDs) are synthesized from bio-waste and are further modified to produce amine-terminated GQDs (Am-GQDs) which have higher dispersibility and photoluminescence intensity than those of GQDs. A strong fluorescence quenching of Am-GQDs (switch-off) is observed for a number of metal ions, but only for the Ag+ ions is the original fluorescence regenerated (switch-on) upon addition of l-cysteine.Graphene quantum dots (GQDs) are synthesized from bio-waste and are further modified to produce amine-terminated GQDs (Am-GQDs) which have higher dispersibility and photoluminescence intensity than those of GQDs. A strong fluorescence quenching of Am-GQDs (switch-off) is observed for a number of metal ions, but only for the Ag+ ions is the original fluorescence regenerated (switch-on) upon addition of l-cysteine. Electronic supplementary information (ESI) available: HRTEM images, GQD SAED patterns and EDAX analysis of Am-GQD@Ag. See DOI: 10.1039/c4nr02494j

  1. A single molecular beacon probe is sufficient for the analysis of multiple nucleic acid sequences.

    PubMed

    Gerasimova, Yulia V; Hayson, Aaron; Ballantyne, Jack; Kolpashchikov, Dmitry M

    2010-08-16

    Molecular beacon (MB) probes are dual-labeled hairpin-shaped oligodeoxyribonucleotides that are extensively used for real-time detection of specific RNA/DNA analytes. In the MB probe, the loop fragment is complementary to the analyte: therefore, a unique probe is required for the analysis of each new analyte sequence. The conjugation of an oligonucleotide with two dyes and subsequent purification procedures add to the cost of MB probes, thus reducing their application in multiplex formats. Here we demonstrate how one MB probe can be used for the analysis of an arbitrary nucleic acid. The approach takes advantage of two oligonucleotide adaptor strands, each of which contains a fragment complementary to the analyte and a fragment complementary to an MB probe. The presence of the analyte leads to association of MB probe and the two DNA strands in quadripartite complex. The MB probe fluorescently reports the formation of this complex. In this design, the MB does not bind the analyte directly; therefore, the MB sequence is independent of the analyte. In this study one universal MB probe was used to genotype three human polymorphic sites. This approach promises to reduce the cost of multiplex real-time assays and improve the accuracy of single-nucleotide polymorphism genotyping.

  2. Structural variations and photoluminescent properties of a series of metal-organic frameworks constructed from 5-(4-carboxybenzoylamino)-isophthalic acid

    SciTech Connect

    Zhao, Wen; Zhang, Li-Juan; Zhao, Xiao-Li

    2013-06-01

    Five new metal-organic frameworks (MOFs) with 5-(4-carboxybenzoylamino)-isophthalic acid (H₃L), namely, [Cd₉L₆(DMA)₆]·4DMA (1), [Cd₃L₂(H₂O)₉]·4H₂O (2), [LaL(H₂O)₄]·2H₂O (3), [CeL(H₂O)₄]·H₂O (4) and [Tb(HL)(H₂L)(H₂O)₃]·5H₂O (5) (DMA=N,N-dimethylacetamide), have been synthesized. Complex 1 shows a three-dimensional architecture generated from linkage of Cd–O chains via L³⁻ ligands. Minor variations in synthetic conditions of 1 afforded 2, which features an interesting 2D→3D catenation architecture containing helical chains. Complexes 3 and 4 are isostructural and each feature a two-dimensional architecture constructed from the linkage of L³⁻ with Ln³⁺. Complex 5 displays a chain-like structure, of which the most interesting feature is the existence of free carboxylic acid (–COOH) group which may confer unique functionality. Moreover, the investigations of the thermal stability, powder X-ray diffractions and solid-state photoluminescent properties for these crystalline materials have been carried out. - Graphical Abstract: Solvothermal reactions of tricarboxylate ligand H₃L with Cd²⁺/Ln³⁺ has yielded a series of new MOFs containing interesting structural motifs. Highlights: • A tricarboxylate ligand whose coordinating functionalities are not symmetry equivalent is employed to construct MOFs. • Complex 2 features an interesting 2D→3D catenation architecture containing helical chains. • Complex 3 feature chain-like structure containing free – COOH group, which may confer unique functionality. • Photoluminescent properties and thermal behaviors for 1–5 have been reported.

  3. Design and synthesis of an activity-based protein profiling probe derived from cinnamic hydroxamic acid.

    PubMed

    Ai, Teng; Qiu, Li; Xie, Jiashu; Geraghty, Robert J; Chen, Liqiang

    2016-02-15

    In our continued effort to discover new anti-hepatitis C virus (HCV) agents, we validated the anti-replicon activity of compound 1, a potent and selective anti-HCV hydroxamic acid recently reported by us. Generally favorable physicochemical and in vitro absorption, distribution, metabolism, and excretion (ADME) properties exhibited by 1 made it an ideal parent compound from which activity-based protein profiling (ABPP) probe 3 was designed and synthesized. Evaluation of probe 3 revealed that it possessed necessary anti-HCV activity and selectivity. Therefore, we have successfully obtained compound 3 as a suitable ABPP probe to identify potential molecular targets of compound 1. Probe 3 and its improved analogs are expected to join a growing list of ABPP probes that have made important contributions to not only the studies of biochemical and cellular functions but also discovery of selective inhibitors of protein targets.

  4. Development of Peptide Nucleic Acid Probes for Detection of the HER2 Oncogene

    PubMed Central

    Song, Young K.; Evangelista, Jennifer; Aschenbach, Konrad; Johansson, Peter; Wen, Xinyu; Chen, Qingrong; Lee, Albert; Hempel, Heidi; Gheeya, Jinesh S.; Getty, Stephanie; Gomez, Romel; Khan, Javed

    2013-01-01

    Peptide nucleic acids (PNAs) have gained much interest as molecular recognition tools in biology, medicine and chemistry. This is due to high hybridization efficiency to complimentary oligonucleotides and stability of the duplexes with RNA or DNA. We have synthesized 15/16-mer PNA probes to detect the HER2 mRNA. The performance of these probes to detect the HER2 target was evaluated by fluorescence imaging and fluorescence bead assays. The PNA probes have sufficiently discriminated between the wild type HER2 target and the mutant target with single base mismatches. Furthermore, the probes exhibited excellent linear concentration dependence between 0.4 to 400 fmol for the target gene. The results demonstrate potential application of PNAs as diagnostic probes with high specificity for quantitative measurements of amplifications or over-expressions of oncogenes. PMID:23593123

  5. Signal-on electrochemical Y or junction probe detection of nucleic acid.

    PubMed

    Shen, Zuliang; Nakayama, Shizuka; Semancik, Steve; Sintim, Herman O

    2012-08-01

    A methylene-blue (MB)-labeled molecular beacon junction probe allows for a signal-on electrochemical detection of nucleic acids via target recycling using endonucleases. Electron transfer is reduced when the MB is intercalated in the stem of the molecular beacon, but then electron transfer from MB to a gold electrode is enhanced upon cleavage of the junction probe due to increased probability of MB approaching the electrode when attached to the more flexible ssDNA.

  6. Photoinduced spectral changes of photoluminescent gold nanoclusters

    NASA Astrophysics Data System (ADS)

    Matulionytė, Marija; Marcinonytė, Raminta; Rotomskis, Ričardas

    2015-05-01

    Ultrasmall photoluminescent gold nanoclusters (Au NCs), composed of several atoms with sizes up to a few nanometers, have recently stimulated extensive interest. Unique molecule-like behaviors, low toxicity, and facile synthesis make photoluminescent Au NCs a very promising alternative to organic fluorophores and semiconductor quantum dots (QDs) in broad ranges of biomedical applications. However, using gold nanoparticles (Au NPs) for bioimaging might cause their degradation under continuous excitation with UV light, which might result in toxicity. We report spectral changes of photoluminescent 2-(N-morpholino) ethanesulfonic acid (MES)-coated (Au-MES) NCs under irradiation with UV/blue light. Photoluminescent water soluble Au-MES NCs with a photoluminescence (PL) band maximum at 476 nm (λex=420 nm) were synthesized. Under irradiation with 402 nm wavelength light the size of photoluminescent Au-MES NCs decreased (λem=430 nm). Irradiating the sample solution with 330 nm wavelength light, nonluminescent Au NPs were disrupted, and photoluminescent Au NCs (λem=476 nm) were formed. Irradiation with 330 nm wavelength light did not directly affect photoluminescent Au-MES NCs, however, increase in PL intensity indicated the formation of photoluminescent Au NCs from the disrupted nonluminescent Au NPs. This study gives a good insight into the photostability of MES-coated Au NPs under continuous excitation with UV/blue light.

  7. Acidity characterization of heterogeneous catalysts by solid-state NMR spectroscopy using probe molecules.

    PubMed

    Zheng, Anmin; Liu, Shang-Bin; Deng, Feng

    2013-01-01

    Characterization of the surface acidic properties of solid acid catalysts is a key issue in heterogeneous catalysis. Important acid features of solid acids, such as their type (Brønsted vs. Lewis acid), distribution and accessibility (internal vs. external sites), concentration (amount), and strength of acid sites are crucial factors dictating their reactivity and selectivity. This short review provides information on different solid-state NMR techniques used for acidity characterization of solid acid catalysts. In particular, different approaches using probe molecules containing a specific nucleus of interest, such as pyridine-d5, 2-(13)C-acetone, trimethylphosphine, and trimethylphosphine oxide, are compared. Incorporation of valuable information (such as the adsorption structure, deprotonation energy, and NMR parameters) from density functional theory (DFT) calculations can yield explicit correlations between the chemical shift of adsorbed probe molecules and the intrinsic acid strength of solid acids. Methods that combine experimental NMR data with DFT calculations can therefore provide both qualitative and quantitative information on acid sites.

  8. The effect of citric acid on morphology and photoluminescence properties of white light emitting ZnO-SiO2 nanocomposites

    NASA Astrophysics Data System (ADS)

    Sivakami, R.; Thiyagarajan, P.

    2016-07-01

    The white light emitting ZnO-SiO2 nanocomposites were synthesized by sol-gel combustion method using zinc nitrate, citric acid and tetraethoxysilane. To analyze the effect of fuel content on the photoluminescence properties of ZnO-SiO2 nanocomposites, the citric acid content was varied as 1, 5, and 10 moles with respect to one mole of zinc. The SEM images of the nanocomposites revealed the spherical, flower and platelet like morphology with variation in citric acid content and annealing temperatures. The ZnO-SiO2 nanocomposites prepared with various Zn:CA ratio excited at UV (280 nm), near UV (365 nm), violet (405 nm) and blue (465 nm) wavelength showed blue and greenish-yellow emission. Among all ratios, the ZnO-SiO2 nanocomposites with Zn:CA - 1:1 ratio showed the intense broad band emission compared to Zn:CA - 1:5 and 1:10 values. This particular composition of sample excited under violet (405 nm) LED source shows white light, as confirmed by the CIE chromaticity coordinates (x = 0.342, y = 0.318).

  9. Probing fatty acid metabolism in bacteria, cyanobacteria, green microalgae and diatoms with natural and unnatural fatty acids.

    PubMed

    Beld, Joris; Abbriano, Raffaela; Finzel, Kara; Hildebrand, Mark; Burkart, Michael D

    2016-04-01

    In both eukaryotes and prokaryotes, fatty acid synthases are responsible for the biosynthesis of fatty acids in an iterative process, extending the fatty acid by two carbon units every cycle. Thus, odd numbered fatty acids are rarely found in nature. We tested whether representatives of diverse microbial phyla have the ability to incorporate odd-chain fatty acids as substrates for their fatty acid synthases and their downstream enzymes. We fed various odd and short chain fatty acids to the bacterium Escherichia coli, cyanobacterium Synechocystis sp. PCC 6803, green microalga Chlamydomonas reinhardtii and diatom Thalassiosira pseudonana. Major differences were observed, specifically in the ability among species to incorporate and elongate short chain fatty acids. We demonstrate that E. coli, C. reinhardtii, and T. pseudonana can produce longer fatty acid products from short chain precursors (C3 and C5), while Synechocystis sp. PCC 6803 lacks this ability. However, Synechocystis can incorporate and elongate longer chain fatty acids due to acyl-acyl carrier protein synthetase (AasS) activity, and knockout of this protein eliminates the ability to incorporate these fatty acids. In addition, expression of a characterized AasS from Vibrio harveyii confers a similar capability to E. coli. The ability to desaturate exogenously added fatty acids was only observed in Synechocystis and C. reinhardtii. We further probed fatty acid metabolism of these organisms by feeding desaturase inhibitors to test the specificity of long-chain fatty acid desaturases. In particular, supplementation with thia fatty acids can alter fatty acid profiles based on the location of the sulfur in the chain. We show that coupling sensitive gas chromatography mass spectrometry to supplementation of unnatural fatty acids can reveal major differences between fatty acid metabolism in various organisms. Often unnatural fatty acids have antibacterial or even therapeutic properties. Feeding of short

  10. Probing fatty acid metabolism in bacteria, cyanobacteria, green microalgae and diatoms with natural and unnatural fatty acids.

    PubMed

    Beld, Joris; Abbriano, Raffaela; Finzel, Kara; Hildebrand, Mark; Burkart, Michael D

    2016-04-01

    In both eukaryotes and prokaryotes, fatty acid synthases are responsible for the biosynthesis of fatty acids in an iterative process, extending the fatty acid by two carbon units every cycle. Thus, odd numbered fatty acids are rarely found in nature. We tested whether representatives of diverse microbial phyla have the ability to incorporate odd-chain fatty acids as substrates for their fatty acid synthases and their downstream enzymes. We fed various odd and short chain fatty acids to the bacterium Escherichia coli, cyanobacterium Synechocystis sp. PCC 6803, green microalga Chlamydomonas reinhardtii and diatom Thalassiosira pseudonana. Major differences were observed, specifically in the ability among species to incorporate and elongate short chain fatty acids. We demonstrate that E. coli, C. reinhardtii, and T. pseudonana can produce longer fatty acid products from short chain precursors (C3 and C5), while Synechocystis sp. PCC 6803 lacks this ability. However, Synechocystis can incorporate and elongate longer chain fatty acids due to acyl-acyl carrier protein synthetase (AasS) activity, and knockout of this protein eliminates the ability to incorporate these fatty acids. In addition, expression of a characterized AasS from Vibrio harveyii confers a similar capability to E. coli. The ability to desaturate exogenously added fatty acids was only observed in Synechocystis and C. reinhardtii. We further probed fatty acid metabolism of these organisms by feeding desaturase inhibitors to test the specificity of long-chain fatty acid desaturases. In particular, supplementation with thia fatty acids can alter fatty acid profiles based on the location of the sulfur in the chain. We show that coupling sensitive gas chromatography mass spectrometry to supplementation of unnatural fatty acids can reveal major differences between fatty acid metabolism in various organisms. Often unnatural fatty acids have antibacterial or even therapeutic properties. Feeding of short

  11. Design and Evaluation of Peptide Nucleic Acid Probes for Specific Identification of Candida albicans

    PubMed Central

    Kim, Hyun-Joong

    2014-01-01

    Candida albicans is an important cause of systemic fungal infections, and rapid diagnostics for identifying and differentiating C. albicans from other Candida species are critical for the timely application of appropriate antimicrobial therapy, improved patient outcomes, and pharmaceutical cost savings. In this work, two 28S rRNA-directed peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH) probes, P-Ca726 (targeting a novel region of the ribosome) and P-CalB2208 (targeting a previously reported region), were evaluated. Hybridization conditions were optimized by using both fluorescence microscopy (FM) and flow cytometry (FCM), and probes were screened for specificity and discriminative ability against a panel of C. albicans and various nontarget Candida spp. The performance of these PNA probes was compared quantitatively against that of DNA probes or DNA probe/helper combinations directed against the same target regions. Ratiometric analyses of FCM results indicated that both the hybridization quality and yield of the PNA probes were higher than those of the DNA probes. In FCM-based comparisons of the PNA probes, P-Ca726 was found to be highly specific, showing 2.5- to 5.5-fold-higher discriminatory power for C. albicans than P-CalB2208. The use of formamide further improved the performance of the new probe. Our results reinforce the significant practical and diagnostic advantages of PNA probes over their DNA counterparts for FISH and indicate that P-Ca726 may be used advantageously for the rapid and specific identification of C. albicans in clinical and related applications, especially when combined with FCM. PMID:25428160

  12. Intra-albumin migration of bound fatty acid probed by spin label ESR

    SciTech Connect

    Gurachevsky, Andrey . E-mail: a.gurachevsky@medinnovation.de; Shimanovitch, Ekaterina; Gurachevskaya, Tatjana; Muravsky, Vladimir

    2007-09-07

    Conventional ESR spectra of 16-doxyl-stearic acid bound to bovine and human serum albumin were recorded at different temperatures in order to investigate the status of spin-labeled fatty acid in the interior of the protein globule. A computer spectrum simulation of measured spectra, performed by non-linear least-squares fits, clearly showed two components corresponding to strongly and weakly immobilized fatty acid molecules. The two-component model was verified on spectra measured at different pH. Thermodynamic parameters of the spin probe exchange between two spin probe states were analyzed. It was concluded that at physiological conditions, fatty acid molecules permanently migrate in the globule interior between the specific binding sites and a space among albumin domains.

  13. Signal turn-on probe for nucleic acid detection based on (19)F nuclear magnetic resonance.

    PubMed

    Sakamoto, Takashi; Shimizu, Yu-ki; Sasaki, Jun; Hayakawa, Hikaru; Fujimoto, Kenzo

    2011-01-01

    To image gene expression in vivo, we designed and synthesized a novel signal turn-on probe for (19)F nuclear magnetic resonance (MR) imaging based on paramagnetic relaxation enhancement. The stem-loop structured oligodeoxyribonucleotide (ODN) having a molecular beacon sequence for point mutated K-ras mRNA was doubly labeled with bis(trifluoromethyl)benzene moiety and Gd-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid chelate moiety at the each termini of the ODN probe, respectively. We found that the (19)F MR signal of the bis(trifluoromethyl)benzene moiety tethered at the 5' termini of the probe turned on by the addition of complementary ODN. The probe has the potential to image gene expressions in vivo.

  14. Probing the Binding Site of Bile Acids in TGR5.

    PubMed

    Macchiarulo, Antonio; Gioiello, Antimo; Thomas, Charles; Pols, Thijs W H; Nuti, Roberto; Ferrari, Cristina; Giacchè, Nicola; De Franco, Francesca; Pruzanski, Mark; Auwerx, Johan; Schoonjans, Kristina; Pellicciari, Roberto

    2013-12-12

    TGR5 is a G-protein-coupled receptor (GPCR) mediating cellular responses to bile acids (BAs). Although some efforts have been devoted to generate homology models of TGR5 and draw structure-activity relationships of BAs, none of these studies has hitherto described how BAs bind to TGR5. Here, we present an integrated computational, chemical, and biological approach that has been instrumental to determine the binding mode of BAs to TGR5. As a result, key residues have been identified that are involved in mediating the binding of BAs to the receptor. Collectively, these results provide new hints to design potent and selective TGR5 agonists. PMID:24900622

  15. Probing the Binding Site of Bile Acids in TGR5

    PubMed Central

    2013-01-01

    TGR5 is a G-protein-coupled receptor (GPCR) mediating cellular responses to bile acids (BAs). Although some efforts have been devoted to generate homology models of TGR5 and draw structure–activity relationships of BAs, none of these studies has hitherto described how BAs bind to TGR5. Here, we present an integrated computational, chemical, and biological approach that has been instrumental to determine the binding mode of BAs to TGR5. As a result, key residues have been identified that are involved in mediating the binding of BAs to the receptor. Collectively, these results provide new hints to design potent and selective TGR5 agonists. PMID:24900622

  16. [Study on recovery and its influencing factors of ferulic acid and tetramethylpyrazine in cerebral microdialysis probe].

    PubMed

    Liao, Wei-guo; Wang, Li-sheng; Fan, Wen-tao; Li, Zhou; Yu, Jian-ye; Liao, Feng-yun; Wu, Yin-ai; Ba, Wen-qiang; Wang, Ding

    2015-11-01

    To establish a method for detecting microdialysis recovery of tetramethylpyrazine (TMP) and ferulic acid (FA) and investigating the influencing factors, providing the basis for further in vivo microdialysis experiments. The concentration of FA and TMP in dialysates were determined by high pressure liquid chromatography ( HPLC) and probe recovery were calculated respectively. The influence of the flow rates, medium concentration, temperature and in vivo probe stability on the recovery of FA and TMP were investigated by using concentration difference method (incremental method and decrement method). The recovery obtained by incremental method were similar to by decrement method. The in vitro recovery rate of FA and TMP decreased with the increase of 1-2.5 μL min(-1), and increased obviously with the temperature of 25-42 degrees C under the same conditions. The concentration of FA and TMP had no obvious effect on the probe recovery under the same flow rate. In addition, the recovery of TMP and FA remained stable and showed similar trends under the condition of four concentration cycles, indicating that the intra day reproducibility of the concentration difference method was good. The recovery of brain microdialysis probes in vivo 8 h maintained a relatively stable, but certain differences existed between different brain microdialysis probes, demonstrating that each probe was required for recovery correction in vivo experiment. Microdialysis sampling can be used for the local brain pharmacokinetic study of FA and TMP, and retrodialysis method can be used in probe recovery of FA and TMP in vivo. PMID:27071270

  17. Ratiometric emission fluorescent pH probe for imaging of living cells in extreme acidity.

    PubMed

    Niu, Weifen; Fan, Li; Nan, Ming; Li, Zengbo; Lu, Dongtao; Wong, Man Shing; Shuang, Shaomin; Dong, Chuan

    2015-03-01

    A novel ratiometric emission fluorescent probe, 1,1-dimethyl-2-[2-(quinolin-4-yl)vinyl]-1H-benzo[e]indole (QVBI), is facilely synthesized via ethylene bridging of benzoindole and quinoline. The probe exhibits ratiometric fluorescence emission (F(522nm)/F(630nm)) characteristics with pKa 3.27 and linear response to extreme-acidity range of 3.8-2.0. Also, its high fluorescence quantum yield (Φ = 0.89) and large Stokes shift (110 nm) are favorable. Moreover, QVBI possesses highly selective response to H(+) over metal ions and some bioactive molecules, good photostability, and excellent reversibility. The probe has excellent cell membrane permeability and is further applied successfully to monitor pH fluctuations in live cells and imaging extreme acidity in Escherichia coli cells without influence of autofluorescence and native cellular species in biological systems. PMID:25664606

  18. Bioavailability of xenobiotics in unsaturated soils – implications for nucleic acid based stable isotope probing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The use of stable isotopes to label phylogenetically informative biomolecules (phospholipid fatty acids, DNA, or RNA), typically referred to as stable isotope probing (SIP) has the potential of providing definitive evidence that a detected population is active in a specific process, if that process ...

  19. Discovery of boronic acid-based fluorescent probes targeting amyloid-beta plaques in Alzheimer's disease.

    PubMed

    Jung, Seung-Jin; Lee, Jun Young; Kim, Tae Ho; Lee, Dong-Eun; Jeon, Jongho; Yang, Seung Dae; Hur, Min Goo; Min, Jung-Joon; Park, Yong Dae

    2016-04-01

    A boronic acid-based fluorescent probe was developed for diagnosis of amyloid-β (Aβ) plaques from Alzheimer's disease (AD). Probe 4c, which included boronic acid as a functional group, exhibited a significant increase (64.37-fold, FAβ/F0) in fluorescence intensity as a response to Aβ aggregates, with a blue shift (105nm) in the maximum emission wavelength. We found that boronic acid as a functional group improved the binding affinity (KD value=0.79±0.05μM for 4c) for Aβ aggregates and confirmed that 4c selectively stained Aβ plaques in brain sections from APP/PS1 mice. Ex vivo fluorescence imaging using mice (normal and APP/PS1) also revealed that 4c was able to penetrate the blood-brain barrier (BBB) and to stain Aβ plaques in the brain. From these results, we believe that 4c will be useful as a fluorescent probe in preclinical research related to AD. Furthermore, we believe that our results with boronic acid also provide valuable information for the development of a probe for Aβ plaques. PMID:26927427

  20. Cross-polarized optical absorption of single-walled carbon nanotubes probed by photoluminescence excitation spectroscopy, UV-Vis-IR and polarized Raman Scatterings

    NASA Astrophysics Data System (ADS)

    Maruyama, Shigeo

    2008-03-01

    Because of the depolarization effect, or so-called antenna effect, optical absorption of single-walled carbon nanotubes (SWNTs) is weak when excited by light polarized perpendicular to the nanotube axis. However, in photoluminescence (PL) excitation spectra of isolated SWNTs, PL peaks due to cross-polarized excitation can be clearly identified. By decomposing the cross-polarized component, the optical transition energy of E12 or E21 can be? measured, and the smaller exciton binding energy for perpendicular excitations is concluded [1]. Cross-polarized absorption is dominant in the absorption of a vertically aligned film of SWNTs [2] when excited from the top of the film. In our previous study, a pi-plasmon absorption at 5.25 eV was revealed in contrast to 4.5 eV for parallel excitation [3]. Resonant Raman scattering from such a film is also influenced by the cross-polarized excitation [4]. Even though a Kataura plot for the E33 and E44 range has been proposed by using such a vertically aligned film [5], polarized Raman scattering spectra reveal more complicated features in the system because of the small bundle size, typically 5-8 nanotubes [6]. References: [1] Y. Miyauchi, M. Oba, S. Maruyama, Phys. Rev. B 74 (2006) 205440. [2] Y. Murakami, S. Chiashi, Y. Miyauchi, M. Hu, M. Ogura, T. Okubo, S. Maruyama, Chem. Phys. Lett. 385 (2004) 298. [3] Y. Murakami, E. Einarsson, T. Edamura, S. Maruyama, Phys. Rev. Lett. 94 (2005) 087402. [4] Y. Murakami, S. Chiashi, E. Einarsson, S. Maruyama, Phys. Rev. B 71 (2005) 085403. [5] P. T. Araujo, S. K. Doorn, S. Kilina, S. Tretiak, E. Einarsson, S. Maruyama, H. Chacham, M. A. Pimenta, A. Jorio, Phys. Rev. Lett. 88 (2007) 067401. [6] E. Einarsson, H. Shiozawa, C. Kramberger, M. H. Ruemmeli, A. Gruneis, T. Pichler, S. Maruyama, J. Phys. Chem. C (2007) published on Web.

  1. Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe

    PubMed Central

    Qin, Peter Z; Haworth, Ian S; Cai, Qi; Kusnetzow, Ana K; Grant, Gian Paola G; Price, Eric A; Sowa, Glenna Z; Popova, Anna; Herreros, Bruno; He, Honghang

    2008-01-01

    This protocol describes the procedures for measuring nanometer distances in nucleic acids using a nitroxide probe that can be attached to any nucleotide within a given sequence. Two nitroxides are attached to phosphorothioates that are chemically substituted at specific sites of DNA or RNA. Inter-nitroxide distances are measured using a four-pulse double electron–electron resonance technique, and the measured distances are correlated to the parent structures using a Web-accessible computer program. Four to five days are needed for sample labeling, purification and distance measurement. The procedures described herein provide a method for probing global structures and studying conformational changes of nucleic acids and protein/nucleic acid complexes. PMID:17947978

  2. Probing the structure of nucleic acids with Ni(II) complexes

    SciTech Connect

    Chen, Xiaoying.

    1992-01-01

    The structure of nucleic acids determines their biological function. Interest in the development of novel probes from structures of nucleic acid has led to the discovery of conformation-specific oxidation of guanine sites in DNA and RNA using Ni(II) complexes. The reaction is highly dependent upon the nature of Ni(II) complexes with the most important feature of a strong in-plane ligand field. The unique properties of Ni(II) complexes combining redox and coordination features provide sensitive probes for nucleic acid conformation. One of these nickel complexes, NiCR, has been shown to selectively promote cleavage of DNA at guanine sites held accessible through the formation of unusual secondary structures such as ends, mismatches, bulges and loops. An unique mechanism for the base and conformation-specific oxidation of DNA promoted by Ni(II) complexes is proposed, involving direct ligation of nickel to N-7 of guanine delivering a non-diffusible oxidizing species. NiCR has been proved to be a sensitive and predictable probe for the tertiary structure of RNAs. The specific sites of oxidation of tRNS[sup phe] promoted by NiCR correspond to the most accessible guanine residues determined by theoretic calculations. NiCR has also been successfully applied to probe the tertiary structure of self-splicing Tetrahymena pre-rRNA intron, and has provided important information about the folding of this intron, especially in the region of the catalytic core.

  3. Superior structure stability and selectivity of hairpin nucleic acid probes with an L-DNA stem.

    PubMed

    Kim, Youngmi; Yang, Chaoyong James; Tan, Weihong

    2007-01-01

    Hairpin nucleic acid probes have been highly useful in many areas, especially for intracellular and in vitro nucleic acid detection. The success of these probes can be attributed to the ease with which their conformational change upon target binding can be coupled to a variety of signal transduction mechanisms. However, false-positive signals arise from the opening of the hairpin due mainly to thermal fluctuations and stem invasions. Stem invasions occur when the stem interacts with its complementary sequence and are especially problematic in complex biological samples. To address the problem of stem invasions in hairpin probes, we have created a modified molecular beacon that incorporates unnatural enantiomeric l-DNA in the stem and natural d-DNA or 2'-O-Me-modified RNA in the loop. l-DNA has the same physical characteristics as d-DNA except that l-DNA cannot form stable duplexes with d-DNA. Here we show that incorporating l-DNA into the stem region of a molecular beacon reduces intra- and intermolecular stem invasions, increases the melting temperature, improves selectivity to its target, and leads to enhanced bio-stability. Our results suggest that l-DNA is useful for designing functional nucleic acid probes especially for biological applications.

  4. Submonolayer Uniformity of Type II InAs/GaInSb W-shaped Quantum Wells Probed by Full-Wafer Photoluminescence Mapping in the Mid-infrared Spectral Range.

    PubMed

    Dyksik, Mateusz; Motyka, Marcin; Sęk, Grzegorz; Misiewicz, Jan; Dallner, Matthias; Weih, Robert; Kamp, Martin; Höfling, Sven

    2015-12-01

    The spatial uniformity of GaSb- and InAs substrate-based structures containing type II quantum wells was probed by means of large-scale photoluminescence (PL) mapping realized utilizing a Fourier transform infrared spectrometer. The active region was designed and grown in a form of a W-shaped structure with InAs and GaInSb layers for confinement of electrons and holes, respectively. The PL spectra were recorded over the entire 2-in. wafers, and the parameters extracted from each spectrum, such as PL peak energy position, its linewidth and integrated intensity, were collected in a form of two-dimensional spatial maps. Throughout the analysis of these maps, the wafers' homogeneity and precision of the growth procedure were investigated. A very small variation of PL peak energy over the wafer indicates InAs quantum well width fluctuation of only a fraction of a monolayer and hence extraordinary thickness accuracy, a conclusion further supported by high uniformity of both the emission intensity and PL linewidth.

  5. Ultramild protein-mediated click chemistry creates efficient oligonucleotide probes for targeting and detecting nucleic acids.

    PubMed

    Nåbo, Lina J; Madsen, Charlotte S; Jensen, Knud J; Kongsted, Jacob; Astakhova, Kira

    2015-05-26

    Functionalized synthetic oligonucleotides are finding growing applications in research, clinical studies, and therapy. However, it is not easy to prepare them in a biocompatible and highly efficient manner. We report a new strategy to synthesize oligonucleotides with promising nucleic acid targeting and detection properties. We focus in particular on the pH sensitivity of these new probes and their high target specificity. For the first time, human copper(I)-binding chaperon Cox17 was applied to effectively catalyze click labeling of oligonucleotides. This was performed under ultramild conditions with fluorophore, peptide, and carbohydrate azide derivatives. In thermal denaturation studies, the modified probes showed specific binding to complementary DNA and RNA targets. Finally, we demonstrated the pH sensitivity of the new rhodamine-based fluorescent probes in vitro and rationalize our results by electronic structure calculations.

  6. Forced intercalation probes (FIT Probes): thiazole orange as a fluorescent base in peptide nucleic acids for homogeneous single-nucleotide-polymorphism detection.

    PubMed

    Köhler, Olaf; Jarikote, Dilip Venkatrao; Seitz, Oliver

    2005-01-01

    Fluorescent base analogues in DNA are versatile probes of nucleic acid-nucleic acid and nucleic acid-protein interactions. New peptide nucleic acid (PNA) based probes are described in which the intercalator dye thiazole orange (TO) serves as a base surrogate. The investigation of six TO derivatives revealed that the linker length and the conjugation site decided whether a base surrogate conveys sequence-selective DNA binding and whether fluorescence is increased or decreased upon single-mismatched hybridization. One TO derivative conferred universal PNA-DNA base pairing while maintaining duplex stability and hybridization selectivity. TO fluorescence increased up to 26-fold upon hybridization. In contrast to most other probes, in which fluorescence is invariant once hybridization had occurred, the emission of TO-containing PNA probes is attenuated when forced to intercalate next to a mismatched base pair. The specificity of DNA detection is therefore not limited by the selectivity of probe-target binding and a DNA target can be distinguished from its single-base mutant under nonstringent hybridization conditions. This property should be of advantage for real-time quantitative PCR and nucleic acid detection within living cells.

  7. Syntheses, structures, and photoluminescence of three-dimensional lanthanide coordination polymers with 2,5-pyridinedicarboxylic acid

    SciTech Connect

    Huang Yan; Song Yishan; Yan, Bing Shao Min

    2008-08-15

    Four new open-framework coordination polymers of lanthanide 2,5-pyridinedicarboxylates, with the formulas Pr2(pydc){sub 3}(H{sub 2}O){sub 2} (1), Ln(pydc)(Hpydc) (Ln=Tb (2), Er (3), Eu (5)), and Gd(pydc)(nic)(H{sub 2}O) (4) (H{sub 2}pydc=2,5-pyridinedicarboxylic acid, Hnic=nicotinic acid), have been hydrothermally synthesized and four of them (except Eu (5)) have been structurally characterized. Complex 1 consists of two types of ligand-binding modes contributing to link the PrO{sub 7}N(H{sub 2}O) polyhedral chains to three-dimensional (3D) open-framework architecture. Complexes 2 and 3 are isostructural and feature unique 3D cage-like supramolecular frameworks remarkably different from that of 1, owing to the different ligand-bridging pattern. Complex 4, however, has the distinct 3D open-framework architecture due to the presence of unexpected nicotinate ligands, which may be derived from pydc ligands via in-situ decarboxylation under the hydrothermal condition. - Graphical abstract: Four new lanthanide coordination polymers have been hydrothermally synthesized by the reaction of 2,5-pyridinedicarboxylic acid with the corresponding lanthanide nitrates, and they show three types of 3D open-framework architecture. Complexes 2 and 5 show strong characteristic green (or red) luminescence and long lifetimes.

  8. Label-free potentiometry for detecting DNA hybridization using peptide nucleic acid and DNA probes.

    PubMed

    Goda, Tatsuro; Singi, Ankit Balram; Maeda, Yasuhiro; Matsumoto, Akira; Torimura, Masaki; Aoki, Hiroshi; Miyahara, Yuji

    2013-02-07

    Peptide nucleic acid (PNA) has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization via Watson-Crick base-pairing. To verify whether PNA probes on an electrode surface enhance sensitivity for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray. Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer (SAM)-formed microelectrodes were directly transformed into potentiometric signals using a high input impedance electrometer. The charge readout allows label-free, reagent-less, and multi-parallel detection of target oligonucleotides without any optical assistance. The differences in the probe lengths between 15- to 22-mer dramatically influenced on the sensitivity of the PNA and DNA sensors. Molecular type of the capturing probe did not affect the degree of potential shift. Theoretical model for charged rod-like duplex using the Gouy-Chapman equation indicates the dominant effect of electrostatic attractive forces between anionic DNA and underlying electrode at the electrolyte/electrode interface in the potentiometry.

  9. Docosahexaenoic acid conjugated near infrared flourescence probe for in vivo early tumor diagnosis

    NASA Astrophysics Data System (ADS)

    Li, Siwen; Cao, Jie; Qin, Jingyi; Zhang, Xin; Achilefu, Samuel; Qian, Zhiyu; Gu, Yueqing

    2013-02-01

    Docosahexaenoic acid(DHA) is an omega-3 C22 natural fatty acid with six cis double bonds and as a constituent of membranes used as a precursor for metabolic and biochemical path ways. In this manuscript,we describe the synthesis of near-infrared(NIR) flourescence ICG-Der-01 labeled DHA for in vitro and vivo tumor targeting.The structure of the probe was intensively characterized by UV and MS. The in vitro and vivo tumor targeting abilities of the DHA-based NIR probes were investigeted in MCF-7 cells and MCF-7 xenograft mice model differently by confocal microscopy and CCD camera. The cell cytotoxicity were tested in tumor cells MCF-7 .The results shows that the DHA-based NIR probes have high affinity with the tumor both in vitro and vivo.In addition ,we also found that the DHA-based NIR probes have the apparent cytotoxicity on MCF-7 cells .which demonstrated that DHA was conjugated with other antitumor drug could increase the abilities of antirumor efficacy .So DHA-ICG-Der-01 is a promising optical agent for diagnosis of tumors especially in their early stage.

  10. A Locked Nucleic Acid Probe Based on Selective Salt-Induced Effect Detects Single Nucleotide Polymorphisms

    PubMed Central

    Zhang, Jing; Wu, Huizhe; Chen, Qiuchen; Zhao, Pengfei; Zhao, Haishan; Yao, Weifan; Wei, Minjie

    2015-01-01

    Detection of single based genetic mutation by using oligonucleotide probes is one of the common methods of detecting single nucleotide polymorphisms at known loci. In this paper, we demonstrated a hybridization system which included a buffer solution that produced selective salt-induced effect and a locked nucleic acid modified 12 nt oligonucleotide probe. The hybridization system is suitable for hybridization under room temperature. By using magnetic nanoparticles as carriers for PCR products, the SNPs (MDR1 C3435T/A) from 45 volunteers were analyzed, and the results were consistent with the results from pyrophosphoric acid sequencing. The method presented in this paper differs from the traditional method of using molecular beacons to detect SNPs in that it is suitable for research institutions lacking real-time quantitative PCR detecting systems, to detect PCR products at room temperature. PMID:26347880

  11. Visible sensing of nucleic acid sequences using a genetically encodable unmodified mRNA probe.

    PubMed

    Narita, Atsushi; Ogawa, Kazumasa; Sando, Shinsuke; Aoyama, Yasuhiro

    2006-01-01

    We previously reported a molecular beacon-mRNA (MB-mRNA) strategy for nucleic acid detection/sensing in a cell-free translation system using unmodified RNA as a probe. Here in this presentation, we report that a combination with RNase H activity, which induces an additional process of irreversible cleavage of MB-domain, achieves an improved sequence selectivity (one nucleotide selectivity) and an enhanced sensitivity. This improved system finally enabled visible sensing of target nucleic acid sequence at a single nucleotide resolution under isothermal conditions.

  12. Immobilization-free electrochemical DNA detection with anthraquinone-labeled pyrrolidinyl peptide nucleic acid probe.

    PubMed

    Kongpeth, Jutatip; Jampasa, Sakda; Chaumpluk, Piyasak; Chailapakul, Orawon; Vilaivan, Tirayut

    2016-01-01

    Electrochemical detection provides a simple, rapid, sensitive and inexpensive method for DNA detection. In traditional electrochemical DNA biosensors, the probe is immobilized onto the electrode. Hybridization with the DNA target causes a change in electrochemical signal, either from the intrinsic signal of the probe/target or through a label or a redox indicator. The major drawback of this approach is the requirement for probe immobilization in a controlled fashion. In this research, we take the advantage of different electrostatic properties between PNA and DNA to develop an immobilization-free approach for highly sequence-specific electrochemical DNA sensing on a screen-printed carbon electrode (SPCE) using a square-wave voltammetric (SWV) technique. Anthraquinone-labeled pyrrolidinyl peptide nucleic acid (AQ-PNA) was employed as a probe together with an SPCE that was modified with a positively-charged polymer (poly quaternized-(dimethylamino-ethyl)methacrylate, PQDMAEMA). The electrostatic attraction between the negatively-charged PNA-DNA duplex and the positively-charged modified SPCE attributes to the higher signal of PNA-DNA duplex than that of the electrostatically neutral PNA probe, resulting in a signal change. The calibration curve of this proposed method exhibited a linear range between 0.35 and 50 nM of DNA target with a limit of detection of 0.13 nM (3SD(blank)/Slope). The sub-nanomolar detection limit together with a small sample volume required (20 μL) allowed detection of <10 fmol (<1 ng) of DNA. With the high specificity of the pyrrolidinyl PNA probe used, excellent discrimination between complementary and various single-mismatched DNA targets was obtained. An application of this new platform for a sensitive and specific detection of isothermally-amplified shrimp's white spot syndrome virus (WSSV) DNA was successfully demonstrated. PMID:26695270

  13. Immobilization-free electrochemical DNA detection with anthraquinone-labeled pyrrolidinyl peptide nucleic acid probe.

    PubMed

    Kongpeth, Jutatip; Jampasa, Sakda; Chaumpluk, Piyasak; Chailapakul, Orawon; Vilaivan, Tirayut

    2016-01-01

    Electrochemical detection provides a simple, rapid, sensitive and inexpensive method for DNA detection. In traditional electrochemical DNA biosensors, the probe is immobilized onto the electrode. Hybridization with the DNA target causes a change in electrochemical signal, either from the intrinsic signal of the probe/target or through a label or a redox indicator. The major drawback of this approach is the requirement for probe immobilization in a controlled fashion. In this research, we take the advantage of different electrostatic properties between PNA and DNA to develop an immobilization-free approach for highly sequence-specific electrochemical DNA sensing on a screen-printed carbon electrode (SPCE) using a square-wave voltammetric (SWV) technique. Anthraquinone-labeled pyrrolidinyl peptide nucleic acid (AQ-PNA) was employed as a probe together with an SPCE that was modified with a positively-charged polymer (poly quaternized-(dimethylamino-ethyl)methacrylate, PQDMAEMA). The electrostatic attraction between the negatively-charged PNA-DNA duplex and the positively-charged modified SPCE attributes to the higher signal of PNA-DNA duplex than that of the electrostatically neutral PNA probe, resulting in a signal change. The calibration curve of this proposed method exhibited a linear range between 0.35 and 50 nM of DNA target with a limit of detection of 0.13 nM (3SD(blank)/Slope). The sub-nanomolar detection limit together with a small sample volume required (20 μL) allowed detection of <10 fmol (<1 ng) of DNA. With the high specificity of the pyrrolidinyl PNA probe used, excellent discrimination between complementary and various single-mismatched DNA targets was obtained. An application of this new platform for a sensitive and specific detection of isothermally-amplified shrimp's white spot syndrome virus (WSSV) DNA was successfully demonstrated.

  14. Electrospun Poly(acrylic acid)/Silica Hydrogel Nanofibers Scaffold for Highly Efficient Adsorption of Lanthanide Ions and Its Photoluminescence Performance.

    PubMed

    Wang, Min; Li, Xiong; Hua, Weikang; Shen, Lingdi; Yu, Xufeng; Wang, Xuefen

    2016-09-14

    Combined with the features of electrospun nanofibers and the nature of hydrogel, a novel choreographed poly(acrylic acid)-silica hydrogel nanofibers (PAA-S HNFs) scaffold with excellent rare earth elements (REEs) recovery performance was fabricated by a facile route consisting of colloid-electrospinning of PAA/SiO2 precursor solution, moderate thermal cross-linking of PAA-S nanofiber matrix, and full swelling in water. The resultant PAA-S HNFs with a loose and spongy porous network structure exhibited a remarkable adsorption capacity of lanthanide ions (Ln(3+)) triggered by the penetration of Ln(3+) from the nanofiber surface to interior through the abundant water channels, which took full advantage of the internal adsorption sites of nanofibers. The effects of initial solution pH, concentration, and contact time on adsorption of Ln(3+) have been investigated comprehensively. The maximum equilibrium adsorption capacities for La(3+), Eu(3+), and Tb(3+) were 232.6, 268.8, and 250.0 mg/g, respectively, at pH 6, and the adsorption data were well-fitted to the Langmuir isotherm and pseudo-second-order models. The resultant PAA-S HNFs scaffolds could be regenerated successfully. Furthermore, the proposed adsorption mechanism of Ln(3+) on PAA-S HNFs scaffolds was the formation of bidentate carboxylates between carboxyl groups and Ln(3+) confirmed by FT-IR and XPS analysis. The well-designed PAA-S HNFs scaffold can be used as a promising alternative for effective REEs recovery. Moreover, benefiting from the unique features of Ln(3+), the Ln-PAA-S HNFs simultaneously exhibited versatile advantages including good photoluminescent performance, tunable emission color, and excellent flexibility and processability, which also hold great potential for applications in luminescent patterning, underwater fluorescent devices, sensors, and biomaterials, among others. PMID:27537710

  15. Synthesis and photoluminescence properties of silver(I) complexes based on N-benzoyl-L-glutamic acid and N-donor ligands with different flexibility

    NASA Astrophysics Data System (ADS)

    Yan, Ming-Jie; Feng, Qi; Song, Hui-Hua

    2016-05-01

    By changing the N-donor ancillary ligand, three novel silver (I) complexes {[Ag(HbzgluO) (4,4‧-bipy)]·H2O}n (1), {[Ag2(HbzgluO)2 (bpe)2]·2H2O}n (2) and {[Ag(HbzgluO)(bpp)]·2H2O}n (3) (H2bzgluO = N-benzoyl-L-glutamic acid, 4,4‧-bipy = 4,4ˊ-bipyridine, bpe = 1,2-di(4-pyridyl)ethane, bpp = 1,3-di(4-pyridyl)propane) were synthesized. Their structures have been determined by single-crystal X-ray diffraction analyses and further characterized by elemental analyses, IR spectra, powder X-ray diffraction (PXRD), and thermogravimetric analyses (TGA). In this study, the N-donor ligands are changed from rigidity (4,4‧-bipy), quasi-flexibility (bpe) to flexibility (bpp), the structures of complexes also change. Complex 1 features a 1D chain structure which is further linked together to construct a 2D supramolecular structure through hydrogen bonds. Complex 2 is a 1D double-chains configuration which eventually forms a 3D supramolecular network via hydrogen bonding interactions. Whereas, complex 3 exhibits a 2D pleated grid structure which is linked by hydrogen bonding interactions into a 3D supramolecular network. The present observations demonstrate that the modulation of coordination polymers with different structures can accomplish by changing the spacer length of N-donor ligands. In addition, the solid-state circular dichroism (CD) spectra indicated that compound 2 exhibited negative cotton effect which originated from the chiral ligands H2bzgluO and the solid-state fluorescence spectra of the three complexes demonstrated the auxiliary ligands have influence on the photoluminescence properties of the complexes.

  16. Copper(II)-lanthanide(III) coordination polymers constructed from pyridine-2,5-dicarboxylic acid: Preparation, crystal structure and photoluminescence

    NASA Astrophysics Data System (ADS)

    Xia, Zheng-Qiang; Wei, Qing; Chen, San-Ping; Feng, Xin-Ming; Xie, Gang; Qiao, Cheng-Fang; Zhang, Guo-Chun; Gao, Sheng-Li

    2013-01-01

    A series of 3d-4f heterometallic coordination polymers, formulated as {[Cu3Ln2(pydc)6(H2O)12]·4H2O}n [Ln=Tb (1), Eu (2), Dy (3), Ho (4), Lu (5)], {[CuNd2(pydc)4(H2O)3]·H2O}n (6) and {[Cu3Pr2(pydc)6(H2O)13]·4H2O}n (7) (where H2pydc=pyridine-2,5-dicarboxylic acid), have been hydrothermally prepared by reactions of H2pydc ligand with lanthanide ions in the presence of Cu(II) ion. X-ray crystal structure analysis reveals that these compounds exhibit rich structural chemistry. 1-5 are isomorphous and present a two-dimensional network constructed from Ln2Cu2L2(H2O)2 SBU rings and CuL2(H2O) building blocks. In 6, two-dimensional ladder-like layers based on Nd(III) belts and CuL2O2 units are assembled by H2pydc ligands into a three-dimensional open framework. Polymer 7 displays a two-dimensional wave-like layer structure containing two distinct ring units, in which a new coordination mode of the pydc2- ligand is observed. The results indicate that the coordination flexibility of the pydc2- ligand and lanthanide contraction effect play cooperative roles in the formation of coordination polymers with different polymeric architectures. Compounds 1-2 exhibit intense green and red luminescence emission characteristics of Tb(III) and Eu(III), respectively. Furthermore, elemental analyses (EA), infrared spectra (IR) and thermogravimetric analyses (TGA) of these compounds were also studied.

  17. Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using

    DOEpatents

    Weier, Heinz-Ulrich G.; Gray, Joe W.

    1995-01-01

    A primer directed DNA amplification method to isolate efficiently chromosome-specific repeated DNA wherein degenerate oligonucleotide primers are used is disclosed. The probes produced are a heterogeneous mixture that can be used with blocking DNA as a chromosome-specific staining reagent, and/or the elements of the mixture can be screened for high specificity, size and/or high degree of repetition among other parameters. The degenerate primers are sets of primers that vary in sequence but are substantially complementary to highly repeated nucleic acid sequences, preferably clustered within the template DNA, for example, pericentromeric alpha satellite repeat sequences. The template DNA is preferably chromosome-specific. Exemplary primers ard probes are disclosed. The probes of this invention can be used to determine the number of chromosomes of a specific type in metaphase spreads, in germ line and/or somatic cell interphase nuclei, micronuclei and/or in tissue sections. Also provided is a method to select arbitrarily repeat sequence probes that can be screened for chromosome-specificity.

  18. Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using

    DOEpatents

    Weier, H.U.G.; Gray, J.W.

    1995-06-27

    A primer directed DNA amplification method to isolate efficiently chromosome-specific repeated DNA wherein degenerate oligonucleotide primers are used is disclosed. The probes produced are a heterogeneous mixture that can be used with blocking DNA as a chromosome-specific staining reagent, and/or the elements of the mixture can be screened for high specificity, size and/or high degree of repetition among other parameters. The degenerate primers are sets of primers that vary in sequence but are substantially complementary to highly repeated nucleic acid sequences, preferably clustered within the template DNA, for example, pericentromeric alpha satellite repeat sequences. The template DNA is preferably chromosome-specific. Exemplary primers and probes are disclosed. The probes of this invention can be used to determine the number of chromosomes of a specific type in metaphase spreads, in germ line and/or somatic cell interphase nuclei, micronuclei and/or in tissue sections. Also provided is a method to select arbitrarily repeat sequence probes that can be screened for chromosome-specificity. 18 figs.

  19. Fluorescence imaging of siRNA delivery by peptide nucleic acid-based probe.

    PubMed

    Sato, Takaya; Sato, Yusuke; Iwai, Kenta; Kuge, Shusuke; Teramae, Norio; Nishizawa, Seiichi

    2015-01-01

    We report on the use of a peptide nucleic acid (PNA)-based fluorescent probe for the analysis of siRNA delivery to living cells. The probe, Py-AA-TO, possesses thiazole orange (TO) and pyrene moieties in the C- and N-termini of PNA, and can function as a light-up probe capable of selective binding to 3'-overhanging nucleotides of target siRNAs. The affinity-labeling of the siRNAs with Py-AA-TO facilitates fluorescence imaging of cellular uptake of polymer-based carriers encapsulating the siRNAs (polyplexes) through endocytosis and subsequent sequestration into lysosome. In addition, flow cytometric measurements reveal that the monitoring of Py-AA-TO fluorescence inside the cells is successfully applicable to the analysis of the polyplex disassembly. These promising functions of Py-AA-TO are presented and discussed as a basis for the design of molecular probes for fluorescent imaging and quantitative analysis of the siRNA delivery process. PMID:25864675

  20. Metal-organic hybrid materials built with tetrachlorophthalate acid and different N-donor coligands: Structure diversity and photoluminescence

    NASA Astrophysics Data System (ADS)

    Xiao, Zhenyu; Yang, Xiao; Zhao, Siwei; Wang, Debao; Yang, Yu; Wang, Lei

    2016-02-01

    Eight new metal-organic hybrid materials, namely {Cd(Tcph)(4,4‧-bipy)1/2} (1), {[Cd2(Tcph)2(1,4-bimb)1/2(H2O)4]·H2O} (2), {Cd2(Tcph)2(1,4-bmimb)1/2(H2O)4} (3), {Cd(Tcph)(1,2-bmimb)} (4), {Cu(Tcph)(1,4-bimb)(H2O)} (5), {[Co(Tcph)(1,4-bimb)1/2(H2O)3]·(H2O)} (6), {Zn(Tcph)(1,2-bimb)} (7), {Cu2(Tcph)2(1,2-bimb)(H2O)4} (8), where Tcph=tetrachlorophthalate acid, 4,4‧-bipy=4,4‧-bipyridine, 1,4-bimb=1,4-bis(imidazol-1-ylmethyl)benzene, 1,4-bmimb=1,4-bis(2-methylimidazol-1-ylmethyl)benzene, 1,2-bimb=1,2-bis(imidazol-1-ylmethyl)-benzene, 1,2-bmimb=1,2-bis(2-methylimidazol-1-ylmethyl)benzene, have been synthesized and characterized. Their structures are determined by single crystal X-ray diffraction and further characterized by infrared spectra (IR) and thermogravimetric (TG) analyses. Complex 1, 4 and 7 display 2D layer structures. 1 possesses two-dimensional sheet containing an unusual [Cd(Tcph)] chains linked by 4,4‧-bipy co-ligand, while 4 and 7 hold the similar 4-connected 44-sql nets. Complex 2 and 3 feature a similar three dimensional (3D) internal compensation structure with a topology of {42·63·8}2{63}. 5 is a novel 2-fold self-penetrating 3D network with 4-coordinated 65·8-CdSO4 subnets. The ladder-like chains of 6 are further connected through O-H···O interactions to yield a 3D supramolecular structure. 8 is a discrete tetranuclear complex. The thermal stabilities of 1-8 and the luminescent properties of 1-4 and 7 in the solid state are also discussed.

  1. Probing the structural dynamics of proteins and nucleic acids with optical tweezers.

    PubMed

    Ritchie, Dustin B; Woodside, Michael T

    2015-10-01

    Conformational changes are an essential feature of most molecular processes in biology. Optical tweezers have emerged as a powerful tool for probing conformational dynamics at the single-molecule level because of their high resolution and sensitivity, opening new windows on phenomena ranging from folding and ligand binding to enzyme function, molecular machines, and protein aggregation. By measuring conformational changes induced in a molecule by forces applied by optical tweezers, new insight has been gained into the relationship between dynamics and function. We discuss recent advances from studies of how structure forms in proteins and RNA, including non-native structures, fluctuations in disordered proteins, and interactions with chaperones assisting native folding. We also review the development of assays probing the dynamics of complex protein-nucleic acid and protein-protein assemblies that reveal the dynamic interactions between biomolecular machines and their substrates.

  2. Ascorbic acid-functionalized Ag NPs as a probe for colorimetric sensing of glutathione

    NASA Astrophysics Data System (ADS)

    D'souza, Stephanie L.; Pati, Ranjan; Kailasa, Suresh Kumar

    2015-08-01

    In this work, we report the use of ascorbic acid-capped silver nanoparticles (AA-Ag NPs) as a probe for selective colorimetric detection of glutathione (GSH) in aqueous solution. This detection system was based on the GSH-induced aggregation of AA-Ag NPs, resulting in drastic changes in the absorption spectra and color of the AA-Ag NPs system. The GSH-induced AA-Ag NPs aggregation was confirmed by UV-visible spectrometry, dynamic light scattering (DLS) and transmission electron microscopic (TEM) techniques. Under optimal conditions, this method exhibited good linearity over the concentration ranges from 5.0 to 50 µM, with the limit of detection 2.4 × 10-7 M. This method was successfully applied to detect GSH in the presence of other biomolecules, which confirms that this probe can be used for the detection of GSH in real samples.

  3. Development of a Radioiodinated Triazolopyrimidine Probe for Nuclear Medical Imaging of Fatty Acid Binding Protein 4

    PubMed Central

    Onoe, Satoru; Sampei, Sotaro; Kimura, Ikuo; Ono, Masahiro; Saji, Hideo

    2014-01-01

    Fatty acid binding protein 4 (FABP4) is the most well-characterized FABP isoform. FABP4 regulates inflammatory pathways in adipocytes and macrophages and is involved in both inflammatory diseases and tumor formation. FABP4 expression was recently reported for glioblastoma, where it may participate in disease malignancy. While FABP4 is a potential molecular imaging target, with the exception of a tritium labeled probe there are no reports of other nuclear imaging probes that target this protein. Here we designed and synthesized a nuclear imaging probe, [123I]TAP1, and evaluated its potential as a FABP4 targeting probe in in vitro and in vivo assays. We focused on the unique structure of a triazolopyrimidine scaffold that lacks a carboxylic acid to design the TAP1 probe that can undergo facilitated delivery across cell membranes. The affinity of synthesized TAP1 was measured using FABP4 and 8-anilino-1-naphthalene sulfonic acid. [125I]TAP1 was synthesized by iododestannylation of a precursor, followed by affinity and selectivity measurements using immobilized FABPs. Biodistributions in normal and C6 glioblastoma-bearing mice were evaluated, and excised tumors were subjected to autoradiography and immunohistochemistry. TAP1 and [125I]TAP1 showed high affinity for FABP4 (Ki = 44.5±9.8 nM, Kd = 69.1±12.3 nM). The FABP4 binding affinity of [125I]TAP1 was 11.5- and 35.5-fold higher than for FABP3 and FABP5, respectively. In an in vivo study [125I]TAP1 displayed high stability against deiodination and degradation, and moderate radioactivity accumulation in C6 tumors (1.37±0.24% dose/g 3 hr after injection). The radioactivity distribution profile in tumors partially corresponded to the FABP4 positive area and was also affected by perfusion. The results indicate that [125I]TAP1 could detect FABP4 in vitro and partly in vivo. As such, [125I]TAP1 is a promising lead compound for further refinement for use in in vivo FABP4 imaging. PMID:24732569

  4. Acidic-pH-activatable fluorescence probes for visualizing exocytosis dynamics.

    PubMed

    Asanuma, Daisuke; Takaoka, Yousuke; Namiki, Shigeyuki; Takikawa, Kenji; Kamiya, Mako; Nagano, Tetsuo; Urano, Yasuteru; Hirose, Kenzo

    2014-06-10

    Live imaging of exocytosis dynamics is crucial for a precise spatiotemporal understanding of secretion phenomena, but current approaches have serious limitations. We designed and synthesized small-molecular fluorescent probes that were chemically optimized for sensing acidic intravesicular pH values, and established that they can be used to sensitively and reliably visualize vesicular dynamics following stimulation. This straightforward technique for the visualization of exocytosis as well as endocytosis/reacidification processes with high spatiotemporal precision is expected to be a powerful tool for investigating dynamic cellular phenomena involving changes in the pH value.

  5. Identification of random nucleic acid sequence aberrations using dual capture probes which hybridize to different chromosome regions

    DOEpatents

    Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

    1998-01-01

    A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration.

  6. Identification of random nucleic acid sequence aberrations using dual capture probes which hybridize to different chromosome regions

    DOEpatents

    Lucas, J.N.; Straume, T.; Bogen, K.T.

    1998-03-24

    A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration. 14 figs.

  7. Folic acid-conjugated europium complexes as luminescent probes for selective targeting of cancer cells.

    PubMed

    Quici, Silvio; Casoni, Alessandro; Foschi, Francesca; Armelao, Lidia; Bottaro, Gregorio; Seraglia, Roberta; Bolzati, Cristina; Salvarese, Nicola; Carpanese, Debora; Rosato, Antonio

    2015-02-26

    We report the synthesis of three optical probes (Eu(3+)⊂1, Eu(3+)⊂2, and Eu(3+)⊂3) having a luminescent Eu complex (signaling unit) bonded in different positions to folic acid (FA), the folate receptor (FR) targeting unit. The structures of the two regioisomers Eu(3+)⊂1 and Eu(3+)⊂2 were assigned by mass spectrometric experiments. The optical properties and stability of these probes were assessed in phosphate-buffered saline, cell culture medium, rat serum, and cellular lysate, and results indicated that they are chemically and photophysically stable. Cytotoxicity was studied with ovarian cancer cells having high (SKOV-3), intermediate (OVCAR-3), low (IGROV-1), or null (A2780) expression of FRs. The internalized probe, evaluated in SKOV-3, IGROV-1, and A2780 cells, was in the order Eu(3+)⊂2 > Eu(3+)⊂1 > Eu(3+)⊂3. No internalization was observed for A2780 cells. Such results, together with those obtained in competition experiments of FA versus Eu(3+)⊂2 and FA or Eu(3+)⊂2 versus (3)H-FA, indicate that internalization is receptor-mediated and that Eu(3+)⊂2 shows high selectivity and specificity for FR.

  8. Structural, electronic and photoluminescence properties of Eu3+-doped CaYAlO4 obtained by using citric acid complexes as precursors

    NASA Astrophysics Data System (ADS)

    Perrella, R. V.; Júnior, C. S. Nascimento; Góes, M. S.; Pecoraro, E.; Schiavon, M. A.; Paiva-Santos, C. O.; Lima, H.; Couto dos Santos, M. A.; Ribeiro, S. J. L.; Ferrari, J. L.

    2016-07-01

    The search for new materials that meet the current technological demands for photonic applications, make the Rare Earth ions embedded in inorganic oxides as excellent candidates for several technological devices. This work presents the synthesis of Eu3+-doped CaYAlO4 using citric acid as ligand to form a complex precursor. The methodology used has big draw due to its easy handling and low cost of the materials. The thermal analysis of viscous solutions was evaluated and the obtained compounds show the formation of a polycrystalline tetragonal phase. Rietveld refinement was used to understand the structural and the cell parameters of the crystalline phase as a function of temperature of heat-treatment. Crystallite size and microstrain were determined and were shown to have a direct relationship with the temperature of the heat-treatment. The band-gap of the CaYAlO4 doped with 1 and 10 mol% of Eu3+ showed values close to 4.30 eV, resulting in their transparency in the visible region between 330 and 750 nm. Besides the intense photoluminescence from Eu3+, a study was conducted to evaluate the possible position of the Eu3+ in the CaYAlO4 as host lattice. Lifetime of the emission decay from Eu3+ excited state 5D0 show that CaYAlO4 is a good host to rare earth ions, once it can avoid clustering of these ions in concentration as high as 10 mol%. The predictions of the sublevels of the 7F1 crystal field level are discussed through the method of equivalent nearest neighbours (MENN). The intensity parameters (Ωλ, λ = 2 and 4) are reproduced with physically reasonable values of average polarizabilities. The set of charge factors used in both calculations are in good agreement with the charge of the europium ion described by the Batista-Longo improved model (BLIM). The quantum efficiencies of the materials were calculated based on Judd-Ofelt theory. Based on the results obtained in this work, the materials have potential use in photonic devices such as lasers and solid

  9. Translational and rotational diffusion of flexible PEG and rigid dendrimer probes in sodium caseinate dispersions and acid gels.

    PubMed

    Salami, Souad; Rondeau-Mouro, Corinne; Barhoum, Myriam; van Duynhoven, John; Mariette, François

    2014-09-01

    The dynamics of rigid dendrimer and flexible PEG probes in sodium caseinate dispersions and acid gels, including both translational diffusion and rotational diffusion, were studied by NMR. Above the onset of the close-packing limit (C ∼ 10 g/100 g H2 O), translational diffusion of the probe depended on its flexibility and on the fluctuations of the matrix chains. The PEG probe diffused more rapidly than the spherical dendrimer probe of corresponding hydrodynamic radius. The greater conformational flexibility of PEG facilitated its motion through the crowded casein matrix. Rotational diffusion was, however, substantially less hindered than the translational diffusion and depended on the local protein-probe friction which became high when the casein concentration increased. The coagulation of the matrix led to the formation of large voids, which resulted in an increase in the translational diffusion of the probes, whereas the rotational diffusion of the probes was retarded in the gel, which could be attributed to the immobilized environment surrounding the probe. Quantitative information from PFG-NMR and SEM micrographs have been combined for characterizing microstructural details in SC acid gels.

  10. Boronic Acid: A Bio-Inspired Strategy To Increase the Sensitivity and Selectivity of Fluorescent NADH Probe.

    PubMed

    Wang, Lu; Zhang, Jingye; Kim, Beomsue; Peng, Juanjuan; Berry, Stuart N; Ni, Yong; Su, Dongdong; Lee, Jungyeol; Yuan, Lin; Chang, Young-Tae

    2016-08-24

    Fluorescent probes have emerged as an essential tool in the molecular recognition events in biological systems; however, due to the complex structures of certain biomolecules, it remains a challenge to design small-molecule fluorescent probes with high sensitivity and selectivity. Inspired by the enzyme-catalyzed reaction between biomolecule and probe, we present a novel combination-reaction two-step sensing strategy to improve sensitivity and selectivity. Based on this strategy, we successfully prepared a turn-on fluorescent reduced nicotinamide adenine dinucleotide (NADH) probe, in which boronic acid was introduced to bind with NADH and subsequently accelerate the sensing process. This probe shows remarkably improved sensitivity (detection limit: 0.084 μM) and selectivity to NADH in the absence of any enzymes. In order to improve the practicality, the boronic acid was further modified to change the measurement conditions from alkalescent (pH 9.5) to physiological environment (pH 7.4). Utilizing these probes, we not only accurately quantified the NADH weight in a health care product but also evaluated intracellular NADH levels in live cell imaging. Thus, these bio-inspired fluorescent probes offer excellent tools for elucidating the roles of NADH in biological systems as well as a practical strategy to develop future sensitive and selective probes for complicated biomolecules. PMID:27500425

  11. Selective local lysis and sampling of live cells for nucleic acid analysis using a microfluidic probe

    PubMed Central

    Kashyap, Aditya; Autebert, Julien; Delamarche, Emmanuel; Kaigala, Govind V.

    2016-01-01

    Heterogeneity is inherent to biology, thus it is imperative to realize methods capable of obtaining spatially-resolved genomic and transcriptomic profiles of heterogeneous biological samples. Here, we present a new method for local lysis of live adherent cells for nucleic acid analyses. This method addresses bottlenecks in current approaches, such as dilution of analytes, one-sample-one-test, and incompatibility to adherent cells. We make use of a scanning probe technology - a microfluidic probe - and implement hierarchical hydrodynamic flow confinement (hHFC) to localize multiple biochemicals on a biological substrate in a non-contact, non-destructive manner. hHFC enables rapid recovery of nucleic acids by coupling cell lysis and lysate collection. We locally lysed ~300 cells with chemical systems adapted for DNA or RNA and obtained lysates of ~70 cells/μL for DNA analysis and ~15 cells/μL for mRNA analysis. The lysates were introduced into PCR-based workflows for genomic and transcriptomic analysis. This strategy further enabled selective local lysis of subpopulations in a co-culture of MCF7 and MDA-MB-231 cells, validated by characteristic E-cadherin gene expression in individually extracted cell types. The developed strategy can be applied to study cell-cell, cell-matrix interactions locally, with implications in understanding growth, progression and drug response of a tumor. PMID:27411740

  12. An aldehyde group-based P-acid probe for selective fluorescence turn-on sensing of cysteine and homocysteine.

    PubMed

    Yang, Chunlei; Wang, Xiu; Shen, Lei; Deng, Wenping; Liu, Haiyun; Ge, Shenguang; Yan, Mei; Song, Xianrang

    2016-06-15

    A highly sensitive and selective turn on fluorescent probe P-acid-aldehyde (P-CHO) is developed for the determination of cysteine (Cys) and homocysteine (Hcy). The probe is designed and synthesized by incorporating the specific functional group aldehyde group for thiols into a stable π-conjugated material 4,4'-(2,5-dimethoxy-1,4-phenylene) bis(ethyne-2,1-diyl) dibenzoic acid (P-acid). The probe fluorescence is quenched through donor photoinduced electron transfer (d-PET) between the fluorophore (P-acid) and the recognition group (aldehyde group). In the presence of thiols, Cys and Hcy can selectively react with aldehyde group of the probe because the inhibition of d-PET between fluorophore and recognition group. Therefore, a turn-on fluorescent sensor was established for the fluorescence recovery. Under the optimized conditions, the fluorescence response of probe is directly proportional to the concentration of Cys in the range of 4-95 NM L(-1), with a detection limit 3.0 nM. In addition, the sensing system exhibits good selectively toward Cys and Hcy in the presence of other amino acids. It has been successfully applied for bioimaging of Cys and Hcy in living cells with low cell toxicity.

  13. Probe design rules and effective enzymes for endonuclease-based detection of nucleic acids.

    PubMed

    Yan, Lei; Nakayama, Shizuka; Sintim, Herman O

    2013-10-15

    Junction probe (JP) platform is an isothermal endonuclease-based detection assay for both RNA and DNA. Herein, we screen 31 REAse and identify effective restriction endonucleases that can be used for JP detection. Secondly, we investigate how different probe architectures affect JP cleavage rates and conclude that although molecular beacon (MB) JP probes give less background noise than linear JP probes, the cleavage of MB JP probes are slower than linear JP probes.

  14. Development of aliphatic biodegradable photoluminescent polymers

    PubMed Central

    Yang, Jian; Zhang, Yi; Gautam, Santosh; Liu, Li; Dey, Jagannath; Chen, Wei; Mason, Ralph P.; Serrano, Carlos A.; Schug, Kevin A.; Tang, Liping

    2009-01-01

    None of the current biodegradable polymers can function as both implant materials and fluorescent imaging probes. The objective of this study was to develop aliphatic biodegradable photoluminescent polymers (BPLPs) and their associated cross-linked variants (CBPLPs) for biomedical applications. BPLPs are degradable oligomers synthesized from biocompatible monomers including citric acid, aliphatic diols, and various amino acids via a convenient and cost-effective polycondensation reaction. BPLPs can be further cross-linked into elastomeric cross-linked polymers, CBPLPs. We have shown representatively that BPLP-cysteine (BPLP-Cys) and BPLP-serine (BPLP-Ser) offer advantages over the traditional fluorescent organic dyes and quantum dots because of their preliminarily demonstrated cytocompatibility in vitro, minimal chronic inflammatory responses in vivo, controlled degradability and high quantum yields (up to 62.33%), tunable fluorescence emission (up to 725 nm), and photostability. The tensile strength of CBPLP-Cys film ranged from 3.25 ± 0.13 MPa to 6.5 ± 0.8 MPa and the initial Modulus was in a range of 3.34 ± 0.15 MPa to 7.02 ± 1.40 MPa. Elastic CBPLP-Cys could be elongated up to 240 ± 36%. The compressive modulus of BPLP-Cys (0.6) (1:1:0.6 OD:CA:Cys) porous scaffold was 39.60 ± 5.90 KPa confirming the soft nature of the scaffolds. BPLPs also possess great processability for micro/nano-fabrication. We demonstrate the feasibility of using BPLP-Ser nanoparticles (“biodegradable quantum dots”) for in vitro cellular labeling and noninvasive in vivo imaging of tissue engineering scaffolds. The development of BPLPs and CBPLPs represents a new direction in developing fluorescent biomaterials and could impact tissue engineering, drug delivery, bioimaging. PMID:19506254

  15. Exploring the Hybridization Thermodynamics of Spherical Nucleic Acids to Tailor Probes for Diagnostic and Therapeutic Applications

    NASA Astrophysics Data System (ADS)

    Randeria, Pratik Shailesh

    Spherical nucleic acids (SNAs), three-dimensional nanoparticle conjugates composed of densely packed and highly oriented oligonucleotides around organic or inorganic nanoparticles, are an emergent class of nanostructures that show promise as single-entity agents for intracellular messenger RNA (mRNA) detection and gene regulation. SNAs exhibit superior biocompatibility and biological properties compared to linear oligonucleotides, enabling them to overcome many of the limitations of linear oligonucleotides for use in biomedical applications. However, the origins of these biologically attractive properties are not well understood. In this dissertation, the chemistry underlying one such property is studied in detail, and the findings are applied towards the rational design of more effective SNAs for diagnostic and therapeutic applications. Chapter 1 introduces the synthesis of SNAs, the unique properties that make them superior to linear nucleic acids for biomedicine, and previously studied applications of these structures. Chapter 2 focuses on quantitatively studying the impact of the chemical structure of the SNA on its ability to hybridize multiple complementary nucleic acids. This chapter lays the groundwork for understanding the factors that govern SNA hybridization thermodynamics and how to tailor SNAs to increase their binding affinity to target mRNA strands. Chapters 3 and 4 capitalize on this knowledge to engineer probes for intracellular mRNA detection and gene regulation applications. Chapter 3 reports the development of an SNA-based probe that can simultaneously report the expression level of two different mRNA transcripts in live cells and differentiate diseased cells from non-diseased cells. Chapter 4 investigates the use of topically-applied SNAs to down-regulate a critical mediator of impaired wound healing in diabetic mice to accelerate wound closure. This study represents the first topical therapeutic application of SNA nanotechnology to treat open

  16. A Sensitive Peptide Nucleic Acid Probe Assay for Detection of BRAF V600 Mutations in Melanoma.

    PubMed

    Chen, Tai-Long; Chang, John Wen-Cheng; Hsieh, Jia-Juan; Cheng, Hsin-Yi; Chiou, Chiuan-Chian

    Mutated v-Raf murine sarcoma viral oncogene homolog B (BRAF) is an important biomarker for the prediction of therapeutic efficacy of several anticancer drugs. The detection of BRAF mutation faces two challenges: Firstly, there are multiple types of mutations, and secondly, tumor samples usually contain various amounts of wild-type, normal tissues. Here, we describe a newly established method for sensitive detection of multiple types of BRAF V600 mutations in excess wild-type background. The method introduced a fluorophore-tagged peptide nucleic acid (PNA) to serve as both polymerase chain reaction (PCR) clamp and sensor probe, which inhibited the amplification of wild-type templates during PCR and revealed multiple types of mutant signals during melting analysis. We demonstrated the design and optimization process of the method, and applied it in the detection of BRAF mutations in 49 melanoma samples. This PNA probe assay method detected three types of mutations in 17 samples, and was much more sensitive than conventional PCR plus Sanger sequencing. PMID:27566656

  17. Peptide nucleic acid probe detection of mutations in Mycobacterium tuberculosis genes associated with drug resistance.

    PubMed

    Bockstahler, L E; Li, Z; Nguyen, N Y; Van Houten, K A; Brennan, M J; Langone, J J; Morris, S L

    2002-03-01

    The emergence of drug-resistant strains of Mycobacterium tuberculosis is a serious public health problem. Many of the specific gene mutations that cause drug resistance in M. tuberculosis are point mutations. We are developing a PCR-peptide nucleic acid (PNA)-based ELISA as a diagnostic method to recognize point mutations in genes associated with isoniazid and rifampin resistance in M. tuberculosis. Specific point mutation-containing sequences and wild-type sequences of cloned mycobacterial genes were PCR-amplified, denatured, and hybridized with PNA probes bound to microplate wells. Using 15-base PNA probes, we established the hybridization temperatures (50 degrees C-55 degrees C) and other experimental conditions suitable for detecting clinically relevant point mutations in the katG and rpoB genes. Hybridization of PCR-amplified sequences that contained these point mutations with complementary mutation-specific PNAs resulted in significant increases in ELISA response compared with hybridization using wild-type-specific PNAs. Conversely, PCR-amplified wild-type sequences hybridized much more efficiently with wild-type PNAs than with the mutation-specific PNAs. Using the M. tuberculosis cloned genes and PCR-PNA-ELISA format developed here, M. tuberculosis sequences containing point mutations associated with drug resistance can be identified in less than 24 h. PMID:11926172

  18. Neutrophil chemotaxis and arachidonic acid metabolism are not linked: evidence from metal ion probe studies

    SciTech Connect

    Turner, S.R.; Turner, R.A.; Smith, D.M.; Johnson, J.A.

    1986-03-05

    Heavy metal ions can inhibit arachidonic acid (AA) metabolism protect against ionophore cytotoxicity (ibid) and inhibit neutrophil chemotaxis. In this study they used Au/sup 3 +/, Zn/sup 2 +/, Cr/sup 3 +/, Mn/sup 2 +/ and Cu/sup 2 +/ as probes of the interrelationships among AA metabolism, ionophore-mediated cytotoxicity, and chemotaxis. Phospholipid deacylation was measured in ionophore-treated cells prelabeled with /sup 3/H-AA. Eicosanoid release from ionophore-treated cells was monitored by radioimmunoassay. Cytoprotection was quantitated as ability to exclude trypan blue. Chemotaxis toward f-met-leu-phe was measured by leading front analysis. The results imply that metal ions attenuate ionophore cytotoxicity by blocking phospholipid deacylation and eicosanoid release. In contrast to previous reports, no correlation between AA metabolism and chemotaxis was demonstrated, suggesting that these 2 processes are not linked.

  19. DNA detection using water-soluble conjugated polymers and peptide nucleic acid probes

    NASA Astrophysics Data System (ADS)

    Gaylord, Brent S.; Heeger, Alan J.; Bazan, Guillermo C.

    2002-08-01

    The light-harvesting properties of cationic conjugated polymers are used to sensitize the emission of a dye on a specific peptide nucleic acid (PNA) sequence for the purpose of homogeneous, "real-time" DNA detection. Signal transduction is controlled by hybridization of the neutral PNA probe and the negative DNA target. Electrostatic interactions bring the hybrid complex and cationic polymer within distances required for Förster energy transfer. Conjugated polymer excitation provides fluorescein emission >25 times higher than that obtained by exciting the dye, allowing detection of target DNA at concentrations of 10 pM with a standard fluorometer. A simple and highly sensitive assay with optical amplification that uses the improved hybridization behavior of PNA/DNA complexes is thus demonstrated.

  20. Probing the Specificity Determinants of Amino Acid Recognition by Arginase†,‡

    PubMed Central

    Shishova, Ekaterina Y.; Di Costanzo, Luigi; Emig, Francis A.; Ash, David E.; Christianson, David W.

    2009-01-01

    Arginase is a binuclear manganese metalloenzyme that serves as a therapeutic target for the treatment of asthma, erectile dysfunction, and atherosclerosis. In order to better understand the molecular basis of inhibitor affinity, we have employed site-directed mutagenesis, enzyme kinetics, and X-ray crystallography to probe the molecular recognition of the amino acid moiety (i.e., the α-amino and α-carboxylate groups) of substrate l-arginine and inhibitors in the active site of human arginase I. Specifically, we focus on: (1) a water-mediated hydrogen bond between the substrate α-carboxylate and T135, (2) a direct hydrogen bond between the substrate α-carboxylate and N130, and (3) a direct charged hydrogen bond between the substrate α-amino group and D183. Amino acid substitutions for T135, N130, and D183 generally compromise substrate affinity as reflected by increased KM values, but have less pronounced effects on catalytic function as reflected by minimal variations of kcat. As with substrate KM values, inhibitor Kd values increase for binding to enzyme mutants and suggest that the relative contribution of intermolecular interactions to amino acid affinity in the arginase active site is: water-mediated hydrogen bond < direct hydrogen bond < direct charged hydrogen bond. Structural comparisons of arginase with the related binuclear manganese metalloenzymes agmatinase and proclavaminic acid amidinohydrolase suggest that the evolution of substrate recognition in the arginase fold occurs by mutation of residues contained in specificity loops flanking the mouth of the active site (especially loops 4 and 5), thereby allowing diverse guanidinium substrates to be accommodated for catalysis. PMID:19093830

  1. Extraordinary adhesion of phenylboronic acid derivatives of polyvinylamine to wet cellulose: a colloidal probe microscopy investigation.

    PubMed

    Notley, Shannon M; Chen, Wei; Pelton, Robert

    2009-06-16

    Typically, the adhesion between cellulose surfaces under aqueous conditions is very poor. Often, adsorbed polymers such as polyvinylamine (PVAm) are used to increase the wet strength; however, this provides only a minimal increase in the adhesion energy. Here, the adhesion between cellulose surfaces with adsorbed layers of phenylboronic acid derivatized polyvinylamine has been studied using colloidal probe microscopy as a function of pH. The adhesion due to the phenylboronic acid (PBA) groups grafted on the polyvinylamine backbone is almost 30 times greater, providing a new, exciting class of polymers using covalent linkages to improve the strength of the joint between cellulose surfaces. The measured surface forces on approach provided key information on the molecular conformation of the polymers at the cellulose-solution interface. At low pH, the three polymers tested, PVAm, PVAm-Ph (with pendant phenol groups), and PVAm-PBA (with phenylboronic acid groups) all had a relatively flat conformation at the interface, which is in agreement with the predictions based upon theory for highly charged polyelectrolytes adsorbing to an oppositely charged interface. With increasing pH, the charge on the polymers is reduced, eventually resulting in a more expansive conformation at the interface at pH 10 and above with the development of a steric interaction force. The onset of this steric force correlates well with the observed significant increase in the pull-off force upon separation of the cellulose surfaces. Furthermore, a greater increase in the adhesion was observed for PVAm-PBA in agreement with previous studies using macroscopic cellulose surfaces. This is attributed to the formation of boronic acid esters between the polymer and the cis diol groups on the cellulose surface.

  2. A highly specific ferrocene-based fluorescent probe for hypochlorous acid and its application to cell imaging.

    PubMed

    Chen, Suming; Lu, Jinxin; Sun, Chengdong; Ma, Huimin

    2010-03-01

    A highly specific ferrocene-based fluorescent probe, (9-anthryl)ethenylferrocene, has been designed, synthesized and characterized for fluorescence imaging of hypochlorous acid (HOCl) in live cells. The design strategy for the probe is based on the strong quenching effect of electron-donor ferrocene on anthracene fluorescence via an intramolecular charge transfer process, and is accomplished through constructing the conjugated molecule by using a cleavable double bond as a linker. The double bond in the probe reacts selectively with HOCl rather than the other reactive oxygen species (e.g., *OH, *O(2)(-), (1)O(2), and H(2)O(2)) in pH 7.4, accompanied by more than 100-fold fluorescence enhancement. Moreover, the probe is cell membrane permeable, and its applicability has been successfully demonstrated for fluorescence imaging of HOCl in HeLa cells.

  3. Real time RNA transcription monitoring by Thiazole Orange (TO)-conjugated Peptide Nucleic Acid (PNA) probes: norovirus detection.

    PubMed

    Tonelli, Alessandro; Tedeschi, Tullia; Germini, Andrea; Sforza, Stefano; Corradini, Roberto; Medici, Maria Cristina; Chezzi, Carlo; Marchelli, Rosangela

    2011-05-01

    Thiazole Orange (TO)-conjugated Peptide Nucleic Acid (PNA) probes have been reported as a valuable strategy for DNA analysis; however, no investigations targeting RNA molecules and no comparisons between different derivatization approaches have been reported so far. In this work, two TO-conjugated PNAs for genogroup II noroviruses (NoV GII) detection were designed and synthesized. Both the probes target the most conserved stretch of nucleotides identified in the open reading frame 1-2 (ORF1-ORF2) junction region and differ for the dye conjugation strategy: one PNA is end-labelled with the TO molecule tethered by a linker; the other probe bears the TO molecule directly linked to the PNA backbone, replacing a conventional nucleobase. The spectroscopic properties of the two PNA probes were studied and their applicability to NoVs detection, using an isothermal assay, was investigated. Both probes showed good specificity and high fluorescence enhancement upon hybridization, especially targeting RNA molecules. Moreover, the two probes were successfully employed for NoVs detection from stool specimens in an isothermal-based amplification assay targeting RNA 'amplicons'. The probes showed to be specific even in the presence of high concentrations of non-target RNA.

  4. A colorimetric and near-infrared fluorescent probe with high sensitivity and selectivity for acid phosphatase and inhibitor screening.

    PubMed

    Xu, Yongqian; Li, Benhao; Xiao, Liangliang; Ouyang, Jia; Sun, Shiguo; Pang, Yi

    2014-08-14

    A dual-channel including a colorimetric and fluorescent probe based on the aggregation-caused quenching (ACQ) and enzymolysis approach has been presented to screen acid phosphatase (ACP) and its inhibitor. Moreover, the ACP activity was determined by real time assay. PMID:24957006

  5. Probe depth matters in dermal microdialysis sampling of benzoic acid after topical application: an ex vivo study in human skin.

    PubMed

    Holmgaard, R; Benfeldt, E; Bangsgaard, N; Sorensen, J A; Brosen, K; Nielsen, F; Nielsen, J B

    2012-01-01

    Microdialysis (MD) in the skin - dermal microdialysis (DMD) - is a unique technique for sampling of topically as well as systemically administered drugs at the site of action, e.g. sampling of dermatological drug concentrations in the dermis. Debate has concerned the existence of a correlation between the depth of the sampling device - the probe - in the dermis and the amount of drug sampled following topical drug administration. This study evaluates the relation between probe depth and drug sampling using dermal DMD sampling ex vivo in human skin. We used superficial (<1 mm), intermediate (1-2 mm) and deep (>2 mm) positioning of the linear MD probe in the dermis of human abdominal skin, followed by topical application of 4 mg/ml of benzoic acid (BA) in skin chambers overlying the probes. Dialysate was sampled every hour for 12 h and analysed for BA content by high-performance liquid chromatography. Probe depth was measured by 20-MHz ultrasound scanning. The area under the time-versus-concentration curve (AUC) describes the drug exposure in the tissue during the experiment and is a relevant parameter to compare for the 3 dermal probe depths investigated. The AUC(0-12) were: superficial probes: 3,335 ± 1,094 μg·h/ml (mean ± SD); intermediate probes: 2,178 ± 1,068 μg·h/ml, and deep probes: 1,159 ± 306 μg·h/ml. AUC(0-12) sampled by the superficial probes was significantly higher than that of samples from the intermediate and deeply positioned probes (p value <0.05). There was a significant inverse correlation between probe depth and AUC(0-12) sampled by the same probe (p value <0.001, r(2) value = 0.5). The mean extrapolated lag-times (±SD) for the superficial probes were 0.8 ± 0.1 h, for the intermediate probes 1.7 ± 0.5 h, and for the deep probes 2.7 ± 0.5 h, which were all significantly different from each other (p value <0.05). In conclusion, this paper demonstrates that there is an inverse relationship between the depth of the probe in the dermis

  6. Probe depth matters in dermal microdialysis sampling of benzoic acid after topical application: an ex vivo study in human skin.

    PubMed

    Holmgaard, R; Benfeldt, E; Bangsgaard, N; Sorensen, J A; Brosen, K; Nielsen, F; Nielsen, J B

    2012-01-01

    Microdialysis (MD) in the skin - dermal microdialysis (DMD) - is a unique technique for sampling of topically as well as systemically administered drugs at the site of action, e.g. sampling of dermatological drug concentrations in the dermis. Debate has concerned the existence of a correlation between the depth of the sampling device - the probe - in the dermis and the amount of drug sampled following topical drug administration. This study evaluates the relation between probe depth and drug sampling using dermal DMD sampling ex vivo in human skin. We used superficial (<1 mm), intermediate (1-2 mm) and deep (>2 mm) positioning of the linear MD probe in the dermis of human abdominal skin, followed by topical application of 4 mg/ml of benzoic acid (BA) in skin chambers overlying the probes. Dialysate was sampled every hour for 12 h and analysed for BA content by high-performance liquid chromatography. Probe depth was measured by 20-MHz ultrasound scanning. The area under the time-versus-concentration curve (AUC) describes the drug exposure in the tissue during the experiment and is a relevant parameter to compare for the 3 dermal probe depths investigated. The AUC(0-12) were: superficial probes: 3,335 ± 1,094 μg·h/ml (mean ± SD); intermediate probes: 2,178 ± 1,068 μg·h/ml, and deep probes: 1,159 ± 306 μg·h/ml. AUC(0-12) sampled by the superficial probes was significantly higher than that of samples from the intermediate and deeply positioned probes (p value <0.05). There was a significant inverse correlation between probe depth and AUC(0-12) sampled by the same probe (p value <0.001, r(2) value = 0.5). The mean extrapolated lag-times (±SD) for the superficial probes were 0.8 ± 0.1 h, for the intermediate probes 1.7 ± 0.5 h, and for the deep probes 2.7 ± 0.5 h, which were all significantly different from each other (p value <0.05). In conclusion, this paper demonstrates that there is an inverse relationship between the depth of the probe in the dermis

  7. Wavelength-ratiometric near-physiological pH sensors based on 6-aminoquinolinium boronic acid probes.

    PubMed

    Badugu, Ramachandram; Lakowicz, Joseph R; Geddes, Chris D

    2005-04-30

    We describe the pH response of a set of isomeric water-soluble fluorescent probes based on both the 6-aminoquinolinium and boronic acid moieties. These probes show spectral shifts and intensity changes with pH, in a wavelength-ratiometric and colorimetric manner. Subsequently, changes in pH can readily be determined around the physiological level. Although boronic acid containing probes are known to exhibit pH sensitivity along with an ability for saccharide binding/chelating, the new probes reported here are considered to be unique and show an unperturbed pH response, even in the presence of high concentrations of background saccharide, such as with glucose and fructose, allowing for the predominant pH sensitivity. The response of the probes is based on the ability of the boronic acid group to interact with strong bases like OH(-), changing from the neutral form of the boronic acid group, R-B(OH)(2), to the anionic ester, R-B(-)(OH)(3), form, which is an electron donating group. The presence of an electron deficient quaternary heterocyclic nitrogen center and a strong electron donating amino group in the 6-position of the quinolinium backbone, provides for the spectral changes observed upon OH(-) complexation. In addition, by comparing the results obtained with systems separately incorporating 6-methoxy or 6-methyl substituents, the suppressed response towards monosaccharides, such as with glucose and fructose, can clearly be observed for these systems. Finally we compare our results to those of a control compound, BAQ, which does not contain the boronic acid group, allowing a rationale of the spectral changes to be made.

  8. Hybridization properties of long nucleic acid probes for detection of variable target sequences, and development of a hybridization prediction algorithm

    PubMed Central

    Öhrmalm, Christina; Jobs, Magnus; Eriksson, Ronnie; Golbob, Sultan; Elfaitouri, Amal; Benachenhou, Farid; Strømme, Maria; Blomberg, Jonas

    2010-01-01

    One of the main problems in nucleic acid-based techniques for detection of infectious agents, such as influenza viruses, is that of nucleic acid sequence variation. DNA probes, 70-nt long, some including the nucleotide analog deoxyribose-Inosine (dInosine), were analyzed for hybridization tolerance to different amounts and distributions of mismatching bases, e.g. synonymous mutations, in target DNA. Microsphere-linked 70-mer probes were hybridized in 3M TMAC buffer to biotinylated single-stranded (ss) DNA for subsequent analysis in a Luminex® system. When mismatches interrupted contiguous matching stretches of 6 nt or longer, it had a strong impact on hybridization. Contiguous matching stretches are more important than the same number of matching nucleotides separated by mismatches into several regions. dInosine, but not 5-nitroindole, substitutions at mismatching positions stabilized hybridization remarkably well, comparable to N (4-fold) wobbles in the same positions. In contrast to shorter probes, 70-nt probes with judiciously placed dInosine substitutions and/or wobble positions were remarkably mismatch tolerant, with preserved specificity. An algorithm, NucZip, was constructed to model the nucleation and zipping phases of hybridization, integrating both local and distant binding contributions. It predicted hybridization more exactly than previous algorithms, and has the potential to guide the design of variation-tolerant yet specific probes. PMID:20864443

  9. Quantification of syntrophic fatty acid-{beta}-oxidizing bacteria in a mesophilic biogas reactor by oligonucleotide probe hybridization

    SciTech Connect

    Hansen, K.H.; Ahring, B.K.; Raskin, L.

    1999-11-01

    Small-subunit rRNA sequences were obtained for two saturated fatty acid-{beta}-oxidizing syntrophic bacteria, Syntrophomonas sapovorans and Syntrophomonas wolfei LYB, and sequence analysis confirmed their classification as members of the family Syntrophomonadaceae. S.wolfei LYB was closely related to S.wolfei subsp. solfei, but S. sapovorans did not cluster with the other members of the genus Syntrophomonas. Five oligonucleotide probes targeting the small-subunit rRNA of different groups within the family Syntrophomonadaceae, which contains all currently known saturated fatty acid-{beta}-oxidizing syntrophic bacteria, were developed and characterized. The probes were designed to be specific at the family, genus, and species levels and were characterized by temperature-of-dissociation and specificity studies. To demonstrate the usefulness of the probes for the detection and quantification of saturated fatty acid-{beta}-oxidizing syntrophic bacteria in methanogenic environments, the microbial community structure of a sample from a full-scale biogas plant was determined. Hybridization results with probes for syntrophic bacteria and methanogens were compared to specific methanogenic activities and microbial numbers determined with most-probable-number estimates. Most of the methanogenic rRNA was comprised of Methanomicrobiales rRNA, suggesting that members of this order served as the main hydrogen-utilizing microorganisms. Between 0.2 and 1% of the rRNA was attributed to the Syntrophomonadaceae, or which the majority was accounted for by the genus Syntrophomonas.

  10. Benzimidazole-based ratiometric two-photon fluorescent probes for acidic pH in live cells and tissues.

    PubMed

    Kim, Hyung Joong; Heo, Cheol Ho; Kim, Hwan Myung

    2013-11-27

    Many aspects of cell metabolism are controlled by acidic pH. We report a new family of small molecule and ratiometric two photon (TP) probes derived from benzimidazole (BH1-3 and BH1L) for monitoring acidic pH values. These probes are characterized by a strong two-photon excited fluorescence, a marked blue-to-green emission color change in response to pH, pKa values ranging from 4.9 to 6.1, a distinctive isoemissive point, negligible cytotoxicity, and high photostability, thereby allowing quantitative analysis of acidic pH. Moreover, we show that BH1L optimized as a lysosomal-targeted probe allows for direct, real-time estimation of the pH values inside lysosomal compartments in live cells as well as in living mouse brain tissues through the use of two-photon microscopy. These findings demonstrate that these probes will find useful applications in biomedical research.

  11. Photoluminescence of Diamondoid Crystals

    SciTech Connect

    Clay, William; Sasagawa, Takao; Iwasa, Akio; Liu, Zhi; Dahl, Jeremy E.; Carlson, Robert M.K.; Kelly, Michael; Melos, Nicholas; Shen, Zhi-Xun; /Stanford U., Phys. Dept. /Stanford U., Appl. Phys. Dept. /Stanford U., Geballe Lab. /SIMES, Stanford

    2012-04-03

    The photoluminescence of diamondoids in the solid state is examined. All of the diamondoids are found to photoluminesce readily with initial excitation wavelengths ranging from 233 nm to 240 nm (5.3 eV). These excitation energies are more than 1 eV lower than any previously studied saturated hydrocarbon material. The emission is found to be heavily shifted from the absorption, with emission wavelengths of roughly 295 nm (4.2 eV) in all cases. In the dissolved state, however, no uorescence is observed for excitation wavelengths as short as 200 nm. We also discuss predictions and measurements of the quantum yield. Our predictions indicate that the maximum yield may be as high as 25%. Our measurement of one species, diamantane, gives a yield of 11%, the highest ever reported for a saturated hydrocarbon, even though it was likely not at the optimal excitation wavelength.

  12. Characterization of Aqueous Oleic Acid/Oleate Dispersions by Fluorescent Probes and Raman Spectroscopy.

    PubMed

    Suga, Keishi; Kondo, Dai; Otsuka, Yoko; Okamoto, Yukihiro; Umakoshi, Hiroshi

    2016-08-01

    Oleic acid (OA) and oleates form self-assembled structures dispersible in aqueous media. Herein, the physicochemical properties of OA/oleate assemblies were characterized using fluorescent probes and Raman spectroscopy, under relatively high dilution (<100 mM of total amphiphile) at 25 °C. Anisotropy analysis using 1,6-diphenyl-1,3,5-hexatriene showed that the microviscosity of the OA/oleate assembly was highest at pH 7.5 (the pH range of 6.9-10.6 was investigated). The fluorescence spectra of 6-lauroyl-2-dimethylaminonaphthalene revealed the dehydrated environments on membrane surfaces at pH < 7.7. The pH-dependent Raman peak intensity ratios, chain torsion (S = I1124/I1096) and chain packing (R = I2850/I2930), showed local maxima, indicating the occurrence of metastable phases, such as dispersed cubic phase (pH = 7.5), vesicle (pH = 8.5), and dispersed cylindrical micelle (pH = 9.7). These results suggest that large-scale OA/oleate assemblies could possess particular membrane properties in a narrow pH region, e.g., at pH 7.5, and 9.7.

  13. Photoluminescence spectroscopy for the discernment of plants within animal diets

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Identification of different animal diets of free ranging herbivores is of much interest. Spectroscopic probes offer the potential for real-time analyses compared to microphitological procedures. The inherent multi-dimensionality of photoluminescence spectroscopy (i.e., fluorescence and phosphoresce...

  14. Two-photon probes for intracellular free metal ions, acidic vesicles, and lipid rafts in live tissues.

    PubMed

    Kim, Hwan Myung; Cho, Bong Rae

    2009-07-21

    Optical imaging with fluorescence microscopy is a vital tool in the study of living systems. The most common method for cell imaging, one-photon microscopy (OPM), uses a single photon of higher energy to excite the fluorophore. However, two-photon microscopy (TPM), which uses two photons of lower energy as the excitation source, is growing in popularity among biologists because of several distinct advantages. Using TPM, researchers can image intact tissue for a long period of time with minimum interference from tissue preparation artifacts, self-absorption, autofluorescence, photobleaching, and photodamage. However, to make TPM a more versatile tool in biology, researchers need a wider variety of two-photon probes for specific applications. In this Account, we describe a series of two-photon probes that we developed that can visualize the distribution of intracellular metal ions, acidic vesicles, and lipid rafts in living cells and tissues. The development of these probes requires a significant two-photon cross section for the bright image and receptors (sensing moieties) that triggers the emission of the two-photon excited fluorescence upon binding with the ions or membrane in the living system. These probes also must be sensitive to the polarity of the environment to allow selective detection of cytosolic and membrane-bound probes. In addition, they need to be cell-permeable, water-soluble for the staining of cells and tissues, and highly photostable for long-term imaging. The resulting probes-AMg1 (Mg(2+)), ACa1-ACa3 (Ca(2+)), AZn1 and AZn2 (Zn(2+)), AH1, AH2, and AL1 (acidic vesicles), and CL2 (membrane)-use 2-acetyl-6-aminonaphthalene as the fluorophore and receptors for the target ions or membrane. All of these two-photon turn-on probes can detect the intracellular free metal ions, acidic vesicles, and lipid rafts at 100-300 microm depth in live tissues. Moreover, with ACa1-AM, we could simultaneously visualize the spontaneous Ca(2+) waves in the somas of

  15. Acid-Activatable Michael-Type Fluorescent Probes for Thiols and for Labeling Lysosomes in Live Cells.

    PubMed

    Dai, Chun-Guang; Du, Xiao-Jiao; Song, Qin-Hua

    2015-12-18

    A Michael addition is usually taken as a base-catalyzed reaction. Most fluorescent probes have been designed to detect thiols in slightly alkaline solutions (pH 7-9). The sensing reactions of almost all Michael-type fluorescent probes for thiols are faster in a high pH solution than in a low pH solution. In this work, we synthesized a series of 7-substituted 2-(quinolin-2-ylmethylene)malonic acids (QMAs, substituents: NEt2, OH, H, Cl, or NO2) and their ethyl esters (QMEs) as Michael-type fluorescent probes for thiols. The sensing reactions of QMAs and QMEs occur in distinct pH ranges, pH < 7 for QMAs and pH > 7 for QMEs. On the basis of experimental and theoretic studies, we have clarified the distinct pH effects on the sensing reactivity between QMAs and QMEs and demonstrated that two QMAs (NEt2, OH) are highly sensitive and selective fluorescent probes for thiols in acidic solutions (pH < 7) and promising dyes that can label lysosomes in live cells.

  16. Intracellular surface-enhanced Raman scattering probe based on gold nanorods functionalized with mercaptohexadecanoic acid with reduced cytotoxicity.

    PubMed

    Liu, Min; Wang, Zhuyuan; Zong, Shenfei; Zhang, Ruohu; Yang, Jing; Cui, Yiping

    2012-01-01

    A surface-enhanced Raman scattering (SERS) probe for intracellular detection was demonstrated by utilizing gold nanorods (GNRs) coated with p-aminothiophenol as the Raman reporters. In this probe, to reduce the cytotoxicity of GNRs, cetyltrimethylammonium bromide (CTAB) molecules adsorbed on the surfaces of GNRs as ligands were replaced by mercaptohexadecanoic acid via a "round-trip" phase change method. Such a ligand exchange can reduce the toxicity of the probe compared to the original CTAB-stabilized GNRs, which were confirmed by both 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay and bright field view of HeLa cells. Meanwhile, the transmission electron microscopy images indicated that there is no significant morphologic change of GNRs before and after the ligand exchange. Moreover, its SERS performance was adequately retained after the incorporation of the probe into living HeLa cells. This new type of SERS probe is expected to have great potential in intracellular imaging or sensing applications.

  17. Detection and quantification of genetically modified organisms using very short, locked nucleic acid TaqMan probes.

    PubMed

    Salvi, Sergio; D'Orso, Fabio; Morelli, Giorgio

    2008-06-25

    Many countries have introduced mandatory labeling requirements on foods derived from genetically modified organisms (GMOs). Real-time quantitative polymerase chain reaction (PCR) based upon the TaqMan probe chemistry has become the method mostly used to support these regulations; moreover, event-specific PCR is the preferred method in GMO detection because of its high specificity based on the flanking sequence of the exogenous integrant. The aim of this study was to evaluate the use of very short (eight-nucleotide long), locked nucleic acid (LNA) TaqMan probes in 5'-nuclease PCR assays for the detection and quantification of GMOs. Classic TaqMan and LNA TaqMan probes were compared for the analysis of the maize MON810 transgene. The performance of the two types of probes was tested on the maize endogenous reference gene hmga, the CaMV 35S promoter, and the hsp70/cryIA(b) construct as well as for the event-specific 5'-integration junction of MON810, using plasmids as standard reference molecules. The results of our study demonstrate that the LNA 5'-nuclease PCR assays represent a valid and reliable analytical system for the detection and quantification of transgenes. Application of very short LNA TaqMan probes to GMO quantification can simplify the design of 5'-nuclease assays. PMID:18494480

  18. Detection and quantification of genetically modified organisms using very short, locked nucleic acid TaqMan probes.

    PubMed

    Salvi, Sergio; D'Orso, Fabio; Morelli, Giorgio

    2008-06-25

    Many countries have introduced mandatory labeling requirements on foods derived from genetically modified organisms (GMOs). Real-time quantitative polymerase chain reaction (PCR) based upon the TaqMan probe chemistry has become the method mostly used to support these regulations; moreover, event-specific PCR is the preferred method in GMO detection because of its high specificity based on the flanking sequence of the exogenous integrant. The aim of this study was to evaluate the use of very short (eight-nucleotide long), locked nucleic acid (LNA) TaqMan probes in 5'-nuclease PCR assays for the detection and quantification of GMOs. Classic TaqMan and LNA TaqMan probes were compared for the analysis of the maize MON810 transgene. The performance of the two types of probes was tested on the maize endogenous reference gene hmga, the CaMV 35S promoter, and the hsp70/cryIA(b) construct as well as for the event-specific 5'-integration junction of MON810, using plasmids as standard reference molecules. The results of our study demonstrate that the LNA 5'-nuclease PCR assays represent a valid and reliable analytical system for the detection and quantification of transgenes. Application of very short LNA TaqMan probes to GMO quantification can simplify the design of 5'-nuclease assays.

  19. Efficient detection of secondary structure folded nucleic acids related to Alzheimer's disease based on junction probes.

    PubMed

    Li, Juan; Qi, Xiu-Juan; Du, Yan-Yan; Fu, Hua-E; Chen, Guo-Nan; Yang, Huang-Hao

    2012-01-01

    Single stranded DNA often forms stable secondary structures under physiological conditions. These DNA secondary structures play important physiological roles. However, the analysis of such secondary structure folded DNA is often complicated because of its high thermodynamic stability and slow hybridization kinetics. In this article, we demonstrate that Y-shaped junction probes could be used for rapid and highly efficient detection of secondary structure folded DNA. Our approach contained a molecular beacon (MB) probe and an assistant probe. In the absence of target, the MB probe failed to hybridize with the assistant probe. Whereas, the MB probe and the assistant probe could cooperatively unwind the secondary structure folded DNA target to form a ternary Y-shaped junction structure. In this condition, the MB probe was also opened, resulting in separating the fluorophores from the quenching moiety and emitting the fluorescence signal. This approach allowed for the highly sensitive detection of secondary structure folded DNA target, such as a tau specific DNA fragment related to Alzheimer's disease in this case. Additionally, this approach showed strong SNPs identifying capability. Furthermore, it was noteworthy that this newly proposed approach was capable of detecting secondary structure folded DNA target in cell lysate samples.

  20. A high-resolution mitochondria-targeting ratiometric fluorescent probe for detection of the endogenous hypochlorous acid

    NASA Astrophysics Data System (ADS)

    Zhou, Liyi; Lu, Dan-Qing; Wang, Qianqian; Hu, Shunqin; Wang, Haifei; Sun, Hongyan; Zhang, Xiaobing

    2016-09-01

    Hypochlorite anion, one of the biologically important reactive oxygen species, plays an essential role in diverse normal biochemical functions and abnormal pathological processes. Herein, an efficient high-resolution mitochondria-targeting ratiometric fluorescent probe for hypochlorous acid detection has been designed, synthesized and characterized. It is easily synthesized by the condensation reaction (Cdbnd C) of a 2-(2-hydroxyphenyl) quinazolin-4(3H)-one fluorophore and a cyanine group (mitochondria-targeting), which made the whole molecular a large Stokes shift (210 nm) and the two well-resolved emission peaks separated by 140 nm. As a result, it is considered as a good candidate for high resolution hypochlorous acid imaging in live cells. The ratiometric fluorescent probe exhibited outstanding features of high sensitivity, high selectivity, rapid response time (within 50 s), and excellent mitochondria-targeting ability. Moreover, the probe can also be successfully applied to imaging endogenously hypochlorous acid in the mitochondria of living cells with low cytotoxicity, and high resolution.

  1. pH-Sensitive Polymeric Micelle-based pH Probe for Detecting and Imaging Acidic Biological Environments

    PubMed Central

    Lee, Young Ju; Kang, Han Chang; Hu, Jun; Nichols, Joseph W.; Jeon, Yong Sun; Bae, You Han

    2012-01-01

    To overcome the limitations of monomeric pH probes for acidic tumor environments, this study designed a mixed micelle pH probe composed of polyethylene glycol (PEG)-b- poly(L-histidine) (PHis) and PEG-b-poly(L-lactic acid) (PLLA), which is well-known as an effective antitumor drug carrier. Unlike monomeric histidine and PHis derivatives, the mixed micelles can be structurally destabilized by changes in pH, leading to a better pH sensing system in nuclear magnetic resonance (NMR) techniques. The acidic pH-induced transformation of the mixed micelles allowed pH detection and pH mapping of 0.2–0.3 pH unit differences by pH-induced “on/off”-like sensing of NMR and magnetic resonance spectroscopy (MRS). The micellar pH probes sensed pH differences in non-biological phosphate buffer and biological buffers such as cell culture medium and rat whole blood. In addition, the pH-sensing ability of the mixed micelles was not compromised by loaded doxorubicin. In conclusion, PHis-based micelles could have potential as a tool to simultaneously treat and map the pH of solid tumors in vivo. PMID:22861824

  2. A novel strategy for functionalizable photoluminescent magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Yan, Huan; Sung, Baeckkyoung; Kim, Min-Ho; Kim, Chanjoong

    2014-12-01

    This study presents functionalizable photoluminescent magnetic iron oxide nanoparticles (PLMNPs) produced by heating magnetic nanoparticles coated with non-photoluminescent hydrophilic poly(acrylic acid) (PAA) but without any add-on photoluminescent chemicals. The photoluminescence of PLMNPs is originated from a carbon nanodot layer that is converted from the PAA polymer coating layer during the heating process. Interestingly, PLMNPs are more photo-stable than conventional organic dyes. Further functionalization of PLMNPs is easily achieved through the coupling reaction with carboxyl groups of the coating layer on the surface. PLMNPs can be remotely heated by applying an alternating magnetic field due to the superparamagnetism, and are found to have good heating efficiency. All these advantages make these nanoparticles appealing for various biomedical applications, such as dual modality imaging and hyperthermia treatment.

  3. Detection of Sialic Acid-Utilising Bacteria in a Caecal Community Batch Culture Using RNA-Based Stable Isotope Probing

    PubMed Central

    Young, Wayne; Egert, Markus; Bassett, Shalome A.; Bibiloni, Rodrigo

    2015-01-01

    Sialic acids are monosaccharides typically found on cell surfaces and attached to soluble proteins, or as essential components of ganglioside structures that play a critical role in brain development and neural transmission. Human milk also contains sialic acid conjugated to oligosaccharides, glycolipids, and glycoproteins. These nutrients can reach the large bowel where they may be metabolised by the microbiota. However, little is known about the members of the microbiota involved in this function. To identify intestinal bacteria that utilise sialic acid within a complex intestinal community, we cultured the caecal microbiota from piglets in the presence of 13C-labelled sialic acid. Using RNA-based stable isotope probing, we identified bacteria that consumed 13C-sialic acid by fractionating total RNA in isopycnic buoyant density gradients followed by 16S rRNA gene analysis. Addition of sialic acid caused significant microbial community changes. A relative rise in Prevotella and Lactobacillus species was accompanied by a corresponding reduction in the genera Escherichia/Shigella, Ruminococcus and Eubacterium. Inspection of isotopically labelled RNA sequences suggests that the labelled sialic acid was consumed by a wide range of bacteria. However, species affiliated with the genus Prevotella were clearly identified as the most prolific users, as solely their RNA showed significantly higher relative shares among the most labelled RNA species. Given the relevance of sialic acid in nutrition, this study contributes to a better understanding of their microbial transformation in the intestinal tract with potential implications for human health. PMID:25816158

  4. Detection of sialic acid-utilising bacteria in a caecal community batch culture using RNA-based stable isotope probing.

    PubMed

    Young, Wayne; Egert, Markus; Bassett, Shalome A; Bibiloni, Rodrigo

    2015-03-25

    Sialic acids are monosaccharides typically found on cell surfaces and attached to soluble proteins, or as essential components of ganglioside structures that play a critical role in brain development and neural transmission. Human milk also contains sialic acid conjugated to oligosaccharides, glycolipids, and glycoproteins. These nutrients can reach the large bowel where they may be metabolised by the microbiota. However, little is known about the members of the microbiota involved in this function. To identify intestinal bacteria that utilise sialic acid within a complex intestinal community, we cultured the caecal microbiota from piglets in the presence of 13C-labelled sialic acid. Using RNA-based stable isotope probing, we identified bacteria that consumed 13C-sialic acid by fractionating total RNA in isopycnic buoyant density gradients followed by 16S rRNA gene analysis. Addition of sialic acid caused significant microbial community changes. A relative rise in Prevotella and Lactobacillus species was accompanied by a corresponding reduction in the genera Escherichia/Shigella, Ruminococcus and Eubacterium. Inspection of isotopically labelled RNA sequences suggests that the labelled sialic acid was consumed by a wide range of bacteria. However, species affiliated with the genus Prevotella were clearly identified as the most prolific users, as solely their RNA showed significantly higher relative shares among the most labelled RNA species. Given the relevance of sialic acid in nutrition, this study contributes to a better understanding of their microbial transformation in the intestinal tract with potential implications for human health.

  5. Detection of Chromosomal Inversions Using Non-Repetitive Nucleic Acid Probes

    NASA Technical Reports Server (NTRS)

    Bailey, Susan M. (Inventor); Ray, F. Andrew (Inventor); Goodwin, Edwin H. (Inventor); Bedford, Joel S. (Inventor); Cornforth, Michael N. (Inventor)

    2014-01-01

    A method and a kit for the identification of chromosomal inversions are described. Single-stranded sister chromatids are generated, for example by CO-FISH. A plurality of non-repetitive, labeled probes of relatively small size are hybridized to portions of only one of a pair of single-stranded sister chromatids. If no inversion exists, all of the probes will hybridize to a first chromatid. If an inversion has occurred, these marker probes will be detected on the sister chromatid at the same location as the inversion on the first chromatid.

  6. Detection of chromosomal inversions using non-repetitive nucleic acid probes

    NASA Technical Reports Server (NTRS)

    Bailey, Susan M. (Inventor); Ray, F. Andrew (Inventor); Goodwin, Edwin H. (Inventor); Bedford, Joel S. (Inventor); Cornforth, Michael N. (Inventor)

    2012-01-01

    A method for the identification of chromosomal inversions is described. Single-stranded sister chromatids are generated, for example by CO-FISH. A plurality of non-repetitive, labeled probes of relatively small size are hybridized to portions of only one of a pair of single-stranded sister chromatids. If no inversion exists, all of the probes will hybridize to a first chromatid. If an inversion has occurred, these marker probes will be detected on the sister chromatid at the same location as the inversion on the first chromatid.

  7. Colorimetric and fluorescence detection of G-quadruplex nucleic acids with a coumarin-benzothiazole probe.

    PubMed

    Yan, Jin-wu; Tian, Yi-guang; Tan, Jia-heng; Huang, Zhi-shu

    2015-11-01

    A colorimetric and red-emitting fluorescent dual probe for G-quadruplexes was devised with a conjugated coumarin-benzothiazole scaffold. Its significant and distinct changes in both color and fluorescence enable the label-free and visual detection of G-quadruplex structures. In addition, this probe gives a distinct strong emission response to the nucleoli in fixed cells imaging, which might be attributed to the interaction between the probe and rDNA G-quadruplex based on the chromatin immunoprecipitation assay. All these results suggest its promising application prospects in the G-quadruplex research field.

  8. Human papillomavirus 35 nucleic acid hybridization probes and methods for employing the same

    SciTech Connect

    Lorincz, A.T.

    1989-07-18

    This patent describes an HPV 35 hybridization probe comprising a member selected from the group consisting of (i) HPV 35 DNA or fragments thereof labelled with a marker and (ii) HPV 35 RNA or fragments thereof labelled with a marker.

  9. Human papillomavirus 43 nucleic acid hybridization probes and methods for employing the same

    SciTech Connect

    Lorincz, A.T.

    1989-07-18

    This patent describes an HPV 43 hybridization probe comprising a member selected from the group consisting of (i) HPV 43 DNA or fragments thereof labelled with a marker and (ii) HPV 43 RNA or fragments thereof labelled with a marker.

  10. Human papillomavirus 44 nucleic acid hybridization probes and methods for employing the same

    SciTech Connect

    Lorincz, A.T.

    1989-07-18

    This patent describes an HPV 44 hybridization probe comprising a member selected from the group consisting of (1) HPV 44 DNA or fragments thereof labelled with a marker and (ii) HPV 44 RNA or fragments thereof labelled with a marker.

  11. Human papillomavirus 56 nucleic acid hybridization probes and methods for employing the same

    SciTech Connect

    Lorinez, A.T.

    1990-03-13

    This patent describes an HPV 56 hybridization probe. It comprises: a member selected from the group consisting of HPV 56 DNA or fragments thereof labelled with a marker and HPV 56 RNA or fragments thereof labelled with a marker.

  12. Y chromosome specific nucleic acid probe and method for determining the Y chromosome in situ

    DOEpatents

    Gray, J.W.; Weier, H.U.

    1998-11-24

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences. 9 figs.

  13. Y chromosome specific nucleic acid probe and method for identifying the Y chromosome in SITU

    DOEpatents

    Gray, Joe W.; Weier, Heinz-Ulrich

    1999-01-01

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences.

  14. Y chromosome specific nucleic acid probe and method for determining the Y chromosome in situ

    DOEpatents

    Gray, Joe W.; Weier, Heinz-Ulrich

    1998-01-01

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences.

  15. Y chromosome specific nucleic acid probe and method for identifying the Y chromosome in SITU

    DOEpatents

    Gray, J.W.; Weier, H.U.

    1999-03-30

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences. 9 figs.

  16. Y chromosome specific nucleic acid probe and method for determining the Y chromosome in situ

    DOEpatents

    Gray, Joe W.; Weier, Heinz-Ulrich

    2001-01-01

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences.

  17. Sensitivity and specificity of nucleic acid probes for potato leafroll luteovirus detection.

    PubMed

    Robinson, D J; Romero, J

    1991-01-01

    Complementary DNA (cDNA) probes, prepared by nick-translation or by oligolabelling of a 520 bp fragment representing residues 4741 to 5261 in the potato leafroll luteovirus (PLRV) sequence, were equally sensitive, with a detection limit equivalent to sap from about 600 micrograms of infected potato or Nicotiana clevelandii leaf tissue and to RNA from about 120 micrograms tissue. Increasing the concentration of oligolabelled probe gave similar results with shorter autoradiographic exposures, but also resulted in positive signals with sap extracts from healthy plants. In contrast, a complementary RNA (cRNA) probe made by in vitro transcription of the cDNA insert could be used at higher concentration without giving rise to reactions with healthy plant extracts, and had a detection limit equivalent to 5 micrograms tissue/spot. Five oligolabelled probes representing different regions of the PLRV genome detected PLRV equally well. A probe that represented a portion of the particle protein gene also detected beet western yellows luteovirus (BWYV), with which it has 69% nucleotide sequence homology, and an English strain of the RPV form of barley yellow dwarf luteovirus, and reacted weakly with extracts from plants infected with groundnut rosette assistor luteovirus or carrot red leaf luteovirus. Probes for regions on either side of the particle protein gene also detected RPV, but not any of the other luteoviruses tested, in agreement with earlier suggestions that RPV is more closely related to PLRV than are BWYV or the other luteoviruses tested. An attempt to improve the detection of weak heterologous reactions by using a cRNA probe was unsuccessful, perhaps because tests using cRNA are more affected by mismatching than tests using cDNA probes. PMID:1804851

  18. Photoluminescence of a Plasmonic Molecule.

    PubMed

    Huang, Da; Byers, Chad P; Wang, Lin-Yung; Hoggard, Anneli; Hoener, Ben; Dominguez-Medina, Sergio; Chen, Sishan; Chang, Wei-Shun; Landes, Christy F; Link, Stephan

    2015-07-28

    Photoluminescent Au nanoparticles are appealing for biosensing and bioimaging applications because of their non-photobleaching and non-photoblinking emission. The mechanism of one-photon photoluminescence from plasmonic nanostructures is still heavily debated though. Here, we report on the one-photon photoluminescence of strongly coupled 50 nm Au nanosphere dimers, the simplest plasmonic molecule. We observe emission from coupled plasmonic modes as revealed by single-particle photoluminescence spectra in comparison to correlated dark-field scattering spectroscopy. The photoluminescence quantum yield of the dimers is found to be surprisingly similar to the constituent monomers, suggesting that the increased local electric field of the dimer plays a minor role, in contradiction to several proposed mechanisms. Aided by electromagnetic simulations of scattering and absorption spectra, we conclude that our data are instead consistent with a multistep mechanism that involves the emission due to radiative decay of surface plasmons generated from excited electron-hole pairs following interband absorption. PMID:26165983

  19. A Far-Red Emitting Probe for Unambiguous Detection of Mobile Zinc in Acidic Vesicles and Deep Tissue†

    PubMed Central

    Rivera-Fuentes, Pablo; Wrobel, Alexandra T.; Zastrow, Melissa L.; Khan, Mustafa; Georgiou, John; Luyben, Thomas T.; Roder, John C.; Okamoto, Kenichi

    2015-01-01

    Imaging mobile zinc in acidic environments remains challenging because most small-molecule optical probes display pH-dependent fluorescence. Here we report a reaction-based sensor that detects mobile zinc unambiguously at low pH. The sensor responds reversibly and with a large dynamic range to exogenously applied Zn2+ in lysosomes of HeLa cells, endogenous Zn2+ in insulin granules of MIN6 cells, and zinc-rich mossy fiber boutons in hippocampal tissue from mice. This long-wavelength probe is compatible with the green-fluorescent protein, enabling multicolor imaging, and facilitates visualization of mossy fiber boutons at depths of >100 µm, as demonstrated by studies in live tissue employing two-photon microscopy. PMID:25815162

  20. Photoluminescence properties of porous silicon

    NASA Astrophysics Data System (ADS)

    Heben, M. J.; Xiao, Y.; McCullough, J. M.; Tsuo, Y. S.; Pankove, J. I.; Deb, S. K.

    1992-12-01

    A porous silicon (PS) layer can be produced on a crystalline silicon substrate by electrochemical or chemical etching in hydrofluoric acid (HF) solutions. There are many properties that make PS thin films interesting for photovoltaic applications, such as a possible direct band gap that can be adjusted between 1.5 and 1.9 eV, textured surfaces for light trapping, the potential for low cost and large-area fabrication, and the possibility of tandem cell structures with Si. We report the fabrication of large area PS (up to 3` diameter) with quite uniform photoluminescence (PL) properties, and studies of the effects of post-hydrogenation treatments on the intensity and stability of the PL from PS. We have observed that a remote-plasma processing treatment can increase the PL emission intensity from PS prepared under certain conditions by 100 times or more. The emission band is narrower and centered more toward the blue for the remote-plasma processed sample, and the PL emission intensity does not degrade in an air ambient over a period of at least several weeks. This result indicates that PS has the potential to become a stable and useful optoelectronic material.

  1. Enhanced photoluminescence by tyrosine-containing bolaamphiphile self-assembly.

    PubMed

    Kwak, Jinyoung; Lee, Sang-Yup

    2013-04-01

    Photoluminescent spherical nanostructures were prepared through the self-assembly of a tyrosine-containing bolaamphiphilic molecule, and their antenna effect was examined. The photoluminescent spherical nanostructures were simply prepared by self-assembly of bolaamphiphile molecules in an aqueous solution in which water-soluble photosensitizers and lanthanide ions were dissolved. The photosensitizers and lanthanide cations were incorporated with the phenol group and the carboxyl end of the tyrosine moiety, respectively. Through fluorescence microscopy and photoluminescence spectroscopy analyses, the various combinations of two lanthanide ions (Eu and Tb) and four photosensitizers were screened for synergetic photoluminescence with bolaamphiphile self-assembly. The bolaamphiphile assembly enhanced the photoluminescence intensity by a factor of around 2 when it was associated with Tb and salicylic acid. This enhancement is driven by the phosphorescence enhancement of the photosensitizer induced by the π-π interactions with the phenol group in tyrosine. These results indicate that the tyrosine-containing bolaamphiphile is a promising molecule that can easily produce a soft nanoscaled host matrix with an antenna effect for photoluminescence.

  2. The influence of capping thioalkyl acid on the growth and photoluminescence efficiency of CdTe and CdSe quantum dots.

    PubMed

    Aldeek, Fadi; Balan, Lavinia; Lambert, Jacques; Schneider, Raphaël

    2008-11-26

    The influence of thioalkyl acid ligand was evaluated during aqueous synthesis at 100 °C and under hydrothermal conditions (150 °C) of CdTe and CdSe quantum dots (QDs). Experiments performed with 3-mercaptopropionic acid (MPA), 6-mercaptohexanoic acid (MHA) and 11-mercaptoundecanoic acid (MUA) demonstrated that the use of MHA and MUA allowed for the preparation of very small nanoparticles (0.6-2.5 nm) in carrying out the reaction under atmospheric pressure or in an autoclave and that the photophysical properties of QDs were dependent on the ligand and on the synthesis conditions. The influence of various experimental conditions, including the Te-to-Cd ratio, temperature, and precursor concentration, on the growth rate of CdTe or CdSe QDs has been systematically investigated. The fluorescence intensities of CdTe QDs capped with MPA, MHA, or MUA versus pH were also found to be related to the surface coverage of the nanoparticles. PMID:21836270

  3. Photoluminescence by Interstellar Dust

    NASA Astrophysics Data System (ADS)

    Vijh, U. P.

    2005-08-01

    In this dissertation, we report on our study of interstellar dust through the process of photoluminescence (PL). We present the discovery of a new band of dust PL, blue luminescence (BL) with λpeak˜370 nm in the proto-planetary nebula known as the Red Rectangle (RR). We attribute this to fluorescence by small, 3-4-ringed polycyclic aromatic hydrocarbon (PAH) molecules. Further analysis reveals additional independent evidence for the presence of small PAHs in this nebula. Detection of BL using long-slit spectroscopic observations in other ordinary reflection nebulae suggests that the BL carrier is an ubiquitous component of the ISM and is not restricted to the particular environment of the RR. We present the spatial distribution of the BL in these nebulae and find that the BL is spatially correlated with IR emission structures attributed to aromatic emission features (AEFs), attributed to PAHs. The carrier of the dust-associated photoluminescence process causing the extended red emission (ERE), known now for over twenty five years, remains unidentified. We constrain the character of the ERE carrier by determining the wavelengths of the radiation that initiates the ERE -- λ < 118 nm. We note that under interstellar conditions most PAH molecules are ionized to the di-cation stage by photons with E > 10.5 eV and that the electronic energy level structure of PAH di-cations is consistent with fluorescence in the wavelength band of the ERE. In the last few chapters of the dissertation we present first results from ongoing work: i) Using narrow-band imaging, we present the optical detection of the circum-binary disk of the RR in the light of the BL, and show that the morphology of the BL and ERE emissions in the RR nebula are almost mutually exclusive. It is very suggestive to attribute them to different ionization stages of the same family of carriers such as PAH molecules. ii) We also present a pure spectrum of the BL free of scattered light, resolved into seven

  4. Probing the Active Center of Benzaldehyde Lyase with Substitutions and the Pseudosubstrate Analogue Benzoylphosphonic Acid Methyl Ester

    SciTech Connect

    Brandt, Gabriel S.; Nemeria, Natalia; Chakraborty, Sumit; McLeish, Michael J.; Yep, Alejandra; Kenyon, George L.; Petsko, Gregory A.; Jordan, Frank; Ringe, Dagmar

    2008-07-28

    Benzaldehyde lyase (BAL) catalyzes the reversible cleavage of (R)-benzoin to benzaldehyde utilizing thiamin diphosphate and Mg{sup 2+} as cofactors. The enzyme is important for the chemoenzymatic synthesis of a wide range of compounds via its carboligation reaction mechanism. In addition to its principal functions, BAL can slowly decarboxylate aromatic amino acids such as benzoylformic acid. It is also intriguing mechanistically due to the paucity of acid-base residues at the active center that can participate in proton transfer steps thought to be necessary for these types of reactions. Here methyl benzoylphosphonate, an excellent electrostatic analogue of benzoylformic acid, is used to probe the mechanism of benzaldehyde lyase. The structure of benzaldehyde lyase in its covalent complex with methyl benzoylphosphonate was determined to 2.49 {angstrom} (Protein Data Bank entry 3D7K) and represents the first structure of this enzyme with a compound bound in the active site. No large structural reorganization was detected compared to the complex of the enzyme with thiamin diphosphate. The configuration of the predecarboxylation thiamin-bound intermediate was clarified by the structure. Both spectroscopic and X-ray structural studies are consistent with inhibition resulting from the binding of MBP to the thiamin diphosphate in the active centers. We also delineated the role of His29 (the sole potential acid-base catalyst in the active site other than the highly conserved Glu50) and Trp163 in cofactor activation and catalysis by benzaldehyde lyase.

  5. Proteomic-based stable isotope probing reveals taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton

    DOE PAGES

    Bryson, Samuel; Li, Zhou; Pett-Ridge, Jennifer; Robert L. Hettich; Mayali, Xavier; Pan, Chongle; Mueller, Ryan S.

    2016-04-26

    Heterotrophic marine bacterioplankton are a critical component of the carbon cycle, processing nearly a quarter of annual global primary production, yet defining how substrate utilization preferences and resource partitioning structure these microbial communities remains a challenge. In this study, we utilized proteomics-based stable isotope probing (proteomic SIP) to characterize the assimilation of amino acids by coastal marine bacterioplankton populations. We incubated microcosms of seawater collected from Newport, OR and Monterey Bay, CA with 1 M 13C-amino acids for 15 and 32 hours. Subsequent analysis of 13C incorporation into protein biomass quantified the frequency and extent of isotope enrichment for identifiedmore » proteins. Using these metrics we tested whether amino acid assimilation patterns were different for specific bacterioplankton populations. Proteins associated with Rhodobacterales and Alteromonadales tended to have a significantly high number of tandem mass spectra from 13C-enriched peptides, while Flavobacteriales and SAR11 proteins generally had significantly low numbers of 13C-enriched spectra. Rhodobacterales proteins associated with amino acid transport and metabolism had an increased frequency of 13C-enriched spectra at time-point 2, while Alteromonadales ribosomal proteins were 13C- enriched across time-points. Overall, proteomic SIP facilitated quantitative comparisons of dissolved free amino acids assimilation by specific taxa, both between sympatric populations and between protein functional groups within discrete populations, allowing an unprecedented examination of population-level metabolic responses to resource acquisition in complex microbial communities.« less

  6. Probing the active center of benzaldehyde lyase with substitutions and the pseudosubstrate analogue benzoylphosphonic acid methyl ester.

    PubMed

    Brandt, Gabriel S; Nemeria, Natalia; Chakraborty, Sumit; McLeish, Michael J; Yep, Alejandra; Kenyon, George L; Petsko, Gregory A; Jordan, Frank; Ringe, Dagmar

    2008-07-22

    Benzaldehyde lyase (BAL) catalyzes the reversible cleavage of ( R)-benzoin to benzaldehyde utilizing thiamin diphosphate and Mg (2+) as cofactors. The enzyme is important for the chemoenzymatic synthesis of a wide range of compounds via its carboligation reaction mechanism. In addition to its principal functions, BAL can slowly decarboxylate aromatic amino acids such as benzoylformic acid. It is also intriguing mechanistically due to the paucity of acid-base residues at the active center that can participate in proton transfer steps thought to be necessary for these types of reactions. Here methyl benzoylphosphonate, an excellent electrostatic analogue of benzoylformic acid, is used to probe the mechanism of benzaldehyde lyase. The structure of benzaldehyde lyase in its covalent complex with methyl benzoylphosphonate was determined to 2.49 A (Protein Data Bank entry 3D7K ) and represents the first structure of this enzyme with a compound bound in the active site. No large structural reorganization was detected compared to the complex of the enzyme with thiamin diphosphate. The configuration of the predecarboxylation thiamin-bound intermediate was clarified by the structure. Both spectroscopic and X-ray structural studies are consistent with inhibition resulting from the binding of MBP to the thiamin diphosphate in the active centers. We also delineated the role of His29 (the sole potential acid-base catalyst in the active site other than the highly conserved Glu50) and Trp163 in cofactor activation and catalysis by benzaldehyde lyase.

  7. Detection of glyceraldehyde 3-phosphate dehydrogenase messenger RNA using a peptide nucleic acid probe in paraffin-embedded archival specimens.

    PubMed

    Hiroyasu, Makoto; Akatsuka, Shinya; Shirase, Tomoyuki; Toda, Yoshinobu; Hiai, Hiroshi; Toyokuni, Shinya

    2004-04-01

    Although the human genome project has been completed, the functions of many genes remain undetermined. In situ hybridization (ISH) is a key method for identifying cells in which a given messenger RNA is transcribed. Paraffin-embedded specimens remain precious materials for research, but preservation of high-quality RNA in these specimens is not expected unless ample caution was taken during fixation. Peptide nucleic acid (PNA) is a recently developed hybrid molecule with genetic information that has high stability and high affinity to the complementary DNA or RNA. We applied a PNA probe to mRNA ISH of liver specimens obtained by autopsy and embedded in paraffin 28-48 years ago. An 18-mer PNA probe for glyceraldehyde 3-phosphate dehydrogenase was used. Staining was then analyzed in association with morphology by hematoxylin and eosin staining, and with the time between death of the patient and tissue fixation. Notably, specimens fixed with formalin and embedded in paraffin 48 years ago yielded excellent results if the time before fixation was short enough (<8 h). There was a significant inverse correlation between the intensity of ISH staining and the time before fixation. Oligonucleotide PNA probe, albeit at high cost, would increase the value of paraffin-embedded specimens in storage for use in human medical research.

  8. Mercaptopropionic acid-capped CdTe quantum dots as fluorescence probe for the determination of salicylic acid in pharmaceutical products.

    PubMed

    Bunkoed, Opas; Kanatharana, Proespichaya

    2015-11-01

    Mercaptopropionic acid (MPA)-capped cadmium telluride (CdTe) quantum dot (QDs) fluorescent probes were synthesized in aqueous solution and used for the determination of salicylic acid. The interaction between the MPA-capped CdTe QDs and salicylic acid was studied using fluorescence spectroscopy and some parameters that could modify the fluorescence were investigated to optimize the measurements. Under optimum conditions, the quenched fluorescence intensity of MPA-capped CdTe QDs was linearly proportional to the concentration of salicylic acid in the range of 0.5-40 µg mL(-1) with a coefficient of determination of 0.998, and the limit of detection was 0.15 µg mL(-1). The method was successfully applied to the determination of salicylic acid in pharmaceutical products, and satisfactory results were obtained that were in agreement with both the high pressure liquid chromatography (HPLC) method and the claimed values. The recovery of the method was in the range 99 ± 3% to 105 ± 9%. The proposed method is simple, rapid, cost effective, highly sensitivity and eminently suitable for the quality control of pharmaceutical preparation. The possible mechanisms for the observed quenching reaction was also discussed.

  9. Fluorescence in situ Hybridization method using Peptide Nucleic Acid probes for rapid detection of Lactobacillus and Gardnerella spp.

    PubMed Central

    2013-01-01

    Background Bacterial vaginosis (BV) is a common vaginal infection occurring in women of reproductive age. It is widely accepted that the microbial switch from normal microflora to BV is characterized by a decrease in vaginal colonization by Lactobacillus species together with an increase of Gardnerella vaginalis and other anaerobes. Our goal was to develop and optimize a novel Peptide Nucleic Acid (PNA) Fluorescence in situ Hybridization assay (PNA FISH) for the detection of Lactobacillus spp. and G. vaginalis in mixed samples. Results Therefore, we evaluated and validated two specific PNA probes by using 36 representative Lactobacillus strains, 22 representative G. vaginalis strains and 27 other taxonomically related or pathogenic bacterial strains commonly found in vaginal samples. The probes were also tested at different concentrations of G. vaginalis and Lactobacillus species in vitro, in the presence of a HeLa cell line. Specificity and sensitivity of the PNA probes were found to be 98.0% (95% confidence interval (CI), from 87.8 to 99.9%) and 100% (95% CI, from 88.0 to 100.0%), for Lactobacillus spp.; and 100% (95% CI, from 92.8 to 100%) and 100% (95% CI, from 81.5 to 100.0%) for G. vaginalis. Moreover, the probes were evaluated in mixed samples mimicking women with BV or normal vaginal microflora, demonstrating efficiency and applicability of our PNA FISH. Conclusions This quick method accurately detects Lactobacillus spp. and G. vaginalis species in mixed samples, thus enabling efficient evaluation of the two bacterial groups, most frequently encountered in the vagina. PMID:23586331

  10. Double-stem Hairpin Probe and Ultrasensitive Colorimetric Detection of Cancer-related Nucleic Acids.

    PubMed

    Xu, Jianguo; Li, Hongling; Wu, Zai-Sheng; Qian, Jun; Xue, Chang; Jia, Lee

    2016-01-01

    The development of a versatile biosensing platform to screen specific DNA sequences is still an essential issue of molecular biology research and clinic diagnosis of genetic disease. In this work, we for the first time reported a double-stem hairpin probe (DHP) that was simultaneously engineered to incorporate a DNAzyme, DNAzyme's complementary fragment and nicking enzyme recognition site. The important aspect of this hairpin probe is that, although it is designed to have a long ds DNA fragment, no intermolecular interaction occurs, circumventing the sticky-end pairing-determined disadvantages encountered by classic molecular beacon. For the DHP-based colorimetric sensing system, as a model analyte, cancer-related DNA sequence can trigger a cascade polymerization/nicking cycle on only one oligonucleotide probe. This led to the dramatic accumulation of G-quadruplexes directly responsible for colorimetric signal conversion without any loss. As a result, the target DNA is capable of being detected to 1 fM (six to eight orders of magnitude lower than that of catalytic molecular beacons) and point mutations are distinguished by the naked eye. The described DHP as a-proof-of-concept would not only promote the design of colorimetric biosensors but also open a good way to promote the diagnosis and treatment of genetic diseases. PMID:26909108

  11. Double-stem Hairpin Probe and Ultrasensitive Colorimetric Detection of Cancer-related Nucleic Acids

    PubMed Central

    Xu, Jianguo; Li, Hongling; Wu, Zai-Sheng; Qian, Jun; Xue, Chang; Jia, Lee

    2016-01-01

    The development of a versatile biosensing platform to screen specific DNA sequences is still an essential issue of molecular biology research and clinic diagnosis of genetic disease. In this work, we for the first time reported a double-stem hairpin probe (DHP) that was simultaneously engineered to incorporate a DNAzyme, DNAzyme's complementary fragment and nicking enzyme recognition site. The important aspect of this hairpin probe is that, although it is designed to have a long ds DNA fragment, no intermolecular interaction occurs, circumventing the sticky-end pairing-determined disadvantages encountered by classic molecular beacon. For the DHP-based colorimetric sensing system, as a model analyte, cancer-related DNA sequence can trigger a cascade polymerization/nicking cycle on only one oligonucleotide probe. This led to the dramatic accumulation of G-quadruplexes directly responsible for colorimetric signal conversion without any loss. As a result, the target DNA is capable of being detected to 1 fM (six to eight orders of magnitude lower than that of catalytic molecular beacons) and point mutations are distinguished by the naked eye. The described DHP as a-proof-of-concept would not only promote the design of colorimetric biosensors but also open a good way to promote the diagnosis and treatment of genetic diseases. PMID:26909108

  12. Double-stem Hairpin Probe and Ultrasensitive Colorimetric Detection of Cancer-related Nucleic Acids.

    PubMed

    Xu, Jianguo; Li, Hongling; Wu, Zai-Sheng; Qian, Jun; Xue, Chang; Jia, Lee

    2016-01-01

    The development of a versatile biosensing platform to screen specific DNA sequences is still an essential issue of molecular biology research and clinic diagnosis of genetic disease. In this work, we for the first time reported a double-stem hairpin probe (DHP) that was simultaneously engineered to incorporate a DNAzyme, DNAzyme's complementary fragment and nicking enzyme recognition site. The important aspect of this hairpin probe is that, although it is designed to have a long ds DNA fragment, no intermolecular interaction occurs, circumventing the sticky-end pairing-determined disadvantages encountered by classic molecular beacon. For the DHP-based colorimetric sensing system, as a model analyte, cancer-related DNA sequence can trigger a cascade polymerization/nicking cycle on only one oligonucleotide probe. This led to the dramatic accumulation of G-quadruplexes directly responsible for colorimetric signal conversion without any loss. As a result, the target DNA is capable of being detected to 1 fM (six to eight orders of magnitude lower than that of catalytic molecular beacons) and point mutations are distinguished by the naked eye. The described DHP as a-proof-of-concept would not only promote the design of colorimetric biosensors but also open a good way to promote the diagnosis and treatment of genetic diseases.

  13. Hybrid materials of MCM-41 functionalized by lanthanide (Tb{sup 3+}, Eu{sup 3+}) complexes of modified meta-methylbenzoic acid: Covalently bonded assembly and photoluminescence

    SciTech Connect

    Li Ying; Yan Bing

    2008-05-15

    Novel organic-inorganic mesoporous hybrid materials were synthesized by linking lanthanide (Tb{sup 3+}, Eu{sup 3+}) complexes to the mesoporous MCM-41 through the modified meta-methylbenzoic acid (MMBA-Si) using co-condensation method in the presence of the cetyltrimethylammonium bromide (CTAB) surfactant as template. The luminescence properties of these resulting materials (denoted as Ln-MMBA-MCM-41, Ln=Tb, Eu) were characterized in detail, and the results reveal that luminescent mesoporous materials have high surface area, uniformity in the ordered mesoporous structure. Moreover, the mesoporous material covalently bonded Tb{sup 3+} complex (Tb-MMBA-MCM-41) exhibits the stronger characteristic emission of Tb{sup 3+} and longer lifetime than Eu-MMBA-MCM-41 due to the triplet state energy of organic legend MMBA-Si matches with the emissive energy level of Tb{sup 3+} very well. - Graphical abstract: Novel organic-inorganic mesoporous luminescent materials were synthesized by linking lanthanide (Tb{sup 3+}, Eu{sup 3+}) complexes to covalently bond the functionalized ordered mesoporous MCM-41 with modified meta-methylbenzoic acid (MMBA)-Si by co-condensation of tetraethoxysilane (TEOS) in the presence of the cetyltrimethylammonium bromide (CTAB) surfactant as template.

  14. Carboxylic Acid Ionophores as Probes of the Role of Calcium in Biological Systems

    NASA Technical Reports Server (NTRS)

    Reed, P. W.

    1983-01-01

    The biological effects of calcium ionophores are described, focusing on arachidonic acid oxygenation, and the formation of a number of oxygenated metabolites of arachidonic acid. These metabolites are involved in a number of bodily functions, and their production may be regulated by calcium.

  15. Probing acid-amide intermolecular hydrogen bonding by NMR spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Chaudhari, Sachin Rama; Suryaprakash, N.

    2012-05-01

    Benzene carboxylic acids and benzamide act as their self-complement in molecular recognition to form inter-molecular hydrogen bonded dimers between amide and carboxylic acid groups, which have been investigated by 1H, 13C and 15N NMR spectroscopy. Extensive NMR studies using diffusion ordered spectroscopy (DOSY), variable temperature 1D, 2D NMR, established the formation of heterodimers of benzamide with benzoic acid, salicylic acid and phenyl acetic acid in deuterated chloroform solution. Association constants for the complex formation in the solution state have been determined. The results are ascertained by X-ray diffraction in the solid state. Intermolecular interactions in solution and in solid state were found to be similar. The structural parameters obtained by X-ray diffraction studies are compared with those obtained by DFT calculations.

  16. Probing the Sophisticated Synergistic Allosteric Regulation of Aromatic Amino Acid Biosynthesis in Mycobacterium tuberculosis Using ᴅ-Amino Acids

    PubMed Central

    Reichau, Sebastian; Blackmore, Nicola J.; Jiao, Wanting; Parker, Emily J.

    2016-01-01

    Chirality plays a major role in recognition and interaction of biologically important molecules. The enzyme 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS) is the first enzyme of the shikimate pathway, which is responsible for the synthesis of aromatic amino acids in bacteria and plants, and a potential target for the development of antibiotics and herbicides. DAH7PS from Mycobacterium tuberculosis (MtuDAH7PS) displays an unprecedented complexity of allosteric regulation, with three interdependent allosteric binding sites and a ternary allosteric response to combinations of the aromatic amino acids l-Trp, l-Phe and l-Tyr. In order to further investigate the intricacies of this system and identify key residues in the allosteric network of MtuDAH7PS, we studied the interaction of MtuDAH7PS with aromatic amino acids that bear the non-natural d-configuration, and showed that the d-amino acids do not elicit an allosteric response. We investigated the binding mode of d-amino acids using X-ray crystallography, site directed mutagenesis and isothermal titration calorimetry. Key differences in the binding mode were identified: in the Phe site, a hydrogen bond between the amino group of the allosteric ligands to the side chain of Asn175 is not established due to the inverted configuration of the ligands. In the Trp site, d-Trp forms no interaction with the main chain carbonyl group of Thr240 and less favourable interactions with Asn237 when compared to the l-Trp binding mode. Investigation of the MtuDAH7PSN175A variant further supports the hypothesis that the lack of key interactions in the binding mode of the aromatic d-amino acids are responsible for the absence of an allosteric response, which gives further insight into which residues of MtuDAH7PS play a key role in the transduction of the allosteric signal. PMID:27128682

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

    NASA Astrophysics Data System (ADS)

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

    2005-03-01

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

  18. ω-Azido fatty acids as probes to detect fatty acid biosynthesis, degradation, and modification[S

    PubMed Central

    Pérez, Alexander J.; Bode, Helge B.

    2014-01-01

    FAs play a central role in the metabolism of almost all known cellular life forms. Although GC-MS is regarded as a standard method for FA analysis, other methods, such as HPLC/MS, are nowadays widespread but are rarely applied to FA analysis. Here we present azido-FAs as probes that can be used to study FA biosynthesis (elongation, desaturation) or degradation (β-oxidation) upon their uptake, activation, and metabolic conversion. These azido-FAs are readily accessible by chemical synthesis and their metabolic products can be easily detected after click-chemistry based derivatization with high sensitivity by HPLC/MS, contributing a powerful tool to FA analysis, and hence, lipid analysis in general. PMID:25013232

  19. Probing the interaction of individual amino acids with inorganic surfaces using atomic force spectroscopy.

    PubMed

    Razvag, Yair; Gutkin, Vitaly; Reches, Meital

    2013-08-13

    This article describes single-molecule force spectroscopy measurements of the interaction between individual amino acid residues and inorganic surfaces in an aqueous solution. In each measurement, there is an amino acid residue, lysine, glutamate, phenylalanine, leucine, or glutamine, and each represents a class of amino acids (positively or negatively charged, aromatic, nonpolar, and polar). Force-distance curves measured the interaction of the individual amino acid bound to a silicon atomic force microscope (AFM) tip with a silcon substrate, cut from a single-crystal wafer, or mica. Using this method, we were able to measure low adhesion forces (below 300 pN) and could clearly determine the strength of interactions between the individual amino acid residues and the inorganic substrate. In addition, we observed how changes in the pH and ionic strength of the solution affected the adsorption of the residues to the substrates. Our results pinpoint the important role of hydrophobic interactions among the amino acids and the substrate, where hydrophobic phenylalanine exhibited the strongest adhesion to a silicon substrate. Additionally, electrostatic interactions also contributed to the adsorption of amino acid residues to inorganic substrates. A change in the pH or ionic strength values of the buffer altered the strength of interactions among the amino acids and the substrate. We concluded that the interplay between the hydrophobic forces and electrostatic interactions will determine the strength of adsorption among the amino acids and the surface. Overall, these results contribute to our understanding of the interaction at the organic-inorganic interface. These results may have implications for our perception of the specificity of peptide binding to inorganic surfaces. Consequently, it would possibly lead to a better design of composite materials and devices.

  20. Probing Protein Structure by Amino Acid-Specific Covalent Labeling and Mass Spectrometry

    PubMed Central

    Mendoza, Vanessa Leah; Vachet, Richard W.

    2009-01-01

    For many years, amino acid-specific covalent labeling has been a valuable tool to study protein structure and protein interactions, especially for systems that are difficult to study by other means. These covalent labeling methods typically map protein structure and interactions by measuring the differential reactivity of amino acid side chains. The reactivity of amino acids in proteins generally depends on the accessibility of the side chain to the reagent, the inherent reactivity of the label and the reactivity of the amino acid side chain. Peptide mass mapping with ESI- or MALDI-MS and peptide sequencing with tandem MS are typically employed to identify modification sites to provide site-specific structural information. In this review, we describe the reagents that are most commonly used in these residue-specific modification reactions, details about the proper use of these covalent labeling reagents, and information about the specific biochemical problems that have been addressed with covalent labeling strategies. PMID:19016300

  1. Probing Phosphorus Efficient Low Phytic Acid Content Soybean Genotypes with Phosphorus Starvation in Hydroponics Growth System.

    PubMed

    Kumar, Varun; Singh, Tiratha Raj; Hada, Alkesh; Jolly, Monica; Ganapathi, Andy; Sachdev, Archana

    2015-10-01

    Phosphorus is an essential nutrient required for soybean growth but is bound in phytic acid which causes negative effects on both the environment as well as the animal nutrition. Lowering of phytic acid levels is associated with reduced agronomic characteristics, and relatively little information is available on the response of soybean plants to phosphorus (P) starvation. In this study, we evaluated the effects of different P starvation concentrations on the phytic acid content, growth, and yield of seven mutant genotypes along with the unirradiated control, JS-335, in a hydroponics growth system. The low phytic acid containing mutant genotypes, IR-JS-101, IR-DS-118, and IR-V-101, showed a relatively high growth rate in low P concentration containing nutrient solution (2 μM), whereas the high P concentration (50 μM) favored the growth of IR-DS-111 and IR-DS-115 mutant genotypes containing moderate phytate levels. The mutant genotypes with high phytic acid content, IR-DS-122, IR-DS-114, and JS-335, responded well under P starvation and did not have any significant effect on the growth and yield of plants. Moreover, the reduction of P concentration in nutrient solution from 50 to 2 μM also reduced the phytic acid content in the seeds of all the soybean genotypes under study. The desirable agronomic performance of low phytic acid containing mutant genotype IR-DS-118 reported in this study suggested it to be a P-efficient genotype which could be considered for agricultural practices under P limiting soils. PMID:26239443

  2. Probing Phosphorus Efficient Low Phytic Acid Content Soybean Genotypes with Phosphorus Starvation in Hydroponics Growth System.

    PubMed

    Kumar, Varun; Singh, Tiratha Raj; Hada, Alkesh; Jolly, Monica; Ganapathi, Andy; Sachdev, Archana

    2015-10-01

    Phosphorus is an essential nutrient required for soybean growth but is bound in phytic acid which causes negative effects on both the environment as well as the animal nutrition. Lowering of phytic acid levels is associated with reduced agronomic characteristics, and relatively little information is available on the response of soybean plants to phosphorus (P) starvation. In this study, we evaluated the effects of different P starvation concentrations on the phytic acid content, growth, and yield of seven mutant genotypes along with the unirradiated control, JS-335, in a hydroponics growth system. The low phytic acid containing mutant genotypes, IR-JS-101, IR-DS-118, and IR-V-101, showed a relatively high growth rate in low P concentration containing nutrient solution (2 μM), whereas the high P concentration (50 μM) favored the growth of IR-DS-111 and IR-DS-115 mutant genotypes containing moderate phytate levels. The mutant genotypes with high phytic acid content, IR-DS-122, IR-DS-114, and JS-335, responded well under P starvation and did not have any significant effect on the growth and yield of plants. Moreover, the reduction of P concentration in nutrient solution from 50 to 2 μM also reduced the phytic acid content in the seeds of all the soybean genotypes under study. The desirable agronomic performance of low phytic acid containing mutant genotype IR-DS-118 reported in this study suggested it to be a P-efficient genotype which could be considered for agricultural practices under P limiting soils.

  3. Diverse Cd(II) compounds based on N-benzoyl-L-glutamic acid and N-donor ligands: Structures and photoluminescent properties

    NASA Astrophysics Data System (ADS)

    Ma, Ning; Guo, Wei-Ying; Song, Hui-Hua; Yu, Hai-Tao

    2016-01-01

    Five new Cd(II) coordination polymers with N-benzoyl-L-glutamic acid (H2bzgluO) and different N-donor ligands, [Cd(bzgluO)(2,2‧-bipy)(H2O)]n (1), [Cd(bzgluO)(2,4‧-bipy)2(H2O)·3H2O]n (2), [Cd(bzgluO)(phen)·H2O]n (3), [Cd(bzgluO)(4,4‧-bipy)(H2O)]n (4), [Cd(bzgluO)(bpp)(H2O)·2H2O]n (5) were synthesized (2,2‧-bipy=2,2‧-bipyridine, 2,4‧-bipy=2,4‧-bipyridine, phen=1,10-phenanthroline, 4,4‧-bipy=4,4‧-bipyridine, bpp=1,3-di(4-pyridyl)propane). Compounds 1-2 exhibit a 1D single-chain structure. Compound 1 generates a 2D supramolecular structure via π-π stacking and hydrogen bonding, 3D architecture of compound 2 is formed by hydrogen bonding. Compound 3 features a 1D double-chain structure, which are linked by π-π interactions into a 2D supramolecular layer. Compounds 4-5 display a 2D network structure. Neighboring layers of 4 are extended into a 3D supramolecular architecture through hydrogen bonding. The structural diversity of these compounds is attributed to the effect of ancillary N-donor ligands and coordination modes of H2bzgluO. Luminescent properties of 1-5 were studied at room temperature. Circular dichroism of compounds 1, 2 and 5 were investigated.

  4. Array of nucleic acid probes on biological chips for diagnosis of HIV and methods of using the same

    DOEpatents

    Chee, Mark; Gingeras, Thomas R.; Fodor, Stephen P. A.; Hubble, Earl A.; Morris, MacDonald S.

    1999-01-19

    The invention provides an array of oligonucleotide probes immobilized on a solid support for analysis of a target sequence from a human immunodeficiency virus. The array comprises at least four sets of oligonucleotide probes 9 to 21 nucleotides in length. A first probe set has a probe corresponding to each nucleotide in a reference sequence from a human immunodeficiency virus. A probe is related to its corresponding nucleotide by being exactly complementary to a subsequence of the reference sequence that includes the corresponding nucleotide. Thus, each probe has a position, designated an interrogation position, that is occupied by a complementary nucleotide to the corresponding nucleotide. The three additional probe sets each have a corresponding probe for each probe in the first probe set. Thus, for each nucleotide in the reference sequence, there are four corresponding probes, one from each of the probe sets. The three corresponding probes in the three additional probe sets are identical to the corresponding probe from the first probe or a subsequence thereof that includes the interrogation position, except that the interrogation position is occupied by a different nucleotide in each of the four corresponding probes.

  5. Functionalized ZnS quantum dots as luminescent probes for detection of amino acids.

    PubMed

    Mobarraz, Mahsa; Ganjali, Mohammad Reza; Chaichi, Mohammad Javad; Norouzi, Parviz

    2012-10-01

    In this work, L-cysteine capped-ZnS quantum dots were synthesized in aqueous medium, and their interaction with some of the amino acids was studied with fluorescence spectra. The results demonstrated that histidine could effectively quench the Quantum dots emission more than other amino acids. Electron transfer process between the capping ligands and histidine was mainly responsible for the remarkable quenching effect of histidine, because according to the structure of histidine, it is the strongest acceptor among essential amino acids. Under optimum conditions, the quenched fluorescence intensity increased linearly with the concentration of histidine ranging from 1.33×10(-6) to 1.49×10(-4) mol L(-1). The limit of detection for histidine was 0.05×10(-7) mol L(-1). PMID:22925905

  6. Facilitating unambiguous NMR assignments and enabling higher probe density through selective labeling of all methyl containing amino acids.

    PubMed

    Proudfoot, Andrew; Frank, Andreas O; Ruggiu, Fiorella; Mamo, Mulugeta; Lingel, Andreas

    2016-05-01

    The deuteration of proteins and selective labeling of side chain methyl groups has greatly enhanced the molecular weight range of proteins and protein complexes which can be studied using solution NMR spectroscopy. Protocols for the selective labeling of all six methyl group containing amino acids individually are available, however to date, only a maximum of five amino acids have been labeled simultaneously. Here, we describe a new methodology for the simultaneous, selective labeling of all six methyl containing amino acids using the 115 kDa homohexameric enzyme CoaD from E. coli as a model system. The utility of the labeling protocol is demonstrated by efficiently and unambiguously assigning all methyl groups in the enzymatic active site using a single 4D (13)C-resolved HMQC-NOESY-HMQC experiment, in conjunction with a crystal structure. Furthermore, the six fold labeled protein was employed to characterize the interaction between the substrate analogue (R)-pantetheine and CoaD by chemical shift perturbations, demonstrating the benefit of the increased probe density. PMID:27130242

  7. Adaptation and Validation of E-Probe Diagnostic Nucleic Acid Analysis for Detection of Escherichia coli O157:H7 in Metagenomic Data from Complex Food Matrices.

    PubMed

    Blagden, Trenna; Schneider, William; Melcher, Ulrich; Daniels, Jon; Fletcher, Jacqueline

    2016-04-01

    The Centers for Disease Control and Prevention recently emphasized the need for enhanced technologies to use in investigations of outbreaks of foodborne illnesses. To address this need, e-probe diagnostic nucleic acid analysis (EDNA) was adapted and validated as a tool for the rapid, effective identification and characterization of multiple pathogens in a food matrix. In EDNA, unassembled next generation sequencing data sets from food sample metagenomes are queried using pathogen-specific sequences known as electronic probes (e-probes). In this study, the query of mock sequence databases demonstrated the potential of EDNA for the detection of foodborne pathogens. The method was then validated using next generation sequencing data sets created by sequencing the metagenome of alfalfa sprouts inoculated with Escherichia coli O157:H7. Nonspecific hits in the negative control sample indicated the need for additional filtration of the e-probes to enhance specificity. There was no significant difference in the ability of an e-probe to detect the target pathogen based upon the length of the probe set oligonucleotides. The results from the queries of the sample database using E. coli e-probe sets were significantly different from those obtained using random decoy probe sets and exhibited 100% precision. The results support the use of EDNA as a rapid response methodology in foodborne outbreaks and investigations for establishing comprehensive microbial profiles of complex food samples. PMID:27052861

  8. Identification and quantification of acetic acid bacteria in wine and vinegar by TaqMan-MGB probes.

    PubMed

    Torija, M J; Mateo, E; Guillamón, J M; Mas, A

    2010-04-01

    A Real-Time PCR (RT-PCR) assay was developed using TaqMan minor groove binder (MGB) probes for the specific detection and quantification of five acetic acid bacteria (AAB) species (Acetobacter pasteurianus, Acetobacter aceti, Gluconacetobacter hansenii, Gluconacetobacter europaeus and Gluconobacter oxydans) in wine and vinegar. The primers and probes, designed from the 16S rRNA gene, showed good specificity with the target AAB species. The technique was tested on AAB grown in glucose medium (GY) and inoculated samples of red wine and wine vinegar. Standard curves were constructed with the five target species in all these matrices. Quantification was linear over at least 5 log units using both serial dilution of purified DNA and cells. When this technique was tested in GY medium and inoculated matrices, at least 10(2)-10(3) cells/ml were detected. To quantify low populations of AAB in microbiologically complex samples, a PCR enrichment including part of the 16S-23S rRNA gene ITS region was needed to increase the amount of target DNA compared to non-target DNA. The RT-PCR assay used in this study is a reliable, specific and fast method for quantifying these five AAB species in wine and vinegar.

  9. Excited States of Nucleic Acids Probed by Proton Relaxation Dispersion NMR Spectroscopy.

    PubMed

    Juen, Michael Andreas; Wunderlich, Christoph Hermann; Nußbaumer, Felix; Tollinger, Martin; Kontaxis, Georg; Konrat, Robert; Hansen, D Flemming; Kreutz, Christoph

    2016-09-19

    In this work an improved stable isotope labeling protocol for nucleic acids is introduced. The novel building blocks eliminate/minimize homonuclear (13) C and (1) H scalar couplings thus allowing proton relaxation dispersion (RD) experiments to report accurately on the chemical exchange of nucleic acids. Using site-specific (2) H and (13) C labeling, spin topologies are introduced into DNA and RNA that make (1) H relaxation dispersion experiments applicable in a straightforward manner. The novel RNA/DNA building blocks were successfully incorporated into two nucleic acids. The A-site RNA was previously shown to undergo a two site exchange process in the micro- to millisecond time regime. Using proton relaxation dispersion experiments the exchange parameters determined earlier could be recapitulated, thus validating the proposed approach. We further investigated the dynamics of the cTAR DNA, a DNA transcript that is involved in the viral replication cycle of HIV-1. Again, an exchange process could be characterized and quantified. This shows the general applicablility of the novel labeling scheme for (1) H RD experiments of nucleic acids.

  10. Excited States of Nucleic Acids Probed by Proton Relaxation Dispersion NMR Spectroscopy.

    PubMed

    Juen, Michael Andreas; Wunderlich, Christoph Hermann; Nußbaumer, Felix; Tollinger, Martin; Kontaxis, Georg; Konrat, Robert; Hansen, D Flemming; Kreutz, Christoph

    2016-09-19

    In this work an improved stable isotope labeling protocol for nucleic acids is introduced. The novel building blocks eliminate/minimize homonuclear (13) C and (1) H scalar couplings thus allowing proton relaxation dispersion (RD) experiments to report accurately on the chemical exchange of nucleic acids. Using site-specific (2) H and (13) C labeling, spin topologies are introduced into DNA and RNA that make (1) H relaxation dispersion experiments applicable in a straightforward manner. The novel RNA/DNA building blocks were successfully incorporated into two nucleic acids. The A-site RNA was previously shown to undergo a two site exchange process in the micro- to millisecond time regime. Using proton relaxation dispersion experiments the exchange parameters determined earlier could be recapitulated, thus validating the proposed approach. We further investigated the dynamics of the cTAR DNA, a DNA transcript that is involved in the viral replication cycle of HIV-1. Again, an exchange process could be characterized and quantified. This shows the general applicablility of the novel labeling scheme for (1) H RD experiments of nucleic acids. PMID:27533469

  11. Water uptake of internally mixed ammonium sulfate and dicarboxylic acid particles probed by infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Miñambres, Lorena; Méndez, Estíbaliz; Sánchez, María N.; Castaño, Fernando; Basterretxea, Francisco J.

    2013-05-01

    Tropospheric aerosols are usually mixtures of inorganic and organic compounds in variable proportions, and the relative amount of organic fraction can influence the hygroscopic properties of the particles. Infrared spectra of submicrometer internally mixed dry particles of ammonium sulfate (AS) with various dicarboxylic acids (oxalic, malonic, maleic, glutaric and pimelic) have been measured in an aerosol flow tube at several solute mass ratios. The spectra show a notable broadening in the bandwidth of sulfate ion ν3 vibrational band near 1115 cm-1 with respect to pure AS. We attribute these perturbations, that are biggest at AS/organic acid mass ratio near unity, to intermolecular interactions between inorganic ions and organic acid molecules in the internally mixed solids. The water uptake behavior of internally mixed particles has been measured by recording the infrared integrated absorbance of liquid water as a function of relative humidity (RH). The amount of water present in the particles prior to deliquescence correlates partially with the water solubilities of the dicarboxylic acids, and also with the relative magnitudes of intermolecular interactions in the internally mixed dry solids. Phase change of ammonium sulfate in the internally mixed particles with RH has been spectrally monitored, and it is shown that water uptaken before full deliquescence produces structural changes in the particles that are revealed by their vibrational spectra.

  12. Ancillary ligand-assisted assembly of C{sub 3}-symmetric 4,4′,4″-nitrilotribenzoic acid with divalent Zn{sup 2+} ions: Syntheses, topological structures, and photoluminescence properties

    SciTech Connect

    Cui, Li-Ting; Niu, Yan-Fei; Han, Jie; Zhao, Xiao-Li

    2015-07-15

    4,4′,4″-nitrilotribenzoic acid (H{sub 3}L), a C{sub 3}-symmetric ligand, was found to self-assemble into two polymorphs driven by intermolecular hydrogen-bonding interactions. Reactions of this ligand with Zn{sup 2+} under solvothermal conditions resulted in four new coordination polymers bearing interesting structural motifs: [Zn{sub 2}(L){sub 2}(py){sub 2}]·2(H{sub 2}NMe{sub 2}){sup +}·DMF·2H{sub 2}O (1), [Zn{sub 2}(L)(H{sub 2}L)(bipy)]·1.5H{sub 2}O·Guest (2), [Zn{sub 2}(L){sub 2}(bipy)]·2(H{sub 2}NMe{sub 2}){sup +}·2DMF (3), and [Zn{sub 3}(L){sub 2}(bpa)]·2H{sub 2}O·Guest (4) (H{sub 3}L=4,4′,4′′-nitrilotribenzoic acid, DMF=dimethylformamide, py=pyridine, bipy=4,4′-bipyridine, bpa=1,2-bis(4-pyridyl)diazene). Single-crystal structural analysis revealed that compound 1 exhibits a rare example of twofold interpenetrating anionic 3D (3,3)-net framework containing helical channels, whereas in 2, the 3D pillar-layer structure generated from bipy-pillared Zn{sub 2}(L)(H{sub 2}L) layer is further reinforced by intermolecular hydrogen bonding among pairs of free –COOH units. Compound 3 shows an interesting entangled architecture of 2D→3D parallel polycatenation consisting five-coordinated Zn{sup 2+} ions. Compound 4 displays a 3D pillar-layer framework with trimeric Zn{sub 3}(CO{sub 2}){sub 6} serving as secondary building unit (SBU). The syntheses, structures, thermal stabilities, powder X-ray diffractions and solid-state photoluminescence properties for these crystalline materials have been carried out. In addition, supramolecular assembly of H{sub 3}L under solvothermal conditions will also be addressed. - Graphical abstract: Supramolecular assembly of 4,4′,4′′-nitrilotribenzoic acid and its ligand behavior toward Zn{sup 2+} were investigated, which exhibit two polymorphs of the free acid and four metal coordination polymers bearing interesting structural motifs. - Highlights: • Two polymorphs of H{sub 3}L showing different hydrogen

  13. Probing inclusion complexes of cyclodextrins with amino acids by physicochemical approach.

    PubMed

    Roy, Mahendra Nath; Roy, Aditi; Saha, Subhadeep

    2016-10-20

    Formations of host-guest inclusion complexes of two natural amino acids, viz., l-Leucine and l-Isoleucine as guests with α and β-cyclodextrins have been investigated which include diverse applications in modern science such as controlled delivery in the field of pharmaceuticals, food processing etc. Surface tension and conductivity studies establish the formation of inclusion complexes with 1:1 stoichiometry. The interactions of cyclodextrins with amino acids have been supported by density, viscosity, refractive index, hydration and solvation number measurements indicating higher degree of inclusion in case of α-cyclodextrin. l-Leucine interacts more with the hydrophobic cavity of cyclodextrin than its isomer. With the help of stability constant by NMR titration, hydrophobic effect, H-bonds and structural effects the formations of inclusion complexes have been explained. PMID:27474589

  14. Energetics of side-chain snorkeling in transmembrane helices probed by nonproteinogenic amino acids

    PubMed Central

    Öjemalm, Karin; Higuchi, Takashi; Lara, Patricia; Lindahl, Erik; Suga, Hiroaki

    2016-01-01

    Cotranslational translocon-mediated insertion of membrane proteins into the endoplasmic reticulum is a key process in membrane protein biogenesis. Although the mechanism is understood in outline, quantitative data on the energetics of the process is scarce. Here, we have measured the effect on membrane integration efficiency of nonproteinogenic analogs of the positively charged amino acids arginine and lysine incorporated into model transmembrane segments. We provide estimates of the influence on the apparent free energy of membrane integration (ΔGapp) of “snorkeling” of charged amino acids toward the lipid–water interface, and of charge neutralization. We further determine the effect of fluorine atoms and backbone hydrogen bonds (H-bonds) on ΔGapp. These results help establish a quantitative basis for our understanding of membrane protein assembly in eukaryotic cells. PMID:27601675

  15. Energetics of side-chain snorkeling in transmembrane helices probed by nonproteinogenic amino acids.

    PubMed

    Öjemalm, Karin; Higuchi, Takashi; Lara, Patricia; Lindahl, Erik; Suga, Hiroaki; von Heijne, Gunnar

    2016-09-20

    Cotranslational translocon-mediated insertion of membrane proteins into the endoplasmic reticulum is a key process in membrane protein biogenesis. Although the mechanism is understood in outline, quantitative data on the energetics of the process is scarce. Here, we have measured the effect on membrane integration efficiency of nonproteinogenic analogs of the positively charged amino acids arginine and lysine incorporated into model transmembrane segments. We provide estimates of the influence on the apparent free energy of membrane integration (ΔGapp) of "snorkeling" of charged amino acids toward the lipid-water interface, and of charge neutralization. We further determine the effect of fluorine atoms and backbone hydrogen bonds (H-bonds) on ΔGapp These results help establish a quantitative basis for our understanding of membrane protein assembly in eukaryotic cells. PMID:27601675

  16. Using modern tools to probe the structure-function relationship of fatty acid synthases

    PubMed Central

    Burkart, Michael D.

    2015-01-01

    Fatty acid biosynthesis is essential to life and represents one of the most conserved pathways in Nature, preserving the same handful of chemical reactions over all species. Recent interest in the molecular details of the de novo fatty acid synthase (FAS) has been heightened by demand for renewable fuels and the emergence of multidrug resistant bacterial strains. Central to FAS is the acyl carrier protein (ACP), a protein chaperone that shuttles the growing acyl chain between catalytic enzymes within the FAS. Human efforts to alter fatty acid biosynthesis for oil production, chemical feedstock or antimicrobial purposes has been met with limited success in part due to a lack of detailed molecular information behind the ACP-partner protein interactions inherent to the pathway. This review will focus on recently developed tools for the modification of ACP and analysis of protein-protein interactions, such as mechanism-based crosslinking, and the studies exploiting them. Discussion specific to each enzymatic domain focuses first on mechanism and known inhibitors, followed by available structures and known interactions with ACP. While significant unknowns remain, new understandings into the intricacies of FAS point to future advances in manipulating this complex molecular factory. PMID:25676190

  17. Re-engineering of CYP2C9 to probe acid-base substrate selectivity.

    PubMed

    Tai, Guoying; Dickmann, Leslie J; Matovic, Nicholas; DeVoss, James J; Gillam, Elizabeth M J; Rettie, Allan E

    2008-10-01

    A common feature of many CYP2C9 ligands is their weak acidity. As revealed by crystallography, the structural basis for this behavior involves a charge-pairing interaction between an anionic moiety on the substrate and an active site R108 residue. In the present study we attempted to re-engineer CYP2C9 to better accept basic ligands by charge reversal at this key residue. We expressed and purified the R108E and R108E/D293N mutants and compared their ability with that of native CYP2C9 to interact with (S)-warfarin, diclofenac, pyrene, propranolol, and ibuprofen amine. As expected, the R108E mutant maintained all the native enzyme's pyrene 1-hydroxylation activity, but catalytic activity toward diclofenac and (S)-warfarin was abrogated. In contrast, the double mutant displayed much less selectivity in its behavior toward these control ligands. Neither of the mutants displayed significant enhancement of propranolol metabolism, and all three preparations exhibited a type II (inhibitor) rather than type I (substrate) spectrum with ibuprofen amine, although binding became progressively weaker with the single and double mutants. Collectively, these data underscore the importance of the amino acid at position 108 in the acid substrate selectivity of CYP2C9, highlight the accommodating nature of the CYP2C9 active site, and provide a cautionary note regarding facile re-engineering of these complex cytochrome P450 active sites.

  18. Mitochondrial, acidic, and cytosolic pHs determination by ³¹P NMR spectroscopy: design of new sensitive targeted pH probes.

    PubMed

    Culcasi, Marcel; Thétiot-Laurent, Sophie; Atteia, Ariane; Pietri, Sylvia

    2015-01-01

    (31)P nuclear magnetic resonance (NMR) is a unique technique to monitor noninvasively the energetics of living systems at real time through the detection of a variety of phosphorylated metabolites. Using adequately designed α-aminophosphonates as external probes, we have shown earlier that (31)P NMR can also give access simultaneously to the accurate pH of cytosolic and acidic compartments in normal and stressed cultured cells or isolated perfused organs, a feature that was not possible using endogenous inorganic phosphate as the probe. More recently, we obtained a series of derivatives of these new pH probes that incorporate a triphenylphosphonium cation as a specific vector to the mitochondrion. Here, we describe the synthesis, (31)P NMR pH titrating properties in buffers, and application in cultures of the green alga Chlamydomonas reinhardtii of two of these mitochondria-targeted pH probes in comparison with one nonvectorized, yet still informative α-aminophosphonate.

  19. Mitochondrial, acidic, and cytosolic pHs determination by ³¹P NMR spectroscopy: design of new sensitive targeted pH probes.

    PubMed

    Culcasi, Marcel; Thétiot-Laurent, Sophie; Atteia, Ariane; Pietri, Sylvia

    2015-01-01

    (31)P nuclear magnetic resonance (NMR) is a unique technique to monitor noninvasively the energetics of living systems at real time through the detection of a variety of phosphorylated metabolites. Using adequately designed α-aminophosphonates as external probes, we have shown earlier that (31)P NMR can also give access simultaneously to the accurate pH of cytosolic and acidic compartments in normal and stressed cultured cells or isolated perfused organs, a feature that was not possible using endogenous inorganic phosphate as the probe. More recently, we obtained a series of derivatives of these new pH probes that incorporate a triphenylphosphonium cation as a specific vector to the mitochondrion. Here, we describe the synthesis, (31)P NMR pH titrating properties in buffers, and application in cultures of the green alga Chlamydomonas reinhardtii of two of these mitochondria-targeted pH probes in comparison with one nonvectorized, yet still informative α-aminophosphonate. PMID:25634273

  20. Primers and a specific DNA probe for detecting lactic acid bacteria producing 3-hydroxypropionaldehyde from glycerol in spoiled ciders.

    PubMed

    Claisse, O; Lonvaud-Funel, A

    2001-06-01

    Of the 40 strains isolated from several spoiled ciders where glycerol was degraded, 36 were identified as Lactobacillus collinoides, three were Lactobacillus hilgardii, and one was Lactobacillus mali. However, only 30 L. collinoides and two L. hilgardii could degrade glycerol. The glycerol dehydratase activity was shown. The main product of the transformation was 1.3 propanediol. Two DNA primers GD1 and GD2 were chosen in the region encoding one of the subunits of glycerol dehydratase of Citrobacter freundii, Klebsiella pneumoniae, Klebsiella oxytoca, Salmonella Typhimurium, and Clostridium pasteurianum. A 279-bp amplicon in polymerase chain reaction amplification was obtained with the genomic L. collinoides IOEB 9527 DNA as template. The amino acid sequence deduced from the amplicon DNA sequence showed a very high similarity and identity with the gene of gram-negative and C. pasteurianum species. After labeling, the amplicon was used as DNA probe in dot-blot hybridization with the genomic DNA of all the tested strains. Only strains that could degrade glycerol hybridized. Moreover, polymerase chain reactions using GDI and GD2 revealed only glycerol dehydratase genes of positive L. collinoides and L. hilgardii strains. The primers and the amplicon proved to be suitable and reliable tools to detect the lactic acid bacteria involved in the deterioration of cider. PMID:11403134

  1. Molecular beacons: a novel DNA probe for nucleic acid and protein studies.

    PubMed

    Tan, W; Fang, X; Li, J; Liu, X

    2000-04-01

    A new concept has been introduced for molecular beacon DNA molecules. Molecular beacons are a new class of oligonucleotides that can report the presence of specific nucleic acids in both homogeneous solutions and at the liquid-solid interface. They emit an intense fluorescent signal only when hybridized to their target DNA or RNA molecules. Biotinylated molecular beacons have been designed and used for the development of ultrasensitive DNA sensors and for DNA molecular interaction studies at a solid-liquid interface. Molecular beacons have also been used to study protein-DNA interactions. They have provided a variety of exciting opportunities in DNA/RNA/protein studies.

  2. On the use of 16-iodohexadecanoic acid (IHDA) as a probe for myocardial beta-oxidation of fatty acids

    SciTech Connect

    De Grado, T.R.; Gatley, S.J.; Ng, C.K.; Holden, J.E.; Bernstein, D.R.

    1984-01-01

    The rate of myocardial clearance of label IHDA was compared with the beta-oxidation rate by coinjection of 125-IHDA and 3-H-Palmitic Acid (THDA) into isolated rat hearts. I-125 residue curves and efflux I-125 and H-3 curves were obtained. Three groups of hearts were studied, control, ischemic and those from rats previously treated with the beta-oxidation inhibitor Ethyl 2(5(4-chlorophenyl)pentyl)-oxiran-2-carboxylate (POCA). Both labels were found to exit ischemic and POCA treated hearts more slowly than controls. In all cases, the clearance of label from IHDA was significantly slower than that of the labelled water from beta-oxidation of THDA, consistent with previous work indicating the efflux of iodide from the mitochondria to be rate-limiting. Assay of heart homogenates showed 60% of the extracted label to be iodide at 1 minute. Thus, iodide is pooled within the mitochondria and diffuses out with a characteristic rate governed by electrochemical and lemmal properties. By assuming parallel utilization of IHDA and THDA and transient clearance of both labelled metabolites from the cytosol, the H-3 curves were interpreted ad equivalent with the production of free iodide in the mitochondria. A rate constant describing the flux of iodide across the mitochondrial membrane was calculated by fitting the I-125 curve (I/sup -/ output) to the H-3 curve (I/sup -/ input) convolved with a single exponential. The rate constant (k/sub I/=2.25 +- .35 x 10/sup -3/ s/sup -1/ for normals) was similar to the largest rate constant from fitted residue curves (k=2.08 +- .05 x 10/sup -3/ s/sup -1/).

  3. Probing determinants of cyclopiazonic acid sensitivity of bacterial Ca2+-ATPases.

    PubMed

    Kotšubei, Aljona; Gorgel, Manuela; Morth, Jens P; Nissen, Poul; Andersen, Jacob L

    2013-11-01

    Cyclopiazonic acid (CPA) is a specific and potent inhibitor of the sarcoplasmic reticulum Ca(2+)-ATPase 1a (SERCA1a). Despite high sequence similarity to SERCA1a, Listeria monocytogenes Ca(2+)-ATPase 1 (LMCA1) is not inhibited by CPA. To test whether a CPA binding site could be created while maintaining the functionality of the ATPase we targeted four amino acid positions in LMCA1 for mutational studies based on a multiple sequence alignment of SERCA-like Ca(2+)-ATPases and structural analysis of the CPA site. The identification of CPA-sensitive gain-of-function mutants pinpointed key determinants of the CPA binding site. The importance of these determinants was further underscored by the characterization of the CPA sensitivity of two additional bacterial Ca(2+)-ATPases from Lactococcus lactis and Bacillus cereus. The CPA sensitivity was predicted from their sequence compared with the LMCA1 results, and this was experimentally confirmed. Interestingly, a cluster of Lactococcus bacteria applied in the production of fermented cheese display Ca(2+)-ATPases that are predictably CPA insensitive and may originate from their coexistence with CPA-producing Penicillum and Aspergillus fungi in the cheese. The differences between bacterial and mammalian binding pockets encompassing the CPA site suggest that CPA derivatives that are specific for bacteria or other pathogens can be developed. PMID:23621633

  4. Locked Nucleic Acid Probe-Based Real-Time PCR Assay for the Rapid Detection of Rifampin-Resistant Mycobacterium tuberculosis.

    PubMed

    Zhao, Yong; Li, Guilian; Sun, Chongyun; Li, Chao; Wang, Xiaochen; Liu, Haican; Zhang, Pingping; Zhao, Xiuqin; Wang, Xinrui; Jiang, Yi; Yang, Ruifu; Wan, Kanglin; Zhou, Lei

    2015-01-01

    Drug-resistant Mycobacterium tuberculosis can be rapidly diagnosed through nucleic acid amplification techniques by analyzing the variations in the associated gene sequences. In the present study, a locked nucleic acid (LNA) probe-based real-time PCR assay was developed to identify the mutations in the rpoB gene associated with rifampin (RFP) resistance in M. tuberculosis. Six LNA probes with the discrimination capability of one-base mismatch were designed to monitor the 23 most frequent rpoB mutations. The target mutations were identified using the probes in a "probe dropout" manner (quantification cycle = 0); thus, the proposed technique exhibited superiority in mutation detection. The LNA probe-based real-time PCR assay was developed in a two-tube format with three LNA probes and one internal amplification control probe in each tube. The assay showed excellent specificity to M. tuberculosis with or without RFP resistance by evaluating 12 strains of common non-tuberculosis mycobacteria. The limit of detection of M. tuberculosis was 10 genomic equivalents (GE)/reaction by further introducing a nested PCR method. In a blind validation of 154 clinical mycobacterium isolates, 142/142 (100%) were correctly detected through the assay. Of these isolates, 88/88 (100%) were determined as RFP susceptible and 52/54 (96.3%) were characterized as RFP resistant. Two unrecognized RFP-resistant strains were sequenced and were found to contain mutations outside the range of the 23 mutation targets. In conclusion, this study established a sensitive, accurate, and low-cost LNA probe-based assay suitable for a four-multiplexing real-time PCR instrument. The proposed method can be used to diagnose RFP-resistant tuberculosis in clinical laboratories.

  5. Photoluminescence response of colloidal quantum dots on VO2 film across metal to insulator transition

    PubMed Central

    2014-01-01

    We have proposed a method to probe metal to insulator transition in VO2 measuring photoluminescence response of colloidal quantum dots deposited on the VO2 film. In addition to linear luminescence intensity decrease with temperature that is well known for quantum dots, temperature ranges with enhanced photoluminescence changes have been found during phase transition in the oxide. Corresponding temperature derived from luminescence dependence on temperature closely correlates with that from resistance measurement during heating. The supporting reflectance data point out that photoluminescence response mimics a reflectance change in VO2 across metal to insulator transition. Time-resolved photoluminescence study did not reveal any significant change of luminescence lifetime of deposited quantum dots under metal to insulator transition. It is a strong argument in favor of the proposed explanation based on the reflectance data. PACS 71.30. + h; 73.21.La; 78.47.jd PMID:25404877

  6. New Real-Time PCR Assay Using Locked Nucleic Acid Probes To Assess Prevalence of ParC Mutations in Fluoroquinolone-Susceptible Streptococcus pneumoniae Isolates from France

    PubMed Central

    Decousser, Jean-Winoc; Methlouthi, Imen; Pina, Patrick; Collignon, Anne; Allouch, Pierre

    2006-01-01

    A real-time PCR assay with locked nucleic acid probes was developed to screen mutations at codons 79 and 83 of the Streptococcus pneumoniae parC gene. Only silent mutations were detected among 236 French invasive fluoroquinolone-susceptible strains. This test could be useful for some high-risk patients or in national surveys. PMID:16569894

  7. ESTIMATION OF BACTERIAL CELL NUMBERS IN HUMIC ACID-RICH SALT MARSH SEDIMENTS WITH PROBES DIRECTED TO 16S RIBOSOMAL DNA

    EPA Science Inventory

    The feasibility of using probes directed towards ribosomal DNAs (rDNAs) as a quantitative approach to estimating cell numbers was examined and applied to study the structure of a bacterial community in humic acid-rich salt marsh sediments. Hybridizations were performed with membr...

  8. Highly water-soluble monoboronic acid probes that show optical sensitivity to glucose based on 4-sulfo-1,8-naphthalic anhydride.

    PubMed

    Cao, Zhi; Nandhikonda, Premchendar; Heagy, Michael D

    2009-05-01

    Two highly water-soluble monoboronic acid probes that display the more desirable off-on fluorescence response were synthesized based on 4-sulfo-1,8-naphthalic anhydride and a remarkable sensitivity for glucose rather than fructose and galactose was also observed.

  9. Adaptation and validation of E-probe diagnostic nucleic acid analysis for detection of Escherichia coli O157:H7 in metagenomic data of complex food matrices

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Foodborne pathogens are an increasing problem threatening the US food supply. The need for rapid sensitive diagnostic tools that can address multiple types and taxonomic classes of foodbourne pathogens is growing. This paper describes the adaptation of E-probe Diagnostic Nucleic acid Analysis (EDNA)...

  10. Radioluminescence and photoluminescence of Th:CaF2 crystals

    PubMed Central

    Stellmer, Simon; Schreitl, Matthias; Schumm, Thorsten

    2015-01-01

    We study thorium-doped CaF2 crystals as a possible platform for optical spectroscopy of the 229Th nuclear isomer transition. We anticipate two major sources of background signal that might cover the nuclear spectroscopy signal: VUV-photoluminescence, caused by the probe light, and radioluminescence, caused by the radioactive decay of 229Th and its daughters. We find a rich photoluminescence spectrum at wavelengths above 260 nm, and radioluminescence emission above 220 nm. This is very promising, as fluorescence originating from the isomer transition, predicted at a wavelength shorter than 200 nm, could be filtered spectrally from the crystal luminescence. Furthermore, we investigate the temperature-dependent decay time of the luminescence, as well as thermoluminescence properties. Our findings allow for an immediate optimization of spectroscopy protocols for both the initial search for the nuclear transition using synchrotron radiation, as well as future optical clock operation with narrow-linewidth lasers. PMID:26502749

  11. Radioluminescence and photoluminescence of Th:CaF2 crystals.

    PubMed

    Stellmer, Simon; Schreitl, Matthias; Schumm, Thorsten

    2015-01-01

    We study thorium-doped CaF2 crystals as a possible platform for optical spectroscopy of the (229)Th nuclear isomer transition. We anticipate two major sources of background signal that might cover the nuclear spectroscopy signal: VUV-photoluminescence, caused by the probe light, and radioluminescence, caused by the radioactive decay of (229)Th and its daughters. We find a rich photoluminescence spectrum at wavelengths above 260 nm, and radioluminescence emission above 220 nm. This is very promising, as fluorescence originating from the isomer transition, predicted at a wavelength shorter than 200 nm, could be filtered spectrally from the crystal luminescence. Furthermore, we investigate the temperature-dependent decay time of the luminescence, as well as thermoluminescence properties. Our findings allow for an immediate optimization of spectroscopy protocols for both the initial search for the nuclear transition using synchrotron radiation, as well as future optical clock operation with narrow-linewidth lasers. PMID:26502749

  12. ESA Mission ROSETTA Will Probe for Chirality of Cometary Amino Acids

    NASA Astrophysics Data System (ADS)

    Thiemann, Wolfram H.-P.; Meierhenrich, Uwe

    2001-02-01

    New crucial theoretical investigations on the origin of biomolecular chirality are reviewed briefly. With the goal to investigate these theories our team is going to perform the `chirality-experiment' in the near future with cometary matter. In 2012 the robotical lander RoLand will detach from the orbiter of the ROSETTA spacecraft and set down on the surface of comet 46P/Wirtanen in order to separate and identify cometary organic compounds via GC-MS in situ. Chiral organics will be separated into their enantiomers by application of 3 capillary columns coated with different kinds of stationary phases. Non-volatile compounds like amino acids will be derivatized in especially developed gas phase alkylation steps avoiding reactions in the liquid phase. The results of these preliminary gas phase reactions are presented in this article.

  13. Label-free and selective sensing of uric acid with gold nanoclusters as optical probe.

    PubMed

    Wang, Jian; Chang, Yong; Wu, Wen Bi; Zhang, Pu; Lie, Shao Qing; Huang, Cheng Zhi

    2016-05-15

    Clinically, the amount of uric acid (UA) in biological fluids is closely related to some diseases such as hyperuricemia and gout, thus it is of great significance to sense UA in clinical samples. In this work, red gold nanoclusters (AuNCs) with relatively high fluorescence quantum yield and strong fluorescence emission were facilely available using bovine serum albumin (BSA) as template. The fluorescence of BSA-protected AuNCs can be sensitively quenched by H2O2, which is further capable of sensing UA through the specific catalytic oxidation with uricase, since it generates stoichiometric quantity of H2O2 by-product. The proposed assay allows for the selective detection of UA in the range of 10-800 μM with a detection limit of 6.6 μM, which is applicable to sense UA in clinical samples with satisfactory results, suggesting its great potential for diagnostic purposes. PMID:26992526

  14. Probing 3D Collective Cancer Invasion Using Double-Stranded Locked Nucleic Acid Biosensors.

    PubMed

    Dean, Zachary S; Elias, Paul; Jamilpour, Nima; Utzinger, Urs; Wong, Pak Kin

    2016-09-01

    Cancer is a leading cause of death worldwide and metastases are responsible for over 90% of human cancer deaths. There is an urgent need to develop novel therapeutics for suppressing cancer invasion, the initial step of metastasis. Nevertheless, the regulation of cancer invasion is poorly understood due to a paucity of tools for monitoring the invasion process in 3D microenvironments. Here, we report a double-stranded locked nucleic acid (dsLNA) biosensor for investigating 3D collective cancer invasion. By incorporating multiphoton microscopy and the dsLNA biosensor, we perform dynamic single cell gene expression analysis while simultaneously characterizing the biomechanical interaction between the invading sprouts and the extracellular matrix. Gene profiling of invasive leader cells and detached cells suggest distinctive signaling mechanisms involved in collective and individual invasion in the 3D microenvironment. Our results underscore the involvement of Notch signaling in 3D collective cancer invasion, which warrants further investigation toward antimetastasis therapy in the future.

  15. Styrene oligomerization as a molecular probe reaction for Brønsted acidity at the nanoscale.

    PubMed

    Aramburo, Luis R; Wirick, Sue; Miedema, Piter S; Buurmans, Inge L C; de Groot, Frank M F; Weckhuysen, Bert M

    2012-05-21

    The Brønsted acid-catalyzed oligomerization of 4-fluorostyrene has been studied on a series of H-ZSM-5 zeolite powders, steamed under different conditions, with a combination of UV-Vis micro-spectroscopy and Scanning Transmission X-ray Microscopy (STXM). UV-Vis micro-spectroscopy and STXM have been used to monitor the relative formation of cyclic and linear dimeric carbocations as a function of the steaming post-treatment (i.e., parent vs. steaming at 600, 700 and 800 °C). It was found that the UV-Vis band intensity ratios of linear to cyclic dimeric species increase from 0.79 (parent H-ZSM-5) over 1.41 (H-ZSM-5 steamed at 600 °C) and 1.88 (H-ZSM-5 steamed at 700 °C) to 2.33 (H-ZSM-5 steamed at 800 °C). STXM confirms this trend in reaction product selectivity, as the relative intensities of the transitions attributed to the presence of the cyclic dimer in the carbon K-edge spectra decrease with increasing severity of the steaming post-treatment. Furthermore, STXM reveals spatial heterogeneities in reaction product formation within the H-ZSM-5 zeolite powders at the nanoscale. More specifically, a shrinking carbon core-shell distribution was detected within the zeolite aggregates, in which the relative amount of cyclic dimeric species is higher in the core relative to the shell of the zeolite aggregate and the relative amount of cyclic dimeric species in the zeolite core gradually decreases with increasing severity of the steaming post-treatment. These differences are rationalized in terms of spatial differences in Brønsted acidity within H-ZSM-5 zeolite powders as well as by changes in the formation process of linear and dimeric carbocations within H-ZSM-5 micro- and mesopores.

  16. Reversible two-photon fluorescent probe for imaging of hypochlorous acid in live cells and in vivo.

    PubMed

    Zhang, Wei; Liu, Wei; Li, Ping; kang, Junqing; Wang, Jiaoyang; Wang, Hui; Tang, Bo

    2015-06-25

    Herein, we have developed a novel reversible two-photon fluorescent probe that is well suited for monitoring HOCl levels selectively and instantaneously. Results showed the reversible and instantaneous responses of the probe towards intracellular HOCl. Moreover, the probe was successfully applied to the imaging of the HOCl levels in zebrafish and mice via two-photon imaging.

  17. Systematic safety evaluation on photoluminescent carbon dots

    NASA Astrophysics Data System (ADS)

    Wang, Kan; Gao, Zhongcai; Gao, Guo; Wo, Yan; Wang, Yuxia; Shen, Guangxia; Cui, Daxiang

    2013-03-01

    Photoluminescent carbon dots (C-dots) were prepared using the improved nitric acid oxidation method. The C-dots were characterized by tapping-mode atomic force microscopy, and UV-vis absorption spectroscopy. The C-dots were subjected to systematic safety evaluation via acute toxicity, subacute toxicity, and genotoxicity experiments (including mouse bone marrow micronuclear test and Salmonella typhimurium mutagenicity test). The results showed that the C-dots were successfully prepared with good stability, high dispersibility, and water solubility. At all studied C-dot dosages, no significant toxic effect, i.e., no abnormality or lesion, was observed in the organs of the animals. Therefore, the C-dots are non-toxic to mice under any dose and have potential use in fluorescence imaging in vivo, tumor cell tracking, and others.

  18. Probing the interaction of the amino acid alanine with the surface of ZnO(1010).

    PubMed

    Gao, Y K; Traeger, F; Shekhah, O; Idriss, H; Wöll, C

    2009-10-01

    The adsorption modes and stability of the amino acid alanine (NH(2)-CH(CH(3))-COOH) have been studied on the nonpolar single crystal surface of zinc oxide, ZnO(1010), experimentally by X-ray photoelectron spectroscopy (XPS) and computationally using density functional theory (DFT). Deposition at 200 K was found to lead to the formation of multilayers identified by an XPS N1s peak at 401.7 eV assigned to the NH(3)(+) group, a fingerprint of the zwitterionic structure of alanine in the solid state. Heating to 300 K resulted in the removal of most of the multilayers with the remaining surface coverage estimated to 0.4 with respect to Zn cations. At this temperature most of the alanine molecules are found to be deprotonated (dissociated), yielding a carboxylate species (NH(2)-CH(CH(3))-COO(-) (a) + OH (s); where O is surface oxygen, (a) for adsorbed and (s) for surface species). Further heating of the surface resulted in a gradual decrease of the surface coverage and by 500 K a large fraction of adsorbed alanine molecules have desorbed from the surface. Total energy DFT computations of different adsorbate species identified two stable dissociative adsorption modes: bidentate and monodentate. The bidentate species with adsorption energy of 1.75 eV was found to be more stable than the monodentate species by about 0.7 eV.

  19. Probing 3D Collective Cancer Invasion Using Double-Stranded Locked Nucleic Acid Biosensors.

    PubMed

    Dean, Zachary S; Elias, Paul; Jamilpour, Nima; Utzinger, Urs; Wong, Pak Kin

    2016-09-01

    Cancer is a leading cause of death worldwide and metastases are responsible for over 90% of human cancer deaths. There is an urgent need to develop novel therapeutics for suppressing cancer invasion, the initial step of metastasis. Nevertheless, the regulation of cancer invasion is poorly understood due to a paucity of tools for monitoring the invasion process in 3D microenvironments. Here, we report a double-stranded locked nucleic acid (dsLNA) biosensor for investigating 3D collective cancer invasion. By incorporating multiphoton microscopy and the dsLNA biosensor, we perform dynamic single cell gene expression analysis while simultaneously characterizing the biomechanical interaction between the invading sprouts and the extracellular matrix. Gene profiling of invasive leader cells and detached cells suggest distinctive signaling mechanisms involved in collective and individual invasion in the 3D microenvironment. Our results underscore the involvement of Notch signaling in 3D collective cancer invasion, which warrants further investigation toward antimetastasis therapy in the future. PMID:27529634

  20. Probing the affinity of polyanions for acidic fibroblast growth factor by unfolding kinetics.

    PubMed

    Mach, H; Middaugh, C R

    1994-02-15

    The relationship between ligand-protein affinity and the extent of protein stabilization induced by such interactions has been investigated using the binding of polyanions to acidic fibroblast growth factor (aFGF) as a model system. It was found that the experimentally observed unfolding rate constant of aFGF consists of two components: one equal to the unfolding rate constant of the aFGF-ligand complex and the other the product of the unfolding rate constant of free aFGF, the aFGF-ligand dissociation constant (Kd), and the reciprocal of the molar ligand concentration. This reflects the presence of two possible unfolding pathways: at high ligand excess dissociation is suppressed and slow unfolding of the aFGF-ligand complex itself prevails. When lower concentrations of ligand allows equilibrium-driven appearance of free aFGF, a more rapid unfolding of dissociated protein predominates. Existence of a steady state of dissociated aFGF undergoing unfolding was demonstrated by computer simulation of the elementary events, using experimentally determined rate constants. The potential applications of such simulations are outlined. An equation allowing estimation of dissociation constants from equilibrium denaturation curves obtained in the presence of a varying amount of ligand is also proposed. In addition, determination of initial unfolding rates in the presence of excess protein permits the the stoichiometry of the interaction to be determined.

  1. Probing Gαi1 Protein Activation at Single Amino Acid Resolution

    PubMed Central

    Sun, Dawei; Maeda, Shoji; Matkovic, Milos; Mendieta, Sandro; Mayer, Daniel; Dawson, Roger; Schertler, Gebhard F.X.; Madan Babu, M.; Veprintsev, Dmitry B.

    2016-01-01

    We present comprehensive single amino acid resolution maps of the residues stabilising the human Gαi1 subunit in nucleotide- and receptor-bound states. We generated these maps by measuring the effects of alanine mutations on the stability of Gαi1 and of the rhodopsin-Gαi1 complex. We identified stabilization clusters in the GTPase and helical domains responsible for structural integrity and the conformational changes associated with activation. In activation cluster I, helices α1 and α5 pack against strands β1-3 to stabilize the nucleotide-bound states. In the receptor-bound state, these interactions are replaced by interactions between α5 and strands β4-6. Key residues in this cluster are Y320, crucial for the stabilization of the receptor-bound state, and F336, which stabilizes nucleotide-bound states. Destabilization of helix α1, caused by rearrangement of this activation cluster, leads to the weakening of the inter-domain interface and release of GDP. PMID:26258638

  2. DNAzyme molecular beacon probes for target-induced signal-amplifying colorimetric detection of nucleic acids.

    PubMed

    Fu, Rongzhan; Li, Taihua; Lee, Soo Suk; Park, Hyun Gyu

    2011-01-15

    A novel DNAzyme molecular beacon (DNAzymeMB) strategy was developed for target-induced signal-amplifying colorimetric detection of target nucleic acids. The DNAzymeMB, which exhibits peroxidase activity in its free hairpin structure, was engineered to form a catalytically inactive hybrid through hybridization with a blocker DNA. The presence of target DNA leads to dissociation of the DNAzymeMB from the inactive hybrid through hybridization with the blocker DNA. This process results in recovery of the catalytically active DNAzymeMB, which can catalyze a colorimetric reaction that signals the presence of the target DNA. In addition, a primer was rationally designed to anneal to the blocker DNA of the blocker/target DNA duplex and displace the bound target DNA during the extension reaction. The released target DNA triggers the next cycle involving hybridization with blocker DNA, DNAzymeMB dissociation, primer extension, and target displacement. This unique amplifying strategy leads to the generation of multiple numbers of active DNAzymeMB molecules from a single target molecule and gives a detection limit down to 1 pM, a value that is nearly 3 or 5 orders of magnitude lower than those of previously reported DNAzyme molecular beacon-based DNA detection methods.

  3. Probing the interaction of the amino acid alanine with the surface of ZnO(1010).

    PubMed

    Gao, Y K; Traeger, F; Shekhah, O; Idriss, H; Wöll, C

    2009-10-01

    The adsorption modes and stability of the amino acid alanine (NH(2)-CH(CH(3))-COOH) have been studied on the nonpolar single crystal surface of zinc oxide, ZnO(1010), experimentally by X-ray photoelectron spectroscopy (XPS) and computationally using density functional theory (DFT). Deposition at 200 K was found to lead to the formation of multilayers identified by an XPS N1s peak at 401.7 eV assigned to the NH(3)(+) group, a fingerprint of the zwitterionic structure of alanine in the solid state. Heating to 300 K resulted in the removal of most of the multilayers with the remaining surface coverage estimated to 0.4 with respect to Zn cations. At this temperature most of the alanine molecules are found to be deprotonated (dissociated), yielding a carboxylate species (NH(2)-CH(CH(3))-COO(-) (a) + OH (s); where O is surface oxygen, (a) for adsorbed and (s) for surface species). Further heating of the surface resulted in a gradual decrease of the surface coverage and by 500 K a large fraction of adsorbed alanine molecules have desorbed from the surface. Total energy DFT computations of different adsorbate species identified two stable dissociative adsorption modes: bidentate and monodentate. The bidentate species with adsorption energy of 1.75 eV was found to be more stable than the monodentate species by about 0.7 eV. PMID:19596338

  4. Design and Performance of rRNA Targeted Oligonucleotide Probes for in Situ Detection and Phylogenetic Identification of Microorganisms Inhabiting Acid Mine Drainage Environments.

    PubMed

    Bond, P.L.; Banfield, J.F.

    2001-02-01

    At Iron Mountain, CA, there is an extreme occurrence of acid mine drainage (AMD). This is a result of past mining activity that has exposed a sulfide ore body to weathering and microbial activity. This study presents seven new oligonucleotide probes for the detection of microorganisms at this AMD site by fluorescent in situ hybridization. In the design of these probes we have accounted for a large body of 16S rRNA sequence data recently compiled by us. This was obtained by PCR and cloning directly from environmental DNA and was mostly represented by novel sequences. The probes were developed to include detection of novel and uncultivated organisms. This includes detection for the Thermoplasmales group, a new group of Leptospirillum, the genus Sulfobacillus, the Acidiphilium genus, Acidimicrobium and relatives, and for organisms within the delta Proteobacteria. These probes have been used to examine the abundance and distribution of organisms, including novel and uncultivated taxa, and to clarify their potential contributions to AMD production at the site. We anticipate that these probes will be useful tools for exploration of the microbiology of other natural acidic environments and bioleaching systems. PMID:12032620

  5. Adsorption of 4-picoline and piperidine to the hydrated SiO2 surface: probing the surface acidity with vibrational sum frequency generation spectroscopy.

    PubMed

    Liu, Dingfang; Ma, Gang; Allen, Heather C

    2005-04-01

    Vapor adsorption is an important process influencing the migration and the fate of many organic pollutants in the environment. In this study, vibrational sum frequency generation (SFG) spectroscopy was used to study the adsorption of two surface acidity probe molecules, 4-picoline (pKa = 5.94) and piperidine (pKa = 11.24), onto the amorphous SiO2 surface. The adsorption of 4-picoline onto the silica surface occurs by forming weak hydrogen bonds between the nitrogen atoms of 4-picoline molecules and the hydrogen atoms of surface silanol OH groups. Piperidine molecules are strongly chemisorbed onto the SiO2 surface through the protonation of piperidine molecules by surface silanol OH groups. The SFG results indicate that the surface acidity constant of silanol OH groups (pKa-(HOSi triple bond)) is in the range of 5.94-11.24 at the air/solid interface. Although this range of surface acidity constants is quite wide, it is possible to narrow it by choosing probe molecules with a smaller pKa range. Together with theoretical prediction methods, adsorption studies using vibrational SFG spectroscopy are capable of quantifying the surface acidity of mineral oxides by carefully choosing the acidity probe molecules.

  6. A streptavidin paramagnetic-particle based competition assay for the evaluation of the optical selectivity of quadruplex nucleic acid fluorescent probes.

    PubMed

    Largy, Eric; Hamon, Florian; Teulade-Fichou, Marie-Paule

    2012-05-01

    Although quadruplex nucleic acids are thought to be involved in many biological processes, they are massively overwhelmed by duplex DNA in the cell. Small molecules, able to probe quadruplex nucleic acids with high optical selectivity, could possibly achieve the visualization of these processes. The aim of the method described herein is to evaluate quickly the optical selectivity of quadruplex nucleic acid probes, in isothermal conditions, using widely available materials, small quantities of oligonucleotides and virtually any kind and quantity of biological competitor. The assay relies on the use of streptavidin-coated paramagnetic particles and biotinylated quadruplex forming oligonucleotides, allowing a quick and easy separation of the quadruplex target from the competitor. In the present study, two quadruplex nucleic acids (the DNA and RNA human telomeric repeats) have been used as targets while a duplex DNA oligonucleotide, total DNA, total RNA, another quadruplex nucleic acid and a protein have been used as competitors. The optical selectivity of various probes, displaying different photophysical properties and binding selectivities, has been successfully examined, allowing the identification of a best candidate for further cell microscopy experiments. This assay allows a quick and reliable assessment of the labeling properties of a quadruplex binder in cellular environment conditions. It is an interesting alternative to gel electrophoresis experiments since it is performed in solution, has a well-resolved separation system and allows easy quantifications.

  7. New organically templated photoluminescence iodocuprates(I)

    SciTech Connect

    Hou Qin; Zhao Jinjing; Zhao Tianqi; Jin Juan; Yu Jiehui; Xu Jiqing

    2011-07-15

    Two types of organic cyclic aliphatic diamine molecules piperazine (pip) and 1,3-bis(4-piperidyl)propane (bpp) were used, respectively, to react with an inorganic mixture of CuI and KI in the acidic CH{sub 3}OH solutions under the solvothermal conditions, generating finally three new organically templated iodocuprates as 2-D layered [(Hpip)Cu{sub 3}I{sub 4}] 1, 1-D chained [tmpip][Cu{sub 2}I{sub 4}] 2 (tmpip=N,N,N',N'-tetramethylpiperazinium) and dinuclear [H{sub 2}bpp]{sub 2}[Cu{sub 2}I{sub 5}] I.2H{sub 2}O 3. Note that the templating agent tmpip{sup 2+} in compound 2 originated from the in situ N-alkylation reaction between the pip molecule and the methanol solvent. The photoluminescence analysis indicates that the title compounds emit the different lights: yellow for 1, blue for 2 and yellow-green for 3, respectively. - Graphical abstract: The solvothermal self-assemblies of CuI, KI and pip/bpp in acidic CH{sub 3}OH solutions created three iodocuprates 2-D layered [(Hpip)Cu{sub 3}I{sub 4}] 1, 1-D chained [tmpip][Cu{sub 2}I{sub 4}] 2 and dinuclear [H{sub 2}bpp]{sub 2}[Cu{sub 2}I{sub 5}] I.2H{sub 2}O 3. Highlights: > A new layered iodocuprate(I) with 20-membered rings was hydrothermally prepared. > A simple approach to prepare the new organic templating agent was reported. > Photoluminescence analysis indicates the emission for iodocuprate(I) is associated with the Cu...Cu interactions.

  8. Nitrogen-doped carbon dots: a facile and general preparation method, photoluminescence investigation, and imaging applications.

    PubMed

    Xu, Yang; Wu, Ming; Liu, Yang; Feng, Xi-Zeng; Yin, Xue-Bo; He, Xi-Wen; Zhang, Yu-Kui

    2013-02-11

    Carbon dots (Cdots) are an important probe for imaging and sensing applications because of their fluorescence property, good biocompatibility, and low toxicity. However, complex procedures and strong acid treatment are often required and Cdots suffer from low photoluminescence (PL) emission. Herein, a facile and general strategy using carbonization of precursors and then extraction with solvents is proposed for the preparation of nitrogen-doped Cdots (N-Cdots) with 3-(3,4-dihydroxyphenyl)-L-alanine (L-DOPA), L-histidine, and L-arginine as precursor models. After they are heated, the precursors become carbonized. Nitrogen-doped Cdots are subsequently extracted into N,N'-dimethylformamide (DMF) from the carbogenic solid. A core-shell structure of Cdots with a carbon core and the oxygen-containing shell was observed. Nitrogen has different forms in N-Cdots and oxidized N-Cdots. The doped nitrogen and low oxidation level in N-Cdots improve their emission significantly. The N-Cdots show an emission with a nitrogen-content-dependent intensity and Cdot-size-dependent emission-peak wavelength. Imaging of HeLa cells, a human cervical cancer cell line, and HepG2 cells, a human hepatocellular liver carcinoma line, was observed with high resolution using N-Cdots as a probe and validates their use in imaging applications and their multicolor property in the living cell system.

  9. pH at the micellar interface: synthesis of pH probes derived from salicylic acid, acid-base dissociation in sodium dodecyl sulfate micelles, and Poisson-Boltzmann simulation.

    PubMed

    Souza, T P; Zanette, D; Kawanami, A E; de Rezende, L; Ishiki, H M; do Amaral, A T; Chaimovich, H; Agostinho-Neto, A; Cuccovia, I M

    2006-05-01

    The study of the H+ concentration at the micellar interface is a convenient system for modeling the distribution of H+ at interfaces. We have synthesized salicylic acid derivatives to analyze the proton dissociation of both the carboxylic and phenol groups of the probes, determining spectrophotometrically the apparent pK(a)'s (pK(ap)) in sodium dodecyl sulfate, SDS, micelles with and without added salt. The synthesized probes were 2-hydroxy-5-(2-trimethylammoniumacetyl)benzoate; 2-hydroxy-5-(2-dimethylhexadecylammoniumacetyl)benzoate; 2-hydroxy-5-(2-dimethylhexadecylammoniumhexanoyl)benzoate; 2-hydroxy-5-(2-dimethylhexadecylammoniumundecanoyl)benzoate; 2-hydroxy-5-acetylbenzoic acid; and 2-hydroxy-5-dodecanoylbenzoic acid. Upon incorporation into SDS micelles the pK(ap)'s of both carboxylic and phenol groups increased by ca. 3 pH units and NaCl addition caused a decrease in the probe-incorporated pK(ap). The experimental results were fitted with a cell model Poisson-Boltzmann (P-B) equation taking in consideration the effect of salt on the aggregation number of SDS and using the distance of the dissociating group as a parameter. The conformations of the probes were analyzed theoretically using two dielectric constants, e.g., 2 and 78. Both the P-B analysis and conformation calculations can be interpreted by assuming that the acid groups dissociate very close to, or at, the interface. Our results are consistent with the assumption that the intrinsic pK(a)'s of both carboxylic and phenol groups of the salicylic acid probes used here can be taken as those in water. Using this assumption the micellar and salt effects on the pK(ap)'s of the (trialkylammonium)benzoate probes were described accurately using a cell model P-B analysis.

  10. Triplex-Forming Peptide Nucleic Acid Probe Having Thiazole Orange as a Base Surrogate for Fluorescence Sensing of Double-stranded RNA.

    PubMed

    Sato, Takaya; Sato, Yusuke; Nishizawa, Seiichi

    2016-08-01

    We have developed a new fluorescent sensing probe for double-stranded RNA (dsRNA) by integrating thiazole orange (TO) as a base surrogate into triplex-forming PNA. Our probe forms the thermally stable triplex with the target dsRNA at acidic pH; and the triplex formation is accompanied by the remarkable light-up response of the TO unit. The binding of our probe to the target dsRNA proceeds very rapidly, allowing real-time monitoring of the triplex formation. Importantly, we found the TO base surrogate in our probe functions as a universal base for the base pair opposite the TO unit in the triplex formation. Furthermore, the TO unit is significantly more responsive for the fully matched dsRNA sequence compared to the mismatch-containing sequences, which enables the analysis of the target dsRNA sequence at the single-base pair resolution. The binding and sensing functions of our probe are described for the development of fluorescent probes applicable to sensing biologically relevant dsRNA. PMID:27442229

  11. Association of fluorescent probes 1-anilinonaphthalene-8-sulfonate and 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid with T7 RNA polymerase.

    PubMed

    Ghosh, Utpal; Das, Mili; Dasgupta, Dipak

    2003-01-01

    T7 RNA polymerase is an enzyme that carries out transcription using DNA as the template and ribonucleotides as the substrates. Here we report the association of the polymerase with 1-anilinonaphthalene-8-sulfonate (ANS) and 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (bis-ANS), which are two fluorescent hydrophobic probes that are frequently used to study structural perturbations in proteins and intermediate states of proteins during folding and unfolding. Our results from the fluorescence titration data show that these two molecules bind to the enzyme with dissociation constants on the micromolar order. The results from the tryptic digestion of the enzyme in the absence and presence of the probes show that they inhibit the rate of tryptic digestion. Circular dichroism spectroscopic studies of the protein in the near UV region indicate that both probes induce tertiary structural changes in the polymerase. There is also a probe (ANS or bis-ANS) induced inhibition of the enzymatic activity. All these results are attributed to association of the probes with the enzyme, leading to an alteration in the conformation of T7 RNA polymerase. This limits the use of these extrinisic probes to the study of the folding properties of the enzyme.

  12. Triplex-Forming Peptide Nucleic Acid Probe Having Thiazole Orange as a Base Surrogate for Fluorescence Sensing of Double-stranded RNA.

    PubMed

    Sato, Takaya; Sato, Yusuke; Nishizawa, Seiichi

    2016-08-01

    We have developed a new fluorescent sensing probe for double-stranded RNA (dsRNA) by integrating thiazole orange (TO) as a base surrogate into triplex-forming PNA. Our probe forms the thermally stable triplex with the target dsRNA at acidic pH; and the triplex formation is accompanied by the remarkable light-up response of the TO unit. The binding of our probe to the target dsRNA proceeds very rapidly, allowing real-time monitoring of the triplex formation. Importantly, we found the TO base surrogate in our probe functions as a universal base for the base pair opposite the TO unit in the triplex formation. Furthermore, the TO unit is significantly more responsive for the fully matched dsRNA sequence compared to the mismatch-containing sequences, which enables the analysis of the target dsRNA sequence at the single-base pair resolution. The binding and sensing functions of our probe are described for the development of fluorescent probes applicable to sensing biologically relevant dsRNA.

  13. Synthesis of fluorescent D-amino acids (FDAAs) and their use for probing peptidoglycan synthesis and bacterial growth in situ

    PubMed Central

    Kuru, Erkin; Tekkam, Srinivas; Hall, Edward

    2015-01-01

    Fluorescent D-amino acids (FDAAs) are efficiently incorporated into the peptidoglycan of diverse bacterial species at the sites of active peptidoglycan biosynthesis, allowing specific and covalent probing of bacterial growth with minimal perturbation. Here, we provide a protocol for the synthesis of four FDAAs emitting light in blue, green or red and for their use in peptidoglycan labeling of live bacteria. Our modular synthesis protocol gives easy access to a library of different FDAAs made with commercially available fluorophores. FDAAs can be synthesized in a typical chemistry laboratory in 2–3 days. The simple labeling procedure involves addition of the FDAAs to the bacterial sample for the desired labeling duration and stopping further label incorporation by fixation or by washing away excess dye. We discuss several scenarios for the use of these labels including short or long labeling durations, and the combination of different labels in pure culture or complex environmental samples. Depending on the experiment, FDAA labeling can take as little as 30 s for a rapidly growing species such as Escherichia coli. PMID:25474031

  14. Denaturant effects on HbGp hemoglobin as monitored by 8-anilino-1-naphtalene-sulfonic acid (ANS) probe.

    PubMed

    Barros, Ana E B; Carvalho, Francisco A O; Alves, Fernanda R; Carvalho, José W P; Tabak, Marcel

    2015-03-01

    Glossoscolex paulistus extracellular hemoglobin (HbGp) stability has been monitored in the presence of denaturant agents. 8-Anilino-1-naphtalene-sulfonic acid (ANS) was used, and spectroscopic and hydrodynamic studies were developed. Dodecyltrimethylammonium bromide (DTAB) induces an increase in ANS fluorescence emission intensity, with maximum emission wavelength blue-shifted from 517 to 493 nm. Two transitions are noticed, at 2.50 and 9.50 mmol/L of DTAB, assigned to ANS interaction with pre-micellar aggregates and micelles, respectively. In oxy-HbGp, ANS binds to protein sites less exposed to solvent, as compared to DTAB micelles. In DTAB-HbGp-ANS ternary system, at pH 7.0, protein aggregation, oligomeric dissociation and unfolding were observed, while, at pH 5.0, aggregation is absent. DTAB induced unfolding process displays two transitions, one due to oligomeric dissociation and the second one, probably, to the denaturation of dissociated subunits. Moreover, guanidine hydrochloride and urea concentrations above 1.5 and 4.0 mol/L, respectively, induce the full HbGp denaturation, with reduction of ANS-bound oxy-HbGp hydrophobic patches, as noticed by fluorescence quenching up to 1.0 and 5.0 mol/L of denaturants. Our results show clearly the differences in probe sensitivity to the surfactant, in the presence and absence of protein, and new insights into the denaturant effects on HbGp unfolding.

  15. Red photoluminescence BCNO synthesized from graphene oxide nanosheets

    NASA Astrophysics Data System (ADS)

    Kang, Yue; Chu, Zeng-yong; Ma, Tian; Li, Wei-ping; Zhang, Dong-jiu; Tang, Xiao-yu

    2016-01-01

    In this paper, we demonstrate the conversion of graphene oxide (GO) into boron carbon oxynitride (BCNO) hybrid nanosheets via a reaction with boric acid and urea, during which the boron and nitrogen atoms are incorporated into graphene nanosheets. The experimental results reveal that GO is important for the photoluminescence (PL) BCNO phosphor particles. More importantly, in this system, the prepared BCNO phosphors can be used to prepare the materials needed for red light emitting diodes (LEDs).

  16. Temperature-dependent photoluminescence of surface-engineered silicon nanocrystals.

    PubMed

    Mitra, Somak; Švrček, Vladimir; Macias-Montero, Manual; Velusamy, Tamilselvan; Mariotti, Davide

    2016-01-01

    In this work we report on temperature-dependent photoluminescence measurements (15-300 K), which have allowed probing radiative transitions and understanding of the appearance of various transitions. We further demonstrate that transitions associated with oxide in SiNCs show characteristic vibronic peaks that vary with surface characteristics. In particular we study differences and similarities between silicon nanocrystals (SiNCs) derived from porous silicon and SiNCs that were surface-treated using a radio-frequency (RF) microplasma system. PMID:27296771

  17. Temperature-dependent photoluminescence of surface-engineered silicon nanocrystals

    PubMed Central

    Mitra, Somak; Švrček, Vladimir; Macias-Montero, Manual; Velusamy, Tamilselvan; Mariotti, Davide

    2016-01-01

    In this work we report on temperature-dependent photoluminescence measurements (15–300 K), which have allowed probing radiative transitions and understanding of the appearance of various transitions. We further demonstrate that transitions associated with oxide in SiNCs show characteristic vibronic peaks that vary with surface characteristics. In particular we study differences and similarities between silicon nanocrystals (SiNCs) derived from porous silicon and SiNCs that were surface-treated using a radio-frequency (RF) microplasma system. PMID:27296771

  18. Intrinsic photoluminescence of diatom shells in sensing applications

    NASA Astrophysics Data System (ADS)

    De Tommasi, E.; Rendina, I.; Rea, I.; De Stefano, M.; Lamberti, A.; De Stefano, L.

    2009-05-01

    Diatoms are monocellular micro-algae provided with external valves, the frustules, made of amorphous hydrated silica. Frustules present patterns of regular arrays of holes, the areolae, characterized by sub-micrometric dimensions. Frustules from centric diatoms are characterized by a radial disposition of areolae and exhibit several optical properties, such as photoluminescence, lens-like behavior and, in general, photonic-crystal-like behavior as long as confinement of electromagnetic field is concerned. In particular, intrinsic photoluminescence from frustules is strongly influenced by the surrounding atmosphere: on exposure to gases, the induced luminescence changes both in the optical intensity and peaks positions. To give specificity against a target analyte, a key feature for an optical sensor, a biomolecular probe, which naturally recognizes its ligand, can be covalently linked to the diatom surface. We explored the photoluminescence emission properties of frustules of Coscinodiscus wailesii centric species, characterized by a diameter of about 100-200 μm, on exposure to different vapours and in presence of specific bioprobes interacting with target analytes. Very high sensitivities have been observed due to the characteristic morphology of diatoms shells. Particular attention has been devoted to the emission properties of single frustules.

  19. Nonlinear photoluminescence spectrum of single gold nanostructures.

    PubMed

    Knittel, Vanessa; Fischer, Marco P; de Roo, Tjaard; Mecking, Stefan; Leitenstorfer, Alfred; Brida, Daniele

    2015-01-27

    We investigate the multiphoton photoluminescence characteristics of gold nanoantennas fabricated from single crystals and polycrystalline films. By exciting these nanostructures with ultrashort pulses tunable in the near-infrared range, we observe distinct features in the broadband photoluminescence spectrum. By comparing antennas of different crystallinity and shape, we demonstrate that the nanoscopic geometry of plasmonic devices determines the shape of the emission spectra. Our findings rule out the contribution of the gold band structure in shaping the photoluminescence.

  20. Simultaneous detection and differentiation of human rhino- and enteroviruses in clinical specimens by real-time PCR with locked nucleic Acid probes.

    PubMed

    Osterback, Riikka; Tevaluoto, Tuire; Ylinen, Tiina; Peltola, Ville; Susi, Petri; Hyypiä, Timo; Waris, Matti

    2013-12-01

    Human rhinoviruses (HRVs) and human enteroviruses (HEVs) are significant respiratory pathogens. While HRV infections are restricted to the respiratory tract, HEV infections may spread to secondary target organs. The method of choice for sensitive specific detection of these viruses is reverse transcription (RT)-PCR with primers targeting the conserved 5' noncoding region of the viral RNA. On the other hand, sequence similarities between HRVs and HEVs complicate their differential detection. In this study, we describe the use of locked nucleic acid (LNA) analogues in short double-dye probes which contained only two selectively HRV- or HEV-specific bases. The double-stranded DNA dye BOXTO (4-[6-(benzoxazole-2-yl-(3-methyl-)-2,3-dihydro-(benzo-1,3-thiazole)-2-methylidene)]-1-methyl-quinolinium chloride) was used with the LNA probes in a tricolor real-time PCR assay to allow specific detection of HRVs (probes labeled with 6-carboxyfluorescein [FAM] [green]) and HEVs (Cy5 [red]) with additional melting curve analysis (BOXTO [yellow]). The functionality of the probes was validated in PCR and RT-PCR assays using plasmids containing viral cDNA, quantified viral RNA transcripts, cultivated rhino- and enterovirus prototypes, and clinical specimens. Of 100 HRV and 63 HEV prototypes, the probes correctly identified all HEVs except one that produced only a BOXTO signal. Among 118 clinical specimens with sequencing results, concordant results were obtained for 116 specimens. Two specimens were reactive with both probes, but sequencing yielded only a single virus. Real-time PCR with LNA probes allowed sensitive group-specific identification of HRVs and HEVs and would enable relative copy number determination. The assay is suitable for rapid and accurate differential detection of HRVs and HEVs in a diagnostic laboratory setting.

  1. A unique "turn-on" fluorescence signalling strategy for highly specific detection of ascorbic acid using carbon dots as sensing probe.

    PubMed

    Fong, Jessica Fung Yee; Chin, Suk Fun; Ng, Sing Muk

    2016-11-15

    Carbon dots (CDs) that showed strong blue fluorescence were successfully synthesised from sodium alginate via furnace pyrolysis. The single step pyrolytic synthesis was simple to perform while yielded CDs with high photostability, good water solubility and minimum by-products. In order to design the probe with "turn-on" sensing capability, the CDs were screened against a series of metal cations to first "turn-off" the fluorescence. It was found that ferric ions (Fe(3+)) were most responsive and effective in quenching the fluorescence of CDs. Based on this observation, the conditioning of the probe was performed to ensure the fluorescence was completely quenched, while not overloading the system with Fe(3+). At the optimised condition, the CDs-Fe(3+) mixture served as a highly specific detection probe for ascorbic acid (AA). The analytical potential of the probe was evaluated and showed a good linear range of response for AA concentration of 24-40μg/mL. The selectivity study against other possible co-existing species was carried out and proved that our unique "turn-on" fluorescence signalling strategy was highly effective and selective towards AA as the target analyte. The probe was demonstrated for quantification of AA in real samples, which was the commercially available vitamin C supplement. The result showed good accuracy with minimum deviation from standard method adopted for validation purpose. PMID:27290666

  2. Unravelling the Bacterial Vaginosis-Associated Biofilm: A Multiplex Gardnerella vaginalis and Atopobium vaginae Fluorescence In Situ Hybridization Assay Using Peptide Nucleic Acid Probes

    PubMed Central

    Hardy, Liselotte; Jespers, Vicky; Dahchour, Nassira; Mwambarangwe, Lambert; Musengamana, Viateur; Vaneechoutte, Mario; Crucitti, Tania

    2015-01-01

    Bacterial vaginosis (BV), a condition defined by increased vaginal discharge without significant inflammation, is characterized by a change in the bacterial composition of the vagina. Lactobacillus spp., associated with a healthy vaginal microbiome, are outnumbered by BV-associated organisms. These bacteria could form a polymicrobial biofilm which allows them to persist in spite of antibiotic treatment. In this study, we examined the presence of Gardnerella vaginalis and Atopobium vaginae in vaginal biofilms using Peptide Nucleic Acid (PNA) probes targeting these bacteria. For this purpose, we developed three new PNA probes for A. vaginae. The most specific A. vaginae probe, AtoITM1, was selected and then used in an assay with two existing probes, Gard162 and BacUni-1, to evaluate multiplex FISH on clinical samples. Using quantitative polymerase chain reaction (qPCR) as the gold standard, we demonstrated a sensitivity of 66.7% (95% confidence interval: 54.5% - 77.1%) and a specificity of 89.4% (95% confidence interval: 76.1% - 96%) of the new AtoITM1 probe. FISH enabled us to show the presence of a polymicrobial biofilm in bacterial vaginosis, in which Atopobium vaginae is part of a Gardnerella vaginalis-dominated biofilm. We showed that the presence of this biofilm is associated with high bacterial loads of A. vaginae and G. vaginalis. PMID:26305575

  3. Fluorescence determination of DNA with 1-pyrenebutyric acid nanoparticles coated with β-cyclodextrin as a fluorescence probe

    NASA Astrophysics Data System (ADS)

    Wang, Lun; Bian, Guirong; Wang, Leyu; Dong, Ling; Chen, Hongqi; Xia, Tingting

    2005-04-01

    A novel ultrasonication method has been successfully developed for the preparation of 1-pyrenebutyric acid (PBAC)/β-cyclodextrin(β-CD) complex nanoparticles. The as-prepared nanoparticles are characterized by transmission electron microscopy (TEM), fluorescence excitation and emission spectroscopy. Complex nanoparticles prepared with ultrasonication are smaller and better dispersed than single PBAC nanoparticles. At pH 3.0, the relative fluorescence intensity of complex nanoparticles of PBAC/β-CD can be quenched by the concentration of DNA. Based on this, a novel fluorimetric method has been developed for rapid determination of DNA. In comparison with single organic fluorophores, these nanoparticle probes are better water-solubility, more stable and do not suffer from blinking. Under optimum conditions, the calibration graphs are linear over the range 0.2-15 μg mL -1 for calf thymus DNA (ct-DNA) and 0.3-12 μg mL -1 for fish sperm DNA (fs-DNA). The corresponding detection limit is 0.01 μg mL -1 for ct-DNA and 0.02 μg mL -1 for fs-DNA. The relative standard deviation of seven replicate measurements is 1.2% for 2.0 μg mL -1 ct-DNA and 1.4% for 2.0 μg mL -1 fs-DNA, respectively. The method is simple and sensitive. The recovery and relative standard deviation are very satisfactory. A mechanism proposed to explain the process also has been studied.

  4. Analysis of Protein–Protein Interactions in MCF-7 and MDA-MB-231 Cell Lines Using Phthalic Acid Chemical Probes

    PubMed Central

    Liang, Shih-Shin; Wang, Tsu-Nai; Tsai, Eing-Mei

    2014-01-01

    Phthalates are a class of plasticizers that have been characterized as endocrine disrupters, and are associated with genital diseases, cardiotoxicity, hepatotoxicity, and nephrotoxicity in the GeneOntology gene/protein database. In this study, we synthesized phthalic acid chemical probes and demonstrated differing protein–protein interactions between MCF-7 cells and MDA-MB-231 breast cancer cell lines. Phthalic acid chemical probes were synthesized using silicon dioxide particle carriers, which were modified using the silanized linker 3-aminopropyl triethoxyslane (APTES). Incubation with cell lysates from breast cancer cell lines revealed interactions between phthalic acid and cellular proteins in MCF-7 and MDA-MB-231 cells. Subsequent proteomics analyses indicated 22 phthalic acid-binding proteins in both cell types, including heat shock cognate 71-kDa protein, ATP synthase subunit beta, and heat shock protein HSP 90-beta. In addition, 21 MCF-7-specific and 32 MDA-MB-231 specific phthalic acid-binding proteins were identified, including related proteasome proteins, heat shock 70-kDa protein, and NADPH dehydrogenase and ribosomal correlated proteins, ras-related proteins, and members of the heat shock protein family, respectively. PMID:25402641

  5. Bioanalytical system for detection of cancer cells with photoluminescent ZnO nanorods

    NASA Astrophysics Data System (ADS)

    Viter, R.; Jekabsons, K.; Kalnina, Z.; Poletaev, N.; Hsu, S. H.; Riekstina, U.

    2016-11-01

    Using photoluminescent ZnO nanorods and carbohydrate marker SSEA-4, a novel cancer cell recognition system was developed. Immobilization of SSEA-4 antibodies (αSSEA-4) on ZnO nanorods was performed in buffer solution (pH = 7.1) over 2 h. The cancer cell line probes were fixed on the glass slide. One hundred microliters of ZnO-αSSEA-4 conjugates were deposited on the cell probe and exposed for 30 min. After washing photoluminescence spectra were recorded. Based on the developed methodology, ZnO-αSSEA-4 probes were tested on patient-derived breast and colorectal carcinoma cells. Our data clearly show that the carbohydrate SSEA-4 molecule is expressed on cancer cell lines and patient-derived cancer cells. Moreover, SSEA-4 targeted ZnO nanorods bind to the patient-derived cancer cells with high selectivity and the photoluminescence signal increased tremendously compared to the signal from the control samples. Furthermore, the photoluminescence intensity increase correlated with the extent of malignancy in the target cell population. A novel portable bioanalytical system, based on optical ZnO nanorods and fiber optic detection system was developed. We propose that carbohydrate SSEA-4 specific ZnO nanorods could be used for the development of cancer diagnostic biosensors and for targeted therapy.

  6. Blue Photoluminescence From Silacyclobutene Compounds

    NASA Astrophysics Data System (ADS)

    Pernisz, Udo

    1999-04-01

    Organosilicon compounds in which the Si atom is bound to an aromatic moiety such as a phenyl group, exhibit strong blue photoluminescence when excited with UV light (for example at a wavelength of 337 nm). This phenomenon was investigated quantitatively at room temperature and at the temperature of liquid nitrogen (78 K) by measuring the emission and excitation spectra of the total luminescence, and of the phosphorescence, for a silacyclobutene compound in which two phenyl groups are joined across the C=C double bond of the ring. The effect of a series of organic substituents on the Si atom was investigated as well as the time dependence of the phosphorescence intensity decay for this class of materials. A tentative model of the energy levels in this compound is proposed. The observation of visible blue emission -- in contrast to photoluminescence in the UV from the aromatic groups -- is explained by the Si-C bond lowering the energy of the molecular orbitals, an effect that is currently under study for a range of Si-containing compounds. Synthesis of the silacyclobutene compounds was performed at the laboratory of Prof. N. Auner, now at J.W. Goethe Universität, Frankfurt, Germany. His contributions, and those of his collaborators, to the work reported here are gratefully acknowledged.

  7. Top-down characterization of nucleic acids modified by structural probes using high-resolution tandem mass spectrometry and automated data interpretation.

    PubMed

    Kellersberger, Katherine A; Yu, Eizadora; Kruppa, Gary H; Young, Malin M; Fabris, Daniele

    2004-05-01

    A top-down approach based on sustained off-resonance irradiation collision-induced dissociation (SORI-CID) has been implemented on an electrospray ionization (ESI) Fourier transform mass spectrometer (FTMS) to characterize nucleic acid substrates modified by structural probes. Solvent accessibility reagents, such as dimethyl sulfate (DMS), 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMCT), and beta-ethoxy-alpha-ketobutyraldehyde (kethoxal, KT) are widely employed to reveal the position of single- vs double-stranded regions and obtain the footprint of bound proteins onto nucleic acids structures. Established methods require end-labeling of the nucleic acid constructs, probe-specific chemistry to produce strand cleavage at the modified nucleotides, and analysis by polyacrylamide gel electrophoresis to determine the position of the susceptible sites. However, these labor-intensive procedures can be avoided when mass spectrometry is used to identify the probe-induced modifications from their characteristic mass signatures. In particular, ESI-FTMS can be directly employed to monitor the conditions of probe application to avoid excessive alkylation, which could induce unwanted distortion or defolding of the substrate of interest. The sequence position of the covalent modifications can be subsequently obtained from classic tandem techniques, which allow for the analysis of individual target adducts present in complex reaction mixtures with no need for separation techniques. Selection and activation by SORI-CID has been employed to reveal the position of adducts in nucleic acid substrates in excess of 6 kDa. The stability of the different covalent modifications under SORI-CID conditions was investigated. Multiple stages of isolation and activation were employed in MS(n)() experiments to obtain the desired sequence information whenever the adduct stability was not particularly favorable, and SORI-CID induced the facile loss of the modified base

  8. Targeting Acidity in Pancreatic Adenocarcinoma: Multispectral Optoacoustic Tomography Detects pH-low Insertion Peptide Probes in vivo

    PubMed Central

    Kimbrough, Charles W; Khanal, Anil; Zeiderman, Matthew; Khanal, Bigya R.; Burton, Neal C; McMasters, Kelly M; Vickers, Selwyn; Grizzle, William E; McNally, Lacey R

    2015-01-01

    Background pH-low Insertion Peptides (pHLIPs) can serve as a targeting moiety that enables pH-sensitive probes to detect solid tumors. Using these probes in conjunction with multispectral optoacoustic tomography (MSOT) is a promising approach to improve imaging for pancreatic cancer. Methods A pH-sensitive pHLIP (V7) was conjugated to 750 NIR fluorescent dye and evaluated as a targeted probe for pancreatic adenocarcinoma. The pH-insensitive K7 pHLIP served as an untargeted control. Probe binding was assessed in vitro at pH 7.4, 6.8, and 6.6 using human pancreatic cell lines S2VP10 and S2013. Using MSOT, semi-quantitative probe accumulation was then assessed in vivo with a murine orthotopic pancreatic adenocarcinoma model. Results In vitro, the V7–750 probe demonstrated significantly higher fluorescence at pH 6.6 compared to pH 7.4 (S2VP10, p=0.0119; S2013, p=0.0160), while no difference was observed with the K7–750 control (S2VP10, p=0.8783; S2013, p=0.921). In the in vivo S2VP10 model, V7–750 probe resulted in 782.5 MSOT a.u. signal compared to 5.3 MSOT a.u. in K7–750 control in tumor (p= 0.0001). Similarly, V7–750 probe signal was 578.3 MSOT a.u. in the S2013 model compared to K7–750 signal at 5.1 MSOT a.u. (p=0.0005). There was minimal off-target accumulation of the V7–750 probe within the liver or kidney, and probe distribution was confirmed with ex vivo imaging. Conclusion Compared to pH-insensitive controls, V7–750 pH-sensitive probe specifically targets pancreatic adenocarcinoma, and has minimal off-target accumulation. The non-invasive detection of pH-targeted probes by means of MSOT represents a promising modality to improve the detection and monitoring of pancreatic cancer. PMID:26124201

  9. Highly Sensitive and Selective Method for Detecting Ultratrace Levels of Aqueous Uranyl Ions by Strongly Photoluminescent-Responsive Amine-Modified Cadmium Sulfide Quantum Dots.

    PubMed

    Dutta, R K; Kumar, Ambika

    2016-09-20

    Detection of ultratrace levels of aqueous uranyl ions without using sophisticated analytical instrumentation and a tedious sample preparation method is a challenge for environmental monitoring and mitigation. Here we present a novel yet simple analytical method for highly sensitive and specific detection of uranyl ions via photoluminescence quenching of CdS quantum dots. We have demonstrated a new approach for synthesizing highly water-soluble and strong photoluminescence-emitting CdS quantum dots (i.e., CdS-MAA and CdS-MAA-TU) of sizes less than 3 nm. The structural, morphological, and optical properties of both the batches of CdS quantum dots were thoroughly characterized by XRD, high-resolution transmission electron microscopy (HRTEM), zeta potential, UV-visible absorption, and photoluminescence spectroscopy. Compared to the batch of CdS quantum dots prepared by capping with only mercaptoacetic acid (CdS-MAA), the batch prepared by capping with mercaptoacetic acid and thiourea in tandem (CdS-MAA-TU) exhibited higher quantum yield= 16.64 ± 1.02%, and more importantly, CdS-MAA-TU exhibited significantly a higher order of photoluminescence quenching responses when treated with ultratrace concentrations of uranyl ions. Under the optimized conditions, the sensitivity of detecting uranyl ion by CdS-MAA-TU was several folds better (0.316 L/ μg) than that of CdS-MAA (0.0053 (L/μg/), as determined from their respective Stern-Volmer plots. Qualitatively, CdS-MAA-TU probe can be used for visual detection of uranyl ions of concentration greater than 5 μg/L. However, the instrumental method of analysis based on photoluminescence spectroscopy confirmed the feasibility for quantitative analysis of ultratrace concentrations of uranyl ions as implied from a very low limit of detection (LoD = 0.07 μg/L) and limit of quantification (LoQ = and 0.231 μg/L). Systematic studies revealed very high selectivity for uranyl ion detection, though minor interference from Cu(2+), Pb(2

  10. A peptide nucleic acid-functionalized carbon nitride nanosheet as a probe for in situ monitoring of intracellular microRNA.

    PubMed

    Liao, Xianjiu; Wang, Quanbo; Ju, Huangxian

    2015-06-21

    A novel probe for recognition of both cancer cells and intracellular microRNA (miRNA) is designed by functionalizing a carbon nitride nanosheet (f-CNNS) with a Cy5-labeled peptide nucleic acid (Cy5-PNA) and folate. The interaction between Cy5-PNA and CNNS quenches the fluorescence of Cy5, and the presence of folate endows the probe with good specificity to folate acceptor overexpressed cells. The probe can be specifically taken up by cancer cells with an incubation step. Upon the recognition of the PNA to complementary miRNA, the hybridization product is released from the CNNS surface, which leads to the fluorescence recovery and provides a specific method for sensing of miRNA. Thus, this probe can be used for cell-specific intracellular miRNA sensing with a confocal microscope. Using miRNA-18a as a target model, the dynamic changes of its expression level inside living cells can be monitored with the proposed method. This method possesses promising applications in the study of miRNA related bioprocesses and biomedicine.

  11. Simultaneous brain and blood microdialysis study with a new removable venous probe. Serotonin and 5-hydroxyindolacetic acid changes after D-norfenfluramine or fluoxetine.

    PubMed

    Páez, X; Hernández, L

    1996-01-01

    A removable intravenous microdialysis probe was developed and simultaneously used with a removable microdialysis probe placed in the lateral hypothalamus (LH). Serotonin (5-HT) and 5-hydroxyindoleacetic acid (5-HIAA) changes in blood and brain dialysates were measured by HPLC-EC after an i.p. injection of 5 mg/kg d-norfenfluramine (dNF) or 10 mg/kg fluoxetine (FLU) in freely moving rats. 5-HT in the LH significantly increased after both drugs, but the rise was larger and faster with dNF [F(7,28)=4.0 p<0.05] than with FLU [F(5,20)=5.0 p<0.01]. By contrast, in venous blood 5-HT increased after FLU [F(5,20)=2.96 p<0.05] but not after dNF. 5-HIAA after both drugs continued decreasing significantly in the LH [dNF F(7,28)=11.4 p<0.01; FLU F(5,20)=22.8 p<0.01], but it did not change in blood. Simultaneous dialysis in brain and blood allowed evaluation of the differential effects of dNF and FLU on 5-HT and 5-HIAA in the two places. Removable venous probes prevented the inflammatory reaction that may occur around permanently implanted probes, and the dialysis could be more efficient and with less risk of clogging.

  12. A label-free fluorescent probe based on DNA-templated silver nanoclusters and exonuclease III-assisted recycling amplification detection of nucleic acid.

    PubMed

    Yang, Wen; Tian, Jianniao; Ma, Yefei; Wang, Lijun; Zhao, Yanchun; Zhao, Shulin

    2015-11-01

    A number of specific nucleic acids are closely related with many serious diseases, in the current research, a platform taking advantage of exonuclease III (Exo III) to realize double recycling amplification and label-free fluorescent DNA-templated silver nanoclusters (DNA-AgNCs) for detecting of nucleic acid had been developed. In this method, a molecular beacon (MB) with 3'-protruding termini and a single-stranded cytosine-rich (C-rich) probe were designed that coexist stably with Exo III. Once the target DNA appeared, portion of the MB could hybridize with target DNA and was digested by Exo III, which allowed the release of target DNA and a residual sequence. Subsequently, the residual sequence could trigger the Exo III to digest C-rich probe, and the DNA-AgNCs was not able to be synthesized because of the C-rich probe was destroyed; finally the fluorescent of solution was quenched. This assay enables to monitor human hemochromatosis gene (as a model) with high sensitivity, the detection limit is as low as 120 pM compared with other fluorescence DNA-AgNCs methods, this assay also exhibits superior specificity even against single base mismatch. The strategy is applied to detect human hemochromatosis gene in real human serum samples successfully. PMID:26572843

  13. A label-free fluorescent probe based on DNA-templated silver nanoclusters and exonuclease III-assisted recycling amplification detection of nucleic acid.

    PubMed

    Yang, Wen; Tian, Jianniao; Ma, Yefei; Wang, Lijun; Zhao, Yanchun; Zhao, Shulin

    2015-11-01

    A number of specific nucleic acids are closely related with many serious diseases, in the current research, a platform taking advantage of exonuclease III (Exo III) to realize double recycling amplification and label-free fluorescent DNA-templated silver nanoclusters (DNA-AgNCs) for detecting of nucleic acid had been developed. In this method, a molecular beacon (MB) with 3'-protruding termini and a single-stranded cytosine-rich (C-rich) probe were designed that coexist stably with Exo III. Once the target DNA appeared, portion of the MB could hybridize with target DNA and was digested by Exo III, which allowed the release of target DNA and a residual sequence. Subsequently, the residual sequence could trigger the Exo III to digest C-rich probe, and the DNA-AgNCs was not able to be synthesized because of the C-rich probe was destroyed; finally the fluorescent of solution was quenched. This assay enables to monitor human hemochromatosis gene (as a model) with high sensitivity, the detection limit is as low as 120 pM compared with other fluorescence DNA-AgNCs methods, this assay also exhibits superior specificity even against single base mismatch. The strategy is applied to detect human hemochromatosis gene in real human serum samples successfully.

  14. Giant blue shifted photoluminescence peak from the edges of CVD grown monolayer MoS2

    NASA Astrophysics Data System (ADS)

    Yore, Alexander; Crumrine, Wendy; Smithe, Kirby; Pop, Eric; Wang, Bin; Newaz, Akm

    To probe the electronic and optical properties of direct band-gap monolayer transition metal dichalcogenides, such as band structure and excitons, micro-photoluminescence spectroscopy has become an attractive and standard tool. Here, we present our experimental work on spatial scanning of photoluminescence of monolayer MoS2 grown by chemical vapor deposition (CVD) using an ultrasmall blue laser (wavelength 405 nm) beam spot with beam diameter as small as ~ 200 nm. We have observed a giant blue shift, as large as ~ 40 nm or ~ 100 meV, of the A-excitonic peak in the photoluminescence spectra from the edges when compared to luminescence from the inside. This giant blue shift may result from the following: (i) compressive strain at the edges; (ii) the enhanced dielectric screening caused by the increased electron density at the metallic Mo-edges; and (iii) chemical impurities.

  15. Assessing the acidity of high silica chabazite H-SSZ-13 by FTIR using CO as molecular probe: Comparison with H-SAPO-34.

    PubMed

    Bordiga, Silvia; Regli, Laura; Cocina, Donato; Lamberti, Carlo; Bjørgen, Morten; Lillerud, Karl Petter

    2005-02-24

    Zeolitic materials based on the chabazite topology, such as H-SAPO-34, possess unique shape-selectivity properties for converting methanol into light olefins. In addition to the topology, zeolite acidity is inherently linked to catalyst activity and selectivity. The acidic properties of high silica chabazite (H-SSZ-13) have attracted much attention in the past decade because the material represents an idealized model system having one acidic site per cage. Conclusions drawn so far have essentially been founded on quantum chemical methods. An experimentally based benchmark of the acidity of H-SSZ-13 has hitherto not been available. In this work, transmission FTIR spectroscopy provides a description of the different acidic sites of H-SSZ-13 by using CO as molecular probe at 70 K. The results demonstrate that H-SSZ-13 is a strongly Brønsted acidic material, essentially having two distinct families of acidic sites. In contrast to numerous preceding reports, we find it fundamental to consider proton distributions among all four possible sites, and do not delimit the interpretations to only two sites. The present data consistently suggest the most abundant family of protons to have three members being located on different crystalline positions on the eight-membered-ring window giving access to the chabazite cage. Consequently, these protons are exposed to two neighboring cages. The second, and less abundant family, is constituted by only one site that is situated on the six-membered ring defining the top/bottom of the barrel-shaped chabazite cage. This proton is therefore only exposed to one cage and requires a higher CO pressure to form adducts. Toward CO, both families of sites possess the same acidity. Parallel experiments were also carried out for the isostructural and commercially important H-SAPO-34 having an equal density of acidic sites. This is the first attempt to directly compare, on an experimental basis, the acidity of these two materials.

  16. Assessing the acidity of high silica chabazite H-SSZ-13 by FTIR using CO as molecular probe: Comparison with H-SAPO-34.

    PubMed

    Bordiga, Silvia; Regli, Laura; Cocina, Donato; Lamberti, Carlo; Bjørgen, Morten; Lillerud, Karl Petter

    2005-02-24

    Zeolitic materials based on the chabazite topology, such as H-SAPO-34, possess unique shape-selectivity properties for converting methanol into light olefins. In addition to the topology, zeolite acidity is inherently linked to catalyst activity and selectivity. The acidic properties of high silica chabazite (H-SSZ-13) have attracted much attention in the past decade because the material represents an idealized model system having one acidic site per cage. Conclusions drawn so far have essentially been founded on quantum chemical methods. An experimentally based benchmark of the acidity of H-SSZ-13 has hitherto not been available. In this work, transmission FTIR spectroscopy provides a description of the different acidic sites of H-SSZ-13 by using CO as molecular probe at 70 K. The results demonstrate that H-SSZ-13 is a strongly Brønsted acidic material, essentially having two distinct families of acidic sites. In contrast to numerous preceding reports, we find it fundamental to consider proton distributions among all four possible sites, and do not delimit the interpretations to only two sites. The present data consistently suggest the most abundant family of protons to have three members being located on different crystalline positions on the eight-membered-ring window giving access to the chabazite cage. Consequently, these protons are exposed to two neighboring cages. The second, and less abundant family, is constituted by only one site that is situated on the six-membered ring defining the top/bottom of the barrel-shaped chabazite cage. This proton is therefore only exposed to one cage and requires a higher CO pressure to form adducts. Toward CO, both families of sites possess the same acidity. Parallel experiments were also carried out for the isostructural and commercially important H-SAPO-34 having an equal density of acidic sites. This is the first attempt to directly compare, on an experimental basis, the acidity of these two materials. PMID:16851287

  17. Identification of PCR-amplified genetically modified organisms (GMOs) DNA by peptide nucleic acid (PNA) probes in anion-exchange chromatographic analysis.

    PubMed

    Rossi, Stefano; Lesignoli, Francesca; Germini, Andrea; Faccini, Andrea; Sforza, Stefano; Corradini, Roberto; Marchelli, Rosangela

    2007-04-01

    PCR products obtained by selective amplification of transgenic DNA derived from food samples containing Roundup Ready soybean or Bt-176 maize have been analyzed by anion-exchange HPLC. Peptide nucleic acids (PNAs), oligonucleotide analogues known to bind to complementary single-stranded DNA with high affinity and specificity, have been used as specific probes in order to assess the identity of the peaks observed. Two different protocols were adopted in order to obtain single-stranded DNA: amplification with an excess of one primer or digestion of one DNA strand. The single-stranded DNA was mixed with the PNA probe, and the presence of a specific sequence was revealed through detection of the corresponding PNA:DNA peak with significantly different retention time. Advantages and limits of this approach are discussed. The method was tested with reference materials and subsequently applied to commercial samples.

  18. Thioglycolic Acid-Capped CdS Quantum Dots Conjugated to α-Amylase as a Fluorescence Probe for Determination of Starch at Low Concentration.

    PubMed

    Tayebi, Mahnoush; Tavakkoli Yaraki, Mohammad; Mogharei, Azadeh; Ahmadieh, Mahnaz; Tahriri, Mohammadreza; Vashaee, Daryoosh; Tayebi, Lobat

    2016-09-01

    In the present research, water soluble thioglycolic acid-capped CdS quantum dots (QDs) were synthesized by chemical precipitation method. The characteristics of prepared quantum dots were determined using X-Ray Diffraction (XRD) and Transmission Electron Microscopy (TEM). The obtained results revealed that CdS QDs have 5.60 nm crystallite size, hexagonal wurtzite structure and spherical morphology with less than 10 nm diameter. The photoluminescence (PL) spectroscopy was performed in order to study the effect of the presence of starch solutions. Blue emission peaks were positioned at 488 nm and its intensity quenched by increasing the concentration of starch solutions. The result of PL quenches in range of studied concentrations (0-100 ppm) was best described by Michaelis-Menten model. The amount of Michaelis constant (Km) for immobilized α-amylase in this system was about 68.08 ppm which showed a great tendency of enzyme to hydrolyze the starch as substrate. Finally, the limit of detection (LOD) was found to be about 2.24 ppm. PMID:27392974

  19. Analysis of oxyluciferin photoluminescence pathways in aqueous solutions.

    PubMed

    Hiyama, Miyabi; Mochizuki, Toshimitsu; Akiyama, Hidefumi; Koga, Nobuaki

    2015-01-01

    We evaluated the pK(a) values of oxyluciferin and its conjugate acids and bases theoretically with the help of experimental correction values, from which free energies for the first excited and the ground states of all the species were estimated. On the basis of these results, we calculated pH-dependent absorption spectra, where the relative absorption intensities of various species strongly depend on photoexcitation energy, and we further analyzed the photoluminescence pathways of oxyluciferin in aqueous solutions with various pH. In the case of 350 nm photoexcitation, in particular, experiments have shown that dominant emission color is green and it attenuates with pH decreasing, while blue (3 < pH < 8) and red (pH < 3) emissions appear. Our present results clarify the pathways of these photoluminescence depending on the pH values and thus should be useful in further analyses of photoluminescence pathways for other photoexcitation wavelength in comparison with experiments. PMID:25334091

  20. Cellular delivery of quantum dot-bound hybridization probe for detection of intracellular pre-microRNA using chitosan/poly(γ-glutamic acid) complex as a carrier.

    PubMed

    Geng, Yao; Lin, Dajie; Shao, Lijia; Yan, Feng; Ju, Huangxian

    2013-01-01

    A quantum dot (QD)-bound hybridization probe was designed for detection of intracellular pre-miRNA using chitosan (CS)/poly(γ-glutamic acid) (γ-PGA) complex as a gene vector. The probe was prepared by assembling thiolated RNA to gold nanoparticle (Au NP) via Au-S bond and then binding 3'-end amine of the RNA to the carboxy group capped on quantum dot surface. The QD-RNA-Au NP probe was assembled on the vector by mixing with aqueous γ-PGA solution and then CS solution to construct a gene delivery system for highly effective cellular uptake and delivery. After the probe was released from CS/γ-PGA complex to the cytoplasm by electrostatic repulsion at intracellular pH, it hybridized with pre-miRNA precursor as target. The formed product was then cleaved by RNase III Dicer, leading to the separation of QDs from Au NPs and fluorescence emission of QDs, which could be detected by confocal microscopic imaging to monitor the amount of the intracellular pre-miRNA precursor. The in vitro assays revealed that the QD-RNA-Au NP was a robust, sensitive and selective probe for quantitative detection of target pre-miRNA. Using MDA-MB231 and MCF-7 breast cancer cells as models, the relative amount of pre-miRNA let-7a could be successfully compared. Since the amount of miRNA is related to the progress and prognosis of cancer, this strategy could be expected to hold promising application potential in medical research and clinical diagnostics.

  1. A naphthalene-based two-photon fluorescent probe for selective and sensitive detection of endogenous hypochlorous acid.

    PubMed

    Zhou, Xiao-Hong; Jiang, Yu-Ren; Zhao, Xiong-Jie; Guo, Dong

    2016-11-01

    An efficient naphthalene-based two-photon fluorescent probe for endogenous HClO has been reported in the present study, which consists of a 6-(2-benzothiazolyl)-2-naphthalenol fluorophore connected with a 4-aminophenol (the fluorescence quenching and response group). This probe exhibits a high selectivity and excellent sensitivity with a detection limit of 7.6nM over other reactive oxygen species and analyte species, and the fluorescence intensity enhanced 103-fold when responsed. Furthermore, it was successfully used for two-photon imaging of endogenous HClO in live cells with high-resolution. PMID:27591640

  2. A naphthalene-based two-photon fluorescent probe for selective and sensitive detection of endogenous hypochlorous acid.

    PubMed

    Zhou, Xiao-Hong; Jiang, Yu-Ren; Zhao, Xiong-Jie; Guo, Dong

    2016-11-01

    An efficient naphthalene-based two-photon fluorescent probe for endogenous HClO has been reported in the present study, which consists of a 6-(2-benzothiazolyl)-2-naphthalenol fluorophore connected with a 4-aminophenol (the fluorescence quenching and response group). This probe exhibits a high selectivity and excellent sensitivity with a detection limit of 7.6nM over other reactive oxygen species and analyte species, and the fluorescence intensity enhanced 103-fold when responsed. Furthermore, it was successfully used for two-photon imaging of endogenous HClO in live cells with high-resolution.

  3. Changing interfaces: Photoluminescent ZnO nanoparticle powders in different aqueous environments

    NASA Astrophysics Data System (ADS)

    Kocsis, Krisztina; Niedermaier, Matthias; Bernardi, Johannes; Berger, Thomas; Diwald, Oliver

    2016-10-01

    We transformed vapor phase grown ZnO nanoparticle powders into aqueous ZnO nanoparticle dispersions and studied the impact of associated microstructure and interface property changes on their spectroscopic properties. With photoluminescence (PL) spectroscopy, we probed oxygen interstitials Oi2 - in the near surface region and tracked their specific PL emission response at hvEM = 2.1 eV during the controlled conversion of the solid-vacuum into the solid-liquid interface. While oxygen adsorption via the gas phase does affect the intensity of the PL emission bands, the O2 contact with ZnO nanoparticles across the solid-liquid interface does not. Moreover, we found that the near band edge emission feature at hvEM = 3.2 eV gains relative intensity with regard to the PL emission features in the visible light region. Searching for potential PL indicators that are specific to early stages of particle dissolution, we addressed for aqueous ZnO nanoparticle dispersions the effect of formic acid adsorption. In the absence of related spectroscopic features, we were able to consistently track ZnO nanoparticle dissolution and the concomitant formation of solvated Zinc formate species by means of PL and FT-IR spectroscopy, dynamic light scattering, and zeta potential measurements. For a more consistent and robust assessment of nanoparticle properties in different continuous phases, we discuss characterization challenges and potential pitfalls that arise upon replacing the solid-gas with the solid-liquid interface.

  4. Sensing of a nucleic acid binding protein via a label-free perylene probe fluorescence recovery assay.

    PubMed

    Liao, Dongli; Li, Wenying; Chen, Jian; Jiao, Huping; Zhou, Huipeng; Wang, Bin; Yu, Cong

    2013-10-01

    A novel label-free fluorescence recovery assay for the sensing of a DNA binding protein has been developed. A transcription factor c-Jun protein, and a 21 base pair duplex DNA containing the c-Jun protein binding site (J-DNA) were selected. J-DNA was mixed with a cationic fluorescent perylene probe (compound 1), and induced aggregation of the probe. Quenching of the probe's fluorescence was observed. However, when c-Jun protein was mixed with the J-DNA, c-Jun bound to the duplex DNA, which reduced the degree of the induced perylene probe aggregation, and a turn on fluorescence signal was observed. The recovered fluorescence intensity was directly related to the amount of c-Jun added. The method is highly selective, six non-DNA binding proteins and one randomly selected 21 base pair duplex DNA (con-1) were tested. No noticeable compound 1 fluorescence recovery was observed. Mutations were also introduced to the c-Jun recognition sequence and much reduced fluorescence recovery was observed. Our assay is label-free, convenient, inexpensive, and fast. It can be used in biomedical research such as high throughput screening of drugs targeted at DNA-binding proteins.

  5. Time-Resolved Photoluminescence and Photovoltaics

    SciTech Connect

    Metzger, W. K.; Ahrenkiel, R. K.; Dippo, P.; Geisz, J.; Wanlass, M. W.; Kurtz, S.

    2005-01-01

    The time-resolved photoluminescence (TRPL) technique and its ability to characterize recombination in bulk photovoltaic semiconductor materials are reviewed. Results from a variety of materials and a few recent studies are summarized and compared.

  6. Sensitive, Efficient Quantitation of 13C-Enriched Nucleic Acids via Ultrahigh-Performance Liquid Chromatography–Tandem Mass Spectrometry for Applications in Stable Isotope Probing

    PubMed Central

    Wilhelm, Roland; Szeitz, András; Klassen, Tara L.

    2014-01-01

    Stable isotope probing (SIP) of nucleic acids is a powerful tool for studying the functional traits of microbial populations within complex communities, but SIP involves a number of technical challenges. Many of the difficulties in DNA-SIP and RNA-SIP experiments can be effectively overcome with an efficient, sensitive method for quantitating the isotopic enrichment of nucleic acids. Here, we present a sensitive method for quantitating 13C enrichment of nucleic acids, requiring a few nanograms of sample, and we demonstrate its utility in typical DNA-SIP and RNA-SIP experiments. All five nucleobases (adenine, guanine, cytosine, thymine, and uracil) were separated and detected by using ultrahigh-performance liquid chromatography–tandem mass spectrometry. We detected all isotopic species in samples with as low as 1.5 atom% 13C above natural abundance, using 1-ng loadings. Quantitation was used to characterize the isotopic enrichment kinetics of cellulose- and lignin-based microcosm experiments and to optimize the recovery of enriched nucleic acids. Application of our method will minimize the quantity of expensive isotopically labeled substrates required and reduce the risk of failed experiments due to insufficient recovery of labeled nucleic acids for sequencing library preparation. PMID:25217022

  7. Sensitive, Efficient Quantitation of 13C-Enriched Nucleic Acids via Ultrahigh-Performance Liquid Chromatography-Tandem Mass Spectrometry for Applications in Stable Isotope Probing.

    PubMed

    Wilhelm, Roland; Szeitz, András; Klassen, Tara L; Mohn, William W

    2014-12-01

    Stable isotope probing (SIP) of nucleic acids is a powerful tool for studying the functional traits of microbial populations within complex communities, but SIP involves a number of technical challenges. Many of the difficulties in DNA-SIP and RNA-SIP experiments can be effectively overcome with an efficient, sensitive method for quantitating the isotopic enrichment of nucleic acids. Here, we present a sensitive method for quantitating (13)C enrichment of nucleic acids, requiring a few nanograms of sample, and we demonstrate its utility in typical DNA-SIP and RNA-SIP experiments. All five nucleobases (adenine, guanine, cytosine, thymine, and uracil) were separated and detected by using ultrahigh-performance liquid chromatography-tandem mass spectrometry. We detected all isotopic species in samples with as low as 1.5 atom% (13)C above natural abundance, using 1-ng loadings. Quantitation was used to characterize the isotopic enrichment kinetics of cellulose- and lignin-based microcosm experiments and to optimize the recovery of enriched nucleic acids. Application of our method will minimize the quantity of expensive isotopically labeled substrates required and reduce the risk of failed experiments due to insufficient recovery of labeled nucleic acids for sequencing library preparation.

  8. Detection of hydrofluoric acid by a SiO2 sol-gel coating fiber-optic probe based on reflection-based localized surface plasmon resonance.

    PubMed

    Chen, I-Cherng; Lin, Shiu-Shiung; Lin, Tsao-Jen; Du, Je-Kang

    2011-01-01

    A novel fiber-optic probe based on reflection-based localized surface plasmon resonance (LSPR) was developed to quantify the concentration of hydrofluoric acid (HF) in aqueous solutions. The LSPR sensor was constructed with a gold nanoparticle-modified PMMA fiber, integrated with a SiO(2) sol-gel coating. This fiber-sensor was utilized to assess the relationship between HF concentration and SiO(2) sol-gel layer etching reduction. The results demonstrated the LSPR sensor was capable of detecting HF-related erosion of hydrofluoric acid solutions of concentrations ranging from 1% to 5% using Relative RI Change Rates. The development of the LSPR sensor constitutes the basis of a detector with significant sensitivity for practical use in monitoring HF solution concentrations.

  9. Detection of Hydrofluoric Acid by a SiO2 Sol-Gel Coating Fiber-Optic Probe Based on Reflection-Based Localized Surface Plasmon Resonance

    PubMed Central

    Chen, I-Cherng; Lin, Shiu-Shiung; Lin, Tsao-Jen; Du, Je-Kang

    2011-01-01

    A novel fiber-optic probe based on reflection-based localized surface plasmon resonance (LSPR) was developed to quantify the concentration of hydrofluoric acid (HF) in aqueous solutions. The LSPR sensor was constructed with a gold nanoparticle-modified PMMA fiber, integrated with a SiO2 sol-gel coating. This fiber-sensor was utilized to assess the relationship between HF concentration and SiO2 sol-gel layer etching reduction. The results demonstrated the LSPR sensor was capable of detecting HF-related erosion of hydrofluoric acid solutions of concentrations ranging from 1% to 5% using Relative RI Change Rates. The development of the LSPR sensor constitutes the basis of a detector with significant sensitivity for practical use in monitoring HF solution concentrations. PMID:22319388

  10. Assay of the human liver citric acid cycle probe phenylacetylglutamine and of phenylacetate in plasma by gas chromatography-mass spectrometry.

    PubMed

    Yang, D; Beylot, M; Agarwal, K C; Soloviev, M V; Brunengraber, H

    1993-07-01

    Phenylacetate, derived from phenylalanine, is converted in human and primate liver to phenylacetylglutamine. The latter has been used to assess the labeling pattern of liver citric acid cycle intermediates. We present gas chromatographic-mass spectrometric assays of phenylacetylglutamine, phenylacetate, and phenylalanine in biological fluids. The compounds are derivatized with dimethylformamide dimethyl acetal. Limits of detection are 0.1 nmol for phenylacetylglutamine and phenylacetate and 2 nmol for phenylalanine. Baseline plasma concentrations of phenylacetate and phenylacetylglutamine and 1 and 3 microM, respectively. The 24-h urinary excretions of phenylacetate and phenylacetylglutamine are about 4 mumol and 1 mmol, respectively. Ingestion of phenylalanine (in the form of aspartame) by a human is followed by sequential increases in phenylacetate and phenylacetylglutamine concentrations in plasma and urine. This assay opens the way to noninvasive probing of the 13C-labeling pattern of liver citric acid cycle intermediates in humans.

  11. Differentiating among plant spectra by combining pH dependent photoluminescence spectroscopy with multi-way principal component analysis (MPCA)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Knowing the botanical composition of the standing crop is essential for managing ecosystem health and herbivory. Photoluminescence spectroscopic probes offer the potential for real-time measurements of animal diet composition. Spectral emission signatures (excitation at 365 nm) from three different ...

  12. Isolation of a human anti-haemophilic factor IX cDNA clone using a unique 52-base synthetic oligonucleotide probe deduced from the amino acid sequence of bovine factor IX.

    PubMed

    Jaye, M; de la Salle, H; Schamber, F; Balland, A; Kohli, V; Findeli, A; Tolstoshev, P; Lecocq, J P

    1983-04-25

    A unique 52mer oligonucleotide deduced from the amino acid sequence of bovine Factor IX was synthesized and used as a probe to screen a human liver cDNA bank. The Factor IX clone isolated shows 5 differences in nucleotide and deduced amino acid sequence as compared to a previously isolated clone. In addition, precisely one codon has been deleted.Images

  13. Photoluminescence Mechanism of DNA-Templated Silver Nanoclusters: Coupling between Surface Plasmon and Emitter and Sensing of Lysozyme.

    PubMed

    Liu, Xiaorong; Hu, Ruoxin; Gao, Zhidan; Shao, Na

    2015-06-01

    DNA-templated silver nanoclusters (DNA-AgNCs) have now been thrust into the limelight with their superior optical properties and potential biological applications. However, the origin of photoluminescence from DNA-AgNCs still remains unclear. In this work, DNA-AgNCs were synthesized and the photoluminescence properties as well as the biosensing applications of the designed DNA-AgNCs were investigated. The photoluminescence properties of the DNA-AgNCs were studied under three regions of excitation wavelength based on the UV-visible absorption spectra. It was deemed that the photoluminescence originated from coupling between the surface plasmon and the emitter in AgNCs when they were excited by visible light above 500 nm, and thus the emission wavelength varied with changing the excitation wavelength. The photoluminescence of the red-emitting-only AgNCs was the intrinsic fluorescence when excited from 200 to 400 nm, which was only related to the emitter; but for two components of blue- and red-emitting AgNCs, the emission wavelength varied with the excitation wavelength ranging from 300 to 360 nm, and the photoluminescence was a coupling between the surface plasmon and the emitter. The photoluminescence was only related to the surface plasmon when the AgNCs were excited from 400 to 500 nm. Four DNA probes were designed and each contained two parts: one part was the template used to synthesize AgNCs and it was same to all, and the other part was the lysozyme binding DNA (LBD) used to bind lysozyme and two kinds of LBD were studied. It was deemed that the difference in DNA bases, sequence, and secondary structure caused the synthesized DNA-AgNCs to be different in photoluminescence properties and sensing ability to lysozyme, and the sensing mechanism based on photoluminescence enhancement was also presented. This work explored the origin of photoluminescence and the sensing ability of DNA-AgNCs, and is hoped to make a better understanding of this kind of

  14. Analysis of cytochrome P450 metabolites of arachidonic acid by stable isotope probe labeling coupled with ultra high-performance liquid chromatography/mass spectrometry.

    PubMed

    Zhu, Quan-Fei; Hao, Yan-Hong; Liu, Ming-Zhou; Yue, Jiang; Ni, Jian; Yuan, Bi-Feng; Feng, Yu-Qi

    2015-09-01

    Cytochrome P450 metabolites of arachidonic acid (AA) belong to eicosanoids and are potent lipid mediators of inflammation. It is well-known that eicosanoids play an important role in numerous pathophysiological processes. Therefore, quantitative analysis of cytochrome P450 metabolites of AA, including hydroxyeicosatetraenoic acids (HETEs), epoxyeicosatreinoic acids (EETs), and dihydroxyeicosatrienoic acids (DHETs) can provide crucial information to uncover underlying mechanisms of cytochrome P450 metabolites of AA related diseases. Herein, we developed a highly sensitive method to identify and quantify HETEs, EETs, and DHETs in lipid extracts of biological samples based on stable isotope probe labeling coupled with ultra high-performance liquid chromatography/mass spectrometry. To this end, a pair of stable isotope probes, 2-dimethylaminoethylamine (DMED) and d4-2-dimethylaminoethylamine (d4-DMED), were utilized to facilely label eicosanoids. The heavy labeled eicosanoid standards were prepared and used as internal standards for quantification to minimize the matrix and ion suppression effects in mass spectrometry analysis. In addition, the detection sensitivities of DMED labeled eicosanoids improved by 3-104 folds in standard solution and 5-138 folds in serum matrix compared with unlabeled analytes. Moreover, a good separation of eicosanoids isomers was achieved upon DMED labeling. The established method provided substantial sensitivity (limit of quantification at sub-picogram), high specificity, and broad linear dynamics range (3 orders of magnitude). We further quantified cytochrome P450 metabolites of AA in rat liver, heart, brain tissues and human serum using the developed method. The results showed that 19 eicosanoids could be distinctly detected and the contents of 11-, 15-, 16-, 20-HETE, 5,6-EET, and 14,15-EET in type 2 diabetes mellitus patients and 5-, 11-, 12-, 15-, 16-, 20-HETE, 8,9-EET, and 5,6-DHET in myeloid leukemia patients had significant changes

  15. Incorporation of extra amino acids in peptide recognition probe to improve specificity and selectivity of an electrochemical peptide-based sensor.

    PubMed

    Zaitouna, Anita J; Maben, Alex J; Lai, Rebecca Y

    2015-07-30

    We investigated the effect of incorporating extra amino acids (AA) at the n-terminus of the thiolated and methylene blue-modified peptide probe on both specificity and selectivity of an electrochemical peptide-based (E-PB) HIV sensor. The addition of a flexible (SG)3 hexapeptide is, in particular, useful in improving sensor selectivity, whereas the addition of a highly hydrophilic (EK)3 hexapeptide has shown to be effective in enhancing sensor specificity. Overall, both E-PB sensors fabricated using peptide probes with the added AA (SG-EAA and EK-EAA) showed better specificity and selectivity, especially when compared to the sensor fabricated using a peptide probe without the extra AA (EAA). For example, the selectivity factor recorded in the 50% saliva was ∼2.5 for the EAA sensor, whereas the selectivity factor was 7.8 for both the SG-EAA and EK-EAA sensors. Other sensor properties such as the limit of detection and dynamic range were minimally affected by the addition of the six AA sequence. The limit of detection was 0.5 nM for the EAA sensor and 1 nM for both SG-EAA and EK-EAA sensors. The saturation target concentration was ∼200 nM for all three sensors. Unlike previously reported E-PB HIV sensors, the peptide probe functions as both the recognition element and antifouling passivating agent; this modification eliminates the need to include an additional antifouling diluent, which simplifies the sensor design and fabrication protocol.

  16. Fluorescence sensing of phosdrin pesticide by the luminescent Eu(III)- and Tb(III)-bis(coumarin-3-carboxylic acid) probes

    NASA Astrophysics Data System (ADS)

    Hussein, Belal H. M.; Khairy, Gasser M.; Kamel, Rasha M.

    2016-04-01

    Luminescence quenching of the Eu(III)- and Tb(III)-bis (coumarin-3-carboxylic acid) (Ln(III)-(CCA)2) probes has been studied in the presence of organophosphorus or organochlorine pesticides; Phosdrin (P1), Malathion (P2), Profenofos (P3), Formothion (P4), Heptachlor (P5), and Endosulfan (P6). The luminescence intensity of lanthanide complex probes Ln(III)-(CCA)2 decreases as the concentration of the Phosdrin pesticide increases, while the other investigated pesticides have no significant influence on the lanthanide fluorescent intensities. It is observed that the quenching of Eu(III) and Tb(III)-coumarin-3-carboxylic acid by Phosdrin proceeds via static quenching processes according to Stern-Volmer plot. The binding constants (K) and the thermodynamic parameters of the interaction of Ln(III)-(CCA)2 with Phosdrin have been determined. A direct method for the determination of the Phosdrin in ethanol has been developed based on the luminescence changes of the Ln(III)-(CCA)2-phosdrin ternary complexes. The detection limits of P1 were 6.28 and 1.07 μM in case of Eu(III) and Tb(III)-complex, respectively. The influence of various interfering species on the detection of P1 has been investigated to assess the analytical applicability of the method. The new method was applied to determine the Phosdrin pesticide in different types of water samples.

  17. Fluorescence sensing of phosdrin pesticide by the luminescent Eu(III)- and Tb(III)-bis(coumarin-3-carboxylic acid) probes.

    PubMed

    Hussein, Belal H M; Khairy, Gasser M; Kamel, Rasha M

    2016-04-01

    Luminescence quenching of the Eu(III)- and Tb(III)-bis (coumarin-3-carboxylic acid) (Ln(III)-(CCA)2) probes has been studied in the presence of organophosphorus or organochlorine pesticides; Phosdrin (P1), Malathion (P2), Profenofos (P3), Formothion (P4), Heptachlor (P5), and Endosulfan (P6). The luminescence intensity of lanthanide complex probes Ln(III)-(CCA)2 decreases as the concentration of the Phosdrin pesticide increases, while the other investigated pesticides have no significant influence on the lanthanide fluorescent intensities. It is observed that the quenching of Eu(III) and Tb(III)-coumarin-3-carboxylic acid by Phosdrin proceeds via static quenching processes according to Stern-Volmer plot. The binding constants (K) and the thermodynamic parameters of the interaction of Ln(III)-(CCA)2 with Phosdrin have been determined. A direct method for the determination of the Phosdrin in ethanol has been developed based on the luminescence changes of the Ln(III)-(CCA)2-phosdrin ternary complexes. The detection limits of P1 were 6.28 and 1.07 μM in case of Eu(III) and Tb(III)-complex, respectively. The influence of various interfering species on the detection of P1 has been investigated to assess the analytical applicability of the method. The new method was applied to determine the Phosdrin pesticide in different types of water samples.

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

    PubMed

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

    2015-02-25

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

  19. Probing the general time scale question of boronic acid binding with sugars in aqueous solution at physiological pH.

    PubMed

    Ni, Nanting; Laughlin, Sarah; Wang, Yingji; Feng, You; Zheng, Yujun; Wang, Binghe

    2012-05-01

    The boronic acid group is widely used in chemosensor design due to its ability to reversibly bind diol-containing compounds. The thermodynamic properties of the boronic acid-diol binding process have been investigated extensively. However, there are few studies of the kinetic properties of such binding processes. In this report, stopped-flow method was used for the first time to study the kinetic properties of the binding between three model arylboronic acids, 4-, 5-, and 8-isoquinolinylboronic acids, and various sugars. With all the boronic acid-diol pairs examined, reactions were complete within seconds. The k(on) values with various sugars follow the order of D-fructose>D-tagatose>D-mannose>D-glucose. This trend tracks the thermodynamic binding affinities for these sugars and demonstrates that the 'on' rate is the key factor determining the binding constant.

  20. Electrospun fluorescein/polymer composite nanofibers and their photoluminescent properties

    NASA Astrophysics Data System (ADS)

    Zhang, Zhi-Hua; Long, Yun-Ze; Yin, Hong-Xin; Sun, Bin; Zheng, Jie; Zhang, Hong-Di; Ji, Xin-Ming; Gu, Chang-Zhi

    2012-09-01

    Fluorescein/polyvinyl pyrrolidone (PVP) composite nanofibers with different fluorescein loadings (with a weight concentration of 0-5.0%) are fabricated via electrospinning. Morphologies, structures and photoluminescent (PL) properties of these straight, helical or wavelike fibers are characterized by scanning electron microscopy (SEM), fluorescence microscopy and a spectrophotometer. It is found that the maximum emission of the as-spun fluorescein/PVP fibers occurs at 510 nm. The PL intensity of the composite fiber increases with fluorescein concentration, then fluorescence quenching appears when the concentration reaches 1.67%. The mechanism of fluorescence quenching of fluorescein is discussed. In addition, the composite fibers exhibit a much stronger PL intensity than fluorescein/PVP bulk film owing to larger specific surface area, which makes them promising materials for biomedical applications such as probes and sensors.

  1. Detection of Human Ig G Using Photoluminescent Porous Silicon Interferometer.

    PubMed

    Cho, Bomin; Kim, Seongwoong; Woo, Hee-Gweon; Kim, Sungsoo; Sohn, Honglae

    2015-02-01

    Photoluminescent porous silicon (PSi) interferometers having dual optical properties, both Fabry-Pérot fringe and photolumincence (PL), have been developed and used as biosensors for detection of Human Immunoglobin G (Ig G). PSi samples were prepared by electrochemical etching of p-type silicon under white light exposure. The surface of PSi was characterized using a cold field emission scanning electron microscope. The sensor system studied consisted of a single layer of porous silicon modified with Protein A. The system was probed with various fragments of aqueous human immunoglobin G (Ig G) analyte. Both reflectivity and PL were simultaneously measured under the exposure of human Ig G. An increase of optical thickness and decrease of PL were obtained under the exposure of human Ig G. Detection limit of 500 fM was observed for the human Ig G.

  2. Hydrophilic Magnetofluorescent Nanobowls: Rapid Magnetic Response and Efficient Photoluminescence.

    PubMed

    Chen, Shun; Zhang, Junjun; Song, Shaokun; Feng, Rui; Ju, Yanyun; Xiong, Chuanxi; Dong, Lijie

    2016-01-19

    Multifunctional integration based on a single nanostructure is emerging as a promising paradigm to future functional materials. In this paper, novel magnetofluorescence nanobowls built with ferroferric mandrel and quantum dots exoderm is reported. Magnetic mandrels are stacked into nanobowls though hydrophobic primary Fe3O4 nanocrystals dragged into anion polyelectrolyte aqueous solution via forced solvent evaporation. Bright luminescence core/shell/shell CdSe/CdS/ZnS quantum dots (QDs) are modified with cationic hyperbranched polyethylenimine (PEI). Through electrostatic interactions, positively charged PEI-coated QDs are anchored on the surface of magnetic mandrel. Under this method, the luminescence of QDs is not quenched by magnetic partners in the resultant magnetoflurescence nanobowls. Such magnetoflurescence nanobowls exhibit high saturation magnetization, superparamagnetic characteristics at room temperature, superior water dispersibility, and excellent photoluminescence properties. The newly developed magnetoflurescence nanobowls open a new dimension in efforts toward multimodal imaging probes combining strong magnetization and efficient fluorescence in tandem for biosensors and clinical diagnostic imaging.

  3. Acid-base equilibrium dynamics in methanol and dimethyl sulfoxide probed by two-dimensional infrared spectroscopy.

    PubMed

    Lee, Chiho; Son, Hyewon; Park, Sungnam

    2015-07-21

    Two-dimensional infrared (2DIR) spectroscopy, which has been proven to be an excellent experimental method for studying thermally-driven chemical processes, was successfully used to investigate the acid dissociation equilibrium of HN3 in methanol (CH3OH) and dimethyl sulfoxide (DMSO) for the first time. Our 2DIR experimental results indicate that the acid-base equilibrium occurs on picosecond timescales in CH3OH but that it occurs on much longer timescales in DMSO. Our results imply that the different timescales of the acid-base equilibrium originate from different proton transfer mechanisms between the acidic (HN3) and basic (N3(-)) species in CH3OH and DMSO. In CH3OH, the acid-base equilibrium is assisted by the surrounding CH3OH molecules which can directly donate H(+) to N3(-) and accept H(+) from HN3 and the proton migrates through the hydrogen-bonded chain of CH3OH. On the other hand, the acid-base equilibrium in DMSO occurs through the mutual diffusion of HN3 and N3(-) or direct proton transfer. Our 2DIR experimental results corroborate different proton transfer mechanisms in the acid-base equilibrium in protic (CH3OH) and aprotic (DMSO) solvents.

  4. Field-Based Stable Isotope Probing Reveals the Identities of Benzoic Acid-Metabolizing Microorganisms and Their In Situ Growth in Agricultural Soil▿

    PubMed Central

    Pumphrey, Graham M.; Madsen, Eugene L.

    2008-01-01

    We used a combination of stable isotope probing (SIP), gas chromatography-mass spectrometry-based respiration, isolation/cultivation, and quantitative PCR procedures to discover the identity and in situ growth of soil microorganisms that metabolize benzoic acid. We added [13C]benzoic acid or [12C]benzoic acid (100 μg) once, four times, or five times at 2-day intervals to agricultural field plots. After monitoring 13CO2 evolution from the benzoic acid-dosed soil, field soils were harvested and used for nucleic acid extraction and for cultivation of benzoate-degrading bacteria. Exposure of soil to benzoate increased the number of culturable benzoate degraders compared to unamended soil, and exposure to benzoate shifted the dominant culturable benzoate degraders from Pseudomonas species to Burkholderia species. Isopycnic separation of heavy [13C]DNA from the unlabeled fraction allowed terminal restriction fragment length polymorphism (T-RFLP) analyses to confirm that distinct 16S rRNA genes were localized in the heavy fraction. Phylogenetic analysis of sequenced 16S rRNA genes revealed a predominance (15 of 58 clones) of Burkholderia species in the heavy fraction. Burkholderia sp. strain EBA09 shared 99.5% 16S rRNA sequence similarity with a group of clones representing the dominant RFLP pattern, and the T-RFLP fragment for strain EBA09 and a clone from that cluster matched the fragment enriched in the [13C]DNA fraction. Growth of the population represented by EBA09 during the field-dosing experiment was demonstrated by using most-probable-number-PCR and primers targeting EBA09 and the closely related species Burkholderia hospita. Thus, the target population identified by SIP not only actively metabolized benzoic acid but reproduced in the field upon the addition of the substrate. PMID:18469130

  5. Field-based stable isotope probing reveals the identities of benzoic acid-metabolizing microorganisms and their in situ growth in agricultural soil.

    PubMed

    Pumphrey, Graham M; Madsen, Eugene L

    2008-07-01

    We used a combination of stable isotope probing (SIP), gas chromatography-mass spectrometry-based respiration, isolation/cultivation, and quantitative PCR procedures to discover the identity and in situ growth of soil microorganisms that metabolize benzoic acid. We added [(13)C]benzoic acid or [(12)C]benzoic acid (100 microg) once, four times, or five times at 2-day intervals to agricultural field plots. After monitoring (13)CO(2) evolution from the benzoic acid-dosed soil, field soils were harvested and used for nucleic acid extraction and for cultivation of benzoate-degrading bacteria. Exposure of soil to benzoate increased the number of culturable benzoate degraders compared to unamended soil, and exposure to benzoate shifted the dominant culturable benzoate degraders from Pseudomonas species to Burkholderia species. Isopycnic separation of heavy [(13)C]DNA from the unlabeled fraction allowed terminal restriction fragment length polymorphism (T-RFLP) analyses to confirm that distinct 16S rRNA genes were localized in the heavy fraction. Phylogenetic analysis of sequenced 16S rRNA genes revealed a predominance (15 of 58 clones) of Burkholderia species in the heavy fraction. Burkholderia sp. strain EBA09 shared 99.5% 16S rRNA sequence similarity with a group of clones representing the dominant RFLP pattern, and the T-RFLP fragment for strain EBA09 and a clone from that cluster matched the fragment enriched in the [(13)C]DNA fraction. Growth of the population represented by EBA09 during the field-dosing experiment was demonstrated by using most-probable-number-PCR and primers targeting EBA09 and the closely related species Burkholderia hospita. Thus, the target population identified by SIP not only actively metabolized benzoic acid but reproduced in the field upon the addition of the substrate.

  6. A Sensitive Gel-based Method Combining Distinct Cyclophellitol-based Probes for the Identification of Acid/Base Residues in Human Retaining β-Glucosidases*

    PubMed Central

    Kallemeijn, Wouter W.; Witte, Martin D.; Voorn-Brouwer, Tineke M.; Walvoort, Marthe T. C.; Li, Kah-Yee; Codée, Jeroen D. C.; van der Marel, Gijsbert A.; Boot, Rolf G.; Overkleeft, Herman S.; Aerts, Johannes M. F. G.

    2014-01-01

    Retaining β-exoglucosidases operate by a mechanism in which the key amino acids driving the glycosidic bond hydrolysis act as catalytic acid/base and nucleophile. Recently we designed two distinct classes of fluorescent cyclophellitol-type activity-based probes (ABPs) that exploit this mechanism to covalently modify the nucleophile of retaining β-glucosidases. Whereas β-epoxide ABPs require a protonated acid/base for irreversible inhibition of retaining β-glucosidases, β-aziridine ABPs do not. Here we describe a novel sensitive method to identify both catalytic residues of retaining β-glucosidases by the combined use of cyclophellitol β-epoxide- and β-aziridine ABPs. In this approach putative catalytic residues are first substituted to noncarboxylic amino acids such as glycine or glutamine through site-directed mutagenesis. Next, the acid/base and nucleophile can be identified via classical sodium azide-mediated rescue of mutants thereof. Selective labeling with fluorescent β-aziridine but not β-epoxide ABPs identifies the acid/base residue in mutagenized enzyme, as only the β-aziridine ABP can bind in its absence. The Absence of the nucleophile abolishes any ABP labeling. We validated the method by using the retaining β-glucosidase GBA (CAZy glycosylhydrolase family GH30) and then applied it to non-homologous (putative) retaining β-glucosidases categorized in GH1 and GH116: GBA2, GBA3, and LPH. The described method is highly sensitive, requiring only femtomoles (nanograms) of ABP-labeled enzymes. PMID:25344605

  7. Dopamine-functionalized InP/ZnS quantum dots as fluorescence probes for the detection of adenosine in microfluidic chip

    PubMed Central

    Ankireddy, Seshadri Reddy; Kim, Jongsung

    2015-01-01

    Microbeads are frequently used as solid supports for biomolecules such as proteins and nucleic acids in heterogeneous microfluidic assays. Chip-based, quantum dot (QD)-bead-biomolecule probes have been used for the detection of various types of DNA. In this study, we developed dopamine (DA)-functionalized InP/ZnS QDs (QDs-DA) as fluorescence probes for the detection of adenosine in microfluidic chips. The photoluminescence (PL) intensity of the QDs-DA is quenched by Zn2+ because of the strong coordination interactions. In the presence of adenosine, Zn2+ cations preferentially bind to adenosine, and the PL intensity of the QDs-DA is recovered. A polydimethylsiloxane-based microfluidic chip was fabricated, and adenosine detection was confirmed using QDs-DA probes. PMID:26347351

  8. Development of a Peptide Nucleic Acid Probe to Trichosporon Species and Identification of Trichosporonosis by Use of In Situ Hybridization in Formalin-Fixed and Paraffin-Embedded (FFPE) Sections

    PubMed Central

    Shinozaki, Minoru; Okubo, Yoichiro; Sasai, Daisuke; Nakayama, Haruo; Murayama, Somay Yamagata; Ide, Tadashi; Wakayama, Megumi; Ishiwatari, Takao; Tochigi, Naobumi; Nemoto, Tetsuo

    2013-01-01

    In order to identify Trichosporon species in formalin-fixed and paraffin-embedded sections from which visual discrimination of non-glabrata Candida species is mostly ineffective but critical for the choice of antifungals, we tested the usefulness of a newly designed peptide nucleic acid probe (PNA) for in situ hybridization (ISH). Results confirmed the usefulness of ISH with our PNA probe in identifying Trichosporon species from Candida albicans. PMID:23100341

  9. Thio-ketosides of sialic acid containing aryl azides: potential photo-affinity probes for analysis of neuraminidases and sialic acid binding proteins

    SciTech Connect

    Warner, T.G.; Lee, L.A.

    1986-05-01

    To date, only a single report describing the synthesis of thio-ketosides of sialic acid has appeared. In this procedure, the pseudo thiourea of acetoneuraminic acid methyl ester (NTU) was used to prepare the sodium thiolate salt. However, in their hands, the preparation of NTU was not straight-forward, and in subsequent reactions thio glycosides were not obtained. Therefore, they have developed an alternate route for introduction of the sulfhydryl group and have prepared novel thio-ketosides with aryl azides. The thio linkage is advantageous since it is not easily cleaved by neuraminidases and it allows incorporation of /sup 35/S as a convenient radioactive label. 2-deoxy-2-S-acetyl-4,7,8,9,- tetra-0-acetyl-N-acetyl neuraminic acid methyl ester was prepared (70% yield) from 2-chloro aceto- neuraminic acid methyl ester and potassium thioacetate in acetone at room temperature (RT) for 90 min. Selective hydrolysis of the thio acetate group was accomplished with equimolar sodium methoxide in DMF. After 10 min at RT, 4-fluoro-3-nitrophenyl azide was added and reaction continued for 60 min. Silicic acid purification, base hydrolysis, and gel filtration chromatography, gave 2'-deoxy-2'-(2-nitro-4-azido-thiophenyl)-..cap alpha..-D-N-acetyl neuraminic acid (35% yield). Other thio-arylazido ketosides were prepared similarly.

  10. Plasmon-assisted photoluminescence enhancement of SiC nanocrystals by proximal silver nanoparticles

    NASA Astrophysics Data System (ADS)

    Zhang, N.; Dai, D. J.; Fan, J. Y.

    2012-10-01

    Plasmon-enhanced photoluminescence has wide application potential in many areas, whereas the underlying mechanism is still in debate. We report the photoluminescence enhancement in SiC nanocrystal-Ag nanoparticle coupled system spaced by the poly(styrene sulfonic acid) sodium salt/poly(allylamine hydrochloride) polyelectrolyte bilayers. The integrated luminescence intensity can be improved by up to 17 times. Our analysis indicates that the strong coupling between the SiC nanocrystals and the surface plasmon oscillation of the silver nanoparticles is the major cause of the luminescence enhancement. These findings will help to understand the photoluminescence enhancement mechanism as well as widen the applications of the SiC nanocrystals in photonics and life sciences.

  11. Di- and triarylmethylium ions as probes for the ambident reactivities of carbanions derived from 5-benzylated Meldrum's acid.

    PubMed

    Chen, Xi; Tan, Yue; Berionni, Guillaume; Ofial, Armin R; Mayr, Herbert

    2014-08-25

    The kinetics of the reactions of carbocations with carbanions 1 derived from 5-benzyl-substituted Meldrum's acids 1-H (Meldrum's acid = 2,2-dimethyl-1,3-dioxane-4,6-dione) were investigated by UV/Vis spectroscopic methods. Benzhydryl cations Ar2CH(+) added exclusively to C-5 of the Meldrum's acid moiety. As the second-order rate constants (kC) of these reactions in DMSO followed the linear free-energy relationship lg k = sN (N+E), the nucleophile-specific reactivity parameters N and sN for the carbanions 1 could be determined. In contrast, trityl cations Ar3C(+) reacted differently. While tritylium ions of low electrophilicity (E<-2) reacted with 1 through rate-determining β-hydride abstraction, more Lewis acidic tritylium ions initially reacted at the carbonyl oxygen of 1 to form trityl enolates, which subsequently reionized and eventually yielded triarylmethanes and 5-benzylidene Meldrum's acids by hydride transfer. PMID:25099696

  12. Photoluminescence of a quantum-dot molecule

    SciTech Connect

    Kruchinin, Stanislav Yu.; Rukhlenko, Ivan D.; Baimuratov, Anvar S.; Leonov, Mikhail Yu.; Turkov, Vadim K.; Baranov, Alexander V.; Fedorov, Anatoly V.; Gun'ko, Yurii K.

    2015-01-07

    The coherent coupling of quantum dots is a sensitive indicator of the energy and phase relaxation processes taking place in the nanostructure components. We formulate a theory of low-temperature, stationary photoluminescence from a quantum-dot molecule composed of two spherical quantum dots whose electronic subsystems are resonantly coupled via the Coulomb interaction. We show that the coupling leads to the hybridization of the first excited states of the quantum dots, manifesting itself as a pair of photoluminescence peaks with intensities and spectral positions strongly dependent on the geometric, material, and relaxation parameters of the quantum-dot molecule. These parameters are explicitly contained in the analytical expression for the photoluminescence differential cross section derived in the paper. The developed theory and expression obtained are essential in interpreting and analyzing spectroscopic data on the secondary emission of coherently coupled quantum systems.

  13. Real-time polymerase chain reaction (PCR) quantitative detection of Brassica napus using a locked nucleic acid TaqMan probe.

    PubMed

    Schmidt, Anna-Mary; Rott, Michael E

    2006-02-22

    Several countries have introduced mandatory labeling requirements on foods derived from genetically modified organisms. Real-time quantitative Polymerase Chain Reaction (PCR) has quickly become the method of choice in support of these regulations and requires the development of separate PCR assays targeting the transgenic sequence as well as a specific endogenous gene sequence. To develop a Brassica napus-specific PCR assay, partial sequences of the acetyl-CoA carboxylase BnACCg8 gene from B. napus and the closely related Brassica rapa were determined and compared, and a region of unique nucleotide sequence was identified. Universal amplification primers were designed to either side of this region, and a locked nucleic acid TaqMan probe was designed to the B. napus-specific sequence. Evaluation of this primer/probe combination indicated a high level of specificity to B. napus: no amplification signal was observed with any other species tested, including five closely related Brassica species. The method was assayed with 14 different B. napus cultivars, and comparable amplification curves were consistently obtained for all. The assay was highly sensitive, with a limit of detection between 1 and 10 haploid copies. Practically, the method was demonstrated to be effective for the detection of processed food samples and for the quantification of Roundup Ready canola content in mixed samples.

  14. A potential fluorescent probe: Maillard reaction product from glutathione and ascorbic acid for rapid and label-free dual detection of Hg(2+) and biothiols.

    PubMed

    Dong, Jiang Xue; Song, Xiao Fang; Shi, Yan; Gao, Zhong Feng; Li, Bang Lin; Li, Nian Bing; Luo, Hong Qun

    2016-07-15

    Maillard reactions and their fluorescent products have drawn much attention in the fields of food and life science, however, the application of fluorescent products separated from the reaction as an indicator for detection of certain substances in sensor field has not been mentioned. In this article, we report on an easy-to-synthesize and water-soluble fluorescent probe separated from the typical Maillard reaction products of glutathione and ascorbic acid, with excellent stability and high quantum yield (18.2%). The further application of the probe has been explored for dual detection of Hg(2+) and biothiols including cysteine, homocysteine, and glutathione, which is based on Hg(2+)-induced fluorescence quenching of the Maillard reaction fluorescent products (MRFPs) and the fluorescence recovery as the introduction of biothiols. This sensing system exhibits a good selectivity and sensitivity, and the linear ranges for Hg(2+), cysteine, homocysteine, and glutathione are 0.05-12, 0.5-10, 0.3-20, and 0.3-20μM, respectively. The detection limits for Hg(2+), cysteine, homocysteine, and glutathione are 22, 47, 96, and 30nM at a signal-to-noise ratio of 3, respectively. Furthermore, the practical applications of this sensor for Hg(2+) and biothiols determination in water samples and human plasma sample have been demonstrated with satisfactory results. PMID:27015151

  15. A potential fluorescent probe: Maillard reaction product from glutathione and ascorbic acid for rapid and label-free dual detection of Hg(2+) and biothiols.

    PubMed

    Dong, Jiang Xue; Song, Xiao Fang; Shi, Yan; Gao, Zhong Feng; Li, Bang Lin; Li, Nian Bing; Luo, Hong Qun

    2016-07-15

    Maillard reactions and their fluorescent products have drawn much attention in the fields of food and life science, however, the application of fluorescent products separated from the reaction as an indicator for detection of certain substances in sensor field has not been mentioned. In this article, we report on an easy-to-synthesize and water-soluble fluorescent probe separated from the typical Maillard reaction products of glutathione and ascorbic acid, with excellent stability and high quantum yield (18.2%). The further application of the probe has been explored for dual detection of Hg(2+) and biothiols including cysteine, homocysteine, and glutathione, which is based on Hg(2+)-induced fluorescence quenching of the Maillard reaction fluorescent products (MRFPs) and the fluorescence recovery as the introduction of biothiols. This sensing system exhibits a good selectivity and sensitivity, and the linear ranges for Hg(2+), cysteine, homocysteine, and glutathione are 0.05-12, 0.5-10, 0.3-20, and 0.3-20μM, respectively. The detection limits for Hg(2+), cysteine, homocysteine, and glutathione are 22, 47, 96, and 30nM at a signal-to-noise ratio of 3, respectively. Furthermore, the practical applications of this sensor for Hg(2+) and biothiols determination in water samples and human plasma sample have been demonstrated with satisfactory results.

  16. Biopolymer-mediated analyte detection via photoluminescence modulation of single-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Heller, Daniel

    Single-walled carbon nanotubes (SWNT) have unique photo-physical properties which, through the work in this dissertation, are investigated and harnessed to produce optical sensors with unique capabilities. Early studies of the modulation of SWNT optical properties---both photoluminescence and resonance Raman scattering---demonstrate their tunable nature. Solution dispersed SWNT are sorted by length and the photoluminescence quantum yield is shown to increase nonlinearly with length, suggesting that SWNT ends quench the exciton. The change in Raman scattering cross section and resonant window is mapped as a function of SWNT aggregation, as well as sonochemical effects on photoluminescence. Nanotube photoluminescence and scattering are then detected, via imaging and spectrometry, from within live murine macrophage cells, and shown to be extremely resilient, demonstrating the potential of nanotube-based molecular probes and biosensors. The work culminates in several major findings in optical sensing. We show that a nanotube-ds(GT)15 DNA complex can detect genotoxic analytes by solvatochromism, and measure this from within live cells and tissues in real-time. We find that such optical signals can be multiplexed, resulting in analyte fingerprinting, and a bioanalyte can be detected at the single-molecule level stochastic operation of such sensors. These concepts are employed to detect, identify, and measure bioanalytes, such as reactive oxygen species, as well as explosives, such as TNT and RDX, with single-molecule sensitivity.

  17. Genotyping of velvet antlers for identification of country of origin using mitochondrial DNA and fluorescence melting curve analysis with locked nucleic acid probes.

    PubMed

    Ahn, Jeong Jin; Kim, Youngjoo; Hong, Ji Young; Kim, Gi Won; Hwang, Seung Yong

    2016-07-01

    Velvet antlers are used medicinally in Asia and possess various therapeutic effects. Prices are set according to the country of origin, which is unidentifiable to the naked eye, and therefore counterfeiting is prevalent. Additionally, antlers of the Canadian elk, which can generate chronic wasting disease, are prevalently smuggled and distributed in the market. Thus, a method for identifying the country of origin of velvet antlers was developed, using polymorphisms in mitochondrial DNA, fluorescence melting curve analysis and analysis of locked nucleic acids (LNA). This combined method is capable of identifying five genotypes of velvet antlers in a single experiment using two probes. It also has advantages in multiplexing, simplicity and efficiency in genotyping, when compared to real-time PCR or microarrays. The developed method can be used to improve identification rates in the velvet antler market and, by extension, research based on polymorphisms in DNA sequences.

  18. Probing thermal stability of the β-lactoglobulin-oleic acid complex by fluorescence spectroscopy and molecular modeling

    NASA Astrophysics Data System (ADS)

    Simion (Ciuciu), Ana-Maria; Aprodu, Iuliana; Dumitrașcu, Loredana; Bahrim, Gabriela Elena; Alexe, Petru; Stănciuc, Nicoleta

    2015-09-01

    Bovine β-lactoglobulin is able to interact with different bioactive compounds, thus being an important candidate in the development of delivery systems with improved functionality. The heat induced changes in the β-lactoglobulin-oleic acid complex were examined by means of fluorescence spectroscopy and molecular modeling techniques. Fluorescence spectroscopy results indicated a rigid protein structure in the temperature range 25-70 °C, whereas at temperatures over 75 °C, the rearrangements of the polypeptide chains led to higher exposure of hydrophobic residues. The most significant increase of the accessible surface area with temperature increase was identified in case of Tyr99 and Tyr102. The phase diagram method indicated an all or none transition between two conformations. Due to conformational changes, no contact between Ile56 or Lys60 and the fatty acid could be identified at 85 °C, but new non-bonding interaction were established with Ile12 and Val15. The results obtained in this study provide important details about thermal induced changes in the conformation of β-lactoglobulin-oleic acid complex. Significant conformational changes were registered above 75 °C, suggesting the possibility of obtaining highly functional complexes between whey proteins and natural unsaturated fatty acids.

  19. Probing High School Students' Cognitive Structures and Key Areas of Learning Difficulties on Ethanoic Acid Using the Flow Map Method

    ERIC Educational Resources Information Center

    Zhou, Qing; Wang, Tingting; Zheng, Qi

    2015-01-01

    The purpose of this study was primarily to explore high school students' cognitive structures and to identify their learning difficulties on ethanoic acid through the flow map method. The subjects of this study were 30 grade 1 students from Dong Yuan Road Senior High School in Xi'an, China. The interviews were conducted a week after the students…

  20. Probing metal ion complexation with salicylic acid and its derivatives with excited state proton transfer and luminescence anisotropy

    SciTech Connect

    Wang, Z.; Friedrich, D.M.; Ainsworth, C.C.

    1996-10-01

    Salicylic acid and its derivatives in which the phenolic proton is preserved show a characteristic dual fluorescence: one band in the UV, due to a {open_quotes}normal{close_quotes} excited state emission, and the other in the visible range, is assigned to excited state intramolecular proton transfer (ESIPT). The transition energy, quantum yield and fluorescence lifetime as well as fluorescence anisotropy are sensitive to the solvent environment, temperature and properties of the substituents (complexation) at the phenolic and carboxylic oxygens. The ESIPT band disappears in molecules in which the intramolecular hydrogen bond between phenolic hydrogen and the carbonyl oxygen is prohibited. In this work, the complexation of Na(I), Ca(II), Al(III) and La(III) with salicylic acid, 3-hydroxybenzoic acid, methylsalicylate and anisic acid in both aqueous and non-aqueous solvents has been studied by absorption and steady state luminescence spectroscopy, picosecond to nanosecond luminescence lifetimes and luminescence anisotropy measurements in a range of solvent and in ethanol at 77 K. Speciation in these complex systems, binding characteristics between the metal ion and the ligand, and ligand-centered energetics are discussed in terms of the spectroscopic properties, luminescence and anisotropy decay kinetics.

  1. Topographic probes of angiotensin and receptor: potent angiotensin II agonist containing diphenylalanine and long-acting antagonists containing biphenylalanine and 2-indan amino acid in position 8.

    PubMed

    Hsieh, K H; LaHann, T R; Speth, R C

    1989-04-01

    A series of phenylalanine-mimicking amino acids with increasing conformational restraint were prepared and incorporated into angiotensin II, in order to develop topographic probes of angiotensin useful for probing receptor boundaries by molecular graphics analysis and for conformational analysis of the ligand by NMR. In binding studies, all analogues displayed high affinity for rat uterus (Ki of 0.74-6.08 nM) and brain (0.46-1.82 nM) receptors. In smooth muscle (rat uterus) contraction assay, the diphenylalanine-containing [Sar1,Dip8]AII and [Sar1,D-Dip8]AII were potent agonists with respectively 284% and 48% activity of [Asn1]AII. In contrast, the biphenylalanine-containing [Sar1,Bip8]AII, [Sar1,D-Bip8]AII, and the 2-indan amino acid containing [Sar1,2-Ind8]AII were potent inhibitors, approximately 9, 2, and 1.4 times more effective than a standard antagonist, [Sar1,Leu8]AII. Their respective pA10 values in rat uterus assay were 8.87, 8.70, and 8.82. By comparison, the pA10 value for [Sar1,Leu8]AII was 8.35. In rats, a single dose of 10 micrograms of [Sar1,2-Ind8]AII or [Sar1,Bip8]AII produced prolonged blockade of the pressor response toward angiotensin II for over 90 min. The very different pharmacological profiles of these rigid aromatic analogues suggest that the angiotensin receptor activation site consists of a relatively wide and elongated pocket with a narrow opening.

  2. Highly photoluminescent MoO(x) quantum dots: Facile synthesis and application in off-on Pi sensing in lake water samples.

    PubMed

    Xiao, Sai Jin; Zhao, Xiao Jing; Zuo, Jun; Huang, Hai Qing; Zhang, Li

    2016-02-01

    Molybdenum oxide (MoOx) is a well-studied transition-metal semiconductor material, and has a wider band gap than MoS2 which makes it become a promising versatile probe in a variety of fields, such as gas sensor, catalysis, energy storage ect. However, few MoOx nanomaterials possessing photoluminescence have been reported until now, not to mention the application as photoluminescent probes. Herein, a one-pot method is developed for facile synthesis of highly photoluminescent MoOx quantum dots (MoOx QDs) in which commercial molybdenum disulfide powder and hydrogen peroxide (H2O2) are involved as the precursor and oxidant, respectively. Compared with current synthesis methods, the proposed one has the advantages of rapid, one-pot, easily prepared, environment friendly as well as strong photoluminescence. The obtained MoOx QDs is further utilized as an efficient photoluminescent probe, and a new off-on sensor has been constructed for phosphate (Pi) determination in complicated lake water samples, attributed to the fact that the binding affinity of Eu(3+) ions to the oxygen atoms from Pi is much higher than that from the surface of MoOx QDs. Under the optimal conditions, a good linear relationship was found between the enhanced photoluminescence intensity and Pi concentration in the range of 0.1-160.0 μM with the detection limit of 56 nM (3σ/k). The first application of the photoluminescent MoOx nanomaterials for ion photochemical sensing will open the gate of employing MoOx nanomaterials as versatile probes in a variety of fields, such as chemi-/bio-sensor, cell imaging, biomedical and so on. PMID:26772134

  3. Hexagonal cobalt oxyhydroxide-carbon dots hybridized surface: high sensitive fluorescence turn-on probe for monitoring of ascorbic acid in rat brain following brain ischemia.

    PubMed

    Li, Linbo; Wang, Chao; Liu, Kangyu; Wang, Yuhan; Liu, Kun; Lin, Yuqing

    2015-03-17

    In this study, we report a novel and efficient fluorescence probe synthesized by Tris(hydroxymethyl)aminomethane-derived carbon dots (CDs)-modified hexagonal cobalt oxyhydroxide(CoOOH) nanoflakes (Tris-derived CDs-CoOOH) for monitoring of cerebral ascorbic acid (AA) in brain microdialysate. The as-prepared Tris-derived CDs with the fluorescence quantum yield of 7.3% are prepared by a one-step pyrolysis strategy of the sole precursor and used as the signal output. After being hybridized with CoOOH nanoflakes to form Tris-derived CDs-CoOOH, the luminescence of the Tris-derived CDs can be efficiently quenched by CoOOH via fluorescence resonance energy transfer (FRET). Due to the specific redox reaction between the enediol group of AA and hexagonal CoOOH nanoflakes, AA can reduce the hexagonal CoOOH nanoflakes in the Tris-derived CDs-CoOOH and lead to collapse of the hybrized structure, then the release of Tris-derived CDs, and thus finally the fluorescence recovery. Moreover, cobalt ions (II), generated by CoOOH nanoflakes oxidizing AA, almost have no obvious interference on the fluorescence probe, i.e., Tris-derived CDs, which could be ascribed to the surface of Tris-derived CDs containing a few strong chelation groups such as amino/carboxyl/thiol groups, instead of plenty of -OH groups with weak chelation with Co(2+). On the basis of this feature, the Tris-derived CDs-CoOOH fluorescent probe demonstrates a linear range from 100 nM to 20 μM with the detection limit of ∼50 nM, i.e., with an improved sensitivity toward AA detection. Compared with other turn-on fluorescent methods using convenient fluorophore-nitroxide fluorescent probes for detection of AA, the method demonstrated here possesses a facial synthesis route, lower limit of detection, and wider linear range, which validates sensing of AA in the cerebral systems during the calm/ischemia process. This study provides a fluorescence assay for the simple yet facial detection of AA in the cerebral systems and

  4. A new dual-channel optical signal probe for Cu2+ detection based on morin and boric acid.

    PubMed

    Wang, Peng; Yuan, Bin Fang; Li, Nian Bing; Luo, Hong Qun

    2014-01-01

    In this work we utilized the common analytical reagent morin to develop a new a dual-channel, cost-effective, and sensitive method for determination of Cu(2+). It is found that morin is only weakly fluorescent by itself, but forms highly fluorescent complexes with boric acid. Moreover, the fluorescence of complexes of morin with boric acid is quenched linearly by Cu(2+) in a certain concentration range. Under optimum conditions, the fluorescence quenching efficiency was linearly proportional to the concentration of cupric ions in the range of 0.5-25 μM with high sensitivity, and the detection limit for Cu(2+) was 0.38 μM. The linear range was 1-25 μM determined by spectrophotometry, and the detection limit for cupric ions was 0.8 μM. Furthermore, the mechanism of sensitive fluorescence quenching response of morin to Cu(2+) is discussed. PMID:25199115

  5. A new dual-channel optical signal probe for Cu2+ detection based on morin and boric acid.

    PubMed

    Wang, Peng; Yuan, Bin Fang; Li, Nian Bing; Luo, Hong Qun

    2014-01-01

    In this work we utilized the common analytical reagent morin to develop a new a dual-channel, cost-effective, and sensitive method for determination of Cu(2+). It is found that morin is only weakly fluorescent by itself, but forms highly fluorescent complexes with boric acid. Moreover, the fluorescence of complexes of morin with boric acid is quenched linearly by Cu(2+) in a certain concentration range. Under optimum conditions, the fluorescence quenching efficiency was linearly proportional to the concentration of cupric ions in the range of 0.5-25 μM with high sensitivity, and the detection limit for Cu(2+) was 0.38 μM. The linear range was 1-25 μM determined by spectrophotometry, and the detection limit for cupric ions was 0.8 μM. Furthermore, the mechanism of sensitive fluorescence quenching response of morin to Cu(2+) is discussed.

  6. Estimation of free energy barriers in the cytoplasmic and mitochondrial aspartate aminotransferase reactions probed by hydrogen-exchange kinetics of C alpha-labeled amino acids with solvent

    SciTech Connect

    Julin, D.A.; Wiesinger, H.; Toney, M.D.; Kirsch, J.F. )

    1989-05-02

    The existence of the postulated quinonoid intermediate in the cytoplasmic aspartate amino-transferase catalyzed transamination of aspartate to oxaloacetate was probed by determining the extent of transfer of tritium from the C alpha position of tritiated L-aspartate to pyridoxamine 5'-phosphate in single turnover experiments in which washout from the back-reaction was obviated by product trapping. The maximum amount of transferred tritium observed was 0.7%, consistent either with a mechanism in which a fraction of the net transamination reaction proceeds through a quinonoid intermediate or with a mechanism in which this intermediate is formed off the main reaction pathway. It is shown that transfer of labeled hydrogen from the amino acid to cofactor cannot be used to differentiate a stepwise from a concerted transamination mechanism. The amount of tritium transferred is a function of the rate constant for torsional equilibration about the epsilon-amino group of Lys-258, the presumptive abstractor of the C alpha proton; the relative rate constants for hydrogen exchange with solvent versus cofactor protonation; and the tritium isotope effect on this ratio. The free energy barriers facing the covalent intermediate between aldimine and keto acid product (i.e., ketimine and possibly quinonoid) were evaluated relatively by comparing the rates of C alpha-hydrogen exchange in starting amino acid with the rates of keto acid formation. The value of theta (= kexge/kprod) was found to be 2.6 for the reaction of cytoplasmic isozyme with aspartate and ca. 0.5 for that of the mitochondrial form with glutamate.

  7. Gold-catalysed cross-coupling between aryldiazonium salts and arylboronic acids: probing the usefulness of photoredox conditions.

    PubMed

    Cornilleau, Thomas; Hermange, Philippe; Fouquet, Eric

    2016-08-21

    The synthesis of biaryl compounds from aryldiazonium salts and arylboronic acids was achieved using PPh3AuCl as catalyst, CsF as base and acetonitrile as solvent. Combined to photosensitizers, irradiation by blue LEDs allowed accelerating the reaction and expanding its scope. Various functional groups were compatible including bromoaryls, iodoaryls, aldehydes and alcohols. A 2-iodobenzyl alcohol moiety was smoothly introduced by this method, enabling its consecutive isotopic labelling by a Pd-catalysed alkoxycarbonylation. PMID:27452177

  8. Spectrophotometric probe

    DOEpatents

    Prather, William S.; O'Rourke, Patrick E.

    1994-01-01

    A support structure bearing at least one probe for making spectrophotometric measurements of a fluid using a source of light and a spectrophotometer. The probe includes a housing with two optical fibers and a planoconvex lens. A sleeve bearing a mirror surrounds the housing. The lens is separated from the mirror by a fixed distance, defining an interior space for receiving a volume of the fluid sample. A plurality of throughholes extending through the sleeve communicate between the sample volume and the exterior of the probe, all but one hole bearing a screen. A protective jacket surrounds the probe. A hollow conduit bearing a tube is formed in the wall of the probe for venting any air in the interior space when fluid enters. The probe is held at an acute angle so the optic fibers carrying the light to and from the probe are not bent severely on emergence from the probe.

  9. Spectrophotometric probe

    DOEpatents

    Prather, W.S.; O'Rourke, P.E.

    1994-08-02

    A support structure is described bearing at least one probe for making spectrophotometric measurements of a fluid using a source of light and a spectrophotometer. The probe includes a housing with two optical fibers and a planoconvex lens. A sleeve bearing a mirror surrounds the housing. The lens is separated from the mirror by a fixed distance, defining an interior space for receiving a volume of the fluid sample. A plurality of throughholes extending through the sleeve communicate between the sample volume and the exterior of the probe, all but one hole bearing a screen. A protective jacket surrounds the probe. A hollow conduit bearing a tube is formed in the wall of the probe for venting any air in the interior space when fluid enters. The probe is held at an acute angle so the optic fibers carrying the light to and from the probe are not bent severely on emergence from the probe. 3 figs.

  10. Blue photoluminescent carbon nanodots from limeade.

    PubMed

    Suvarnaphaet, Phitsini; Tiwary, Chandra Sekhar; Wetcharungsri, Jutaphet; Porntheeraphat, Supanit; Hoonsawat, Rassmidara; Ajayan, Pulickel Madhavapanicker; Tang, I-Ming; Asanithi, Piyapong

    2016-12-01

    Carbon-based photoluminescent nanodot has currently been one of the promising materials for various applications. The remaining challenges are the carbon sources and the simple synthetic processes that enhance the quantum yield, photostability and biocompatibility of the nanodots. In this work, the synthesis of blue photoluminescent carbon nanodots from limeade via a single-step hydrothermal carbonization process is presented. Lime carbon nanodot (L-CnD), whose the quantum yield exceeding 50% for the 490nm emission in gram-scale amounts, has the structure of graphene core functionalized with the oxygen functional groups. The micron-sized flake of the as-prepared L-CnD powder exhibits multicolor emission depending on an excitation wavelength. The L-CnDs are demonstrated for rapidly ferric-ion (Fe(3+)) detection in water compared to Fe(2+), Cu(2+), Co(2+), Zn(2+), Mn(2+) and Ni(2+) ions. The photoluminescence quenching of L-CnD solution under UV light is used to distinguish the Fe(3+) ions from others by naked eyes as low concentration as 100μM. Additionally, L-CnDs provide exceptional photostability and biocompatibility for imaging yeast cell morphology. Changes in morphology of living yeast cells, i.e. cell shape variation, and budding, can be observed in a minute-period until more than an hour without the photoluminescent intensity loss. PMID:27612786

  11. Diagnostic meaning of intestinal wall photoluminescence changes

    NASA Astrophysics Data System (ADS)

    Besaha, R. M.; Hrynchuk, F. V.; Polyansky, I. Y.

    2006-05-01

    Diagnostics of inflammatory-destructive diseases of the abdominal cavity organs is performed by the determined spectra of luminescence of venous blood plasma. The shift of the photoluminescence maximum beginning with the wave-length 469 nm into short-wave zone proves the presence of the acute inflammatory-destructive diseases and exacerbation of the pathological process.

  12. Probing the chemical mechanism and critical regulatory amino acid residues of Drosophila melanogaster arylalkylamine N-acyltransferase like 2.

    PubMed

    Dempsey, Daniel R; Carpenter, Anne-Marie; Ospina, Santiago Rodriguez; Merkler, David J

    2015-11-01

    Arylalkylamine N-acyltransferase like 2 (AANATL2) catalyzes the formation of N-acylarylalkylamides from the corresponding acyl-CoA and arylalkylamine. The N-acylation of biogenic amines in Drosophila melanogaster is a critical step for the inactivation of neurotransmitters, cuticle sclerotization, and melatonin biosynthesis. In addition, D. melanogaster has been used as a model system to evaluate the biosynthesis of fatty acid amides: a family of potent cell signaling lipids. We have previously showed that AANATL2 catalyzes the formation of N-acylarylakylamides, including long-chain N-acylserotonins and N-acyldopamines. Herein, we define the kinetic mechanism for AANATL2 as an ordered sequential mechanism with acetyl-CoA binding first followed by tyramine to generate the ternary complex prior to catalysis. Bell shaped kcat,app - acetyl-CoA and (kcat/Km)app - acetyl-CoA pH-rate profiles identified two apparent pKa,app values of ∼7.4 and ∼8.9 that are critical to catalysis, suggesting the AANATL2-catalyzed formation of N-acetyltyramine occurs through an acid/base chemical mechanism. Site-directed mutagenesis of a conserved glutamate that corresponds to the catalytic base for other D. melanogaster AANATL enzymes did not produce a substantial depression in the kcat,app value nor did it abolish the pKa,app value attributed to the general base in catalysis (pKa ∼7.4). These data suggest that AANATL2 catalyzes the formation of N-acylarylalkylamides using either different catalytic residues or a different chemical mechanism relative to other D. melanogaster AANATL enzymes. In addition, we constructed other site-directed mutants of AANATL2 to help define the role of targeted amino acids in substrate binding and/or enzyme catalysis.

  13. Folic acid-targeted magnetic Tb-doped CeF3 fluorescent nanoparticles as bimodal probes for cellular fluorescence and magnetic resonance imaging.

    PubMed

    Ma, Zhi-Ya; Liu, Yu-Ping; Bai, Ling-Yu; An, Jie; Zhang, Lin; Xuan, Yang; Zhang, Xiao-Shuai; Zhao, Yuan-Di

    2015-10-01

    Magnetic fluorescent nanoparticles (NPs) have great potential applications for diagnostics, imaging and therapy. We developed a facile polyol method to synthesize multifunctional Fe3O4@CeF3:Tb@CeF3 NPs with small size (<20 nm), high water solubility and good biocompatibility. The NPs were modified by ligand exchange reactions with citric acid (CA) to obtain carboxyl-functionalized NPs (Fe3O4@CeF3:Tb@CeF3-COOH). Folic acid (FA) as an affinity ligand was then covalently conjugated onto NPs to yield Fe3O4@CeF3:Tb@CeF3-FA NPs. They were then applied as multimodal imaging agents for simultaneous in vitro targeted fluorescence imaging and magnetic resonance imaging (MRI) of HeLa cells with overexpressed folate receptors (FR). The results indicated that these NPs had strong luminescence and enhanced T2-weighted MR contrast and would be promising candidates as multimodal probes for both fluorescence and MRI imaging.

  14. Probing the active site of MIO-dependent 2,3-aminomutases, key catalysts in the biosynthesis of beta-amino acids incorporated in secondary metabolites

    PubMed Central

    Bruner, Steven D.; Cooke, Heather

    2012-01-01

    The tyrosine aminomutase SgTAM produces (S)-β-tyrosine from l-tyrosine in the biosynthesis of the enediyne antitumor antibiotic C-1027. This conversion is promoted by the methylideneimidazole-5-one (MIO) prosthetic group. MIO was first identified in the homologous family of ammonia lyases, which deaminate aromatic amino acids to form α,β-unsaturated carboxylates. Studies of substrate specificity have been described for lyases but there have been no reports in altering the substrate specificity of aminomutases. Furthermore, it remains unclear as to what structural properties are responsible for catalyzing the presumed readdition of the amino group into the α,β-unsaturated intermediates to form β-amino acids. Attempts to elucidate specificity and mechanistic determinants of SgTAM have also proved to be difficult as it is recalcitrant to perturbations to the active site via mutagenesis. An X-ray co-crystal structure of the SgTAM mutant of the catalytic base with l-tyrosine verified important substrate binding residues as well as the enzymatic base. Further mutagenesis revealed that removal of these crucial interactions renders the enzyme inactive. Proposed structural determinants for mutase activity probed via mutagenesis, time-point assays and X-ray crystallography revealed a complicated role for these residues in maintaining key quaternary structure properties that aid in catalysis. PMID:20577998

  15. Probing the Active Site of MIO-dependent Aminomutases, Key Catalysts in the Biosynthesis of amino Acids Incorporated in Secondary Metabolites

    SciTech Connect

    Cooke, H.; Bruner, S

    2010-01-01

    The tyrosine aminomutase SgTAM produces (S)-{beta}-tyrosine from L-tyrosine in the biosynthesis of the enediyne antitumor antibiotic C-1027. This conversion is promoted by the methylideneimidazole-5-one (MIO) prosthetic group. MIO was first identified in the homologous family of ammonia lyases, which deaminate aromatic amino acids to form {alpha},{beta}-unsaturated carboxylates. Studies of substrate specificity have been described for lyases but there have been limited reports in altering the substrate specificity of aminomutases. Furthermore, it remains unclear as to what structural properties are responsible for catalyzing the presumed readdition of the amino group into the {alpha},{beta}-unsaturated intermediates to form {beta}-amino acids. Attempts to elucidate specificity and mechanistic determinants of SgTAM have also proved to be difficult as it is recalcitrant to perturbations to the active site via mutagenesis. An X-ray cocrystal structure of the SgTAM mutant of the catalytic base with L-tyrosine verified important substrate binding residues as well as the enzymatic base. Further mutagenesis revealed that removal of these crucial interactions renders the enzyme inactive. Proposed structural determinants for mutase activity probed via mutagenesis, time-point assays and X-ray crystallography revealed a complicated role for these residues in maintaining key quaternary structure properties that aid in catalysis.

  16. Investigation of Humidity Dependent Surface Morphology and Proton Conduction in Multi-Acid Side Chain Membranes by Conductive Probe Atomic Force Microscopy.

    PubMed

    Economou, Nicholas J; Barnes, Austin M; Wheat, Andrew J; Schaberg, Mark S; Hamrock, Steven J; Buratto, Steven K

    2015-11-01

    In this report, we employ phase-contrast tapping mode and conductive probe atomic force microscopy (cp-AFM) as tools to investigate the nanoscale morphology and proton conductance of a 3M perfluoro-imide acid (PFIA) membrane (625 EW) over a large range of relative humidity (3-95% RH). As a point of comparison, we also investigate 3M perfluorosulfonic acid (PFSA) (825 EW) and Nafion 212. With AFM, we assess the membrane's water retention and mechanical stability at low RH and high RH, respectively. Cp-AFM allows us to spatially resolve the hydrophilic and electrochemically active domains under a similar set of conditions and observe directly the ties between membrane morphology and proton conductance. From our data, we are able to correlate the improved water retention indicated by the size of the hydrophilic domains with the proton conductance in the PFIA membrane at elevated temperature and compare the result with that observed for the PFSA and Nafion. At high RH conditions, we see evidence of a nearly continuous hydrophilic phase, which indicates a high degree of swelling. PMID:26439098

  17. Use of Dimedone-Based Chemical Probes for Sulfenic Acid Detection: Methods to Visualize and Identify Labeled Proteins

    PubMed Central

    Nelson, Kimberly J.; Klomsiri, Chananat; Codreanu, Simona G.; Soito, Laura; Liebler, Daniel C.; Rogers, LeAnn C.; Daniel, Larry W.; Poole, Leslie B.

    2013-01-01

    Reversible thiol modification is a major component of the modulation of cell-signaling pathways by reactive oxygen species. Hydrogen peroxide, peroxynitrite, or lipid hydroperoxides are all able to oxidize cysteines to form cysteine sulfenic acids; this reactive intermediate can be directly reduced to thiol by cellular reductants such as thioredoxin or further participate in disulfide bond formation with glutathione or cysteine residues in the same or another protein. To identify the direct protein targets of cysteine modification and the conditions under which they are oxidized, a series of dimedone-based reagents linked to affinity or fluorescent tags have been developed that specifically alkylate and trap cysteine sulfenic acids. In this chapter, we provide detailed methods using one of our biotin-tagged reagents, DCP-Bio1, to identify and monitor proteins that are oxidized in vitro and in vivo. Using streptavidin-linked agarose beads, this biotin-linked reagent can be used to affinity capture labeled proteins. Stringent washing of the beads prior to elution minimizes the contamination of the enriched material with unlabeled proteins through coimmunoprecipitation or nonspecific binding. In particular, we suggest including DTT in one of the washes to remove proteins covalently linked to biotinylated proteins through a disulfide bond, except in cases where these linked proteins are of interest. We also provide methods for targeted approaches monitoring cysteine oxidation in individual proteins, global approaches to follow total cysteine oxidation in the cell, and guidelines for proteomic analyses to identify novel proteins with redox sensitive cysteines. PMID:20513473

  18. A novel magnetic field probing technique for determining state of health of sealed lead-acid batteries

    NASA Astrophysics Data System (ADS)

    Khare, Neeta; Singh, Pritpal; Vassiliou, John K.

    2012-11-01

    State of Health (SOH) is a critical index for a Sealed Lead-Acid (SLA) battery diagnostic which provides the information about battery replacement and aging effects. SOH is a complex function of chemical parameters of a battery such as stratification in electrolyte, electrode structure (sulfation and hard sulfation) in addition to electrical parameters of a battery. This paper describes a method of online determination of stratification, electrode structure, electrode polarization and current profile within the battery under the influence of a magnetic field. An AC magnetic field is used as a noninvasive tool during battery cycles. An induced emf in a secondary coil (SCV) is used as a measure of change in the magnetic field. The H+ proton density varies with change in sulfuric acid (electrolyte) concentration during battery cycles. The magnetic flux lines are affected by the density of H+ protons whose magnetic dipole moments try to align along the magnetic flux lines. The stratification is seen by a 12% decrease in magnetic flux linking from the top to the bottom of the electrolyte in a battery. Additional experimental results demonstrate the variation in magnetic flux linking which correlates with current profile across the electrode and electrode structure.

  19. Probing the adsorption of weak acids on graphite using amplitude modulation-frequency modulation atomic force microscopy.

    PubMed

    Moustafa, Ahmed M A; Huang, Jun; McPhedran, Kerry N; Zeng, Hongbo; El-Din, Mohamed Gamal

    2015-03-17

    Recent thermodynamics calculations and adsorption isotherms showed that the adsorption of a self-assembled layer (SAL) of ionized weak acids to carbon was attributed to the negatively charged hydrogen bonding (-CAHB), yet the direct visualization and characterization of this adsorption behavior have not been reported. Here, an amplitude modulation-frequency modulation atomic force microscopy (AM-FM AFM) technique was applied to discriminate the adsorption of decanoic acids (DA) on highly ordered pyrolytic graphite (HOPG). Thermodynamics calculations revealed that the adsorption of SAL was driven by the formation of -CAHB with negatively charged functional groups of HOPG. Multilayer adsorption could occur over the adsorbed ionized SAL, leading to the development of aggregates. AM-FM AFM imaging showed that the adsorption of the DA molecules forming aggregates occurred only for the HOPG-functionalized steps, while DA molecules were found to adsorb over the entire functionalized HOPG surface after water-plasma treatment, as evident from the frequency shifts identified in AFM images. PMID:25710305

  20. Probing the adsorption of weak acids on graphite using amplitude modulation-frequency modulation atomic force microscopy.

    PubMed

    Moustafa, Ahmed M A; Huang, Jun; McPhedran, Kerry N; Zeng, Hongbo; El-Din, Mohamed Gamal

    2015-03-17

    Recent thermodynamics calculations and adsorption isotherms showed that the adsorption of a self-assembled layer (SAL) of ionized weak acids to carbon was attributed to the negatively charged hydrogen bonding (-CAHB), yet the direct visualization and characterization of this adsorption behavior have not been reported. Here, an amplitude modulation-frequency modulation atomic force microscopy (AM-FM AFM) technique was applied to discriminate the adsorption of decanoic acids (DA) on highly ordered pyrolytic graphite (HOPG). Thermodynamics calculations revealed that the adsorption of SAL was driven by the formation of -CAHB with negatively charged functional groups of HOPG. Multilayer adsorption could occur over the adsorbed ionized SAL, leading to the development of aggregates. AM-FM AFM imaging showed that the adsorption of the DA molecules forming aggregates occurred only for the HOPG-functionalized steps, while DA molecules were found to adsorb over the entire functionalized HOPG surface after water-plasma treatment, as evident from the frequency shifts identified in AFM images.

  1. Mefenamic acid anti-inflammatory drug: probing its polymorphs by vibrational (IR and Raman) and solid-state NMR spectroscopies.

    PubMed

    Cunha, Vanessa R R; Izumi, Celly M S; Petersen, Philippe A D; Magalhães, Alviclér; Temperini, Marcia L A; Petrilli, Helena M; Constantino, Vera R L

    2014-04-24

    This work deals with the spectroscopic (supported by quantum chemistry calculations), structural, and morphological characterization of mefenamic acid (2-[(2,3-(dimethylphenyl)amino] benzoic acid) polymorphs, known as forms I and II. Polymorph I was obtained by recrystallization in ethanol, while form II was reached by heating form I up to 175 °C, to promote the solid phase transition. Experimental and theoretical vibrational band assignments were performed considering the presence of centrosymmetric dimers. Besides band shifts in the 3345-3310 cm(-1) range, important vibrational modes to distinguish the polymorphs are related to out-of-phase and in-phase N-H bending at 1582 (Raman)/1577 (IR) cm(-1) and 1575 (Raman)/1568 (IR) cm(-1) for forms I and II, respectively. In IR spectra, bands assigned to N-H bending out of plane are observed at 626 and 575 cm(-1) for polymorphs I and II, respectively. Solid-state (13)C NMR spectra pointed out distinct chemical shifts for the dimethylphenyl group: 135.8 to 127.6 ppm (carbon bonded to N) and 139.4 to 143.3 ppm (carbon bonded to methyl group) for forms I and II, respectively. PMID:24654805

  2. Using rumen probes to examine effects of conjugated linoleic acids and dietary concentrate proportion on rumen pH and rumen temperature of periparturient dairy cows.

    PubMed

    Petzold, M; Meyer, U; Spilke, J; Dänicke, S

    2014-08-01

    The study aimed to examine the influence of supplemented conjugated linoleic acids (CLA) to periparturient cows receiving different concentrate proportions antepartum on rumen pH (RpH) and rumen temperature (RT). Twenty pregnant German Holstein cows were equipped with rumen probes for continuous RpH and RT measurement in a frequency of 15 min to investigate effects of dietary concentrate and CLA around parturition and the impact of parturition itself on RpH and RT. Cows had ad libitum access to partial mixed rations, 3 weeks prior to calving until day 7 post-partum. Antepartum, cows received 100 g/day control fat (CON) or CLA supplement, either in low (20%; CON-20, CLA-20) or high concentrate diet (60%; CON-60, CLA-60). Post-partum, concentrate proportion was adjusted to 50% while fat supplementation continued. Compared with adapted feeding, high concentrate proportions antepartum tended to increase DMI and reduced RpH. Groups CON-60 and CLA-60 spent more than 4 h per day below RpH 5.6 during late pregnancy, indicating the presence of subacute rumen acidosis (SARA). The RT remained unaffected antepartum. Before calving, cows spent less time below RpH 5.6 and SARA could be detected in each group post-partum. Mean RpH increased slightly antepartum, whereas few hours before parturition a sharp decrease in RpH could be observed, accompanied with increased RT. Overall, it seems that CLA supplementation influences RpH and RT. Bearing in mind that rumen parameters fluctuate during day and herd level must be known, rumen probes for continuous RpH and RT measurement could be a useful management tool for animal health surveillance and may also help to predict parturition.

  3. Development of a fatty acid and RNA stable isotope probing-based method for tracking protist grazing on bacteria in wastewater.

    PubMed

    Kuppardt, Steffen; Chatzinotas, Antonis; Kästner, Matthias

    2010-12-01

    Removal of potential pathogenic bacteria, for example, during wastewater treatment, is effected by sorption, filtration, natural die-off, lysis by viruses, and grazing by protists, but the actual contribution of grazing has never been assessed quantitatively. A methodical approach for analyzing the grazing of protists on (13)C-labeled prey bacteria was developed which enables mass balances of the carbon turnover to be drawn, including yield estimation. Model experiments for validating the approach were performed in closed microcosms with the ciliate Uronema sp. and (13)C-labeled Escherichia coli as model prey. The transfer of bacterial (13)C into grazing protist biomass was investigated by fatty acid (FA) and RNA stable isotope probing (SIP). Uronema sp. showed ingestion rates of ∼390 bacteria protist(-1) h(-1), and the temporal patterns of (13)C assimilation from the prey bacteria to the protist FA were identified. Nine fatty acids specific for Uronema sp. were found (20:0, i20:0, 22:0, 24:0, 20:1ω9c, 20:1ω9t, 22:1ω9c, 22:1ω9t, and 24:1). Four of these fatty acids (22:0, 20:1ω9t, 22:1ω9c, and 22:1ω9t) were enriched very rapidly after 3 h, indicating grazing on bacteria without concomitant cell division. Other fatty acids (20:0, i20:0, and 20:1ω9c) were found to be indicative of growth with cell division. The fatty acids were found to be labeled with a percentage of labeled carbon (atoms percent [atom%]) up to 50. Eighteen percent of the E. coli-derived (13)C was incorporated into Uronema biomass, whereas 11% was mineralized. Around 5 mol bacterial carbon was necessary in order to produce 1 mol protist carbon (y(x)(/)(s) ≈ 0.2), and the temporal pattern of (13)C labeling of protist rRNA was also shown. A consumption of around 1,000 prey bacteria (∼98 atom% (13)C) per protist cell appears to be sufficient to provide detectable amounts of label in the protist RNA. The large shift in the buoyant density fraction of (13)C-labeled protist RNA demonstrated

  4. Plasmon-modulated photoluminescence of individual gold nanostructures.

    PubMed

    Hu, Hailong; Duan, Huigao; Yang, Joel K W; Shen, Ze Xiang

    2012-11-27

    In this work, we performed a systematic study on the photoluminescence and scattering spectra of individual gold nanostructures that were lithographically defined. We identify the role of plasmons in photoluminescence as modulating the energy transfer between excited electrons and emitted photons. By comparing photoluminescence spectra with scattering spectra, we observed that the photoluminescence of individual gold nanostructures showed the same dependencies on shape, size, and plasmon coupling as the particle plasmon resonances. Our results provide conclusive evidence that the photoluminescence in gold nanostructures indeed occurs via radiative damping of plasmon resonances driven by excited electrons in the metal itself. Moreover, we provide new insight on the underlying mechanism based on our analysis of a reproducible blue shift of the photoluminescence peak (relative to the scattering peak) and observation of an incomplete depolarization of the photoluminescence. PMID:23072661

  5. Photoluminescence characteristics of rare earth-doped nanoporous aluminum oxide

    NASA Astrophysics Data System (ADS)

    de Azevedo, W. M.; de Carvalho, D. D.; de Vasconcelos, E. A.; da Silva, E. F.

    2004-07-01

    In this work we present photoluminescence characterization of rare earth ion-doped nanoporous aluminum oxide synthesized by the anodization process in diverse solvents. We find that the luminescence of doped aluminum oxide strongly depends on the synthesis medium. When synthesized in an inorganic acid only rare earth fluorescence is present, whereas nanoporous aluminum oxide synthesized in organic solvent presents two strong unexpected luminescence emission lines, one at 429 nm and the other at 491 nm, with quite long decay time when excited with long wavelength ultraviolet light. The results suggest that light simulation of primary colors and chromaticity control of the emitted light can be done by the a combination of different rare earth ions present in the sample.

  6. Effect of chemical heterogeneity on photoluminescence of graphite oxide treated with S-/N-containing modifiers

    NASA Astrophysics Data System (ADS)

    Ebrahim, Amani M.; Rodríguez-Castellón, Enrique; Montenegro, José María; Bandosz, Teresa J.

    2015-03-01

    Graphite oxide (GO) obtained using Hummers method was modified by hydrothermal treatment either with sulfanilic acid or polystyrene (3-ammonium) sulfonate at 100 °C or 85 °C, respectively. Both modifiers contain sulfur in the oxidized forms and nitrogen in the reduced forms. The materials were characterized using FTIR, XPS, thermal analysis, potentiometric titration and SEM. Their photoluminescent properties and their alteration with an addition of Ag+ were also measured. As a result of these modifications nitrogen was introduced to the graphene layers as amines, imides, amides, and sulfur as sulfones and sulfonic acids. Moreover, the presence of polyaniline was detected. This significantly affected the polarity, acid-base character, and conductivity of the materials. Apparently carboxylic groups of GO were involved in the surface reactions. The modified GOs lost their layered structure and the modifications resulted in the high degree of structural and chemical heterogeneity. Photoluminescence in visible light was recorded and linked to the presence of heteroatoms. For the polystyrene (3-ammonium) sulfonate modified sample addition of Ag+ quenched the photoluminescence at low wavelength showing sensitivity as a possible optical detector. No apparent effect was found for the sulfanilic acid modified sample.

  7. A Comprehensive Spectroscopic and Computational Investigation to Probe the Interaction of Antineoplastic Drug Nordihydroguaiaretic Acid with Serum Albumins.

    PubMed

    Nusrat, Saima; Siddiqi, Mohammad Khursheed; Zaman, Masihuz; Zaidi, Nida; Ajmal, Mohammad Rehan; Alam, Parvez; Qadeer, Atiyatul; Abdelhameed, Ali Saber; Khan, Rizwan Hasan

    2016-01-01

    Exogenous drugs that are used as antidote against chemotheray, inflammation or viral infection, gets absorbed and interacts reversibly to the major serum transport protein i.e. albumins, upon entering the circulatory system. To have a structural guideline in the rational drug designing and in the synthesis of drugs with greater efficacy, the binding mechanism of an antineoplastic and anti-inflammatory drug Nordihydroguaiaretic acid (NDGA) with human and bovine serum albumins (HSA & BSA) were examined by spectroscopic and computational methods. NDGA binds to site II of HSA with binding constant (Kb) ~105 M-1 and free energy (ΔG) ~ -7.5 kcal.mol-1. It also binds at site II of BSA but with lesser binding affinity (Kb) ~105 M-1 and ΔG ~ -6.5 kcal.mol-1. The negative value of ΔG, ΔH and ΔS for both the albumins at three different temperatures confirmed that the complex formation process between albumins and NDGA is spontaneous and exothermic. Furthermore, hydrogen bonds and hydrophobic interactions are the main forces involved in complex formation of NDGA with both the albumins as evaluated from fluorescence and molecular docking results. Binding of NDGA to both the albumins alter the conformation and causes minor change in the secondary structure of proteins as indicated by the CD spectra. PMID:27391941

  8. Probing roles of lipopolysaccharide, type 1 fimbria, and colanic acid in the attachment of Escherichia coli strains on inert surfaces.

    PubMed

    Chao, Yuanqing; Zhang, Tong

    2011-09-20

    The roles of bacterial surface polymers in reversible (phase I) and irreversible (phase II) attachment (i.e., lipopolysaccharides (LPS), type 1 fimbria, and capsular colanic acid (CA)) were investigated in situ by combining fluorescence microscopy and atomic force microscopy. Fluorescence microscopy was used to evaluate the phase I attachment by counting the total number of cells on the substrata, and AFM was applied to image the phase II cells and measure the lateral detachment force to characterize phase II attachment. Also, by comparing the number of cells in phases I and II, the transformation ratio was calculated and used as an index to evaluate the roles of different polymers in the attachment process. Escherichia coli K-12 and its six mutants, which had different surface polymers in terms of LPS structures, CA contents, and type 1 fimbriae, were used as the test strains. Six different materials were applied as substrata, including glass, two metals (aluminum and stainless steel), and three plastics (polyvinyl chloride, polycarbonate, and polyethylene). The results indicated that LPS significantly enhanced phases I and II attachment as well as the transformation ratio from phase I to II. Like LPS, type 1 fimbriae largely increased the phase I attachment and the transformation ratio; however, they did not significantly influence the adhesion strength in phase II. CA had a negative effect on attachment in phases I and II by decreasing the adhered number of cells and the lateral detachment force, respectively, but had no influence on the transformation ratio. PMID:21842859

  9. A Comprehensive Spectroscopic and Computational Investigation to Probe the Interaction of Antineoplastic Drug Nordihydroguaiaretic Acid with Serum Albumins

    PubMed Central

    Nusrat, Saima; Siddiqi, Mohammad Khursheed; Zaman, Masihuz; Zaidi, Nida; Ajmal, Mohammad Rehan; Alam, Parvez; Qadeer, Atiyatul; Abdelhameed, Ali Saber

    2016-01-01

    Exogenous drugs that are used as antidote against chemotheray, inflammation or viral infection, gets absorbed and interacts reversibly to the major serum transport protein i.e. albumins, upon entering the circulatory system. To have a structural guideline in the rational drug designing and in the synthesis of drugs with greater efficacy, the binding mechanism of an antineoplastic and anti-inflammatory drug Nordihydroguaiaretic acid (NDGA) with human and bovine serum albumins (HSA & BSA) were examined by spectroscopic and computational methods. NDGA binds to site II of HSA with binding constant (Kb) ~105 M-1 and free energy (ΔG) ~ -7.5 kcal.mol-1. It also binds at site II of BSA but with lesser binding affinity (Kb) ~105 M-1 and ΔG ~ -6.5 kcal.mol-1. The negative value of ΔG, ΔH and ΔS for both the albumins at three different temperatures confirmed that the complex formation process between albumins and NDGA is spontaneous and exothermic. Furthermore, hydrogen bonds and hydrophobic interactions are the main forces involved in complex formation of NDGA with both the albumins as evaluated from fluorescence and molecular docking results. Binding of NDGA to both the albumins alter the conformation and causes minor change in the secondary structure of proteins as indicated by the CD spectra. PMID:27391941

  10. Effects of macromolecular crowding on a small lipid binding protein probed at the single-amino acid level.

    PubMed

    Pérez Santero, Silvia; Favretto, Filippo; Zanzoni, Serena; Chignola, Roberto; Assfalg, Michael; D'Onofrio, Mariapina

    2016-09-15

    Macromolecular crowding is a distinctive feature of the cellular interior, influencing the behaviour of biomacromolecules. Despite significant advancements in the description of the effects of crowding on global protein properties, the influence of cellular components on local protein attributes has received limited attention. Here, we describe a residue-level systematic interrogation of the structural, dynamic, and binding properties of the liver fatty acid binding protein (LFABP) in crowded solutions. Two-dimensional NMR spectral fingerprints and relaxation data were collected on LFABP in the presence of polymeric and biomolecular crowders. Non-interacting crowders produced minimal site-specific spectral perturbations on ligand-free and lipid-bound LFABP. Conformational adaptations upon ligand binding reproduced those observed in dilute solution, but a perturbation of the free oleate state resulted in less favorable uptake. When LFABP engaged in direct interactions with background molecules, changes in local chemical environments were detected for residues of the internal binding pocket and of the external surface. Enhanced complexity was introduced by investigating LFABP in cell lysates, and in membrane-bounded compartments. LFABP was able to capture ligands from prokaryotic and eukaryotic cell lysates, and from artificial cells (water-in-oil emulsion droplets). The data suggest that promiscuous interactions are a major factor influencing protein function in the cell. PMID:27457417

  11. ANTS-anchored Zn-Al-CO3-LDH particles as fluorescent probe for sensing of folic acid

    NASA Astrophysics Data System (ADS)

    Liu, Pengfei; Liu, Dan; Liu, Yanhuan; Li, Lei

    2016-09-01

    A novel fluorescent nanosensor for detecting folic acid (FA) in aqueous media has been developed based on 8-aminonaphthalene-1,3,6-trisulfonate (ANTS) anchored to the surface of Zn-Al-CO3-layered double hydroxides (LDH) particles. The nanosensor showed high fluorescence intensity and good photostability due to a strong coordination interaction between surface Zn2+ ions of Zn-Al-CO3-LDH and N atoms of ANTS, which were verified by result of X-ray photoelectron spectroscopy (XPS). ANTS-anchored on the surface of Zn-Al-CO3-LDH restricted the intra-molecular rotation leading to ANTS-anchored J-type aggregation emission enhancement. ANTS-anchored Zn-Al-CO3-LDH particles exhibited highly sensitive and selective response to FA over other common metal ions and saccharides present in biological fluids. The proposed mechanism was that oxygen atoms of -SO3 groups in ANTS-anchored on the surface of Zn-Al-CO3-LDH were easily collided by FA molecules to form potential hydrogen bonds between ANTS-anchored and FA molecules, which could effectively quench the ANTS-anchored fluorescence. Under the simulated physiological conditions (pH of 7.4), the fluorescence quenching was fitted to Stern-Volmer equation with a linear response in the concentration range of 1 μM to 200 μM with a limit of detection of 0.1 μM. The results indicate that ANTS-anchored Zn-Al-CO3-LDH particles can afford a very sensitive system for the sensing FA in aqueous solution.

  12. Photoluminescence of Mn+ doped GaAs

    NASA Astrophysics Data System (ADS)

    Zhou, Huiying; Qu, Shengchun; Liao, Shuzhi; Zhang, Fasheng; Liu, Junpeng; Wang, Zhanguo

    2010-10-01

    Photoluminescence is one of the most useful techniques to obtain information about optoelectronic properties and defect structures of materials. In this work, the room-temperature and low temperature photoluminescence of Mn-doped GaAs were investigated, respectively. Mn-doped GaAs structure materials were prepared by Mn+ ion implantation at room temperature into GaAs. The implanted samples were subsequently annealed at various temperatures under N2 atmosphere to recrystallize the samples and remove implant damage. A strong peak was found for the sample annealed at 950 °C for 5 s. Transitions near 0.989 eV (1254 nm), 1.155 eV (1074 nm) and 1.329 eV (933 nm) were identified and formation of these emissions was analyzed for all prepared samples. This structure material could have myriad applications, including information storage, magnet-optical properties and energy level engineering.

  13. Self-assembly drives quantum dot photoluminescence.

    PubMed

    Plain, J; Sonnefraud, Y; Viste, P; Lérondel, G; Huant, S; Royer, P

    2009-03-01

    Engineering the spectral properties of quantum dots can be achieved by a control of the quantum dots organization on a substrate. Indeed, many applications of quantum dots as LEDs are based on the realization of a 3D architecture of quantum dots. In this contribution, we present a systematic study of the quantum dot organization obtained on different chemically modified substrates. By varying the chemical affinity between the quantum dots and the substrate, the quantum dot organization is strongly modified from the 2D monolayer to the 3D aggregates. Then the photoluminescence of the different obtained samples has been systematically studied and correlated with the quantum dot film organization. We clearly show that the interaction between the substrate and the quantum dot must be stronger than the quantum dot-quantum dot interaction to avoid 3D aggregation and that these organization strongly modified the photoluminescence of the film rather than intrinsic changes of the quantum dot induced by pure surface chemistry.

  14. Investigation of the Binding Interaction of Fatty Acids with Human G Protein-Coupled Receptor 40 Using a Site-Specific Fluorescence Probe by Flow Cytometry.

    PubMed

    Ren, Xiao-Min; Cao, Lin-Ying; Zhang, Jing; Qin, Wei-Ping; Yang, Yu; Wan, Bin; Guo, Liang-Hong

    2016-04-01

    Human G protein-coupled receptor 40 (hGPR40), with medium- and long-chain free fatty acids (FFAs) as its natural ligands, plays an important role in the enhancement of glucose-dependent insulin secretion. To date, information about the direct binding of FFAs to hGPR40 is very limited, and how carbon-chain length affects the activities of FFAs on hGPR40 is not yet understood. In this study, a fluorescein-fasiglifam analogue (F-TAK-875A) conjugate was designed and synthesized as a site-specific fluorescence probe to study the interaction of FFAs with hGPR40. hGPR40 was expressed in human embryonic kidney 293 cells and labeled with F-TAK-875A. By using flow cytometry, competitive binding of FFA and F-TAK-875A to hGPR40-expressed cells was measured. Binding affinities of 18 saturated FFAs, with carbon-chain lengths ranging from C6 to C23, were analyzed. The results showed that the binding potencies of FFAs to hGPR40 were dependent on carbon length. There was a positive correlation between length and binding potency for seven FFAs (C9-C15), with myristic acid (C15) showing the highest potency, 0.2% relative to TAK-875. For FFAs with a length of fewer than C9 or more than C15, they had very weak or no binding. Molecular docking results showed that the binding pocket of TAK-875 in hGPR40 could enclose FFAs with lengths of C15 or fewer. However, for FFAs with lengths longer than C15, part of the alkyl chain extended out of the binding pocket. This study provided insights into the structural dependence of FFAs binding to and activation of hGPR40.

  15. Central-metal exchange, improved catalytic activity, photoluminescence properties of a new family of d(10) coordination polymers based on the 5,5'-(1H-2,3,5-triazole-1,4-diyl)diisophthalic acid ligand.

    PubMed

    Wang, Huarui; Huang, Chao; Han, Yanbing; Shao, Zhichao; Hou, Hongwei; Fan, Yaoting

    2016-05-01

    The rigid and planar tetracarboxylic acid 5,5'-(1H-2,3,5-triazole-1,4-diyl)diisophthalic acid (H4L), incorporating a triazole group, has been used with no or different pyridine-based linkers to construct a family of d(10) coordination polymers, namely, {[H2N(CH3)2]3[Cd3(L)2(HCOO)]}n (), {[Cd2(L)(py)6]·H2O}n (), {[H2N(CH3)2] [Cd2(L)(HCOO)(H2O)4]}n (), {[Zn(H2L)]·H2O}n (), and {[Zn(H2L)(4,4'-bipy)0.5]·C2H5OH·H2O}n () (py = pyridine, 4,4'-bipy = 4,4'-bipyridine). constructs a 3D porous network containing two kinds of channels: one is filled with coordinated HCOO(-) anions, and the other with [H2N(CH3)2](+) cations. The framework of can be described as a rare (5,6,7)-connected net with the Schläfli symbol of (4(12)·5·6(2))(4(5)·5(3)·6(2))2(4(8)·5(3)·6(8)·8(2))2. The Cd(ii) ions in are connected through the carboxylate ligands to form a 2D layer, with aperture dimensions of ∼15.1 Å × 16.2 Å. The network of features a 3D (3,4)-connected (6·8·10)2(6·8(3)·10(2)) topology. A 3D network with the (4(2)·6·8(3)) topology of possesses an open 1D channel with the free volume of 29.2%. is a 2D layer structure with the (4(2)·6(3)·8)(4(2)·6) topology. The fluorescence lifetime τ values of are on the nanosecond timescale at room temperature. In particular, central-metal exchange in leads to a series of isostructural M(ii)-Cd frameworks [M = Cu (), Co (), Ni ()] showing improved catalytic activity for the synthesis of 1,4,5,6-tetrahydropyrimidine derivatives. Based on this, a plausible mechanism for the catalytic reaction has been proposed and the reactivity-structure relationship has been further clarified. PMID:27063339

  16. Syntheses, structures and photoluminescent properties of Zn(Ⅱ)/Co(Ⅱ) coordination polymers based on flexible tetracarboxylate ligand of 5,5‧-(butane-1,4-diyl)-bis(oxy)-di isophthalic acid

    NASA Astrophysics Data System (ADS)

    Gao, Yan-Peng; Guo, Le; Dong, Wei; Jia, Min; Zhang, Jing-Xue; Sun, Zhong; Chang, Fei

    2016-08-01

    Three new mixed-ligand metal-organic frameworks based on 5,5‧-(butane-1,4- diyl)-bis(oxy)-diisophthalic acid and transitional metal cations with the help of two ancillary bridging N-donor pyridyl and imidazole linkers, [Zn(L)0.5(4,4‧-bpy)]·2(H2O) (1), [M(L)0.5(bib)]·4(H2O) (M = Zn (2), Co (3)), (4,4‧-bpy=4,4‧-bipyridine, bib=1,4-bis (1H-imidazol-1-yl)-butane), have been synthesized under solvothermal conditions. Their structures and properties were determined by single-crystal and powder X-ray diffraction analyses, IR spectra, elemental analyses and thermogravimetric analyses (TGA). Compounds 1-3 display a 3D 3-fold interpenetrated frameworks linked by the L4- ligands, ancillary N-donor linkers and the free water molecules in the crystal lattice. Topological analysis reveals that 1-3 are a (4,4)-connected bbf topology net with the (64·82)(66) topology. The effects of the L4- anions, the N-donor ligands, and the metal ions on the structures of the coordination polymers have been discussed. Furthermore, luminescence properties and thermogravimetric properties of these compounds were investigated.

  17. Effect of glucose on the fatty acid composition of Cupriavidus necator JMP134 during 2,4-dichlorophenoxyacetic acid degradation: implications for lipid-based stable isotope probing methods.

    PubMed

    Lerch, Thomas Z; Dignac, Marie-France; Barriuso, Enrique; Mariotti, André

    2011-10-01

    Combining lipid biomarker profiling with stable isotope probing (SIP) is a powerful technique for studying specific microbial populations responsible for the degradation of organic pollutants in various natural environments. However, the presence of other easily degradable substrates may induce significant physiological changes by altering both the rate of incorporation of the target compound into the biomass and the microbial lipid profiles. In order to test this hypothesis, Cupriavidus necator JMP134, a 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium, was incubated with [(13)C]2,4-D, [(13)C]glucose, or mixtures of both substrates alternatively labeled with (13)C. C. necator JMP134 exhibited a preferential use of 2,4-D over glucose. The isotopic analysis showed that glucose had only a small effect on the incorporation of the acetic chain of 2,4-D into the biomass (at days 2 and 3) and no effect on that of the benzenic ring. The addition of glucose did change the fatty acid methyl ester (FAME) composition. However, the overall FAME isotopic signature reflected that of the entire biomass. Compound-specific individual isotopic analyses of FAME composition showed that the (13)C-enriched FAME profiles were slightly or not affected when tracing the 2,4-D acetic chain or 2,4-D benzenic ring, respectively. This batch study is a necessary step for validating the use of lipid-based SIP methods in complex environments.

  18. Probing the interaction induced conformation transitions in acid phosphatase with cobalt ferrite nanoparticles: Relation to inhibition and bio-activity of Chlorella vulgaris acid phosphatase.

    PubMed

    Ahmad, Farooq; Zhou, Xing; Yao, Hongzhou; Zhou, Ying; Xu, Chao

    2016-09-01

    The present study explored the interaction and kinetics of cobalt ferrite nanoparticles (NPs) with acid phosphatase (ACP) by utilizing diverse range of spectroscopic techniques. The results corroborate, the CoFe2O4 NPs cause fluorescence quenching in ACP by static quenching mechanism. The negative values of van't Hoff thermodynamic expressions (ΔH=-0.3293Jmol(-1)K(-1) and ΔG=-3.960kJmol(-1)K(-1)) corroborate the spontaneity and exothermic nature of static quenching. The positive value of ΔS (13.2893Jmol(-1)K(-1)) corroborate that major contributors of higher and stronger binding affinity among CoFe2O4 NPs with ACP were electrostatic. In addition, FTIR, UV-CD, UV-vis spectroscopy and three dimensional fluorescence (3D) techniques confirmed that CoFe2O4 NPs binding induces microenvironment perturbations leading to secondary and tertiary conformation changes in ACP to a great extent. Furthermore, synchronous fluorescence spectroscopy (SFS) affirmed the comparatively significant changes in microenvironment around tryptophan (Trp) residue by CoFe2O4 NPs. The effect of CoFe2O4 NPs on the activation kinetics of ACP was further examined in Chlorella vulgaris. Apparent Michaelis constant (Km) values of 0.57 and 26.5mM with activation energy values of 0.538 and 3.428kJmol(-1) were determined without and with 200μM CoFe2O4 NPs. Apparent Vmax value of -7Umml(-1) corroborate that enzyme active sites were completely captured by the NPs leaving no space for the substrate. The results confirmed that CoFe2O4 NPs ceased the activity by unfolding of ACP enzyme. This suggests CoFe2O4 NPs perturbed the enzyme activity by transitions in conformation and hence the metabolic activity of ACP. This study provides the pavement for novel and simple approach of using sensitive biomarkers for sensing NPs in environment. PMID:27209386

  19. DNA detection using plasmonic enhanced near-infrared photoluminescence of gallium arsenide.

    PubMed

    Tang, Longhua; Chun, Ik Su; Wang, Zidong; Li, Jinghong; Li, Xiuling; Lu, Yi

    2013-10-15

    Efficient near-infrared detection of specific DNA with single nucleotide polymorphism selectivity is important for diagnostics and biomedical research. Herein, we report the use of gallium arsenide (GaAs) as a sensing platform for probing DNA immobilization and targeting DNA hybridization, resulting in ∼8-fold enhanced GaAs photoluminescence (PL) at ∼875 nm. The new signal amplification strategy, further coupled with the plasmonic effect of Au nanoparticles, is capable of detecting DNA molecules with a detection limit of 0.8 pM and selectivity against single base mismatches. Such an ultrasensitive near-infrared sensor can find a wide range of biochemical and biomedical applications.

  20. Photoluminescence imaging of solitary dopant sites in covalently doped single-wall carbon nanotubes.

    PubMed

    Hartmann, Nicolai F; Yalcin, Sibel Ebru; Adamska, Lyudmyla; Hároz, Erik H; Ma, Xuedan; Tretiak, Sergei; Htoon, Han; Doorn, Stephen K

    2015-12-28

    Covalent dopants in semiconducting single wall carbon nanotubes (SWCNTs) are becoming important as routes for introducing new photoluminescent emitting states with potential for enhanced quantum yields, new functionality, and as species capable of near-IR room-temperature single photon emission. The origin and behavior of the dopant-induced emission is thus important to understand as a key requirement for successful room-T photonics and optoelectronics applications. Here, we use direct correlated two-color photoluminescence imaging to probe how the interplay between the SWCNT bright E(11) exciton and solitary dopant sites yields the dopant-induced emission for three different dopant species: oxygen, 4-methoxybenzene, and 4-bromobenzene. We introduce a route to control dopant functionalization to a low level as a means for introducing spatially well-separated solitary dopant sites. Resolution of emission from solitary dopant sites and correlation to their impact on E(11) emission allows confirmation of dopants as trapping sites for localization of E(11) excitons following their diffusive transport to the dopant site. Imaging of the dopant emission also reveals photoluminescence intermittency (blinking), with blinking dynamics being dependent on the specific dopant. Density functional theory calculations were performed to evaluate the stability of dopants and delineate the possible mechanisms of blinking. Theoretical modeling suggests that the trapping of free charges in the potential well created by permanent dipoles introduced by dopant atoms/groups is likely responsible for the blinking, with the strongest effects being predicted and observed for oxygen-doped SWCNTs. PMID:26586162

  1. Chemical Cleavage of Layered Carbon Nitride with Enhanced Photoluminescent Performances and Photoconduction.

    PubMed

    Zhou, Zhixin; Shen, Yanfei; Li, Ying; Liu, Anran; Liu, Songqin; Zhang, Yuanjian

    2015-12-22

    Graphene quantum dots (GQDs) and carbon dots (C-dots) have various alluring properties and potential applications, but they are often limited by unsatisfied optical performance such as low quantum yield, ambiguous fluorescence emission mechanism, and narrow emission wavelength. Herein, we report that bulk polymeric carbon nitride could be utilized as a layered precursor to prepare carbon nitride nanostructures such as nanorods, nanoleaves and quantum dots by chemical tailoring. As doped carbon materials, these carbon nitride nanostructures not only intrinsically emitted UV lights but also well inherited the explicit photoluminescence mechanism of the bulk pristine precursor, both of which were rarely reported for GQDs and C-dots. Especially, carbon nitride quantum dots (CNQDs) had a photoluminescence quantum yield (QY) up to 46%, among the highest QY for metal-free quantum dots so far. As examples, the CNQDs were utilized as a photoluminescence probe for rapid detection of Fe(3+) with a detection limit of 1 μM in 2 min and a photoconductor in an all-solid-state device. This work would open up an avenue for doped nanocarbon in developing photoelectrical devices and sensors.

  2. Microscopic view on the ultrafast photoluminescence from photoexcited graphene.

    PubMed

    Winzer, Torben; Ciesielski, Richard; Handloser, Matthias; Comin, Alberto; Hartschuh, Achim; Malic, Ermin

    2015-02-11

    We present a joint theory-experiment study on ultrafast photoluminescence from photoexcited graphene. On the basis of a microscopic theory, we reveal two distinct mechanisms behind the occurring photoluminescence: besides the well-known incoherent contribution driven by nonequilibrium carrier occupations, we found a coherent part that spectrally shifts with the excitation energy. In our experiments, we demonstrate for the first time the predicted appearance and spectral shift of the coherent photoluminescence. PMID:25616043

  3. Terbium photoluminescence in yttrium aluminum garnet xerogels

    SciTech Connect

    Maliarevich, G. K.; Gaponenko, N. V. Mudryi, A. V.; Drozdov, Yu. N.; Stepikhova, M. V.; Stepanova, E. A.

    2009-02-15

    Based on a colloidal solution containing terbium, yttrium, and aluminum metal ions, a powder was synthesized and films of terbium-doped yttrium aluminum garnet Tb{sub 0.15}Y{sub 2.85}Al{sub 5}O{sub 12} were grown on single-crystal silicon and porous anodic alumina. Annealing of the sample in a temperature range from 200-1100 deg. C results in an increase in the photoluminescence intensity in the wavelength range from 480-640 nm, which is caused by Tb{sup 3+} ion intra-atomic transitions {sup 5}D{sub 4}{sup {yields}}{sup 7}F{sub j} (j = 3, 4, 5, 6). Annealing at 900 deg. C and higher temperatures gives rise to low-intensity photoluminescence bands in the region of 667 and 681 nm, which correspond to transitions {sup 5}D{sub 4}{sup {yields}}{sup 7}F{sub 0}, {sup 5}D{sub 4}{sup {yields}}{sup 7}F{sub 1}, and room-temperature Stark term splitting, which suggests the existence of a crystalline environment of Tb{sup 3+} ions. The FWHM of spectral lines in the region of 543 nm decreases from {approx}10 to {approx}(2-3) nm as the xerogel annealing temperature is increased from 700 to 900 deg. C and higher. Three bands with maxima at 280, 330, and 376 nm, which correspond to Tb{sup 3+} ion transitions {sup 7}F{sub 6}{sup {yields}}{sup 5}I{sub 8}, {sup 5}L{sub 6}, {sup 5}G{sub 6}, {sup 5}D{sub 3}, are observed in the photoluminescence excitation spectra of the studied structures for the emission wavelength at 543 nm. X-ray diffraction detected the formation of a crystalline phase for a terbium-doped yttrium aluminum garnet powder after annealing at 1100 deg. C.

  4. A turn-on highly selective and ultrasensitive determination of copper (II) in an aqueous medium using folic acid capped gold nanoparticles as the probe

    NASA Astrophysics Data System (ADS)

    Vasimalai, N.; Prabhakarn, A.; John, S. Abraham

    2013-12-01

    This paper describes a ‘turn-on’ fluorescent determination of Cu(II) in an aqueous medium using folic acid capped gold nanoparticles (FA-AuNPs) as the probe. The FA-AuNPs were synthesized by the wet chemical method and were characterized by UV-visible, fluorescence, HR-TEM, XRD, zeta potential, and DLS techniques. The FA-AuNPs show an absorption maximum at 510 nm and an emission maximum at 780 nm (λex: 510 nm). On adding 10 μM Cu(II), the wine-red color of FA-AuNPs changed to purple and the absorbance at 510 nm decreased. The observed changes were ascribed to the aggregation of AuNPs. This was confirmed by DLS and HR-TEM studies. Interestingly, the emission intensity of FA-AuNPs was enhanced even in the presence of a picomolar concentration of Cu(II). Based on the enhancement of the emission intensity, the concentration of Cu(II) was determined. The FA-AuNPs showed an extreme selectivity towards the determination of 10 nM Cu(II) in the presence of 10 000-fold higher concentration of interferences except EDTA and the carboxylate anion. A good linearity was observed from 10 × 10-9 to 1 × 10-12 M Cu(II), and the detection limit was found to be 50 fM l-1 (S/N = 3). The proposed method was successfully applied to determine Cu(II) in real samples. The results obtained were validated with ICP-AES.

  5. Nanoparticle-based luminescent probes for intracellular sensing and imaging of pH.

    PubMed

    Schäferling, Michael

    2016-05-01

    Fluorescence imaging microscopy is an essential tool in biomedical research. Meanwhile, various fluorescent probes are available for the staining of cells, cell membranes, and organelles. Though, to monitor intracellular processes and dysfunctions, probes that respond to ubiquitous chemical parameters determining the cellular function such as pH, pO2 , and Ca(2+) are required. This review is focused on the progress in the design, fabrication, and application of photoluminescent nanoprobes for sensing and imaging of pH in living cells. The advantages of using nanoprobes carrying fluorescent pH indicators compared to single molecule probes are discussed as well as their limitations due to the mostly lysosomal uptake by cells. Particular attention is paid to ratiometric dual wavelength nanosensors that enable intrinsic referenced measurements. Referencing and proper calibration procedures are basic prerequisites to carry out reliable quantitative pH determinations in complex samples such as living cells. A variety of examples will be presented that highlight the diverseness of nanocarrier materials (polymers, micelles, silica, quantum dots, carbon dots, gold, photon upconversion nanocrystals, or bacteriophages), fluorescent pH indicators for the weak acidic range, and referenced sensing mechanisms, that have been applied intracellularly up to now. WIREs Nanomed Nanobiotechnol 2016, 8:378-413. doi: 10.1002/wnan.1366 For further resources related to this article, please visit the WIREs website.

  6. Photoluminescence study in diaminobenzene functionalized graphene oxide

    SciTech Connect

    Gupta, Abhisek E-mail: cnssks@iacs.res.in; Saha, Shyamal K. E-mail: cnssks@iacs.res.in

    2014-10-15

    Being an excellent electronic material graphene is a very poor candidate for optoelectronic applications. One of the major strategies to develop the optical property in GO is the functionalization of graphene oxide (GO). In the present work GO sheets are functionalized by o-phenylenediamine to achieve diaminobenzene functionalized GO composite (DAB-GO). Formation of DAB-GO composite is further characterized by FTIR, UV, Raman studies. Excellent photoluminescence is observed in DAB-GO composite via passivation of the surface reactive sites by ring-opening amination of epoxides of GO.

  7. Photoluminescence study in diaminobenzene functionalized graphene oxide

    NASA Astrophysics Data System (ADS)

    Gupta, Abhisek; Saha, Shyamal K.

    2014-10-01

    Being an excellent electronic material graphene is a very poor candidate for optoelectronic applications. One of the major strategies to develop the optical property in GO is the functionalization of graphene oxide (GO). In the present work GO sheets are functionalized by o-phenylenediamine to achieve diaminobenzene functionalized GO composite (DAB-GO). Formation of DAB-GO composite is further characterized by FTIR, UV, Raman studies. Excellent photoluminescence is observed in DAB-GO composite via passivation of the surface reactive sites by ring-opening amination of epoxides of GO.

  8. Photoluminescence in anthracene and it's derivatives

    NASA Astrophysics Data System (ADS)

    Vyas, Arpita; Mirgane, Nitin A.; Moharil, S. V.; Muley, Aarti Iyer

    2016-05-01

    The anthracene and it's derivative 9-chloro acridine and Anthracene-9-ylmethylacetate have prepared in Poly vinyl alcohol(PVOH). Their photoluminescence properties have studied. The pure anthracene has an emission at 424 and 443nm. The intense peak is observed at 465nm and shoulder at 407nm. The derivatives of anthracene Anthracene-9-ylmethylacetate shows an emission around 440nm for the excitation at 393nm and 9-chloro acridine shows emission around 360nm for the excitation at 290nm. The major problem of this organic material is the stability. The composites prepared in the medium of PVOH are more stable.

  9. Photoluminescence of strained-layer superlattices

    NASA Astrophysics Data System (ADS)

    Kato, H.; Nakayama, M.; Chika, S.; Sano, N.

    1984-11-01

    The strained-layer superlattices (SLS's) of In xGa 1- xAsGaAs and the single hetero-structure of In xGa 1- xAs on GaAs were grown by MBE method. The samples obtained have a perfect surface morphology. The alloy composition of In xGa 1- xAs layer and the growth rate were determined with high accuracy by in situ observation of the intensity oscillation of RHEED pattern. Photoluminescence peak energies of SLS's are in agreement with the calculated value by the Kronig-Penny analysis.

  10. Optical probe

    DOEpatents

    Hencken, Kenneth; Flower, William L.

    1999-01-01

    A compact optical probe is disclosed particularly useful for analysis of emissions in industrial environments. The instant invention provides a geometry for optically-based measurements that allows all optical components (source, detector, rely optics, etc.) to be located in proximity to one another. The geometry of the probe disclosed herein provides a means for making optical measurements in environments where it is difficult and/or expensive to gain access to the vicinity of a flow stream to be measured. Significantly, the lens geometry of the optical probe allows the analysis location within a flow stream being monitored to be moved while maintaining optical alignment of all components even when the optical probe is focused on a plurality of different analysis points within the flow stream.

  11. Solid-state (17)O NMR as a sensitive probe of keto and gem-diol forms of alpha-keto acid derivatives.

    PubMed

    Zhu, Jianfeng; Geris, Amanda J; Wu, Gang

    2009-08-28

    We have used solid-state (17)O NMR experiments to measure the (17)O quadrupole coupling (QC) and chemical shift (CS) tensors for two alpha-keto acids: sodium [2-(17)O]pyruvate and lithium [2,2'-(17)O(2)]pyruvate. In the solid state, sodium [2-(17)O]pyruvate is in the keto form (-C(double bond (17)O)-) whereas lithium [2,2'-(17)O(2)]pyruvate takes the gem-diol form (-C((17)OH)(2)-). This study represents the first time that a full set of (17)O NMR tensors are experimentally determined for alpha-keto acids in these two different tautomeric forms. We have found that the two forms exhibit drastically different (17)O QC and CS tensors: for the keto form, delta(iso) = 543 +/- 1 ppm, C(Q) = 10.8 +/- 0.2 MHz, eta(Q) = 0.48 +/- 0.05, delta(11) = 1020 +/- 10, delta(22) = 640 +/- 10, delta(33) = -40 +/- 10 ppm, alpha = 80 +/- 5 degrees, beta = 90 +/- 2 degrees, and gamma = 83 +/- 2 degrees; for the gem-diol form, delta(iso) = 62 +/- 1 ppm, C(Q) = 8.5 +/- 0.5 MHz, eta(Q) = 1.0 +/- 0.05, delta(11) = 140 +/- 5, delta(22) = 45 +/- 5, delta(33) = 0 +/- 5 ppm, alpha = 55 +/- 5 degrees, beta = 90 +/- 5 degrees, and gamma = 80 +/- 2 degrees. The (17)O chemical shift tensor observed for the gem-diol functional group also represents the first such measurement for any -ol functional group (e.g., alcohols, phenols, carbohydrates, etc.) Using these accurate experimental (17)O NMR tensors, we were able to evaluate the accuracy of quantum chemical calculations. Our results showed that quantum chemical calculations using the crystal lattice approach are in much better agreement with the experimental solid-state (17)O NMR data than those calculated using the molecular cluster approach. Quantum chemical calculations have also provided information about the sign of the (17)O quadrupolar coupling constants and about the (17)O NMR tensor orientations in the molecular frame of reference. Our findings suggest that solid-state (17)O NMR may be useful in probing the tautomeric form of the alpha

  12. Efficient Synthesis of Highly Photoluminescent Short Dendritic CdSeS/ZnS Quantum Dots for Biolabeling.

    PubMed

    Kong, Peng; Zhou, Guangjun; Zhou, Haifeng; Zhou, Juan; Zhang, Xingshuang; Yu, Zhichao

    2016-03-01

    A convenient and efficient approach is reported to synthesize CdSeS with low-cost and low-toxic materials. The influence of the Se/S ratio and reaction time on the photoluminescent properties of CdSeS QDs is investigated through researching the temporal evolution of the absorption and the emission. Following, the high photoluminescent short dendritic green-emitting CdSeS/ZnS QDs are prepared using the method inspired by the successive ion layer adsorption and reaction procedure, which are composed of a CdSeS core and ZnS branches. Transmission electronic microscopy and X-ray diffraction show that the CdSeS/ZnS QDs is in a cubic zinc blende structure. The photoluminescence intensity increase significantly when the ZnS branches form as a result of the charge carriers being confined in the core. The photoluminescence quantum yield of the obtained CdSeS/ZnS core-shell QDs can be up to 90%, which is much higher than that of initial CdSeS QDs (39%). In addition, CdSeS/ZnS QDs have good photoluminescence intensity after they are transferred from organic solvent into aqueous media through ligand replacement using mercaptoacetic acid. Afterwards, the E. Coli O-157 are not only successfully conjugated with CdSeS/ZnS QDs but also present clear images under UV irradiation. PMID:27455651

  13. Hydrothermal synthesis, crystal structures and photoluminescence properties of mixed europium-yttrium organic frameworks

    NASA Astrophysics Data System (ADS)

    Han, Yinfeng; Fu, Lianshe; Mafra, Luís; Shi, Fa-Nian

    2012-02-01

    Three mixed europium-yttrium organic frameworks: Eu2-xYx(Mel)(H2O)6 (Mel=mellitic acid or benzene-1,2,3,4,5,6-hexacarboxylic acid, x=0.38 1, 0.74 2, and 0.86 3) have been synthesized and characterized. All the compounds contain a 3-D net with (4, 8)-flu topology. The study indicates that the photoluminescence properties are effectively affected by the different ratios of europium and yttrium ions, the quantum efficiency is increased and the Eu3+ lifetime becomes longer in these MOFs than those of the Eu analog.

  14. Influence of cysteine doping on photoluminescence intensity from semiconducting single-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Kurnosov, N. V.; Leontiev, V. S.; Linnik, A. S.; Karachevtsev, V. A.

    2015-03-01

    Photoluminescence (PL) from semiconducting single-walled carbon nanotubes can be applied for detection of cysteine. It is shown that cysteine doping (from 10-8 to 10-3 M) into aqueous suspension of nanotubes with adsorbed DNA leads to increase of PL intensity. The PL intensity was enhanced by 27% at 10-3 M cysteine concentration in suspension. Most likely, the PL intensity increases due to the passivation of p-defects on the nanotube by the cysteine containing reactive thiol group. The effect of doping with other amino acids without this group (methionine, serine, aspartic acid, lysine, proline) on the PL intensity is essentially weaker.

  15. The correlation of blue shift of photoluminescence and morphology of silicon nanoporous

    NASA Astrophysics Data System (ADS)

    Al-Jumaili, Batool E. B.; Talib, Zainal A.; Josephine L., Y.; Paiman, Suriati B.; Ahmed, Naser M.; Al-Jumaily, Abdulmajeed H. J.; Ramizy, Asmiet; Abdulateef, Sinan A.; Muh'd, Ibrahim B.; Mofdal, Manahil E. E.

    2016-07-01

    Porous silicon with diameters ranging from 6.41 to 7.12 nm were synthesized via electrochemical etching by varied anodization current density in ethanoic solutions containing aqueous hydrofluoric acid up to 65mA/cm2.The luminescence properties of the nanoporous at room temperature were analyzed via photoluminescence spectroscopy. Photoluminescence PL spectra exhibit a broad emission band in the range of 360-700 nm photon energy. The PL spectrum has a blue shift in varied anodization current density; the blue shift incremented as the existing of anodization although the intensity decreased. The current blue shift is owning to alteration of silicon nanocrystal structure at the superficies. The superficial morphology of the PS layers consists of unified and orderly distribution of nanocrystalline Si structures, have high porosity around (93.75%) and high thickness 39.52 µm.

  16. Environmental applications of photoluminescence-based biosensors.

    PubMed

    Reardon, Kenneth F; Zhong, Zhong; Lear, Kevin L

    2009-01-01

    For monitoring and treatment of soil and water, environmental scientists and engineers require measurements of the concentration of chemical contaminants. Although laboratory-based methods relying on gas or liquid chromatography can yield very accurate measurements, they are also complex, time consuming, expensive, and require sample pretreatment. Furthermore, they are not readily adapted for in situ measurements.Sensors are devices that can provide continuous, in situ measurements, ideally without the addition of reagents. A biosensor incorporates a biological component coupled to a transducer, which translates the interaction between the analyte and the biocomponent into a signal that can be processed and reported. A wide range of transducers have been employed in biosensors, the most common of which are electrochemical and optical. In this contribution, we focus on photoluminescence-based biosensors of potential use in the applications described above.Following a review of photoluminescence and a discussion of the optoelectronic hardware part of these biosensor systems, we provide explanations and examples of optical biosensors for specific chemical groups: hydrocarbons and alcohols, halogenated organics, nitro-, phospho-, sulfo-, and other substituted organics, and metals and other inorganics. We also describe approaches that have been taken to describe chemical mixtures as a whole (biological oxygen demand and toxicity) since most environmental samples contain mixtures of unknown (and changing) composition. Finally, we end with some thoughts on future research directions that are necessary to achieve the full potential of environmental biosensors.

  17. Highly Photoluminescent Molybdenum Oxide Quantum Dots: One-Pot Synthesis and Application in 2,4,6-Trinitrotoluene Determination.

    PubMed

    Xiao, Sai Jin; Zhao, Xiao Jing; Hu, Ping Ping; Chu, Zhao Jun; Huang, Cheng Zhi; Zhang, Li

    2016-03-01

    As a well-studied transition-metal semiconductor material, MoOx has a wider band gap than molybdenum disulfide (MoS2), and its property varies dramatically for the existence of several different allotropes and suboxide phases of molybdenum oxides (MoOx, x < 3). In this manuscript, a one-pot method possessing the advantages of one pot, easily prepared, rapid, and environmentally friendly, has been developed for facile synthesis of highly photoluminescent MoOx quantum dots (MoOx QDs), in which commercial molybdenum disulfide (MoS2) powder and hydrogen peroxide (H2O2) are employed as the precursor and oxidant, respectively. The obtained MoOx QDs can be further utilized as an efficient photoluminescent probe, and a new turn-off sensor is developed for 2,4,6-trinitrotoluene (TNT) determination based on the fact that the photoluminescence of MoOx QDs can be quenched by the Meisenheimer complexes formed in the strong alkali solution through the inner filter effect (IFE). Under the optimal conditions, the decreased photoluminescence of MoOx QDs shows a good linear relationship to the concentration of TNT ranging from 0.5 to 240.0 μM, and the limit of detection was 0.12 μM (3σ/k). With the present turn-off sensor, TNT in river water samples can be rapidly and selectively detected without tedious sample pretreatment processes.

  18. Photoluminescence spectroscopy of YVO4:Eu3+ nanoparticles with aromatic linker molecules: A precursor to biomedical functionalization

    NASA Astrophysics Data System (ADS)

    Senty, T. R.; Yalamanchi, M.; Zhang, Y.; Cushing, S. K.; Seehra, M. S.; Shi, X.; Bristow, A. D.

    2014-04-01

    Photoluminescence spectra of YVO4:Eu3+ nanoparticles are presented, with and without the attachment of organic molecules that are proposed for linking to biomolecules. YVO4:Eu3+ nanoparticles with 5% dopant concentration were synthesized via wet chemical synthesis. X-ray diffraction and transmission electron microscopy show the expected wakefieldite structure of tetragonal particles with an average size of 17 nm. Fourier-transform infrared spectroscopy determines that metal-carboxylate coordination is successful in replacing native metal-hydroxyl bonds with three organic linkers, namely, benzoic acid, 3-nitro 4-chloro-benzoic acid, and 3,4-dihydroxybenzoic acid, in separate treatments. UV-excitation photoluminescence spectra show that the position and intensity of the dominant 5D0 - 7F2 electric-dipole transition at 619 nm are unaffected by the benzoic acid and 3-nitro 4-chloro-benzoic acid treatments. Attachment of 3,4-dihydroxybenzoic acid produces an order-of-magnitude quenching in the photoluminescence, due to the presence of high-frequency vibrational modes in the linker. Ratios of the dominant electric- and magnetic-dipole transitions confirm infrared measurements, which indicate that the bulk crystal of the nanoparticle is unchanged by all three treatments.

  19. Enhanced photoluminescence of C 60 incorporated into interlayers of hydrotalcite

    NASA Astrophysics Data System (ADS)

    Ding, Weiping; Gu, Gang; Zhong, Wei; Zang, Wen-Cheng; Du, Youwei

    1996-11-01

    Strong photoluminescence of sodium-reduced C 60 incorporated into interlayers of hydrotalcite is observed. This phenomenon is correlated to the fact that the reduced C 60 is positioned between positively charged layers of the anion clay. The interaction between the layers and reduced C 60 alters the photophysical properties of C 60 and relaxes the electron transition inhibition, thus enhancing photoluminescence.

  20. Amino acid precursors from a simulated lower atmosphere of titan: experiments of cosmic ray energy source with ¹³C- and ¹⁸O-stable isotope probing mass spectrometry.

    PubMed

    Taniuchi, Toshinori; Takano, Yoshinori; Kobayashi, Kensei

    2013-01-01

    The organic haze of aerosols that shrouds the Saturnian moon Titan has previously been studied by both observations and laboratory simulation experiments. Here we report the abiotic formation of amino acid precursors in complex organic molecules during experimental simulation of the environment near Titan's surface with proton irradiation. Pyrolysis of the organic molecules formed in the simulated Titan atmosphere by proton irradiation at 600°C yielded compounds that contained HCN and NH₃ (m/z = 27 and 17). These experimental results are consistent with the molecular information obtained by pyrolysis gas chromatography/mass spectrometry (pyrolysis GC/MS) of samples collected by the Huygens probe to Titan. Scanning electron microscopy (SEM) and three-dimensional atomic force microscopy (AFM) images of the irradiation products reveal nanometer-scale filaments and globules in complex amorphous structures (approximately 1000 Da). Isotope probing experiments by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) show that oxygen atoms were incorporated into the racemic amino acids by hydrolysis of ¹⁸O-labeled water. We suggest that the amino acid precursors possibly formed after water hydrolysis, as suggested in a previous observational study (C. A. Griffith, T. Owen, T. R. Geballe, J. Rayner, and P. Rannou, Science, 2003, 300, 628). We propose that cosmic rays are a significant and effective energy source for producing complex organics and amino acid precursors in Titan's atmospheric haze.

  1. Conductivity Probe

    NASA Technical Reports Server (NTRS)

    2008-01-01

    The Thermal and Electrical Conductivity Probe (TECP) for NASA's Phoenix Mars Lander took measurements in Martian soil and in the air.

    The needles on the end of the instrument were inserted into the Martian soil, allowing TECP to measure the propagation of both thermal and electrical energy. TECP also measured the humidity in the surrounding air.

    The needles on the probe are 15 millimeters (0.6 inch) long.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  2. Design, synthesis, and biological evaluation of 4-(5-dimethylamino-naphthalene-1-sulfon-amido)-3-(4-iodophenyl)butanoic acid as a novel molecular probe for apoptosis imaging

    SciTech Connect

    Zeng, Wenbin; Miao, Weimin; Le Puil, Michael; Shi, Guangqing; Biggerstaff, John; Kabalka, George W.; Townsend, David

    2010-07-30

    Research highlights: {yields} Annexin V is the gold standard probe for imaging apoptosis. {yields} Unfavorable profiles of Annexin V make it difficult to apply in the clinic. {yields} A novel small-molecular probe DNSBA was designed as an alternative to Annexin V. {yields} DNSBA specifically and selectively detect apoptotic cancer cells at all stages. {yields} DNSBA is a potential SPECT and PET agent when labeled with radioiodine. -- Abstract: Apoptosis (programmed cell death) plays a crucial role in the pathogenesis of many disorders, thus the detection of apoptotic cells can provide the physician with important information to further therapeutic strategies and would substantially advance patient care. A small molecule, 4-(5-dimethylamino-naphthalene-1-sulfonamido)-3-(4-iodo-phenyl)butanoic acid (DNSBA), was designed as a novel probe for imaging apoptosis and synthesized with good yield. The biological characterization demonstrated that DNSBA can be used to specifically and selectively detect apoptotic cancer cells at all stages. DNSBA is also designed as a potential SPECT and PET probe when labeled with radioiodine (I-123, -124, and -131).

  3. Poly(vinylpyrrolidone) supported copper nanoclusters: glutathione enhanced blue photoluminescence for application in phosphor converted light emitting devices

    NASA Astrophysics Data System (ADS)

    Wang, Zhenguang; Susha, Andrei S.; Chen, Bingkun; Reckmeier, Claas; Tomanec, Ondrej; Zboril, Radek; Zhong, Haizheng; Rogach, Andrey L.

    2016-03-01

    Poly(vinylpyrrolidone) supported Cu nanoclusters were synthesized by reduction of Cu(ii) ions with ascorbic acid in water, and initially showed blue photoluminescence with a quantum yield of 8%. An enhancement of the emission quantum yield has been achieved by treatment of Cu clusters with different electron-rich ligands, with the most pronounced effect (photoluminescence quantum yield of 27%) achieved with glutathione. The bright blue emission of glutathione treated Cu NCs is fully preserved in the solid state powder, which has been combined with commercial green and red phosphors to fabricate down-conversion white light emitting diodes with a high colour rendering index of 92.Poly(vinylpyrrolidone) supported Cu nanoclusters were synthesized by reduction of Cu(ii) ions with ascorbic acid in water, and initially showed blue photoluminescence with a quantum yield of 8%. An enhancement of the emission quantum yield has been achieved by treatment of Cu clusters with different electron-rich ligands, with the most pronounced effect (photoluminescence quantum yield of 27%) achieved with glutathione. The bright blue emission of glutathione treated Cu NCs is fully preserved in the solid state powder, which has been combined with commercial green and red phosphors to fabricate down-conversion white light emitting diodes with a high colour rendering index of 92. Electronic supplementary information (ESI) available: The optical spectra of control experiments for Cu NC synthesis, optimization of the reaction conditions, and spectra for LEDs chips and blue LEDs. See DOI: 10.1039/c6nr00806b

  4. Scanning photoluminescent spectroscopy of bioconjugated quantum dots

    NASA Astrophysics Data System (ADS)

    Chornokur, G.; Ostapenko, S.; Oleynik, E.; Phelan, C.; Korsunska, N.; Kryshtab, T.; Zhang, J.; Wolcott, A.; Sellers, T.

    2009-04-01

    We report on the application of the bio-conjugated quantum dots (QDs) for a "sandwich" enzyme-linked immunosorbent assay (ELISA) cancer testing technique. Quantum dot ELISA detection of the cancer PSA antigen at concentrations as low as 0.01 ng/ml which is ˜50 times lower than the classic "sandwich" ELISA was demonstrated. Scanning photoluminescence (PL) spectroscopy was performed on dried ELISA wells and the results compared with the same QD samples dried on a solid substrate. We confirmed a "blue" up to 37 nm PL spectral shift in a case of QDs conjugated to PSA antibodies. Increasing of the "blue" spectral shift was observed at lower PSA antigen concentrations. The results can be used to improve sensitivity of "sandwich" ELISA cancer antigen detection.

  5. Photoluminescence of a single complex plasmonic nanoparticle

    PubMed Central

    Zhang, Tianyue; Lu, Guowei; Shen, Hongming; Shi, Kebin; Jiang, Yuanyuan; Xu, Dongsheng; Gong, Qihuang

    2014-01-01

    We report detailed investigations of the photoluminescence (PL) generated from an individual gold nanoflower, a highly branched plasmonic nanoparticle. Compared to nanostructures with simple shapes, such as spheres, nanorods, and bipyramids, nanoflowers exhibit more distinct features, i.e., the PL spectra and far-field emission patterns are strongly dependent on the wavelength and polarization of the excitation light. The experimental results are qualitatively explained using theoretical calculations. In addition, the intrinsic PL signal is highly dominated by localized surface plasmon resonances. The crucial role of plasmonic coupling in complex nanostructures during the plasmon-enhanced PL process is highlighted. The findings contribute to a deeper understanding of the PL properties of metallic nanoparticles. This study will be beneficial for several potential applications, including optical imaging and sensing in the fields of materials science and biology. PMID:24463794

  6. Simulation of J-aggregate microcavity photoluminescence

    NASA Astrophysics Data System (ADS)

    Michetti, Paolo; La Rocca, Giuseppe C.

    2008-05-01

    We have developed a model in order to account for the photoexcitation dynamics of J-aggregate films and strongly coupled J-aggregate microcavities. The J aggregates are described as a disordered Frenkel exciton system in which relaxation occurs due to the presence of a thermal bath of molecular vibrations. The correspondence between the photophysics in J-aggregate films and that in J-aggregate microcavities is obtained by introducing a model polariton wave function mixing cavity photon modes and J-aggregate super-radiant excitons. With the same description of the material properties, we have calculated both absorption and luminescence spectra for the J-aggregate film and the photoluminescence of strongly coupled organic microcavities. The model is able to account for the fast relaxation dynamics in organic microcavities following nonresonant pumping and explains the temperature dependence of the ratio between the upper polariton and the lower polariton luminescence.

  7. Photoluminescence studies in epitaxial CZTSe thin films

    NASA Astrophysics Data System (ADS)

    Sendler, Jan; Thevenin, Maxime; Werner, Florian; Redinger, Alex; Li, Shuyi; Hägglund, Carl; Platzer-Björkman, Charlotte; Siebentritt, Susanne

    2016-09-01

    Epitaxial Cu 2 ZnSnSe 4 (CZTSe) thin films were grown by molecular beam epitaxy on GaAs(001) using two different growth processes, one containing an in-situ annealing stage as used for solar cell absorbers and one for which this step was omitted. Photoluminescences (PL) measurements carried out on these samples show no dependence of the emission shape on the excitation intensity at different temperatures ranging from 4 K to 300 K . To describe the PL measurements, we employ a model with fluctuating band edges in which the density of states of the resulting tail states does not seem to depend on the excited charge carrier density. In this interpretation, the PL measurements show that the annealing stage removes a defect level, which is present in the samples without this annealing.

  8. Pollution Probe.

    ERIC Educational Resources Information Center

    Chant, Donald A.

    This book is written as a statement of concern about pollution by members of Pollution Probe, a citizens' anti-pollution group in Canada. Its purpose is to create public awareness and pressure for the eventual solution to pollution problems. The need for effective government policies to control the population explosion, conserve natural resources,…

  9. New approach to real-time nucleic acids detection: folding polymerase chain reaction amplicons into a secondary structure to improve cleavage of Forster resonance energy transfer probes in 5'-nuclease assays.

    PubMed

    Kutyavin, Igor V

    2010-03-01

    The article describes a new technology for real-time polymerase chain reaction (PCR) detection of nucleic acids. Similar to Taqman, this new method, named Snake, utilizes the 5'-nuclease activity of Thermus aquaticus (Taq) DNA polymerase that cleaves dual-labeled Förster resonance energy transfer (FRET) probes and generates a fluorescent signal during PCR. However, the mechanism of the probe cleavage in Snake is different. In this assay, PCR amplicons fold into stem-loop secondary structures. Hybridization of FRET probes to one of these structures leads to the formation of optimal substrates for the 5'-nuclease activity of Taq. The stem-loop structures in the Snake amplicons are introduced by the unique design of one of the PCR primers, which carries a special 5'-flap sequence. It was found that at a certain length of these 5'-flap sequences the folded Snake amplicons have very little, if any, effect on PCR yield but benefit many aspects of the detection process, particularly the signal productivity. Unlike Taqman, the Snake system favors the use of short FRET probes with improved fluorescence background. The head-to-head comparison study of Snake and Taqman revealed that these two technologies have more differences than similarities with respect to their responses to changes in PCR protocol, e.g. the variations in primer concentration, annealing time, PCR asymmetry. The optimal PCR protocol for Snake has been identified. The technology's real-time performance was compared to a number of conventional assays including Taqman, 3'-MGB-Taqman, Molecular Beacon and Scorpion primers. The test trial showed that Snake supersedes the conventional assays in the signal productivity and detection of sequence variations as small as single nucleotide polymorphisms. Due to the assay's cost-effectiveness and simplicity of design, the technology is anticipated to quickly replace all known conventional methods currently used for real-time nucleic acid detection.

  10. Photoluminescence from silicon nanoparticles embedded in ammonium silicon hexafluoride.

    PubMed

    Kalem, Seref; Werner, Peter; Talalaev, Vadim; Becker, Michael; Arthursson, Orjan; Zakharov, Nikolai

    2010-10-29

    Silicon (Si) nanoparticles (NPs) were synthesized by transforming a Si wafer surface to ammonium silicon hexafluoride (ASH) or (NH(4))(2)SiF(6) under acid vapor treatment. Si-NPs which were found to be embedded within the polycrystalline (ASH) layer exhibit a strong green-orange photoluminescence (PL). Differential PL measurements revealed a major double component spectrum consisting of a broad band associated with the ASH-Si wafer interfacial porous oxide layer and a high energy band attributable to Si-NPs embedded in the ASH. The origin of the latter emission can be explained in terms of quantum/spatial confinement effects probably mediated by oxygen related defects in or around Si-NPs. Although Si-NPs are derived from the interface they are much smaller in size than those embedded within the interfacial porous oxide layer (SiO(x), x > 1.5). Transmission electron microscopy (TEM) combined with Raman scattering and Fourier transformed infrared (FTIR) analysis confirmed the presence of Si-NP and Si-O bondings pointing to the role of oxygen related defects in a porous/amorphous structure. The presence of oxygen of up to 4.5 at.% in the (NH(4))(2)SiF(6) layer was confirmed by energy dispersive spectroscopy (EDS) analysis.

  11. Enhanced photoluminescence of porous silicon nanoparticles coated by bioresorbable polymers

    PubMed Central

    2012-01-01

    A significant enhancement of the photoluminescence (PL) efficiency is observed for aqueous suspensions of porous silicon nanoparticles (PSiNPs) coated by bioresorbable polymers, i.e., polylactic-co-glycolic acid (PLGA) and polyvinyl alcohol (PVA). PSiNPs with average size about 100 nm prepared by mechanical grinding of electrochemically etched porous silicon were dispersed in water to prepare the stable suspension. The inner hydrophobic PLGA layer prevents the PSiNPs from the dissolution in water, while the outer PVA layer makes the PSiNPs hydrophilic. The PL quantum yield of PLGA/PVA-coated PSiNPs was found to increase by three times for 2 weeks of the storage in water. The observed effect is explained by taking into account both suppression of the dissolution of PSiNPs in water and a process of the passivation of nonradiative defects in PSiNPs. The obtained results are interesting in view of the potential applications of PSiNPs in bioimaging. PMID:22873790

  12. From natural attapulgite to phosphor materials: Characterization, photoluminescence and structure

    SciTech Connect

    Wang, Wenjie; Gu, Zheng; Gao, Xiuping; Jiang, Huie; Liu, Weisheng

    2014-08-15

    Highlights: • Sr{sub 2.965}Al{sub 0.08}Si{sub 0.92}O{sub 5}:0.025Ce{sup 3+}, 0.01Eu{sup 2+} phosphor was synthesized from natural attapulgite. • Pure Sr{sub 3}SiO{sub 5} phase can be easily obtained. • It provides a new application field as phosphor for natural attapulgite. - Abstract: Sr{sub 2.965}Al{sub 0.08}Si{sub 0.92}O{sub 5}:0.025Ce{sup 3+}, 0.01Eu{sup 2+} (SrAlSiO:Ce{sup 3+}, Eu{sup 2+}) phosphor from natural attapulgite (ATP) was synthesized by solid-state reaction method. For the use of ATP as a source of Si and Al, pretreatment process including mechanical grinding and acid leaching were involved. X-ray diffraction patterns confirmed the formation of silicates in a wide temperature field, whereas Sr{sub 3}SiO{sub 5} within a single step. The ATP fibers were tuning into phosphor particles (about 1.5–3.0 μm) after calcination. Furthermore, photoluminescence spectra of the SrAlSiO:Ce{sup 3+}, Eu{sup 2+} phosphor was also in good agreement with the literature results, indicating a promising potential application as an effective candidate for warm-white LEDs materials.

  13. Upconverted photoluminescence induced by radiative coupling between excitons

    NASA Astrophysics Data System (ADS)

    Matsuda, Takuya; Yokoshi, Nobuhiko; Ishihara, Hajime

    2016-04-01

    We propose an unconventional scheme of photoluminescence in a semiconductor thin film, where the nonlocal correlation between an excitonic wave and light wave prominently enhances the interaction between different excitonic states via radiation beyond the long-wavelength approximation (the so-called excitonic superradiance regime). On the basis of the developed method extending input-output theory, we elucidate atypical photoluminescence effects due to the strong wave-wave correlation. In particular, the upconverted photoluminescence based on the coherent quantum superposition of excitons is found to be highly efficient, i.e., it can be realized by weak pumping without auxiliary systems such as cavities or photonic antennas.

  14. Three new Ag(I) coordination architectures based on mixed ligands: Syntheses, structures and photoluminescent properties

    SciTech Connect

    Li, Yamin; Xiao, Changyu; Li, Shu; Chen, Qi; Li, Beibei; Liao, Qian; Niu, Jingyang

    2013-04-15

    Three new silver (I) coordination complexes, [Ag{sub 2}(1,2-bdc)(phdat)]{sub n} (1), [Ag{sub 2}(NO{sub 2}-bdc)(phdat)]{sub n} (2), [Ag{sub 4}(nta){sub 3}(phdat)NO{sub 3}]{sub n} (3) (1,2-bdc=phthalic acid dianion, NO{sub 2}-bdc=5-nitro-1,3-benzenedicarboxylic acid dianion, nta=nicotinic acid anion, phdat=2,4-diamine-6-phenyl-1,3,5-triazine) have been hydrothermally synthesized by the reactions of silver nitrate and phdat with the homologous ligands 1,2-H{sub 2}bdc, NO{sub 2}-H{sub 2}bdc, and Hnta, respectively, and characterized by single-crystal X-ray diffractions, IR spectra, elemental analyses thermogravimetric analyses (TGA). The compound 1 exhibits a chiral 3D network with cbs/CrB self-dual topological net, which contains two kinds of single helical chains. For compound 2, the 3D network is comprised of two kinds of similar 2D sheets with the topological symbol of sql-type packed in AABBAA mode by Ag–N/O weakly contacts. And compound 3 has 2D double layer architecture, consisting of the 2D plane with hcb-type topological symbol connected by Ag–O weakly coordinations. The photoluminescent properties associated with the crystal structures of three compounds have also been measured. - Graphical abstract: Three new silver(I) coordination complexes 1–3 have been synthesized and characterized by single-crystal X-ray diffractions, IR spectra, elemental analyses, thermogravimetric analyses (TGA) and photoluminescent spectra. Highlights: ► The compound 1 exhibits a novel chiral 3D network with two kinds of single helical chains. ► 3D or 2D new Ag coordination complexes. ► The photoluminescent properties have been measured.

  15. A biomimetic tongue by photoluminescent metal-organic frameworks.

    PubMed

    Lee, Tu; Lin Lee, Hung; Hsun Tsai, Meng; Cheng, Shao-Liang; Lee, Sheng-Wei; Hu, Jung-Chih; Chen, Lien-Tai

    2013-05-15

    The taste sensing capabilities of a "biomimetic tongue" based on the photoluminescence (PL) responses of metal-organic frameworks (MOFs), [In(OH)(bdc)]n (bdc=1,4-benzenedicarboxylate), [Tb(btc)]n (MOF-76, btc=benzene-1,3,5-tricarboxylate), and [Ca3(btc)2(DMF)2(H2O)2]·3H2O are proven on aqueous solutions of five basic tastants: sucrose (sweet), caffeine (bitter), citric acid (sour), sodium chloride (salty) and monosodium glutamate (umami). For [In(OH)(bdc)]n, the tastant interacts stereochemically with poly(acrylic acid) (PAA) and alters its conformations. The frequency and magnitude of chelation between COO(-) pendant groups of PAA and In(3+) nodes of [In(OH)(bdc)]n framework influence the corresponding PL reponses. For MOF-76, the tastant interacts with incorporated water in MOF-76 through hydrogen bonding. The limitation of O-H bond stretching of water results in the enhancement of the PL intensity. For [Ca3(BTC)2(DMF)2(H2O)2]·3H2O, it is added as a third MOF component to increase the precision on taste discrimination. The significance of MOF-based "biomimetic tongue" includes: (1) PAA on [In(OH)(bdc)]n mimics the taste receptor cells (TRCs) for their structural flexibility, (2) the Weber-Fechner law of human sensing that sensation is proportional to the logarithm of the stimulus intensity is observed between the PL emission response of MOF-76 and the concentration of tastant, (3) the strength of taste is quantified by the τ scale and the PL emission intensity of MOF-76, which are dependent on the logarithmic tastant concentration, (4) the tastant is identified by the shape of the 3D principal component analysis contour map (i.e., pattern recognition method), and (5) the fabrication of [In(OH)(bdc)]n/PAA film by brushing is illustrated. PMID:23277340

  16. Surface plasmon enhanced photoluminescence from copper nanoparticles: Influence of temperature

    SciTech Connect

    Yeshchenko, Oleg A. Bondarchuk, Illya S.; Losytskyy, Mykhaylo Yu.

    2014-08-07

    Anomalous temperature dependence of surface plasmon enhanced photoluminescence from copper nanoparticles embedded in a silica host matrix has been observed. The quantum yield of photoluminescence increases as the temperature increases. The key role of such an effect is the interplay between the surface plasmon resonance and the interband transitions in the copper nanoparticles occurring at change of the temperature. Namely, the increase of temperature leads to the red shift of the resonance. The shift leads to increase of the spectral overlap of the resonance with photoluminescence band of copper as well as to the decrease of plasmon damping caused by interband transitions. Such mechanisms lead to the increase of surface plasmon enhancement factor and, consequently, to increase of the quantum yield of the photoluminescence.

  17. Understanding ligand-centred photoluminescence through flexibility and bonding of anthraquinone inorganic-organic frameworks

    SciTech Connect

    Furman, Joshua D; Burwood, Ryan P; Tang, Min; Mikhailovsky, Alexander A; Cheetham, Anthony K

    2011-11-17

    Five novel inorganic-organic framework compounds containing the organic chromophore ligand anthraquinone-2,3-dicarboxylic acid (abbreviated H2AQDC) and calcium (CaAQDC), zinc (ZnAQDC), cadmium (CdAQDC), manganese (MnAQDC), and nickel (NiAQDC), respectively, have been synthesized. The photoluminescence of these materials is only visible at low temperatures and this behaviour has been evaluated in terms of ligand rigidity. It is proposed that the 2,3 position bonding sites result in luminescence-quenching ligand motion, as supported by X-ray diffraction and temperature-dependent luminescence studies.

  18. Combustion synthesis and photoluminescence of Eu3+ doped LaAlO3 nanophosphors

    NASA Astrophysics Data System (ADS)

    Dhahri, A.; Horchani-Naifer, K.; Benedetti, A.; Enrichi, F.; Ferid, M.

    2012-09-01

    Eu3+ doped LaAlO3 nanophosphors were successfully synthesized by a combustion process using concentrated solution of lanthanum nitrates and aluminate as oxidiser, and glycine acid as fuel. The powders were characterized by infrared spectroscopy (IR), X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and fluorescence spectroscopy. Pure LaAlO3 phase was obtained at 800 °C heated for 4 h, without formation of any intermediate phase, with an average crystal size, as determined by TEM, of 60 nm. Intense photoluminescence emission is reported at 616 nm, allowing the use of this material as red phosphor.

  19. Synthesis and Photoluminescent Properties of Eu²⁺-Doped BaSiF₆ Nanoparticles.

    PubMed

    Zhao, Xin; Hua, Ruinian; Zhang, Wei; Zhao, Jun; Tang, Dongxin; Sun, Zhengang

    2016-01-01

    By adjusting the molar ratio of oleic acid (OA), oleylamine (OM), and 1-octadecene (OD) ligands in reaction solution, Eu²⁺-doped BaSiF₆ nanoparticles were synthesized using a thermal decomposition synthesis route. Eu²⁺ ions have been successfully doped into BaSiF₆ host lattice and strong 4f-4f line emission of the Eu²⁺ in BaSiF₆ matrix is observed. Meanwhile, the photoluminescent (PL) properties of BaSiF₆:Eu²⁺ nanoparticles doping Eu²⁺ ions at different concentrations were also studied. PMID:27398531

  20. Photoluminescence imaging of solitary dopant sites in covalently doped single-wall carbon nanotubes

    SciTech Connect

    Hartmann, Nicolai F.; Yalcin, Sibel Ebru; Adamska, Lyudmyla; Haroz, Erik H.; Ma, Xuedan; Tretiak, Sergei; Htoon, Han; Doorn, Stephen K.

    2015-11-11

    Covalent dopants in semiconducting single wall carbon nanotubes (SWCNTs) are becoming important as routes for introducing new photoluminescent emitting states with potential for enhanced quantum yields, new functionality, and as species capable of near-IR room-temperature single photon emission. The origin and behavior of the dopant-induced emission is thus important to understand as a key requirement for successful room-T photonics and optoelectronics applications. Here, we use direct correlated two-color photoluminescence imaging to probe how the interplay between the SWCNT bright E11 exciton and solitary dopant sites yields the dopant-induced emission for three different dopant species: oxygen, 4-methoxybenzene, and 4-bromobenzene. We introduce a route to control dopant functionalization to a low level as a means for introducing spatially well-separated solitary dopant sites. Resolution of emission from solitary dopant sites and correlation to their impact on E11 emission allows confirmation of dopants as trapping sites for localization of E11 excitons following their diffusive transport to the dopant site. Imaging of the dopant emission also reveals photoluminescence intermittency (blinking), with blinking dynamics being dependent on the specific dopant. Density functional theory calculations were performed to evaluate the stability of dopants and delineate the possible mechanisms of blinking. Furthermore, theoretical modeling suggests that the trapping of free charges in the potential well created by permanent dipoles introduced by dopant atoms/groups is likely responsible for the blinking, with the strongest effects being predicted and observed for oxygen-doped SWCNTs.

  1. Photoluminescence imaging of solitary dopant sites in covalently doped single-wall carbon nanotubes

    DOE PAGES

    Hartmann, Nicolai F.; Yalcin, Sibel Ebru; Adamska, Lyudmyla; Haroz, Erik H.; Ma, Xuedan; Tretiak, Sergei; Htoon, Han; Doorn, Stephen K.

    2015-11-11

    Covalent dopants in semiconducting single wall carbon nanotubes (SWCNTs) are becoming important as routes for introducing new photoluminescent emitting states with potential for enhanced quantum yields, new functionality, and as species capable of near-IR room-temperature single photon emission. The origin and behavior of the dopant-induced emission is thus important to understand as a key requirement for successful room-T photonics and optoelectronics applications. Here, we use direct correlated two-color photoluminescence imaging to probe how the interplay between the SWCNT bright E11 exciton and solitary dopant sites yields the dopant-induced emission for three different dopant species: oxygen, 4-methoxybenzene, and 4-bromobenzene. We introducemore » a route to control dopant functionalization to a low level as a means for introducing spatially well-separated solitary dopant sites. Resolution of emission from solitary dopant sites and correlation to their impact on E11 emission allows confirmation of dopants as trapping sites for localization of E11 excitons following their diffusive transport to the dopant site. Imaging of the dopant emission also reveals photoluminescence intermittency (blinking), with blinking dynamics being dependent on the specific dopant. Density functional theory calculations were performed to evaluate the stability of dopants and delineate the possible mechanisms of blinking. Furthermore, theoretical modeling suggests that the trapping of free charges in the potential well created by permanent dipoles introduced by dopant atoms/groups is likely responsible for the blinking, with the strongest effects being predicted and observed for oxygen-doped SWCNTs.« less

  2. Synthesis and Photoluminescence Properties of Li2SrSiO4 Activated with Dy3+ and Sm3+

    NASA Astrophysics Data System (ADS)

    Erdoğmuş, E.

    2015-01-01

    Li2SrSiO4:M (M: Dy3+ and Sm3+) phosphors were synthesized by the conventional solid state reaction. The synthesized materials were characterized by powder XRD. The emission and excitation spectra of these phosphors were measured at room temperature with a spectrofluorometer. The first phosphor, Li2SrSiO4:Dy3+, emits at 479, 573, and 666 nm upon 351 nm excitation. The second phosphor, Li2SrSiO4:Sm3+, emits at 561-571, 594, 647-655, and 703-713 nm upon 399 nm excitation. Also, the dependence of the photoluminescence properties of both phosphors on boric acid concentration was investigated. The results showed that boric acid was effective in improving the photoluminescence intensity of both phosphors.

  3. Photoluminescence of P3HT nanoparticles

    NASA Astrophysics Data System (ADS)

    Dujovne, Irene; Labastide, Joelle; Baghgar, Mina; McKenna, Aidan; Barnes, Austin M.; Venkataraman, D.; Barnes, Michael D.

    2012-02-01

    Polythiophenes are semiconducting polymers that have been designed to crystallize. The photophysics of semicrystalline polythiophene and polythiophene-blends are the focus of intense research efforts across different disciplines. In these systems there is a competition between charge separation and recombination. Exciton diffusion length in organic-semiconductors is a major road-block for efficient solar energy harvesting devices since, for direct bandgap organic materials, this distance is about 10 nanometers. Thus, efficient extraction of photogenerated electrons and holes requires engineering polymer domain dimensions in this size range. In our initial investigations of the photophysics of isolated P3HT nanoparticles (15 - 130 nm), we have observed several intriguing size-dependent features in the single-particle photoluminescence (PL) connected with exciton diffusion and dissociation dynamics. In addition to the short-time behavior, we also observe size-dependent differences in PL decay at long times. In the 10 - 100 ns time regime, the PL originates not from radiative transitions of bound excitons, but rather from charge-separation followed by bi-polaron recombination--and thus provides an interesting measure of exciton fission probability within the nanoparticle.

  4. Photoluminescence of carbon dots from mesoporous silica

    NASA Astrophysics Data System (ADS)

    Nelson, D. K.; Razbirin, B. S.; Starukhin, A. N.; Eurov, D. A.; Kurdyukov, D. A.; Stovpiaga, E. Yu; Golubev, V. G.

    2016-09-01

    Photophysical properties of carbon dots were investigated under various excitation conditions and over a wide temperature region - from room to liquid helium temperatures. The carbon dots (CDs) were synthesized using mesoporous silica particles as a reactor and (3-aminopropyl)triethoxysilane (APTES) as a precursor. The photoluminescence spectra of CDs exhibit a strong dependence on the excitation wavelength and demonstrate a significant inhomogeneous broadening. Lowering sample temperature reveals the doublet structure of the spectra, which is associated with the vibronic structure of radiative transitions. The vibration energy ∼1200 cm-1 is close to the energy of Csbnd O stretching vibration. Long-lived phosphorescence of carbon dots with its decay time ∼0.2 s at T = 80 K was observed. The fluorescence and phosphorescence spectra are shown to be spectrally separated. The long-lived component of the emission was ascribed to optically forbidden triplet-singlet transitions. The value of the singlet-triplet splitting was found to be about 0.3 eV. Photo-induced polarization of the luminescence of carbon dots was revealed. The degree of the linear polarization is dependent on the wavelengths of both excitation and emitted light. The effect indicates a hidden anisotropy of optical dipole transitions in the dots and demonstrates the loss of the dipole orientation during the electron energy relaxation.

  5. Using quantum dot photoluminescence for load detection

    NASA Astrophysics Data System (ADS)

    Moebius, M.; Martin, J.; Hartwig, M.; Baumann, R. R.; Otto, T.; Gessner, T.

    2016-08-01

    We propose a novel concept for an integrable and flexible sensor capable to visualize mechanical impacts on lightweight structures by quenching the photoluminescence (PL) of CdSe quantum dots. Considering the requirements such as visibility, storage time and high optical contrast of PL quenching with low power consumption, we have investigated a symmetrical and an asymmetrical layer stack consisting of semiconductor organic N,N,N',N'-Tetrakis(3-methylphenyl)-3,3'-dimethylbenzidine (HMTPD) and CdSe quantum dots with elongated CdS shell. Time-resolved series of PL spectra from layer stacks with applied voltages of different polarity and simultaneous observation of power consumption have shown that a variety of mechanisms such as photo-induced charge separation and charge injection, cause PL quenching. However, mechanisms such as screening of external field as well as Auger-assisted charge ejection is working contrary to that. Investigations regarding the influence of illumination revealed that the positive biased asymmetrical layer stack is the preferred sensor configuration, due to a charge carrier injection at voltages of 10 V without the need of coincident illumination.

  6. Plasmonic enhancement of photoluminescence from aluminium nitride

    NASA Astrophysics Data System (ADS)

    Flynn, Chris; Stewart, Matthew

    2016-03-01

    Aluminium nitride (AlN) films were grown on c-plane sapphire wafers by molecular beam epitaxy (MBE) under aluminium-rich conditions. The excess aluminium (Al) accumulated on the surface of the films as micro-scale droplets 1-10 μm in size, and as Al nanoparticles with diameters in the range 10-110 nm. Photoluminescence (PL) measurements were performed on the AlN samples using a 193 nm Excimer laser as the excitation source. Prior to PL measurements the wafers were cleaved in half. One half of each wafer was submitted to a 10 min treatment in H3PO4 heated to 70 °C to remove the excess Al from the film surface. The remaining half was left in the as-deposited condition. The mean intensities of the near-band-edge PL peaks of the as-deposited samples were 2.0-3.4 times higher compared to the samples subjected to the H3PO4 Al-removal treatment. This observation motivated calculations to determine the optimal Al surface nanosphere size for plasmonic enhancement of PL from AlN. The PL enhancement was found to peak for an Al nanosphere radius of 15 nm, which is within the range of the experimentally-observed Al nanoparticle sizes.

  7. Photoluminescence of etched SiC nanowires

    NASA Astrophysics Data System (ADS)

    Stewart, Polite D., Jr.; Rich, Ryan; Zerda, T. W.

    2010-10-01

    SiC nanowires were produced from carbon nanotubes and nanosize silicon powder in a tube furnace at temperatures between 1100^oC and 1350^oC. SiC nanowires had average diameter of 30 nm and very narrow size distribution. The compound possesses a high melting point, high thermal conductivity, and excellent wear resistance. The surface of the SiC nanowires after formation is covered by an amorphous layer. The composition of that layer is not fully understood, but it is believed that in addition to amorphous SiC it contains various carbon and silicon compounds, and SiO2. The objective of the research was to modify the surface structure of these SiC nanowires. Modification of the surface was done using the wet etching method. The etched nanowires were then analyzed using Fourier Transform Infrared spectroscopy (FTIR), transmission electron microscopy (TEM), and photoluminescence (PL). FTIR and TEM analysis provided valid proof that the SiC nanowires were successfully etched. Also, the PL results showed that the SiC nanowire core did possess a fluorescent signal.

  8. A nucleic acid probe labeled with desmethyl thiazole orange: a new type of hybridization-sensitive fluorescent oligonucleotide for live-cell RNA imaging.

    PubMed

    Okamoto, Akimitsu; Sugizaki, Kaori; Yuki, Mizue; Yanagisawa, Hiroyuki; Ikeda, Shuji; Sueoka, Takuma; Hayashi, Gosuke; Wang, Dan Ohtan

    2013-01-14

    A new fluorescent nucleotide with desmethyl thiazole orange dyes, D'(505), has been developed for expansion of the function of fluorescent probes for live-cell RNA imaging. The nucleoside unit of D'(505) for DNA autosynthesis was soluble in organic solvents, which made the preparation of nucleoside units and the reactions in the cycles of DNA synthesis more efficient. The dyes of D'(505)-containing oligodeoxynucleotide were protonated below pH 7 and the oligodeoxynucleotide exhibited hybridization-sensitive fluorescence emission through the control of excitonic interactions of the dyes of D'(505). The simplified procedure and effective hybridization-sensitive fluorescence emission produced multicolored hybridization-sensitive fluorescent probes, which were useful for live-cell RNA imaging. The acceptor-bleaching method gave us information on RNA in a specific cell among many living cells.

  9. Investigation of an unnatural amino acid for use as a resonance Raman probe: Detection limits, solvent and temperature dependence of the νC≡N band of 4-cyanophenylalanine.

    PubMed

    Weeks, Colin L; Polishchuk, Alexei; Getahun, Zelleka; Degrado, William F; Spiro, Thomas G

    2008-11-01

    The incorporation of unnatural amino acids into proteins that act as spectroscopic probes can be used to study protein structure and function. One such probe is 4-cyanophenylalanine (PheCN), the nitrile group of which has a stretching mode that occurs in a region of the vibrational spectrum that does not contain any modes from the usual components of proteins and the wavenumber is sensitive to the polarity of its environment. In this work we evaluate the potential of UV resonance Raman spectroscopy for monitoring the sensitivity of the νC≡N band of PheCN incorporated into proteins to the protein environment. Measurement of the Raman excitation profile of PheCN showed that considerable resonance enhancement of the Raman signal was obtained using UV excitation and the best signal-to-noise ratios were obtained with excitation wavelengths of 229 and 244 nm. The detection limit for PheCN in proteins was ~10 μM, approximately a hundred-fold lower than the concentrations used in IR studies, which increases the potential applications of PheCN as a vibrational probe. The wavenumber of the PheCN νC≡N band was strongly dependent on the polarity of its environment, when the solvent was changed from H(2)O to THF it decreased by 8 cm(-1). The presence of liposomes caused a similar though smaller decrease in νC≡N for a peptide, mastoparan X, modified to contain PheCN. The selectivity and sensitivity of resonance Raman spectroscopy of PheCN mean that it can be a useful probe of intra- and intermolecular interactions in proteins and opens the door to its application in the study of protein dynamics using time-resolved resonance Raman spectroscopy.

  10. Measuring long-range carrier diffusion across multiple grains in polycrystalline semiconductors by photoluminescence imaging

    PubMed Central

    Alberi, K.; Fluegel, B.; Moutinho, H.; Dhere, R. G.; Li, J. V.; Mascarenhas, A.

    2013-01-01

    Thin-film polycrystalline semiconductors are currently at the forefront of inexpensive large-area solar cell and integrated circuit technologies because of their reduced processing and substrate selection constraints. Understanding the extent to which structural and electronic defects influence carrier transport in these materials is critical to controlling the optoelectronic properties, yet many measurement techniques are only capable of indirectly probing their effects. Here we apply a novel photoluminescence imaging technique to directly observe the low temperature diffusion of photocarriers through and across defect states in polycrystalline CdTe thin films. Our measurements show that an inhomogeneous distribution of localized defect states mediates long-range hole transport across multiple grain boundaries to locations exceeding 10 μm from the point of photogeneration. These results provide new insight into the key role deep trap states have in low temperature carrier transport in polycrystalline CdTe by revealing their propensity to act as networks for hopping conduction. PMID:24158163

  11. Convenient synthesis of stable silver quantum dots with enhanced photoluminescence emission by laser fragmentation

    NASA Astrophysics Data System (ADS)

    Shuang, Li; Ming, Chen

    2016-04-01

    A new strategy for the facile synthesis of very stable and mono-dispersed silver (Ag) quantum dots (QDs) is developed by laser fragmentation of bulk Ag in water using polysorbate 80 as a dispersing and stabilizing agent. The surfactant plays an important role in the formation of size-controlled Ag nano-structures. The Ag QDs have excellent photo-stability of ∼500 h and enhanced photoluminescence (PL) at 510 nm. This has significant implications for selective and ultrasensitive PL probes. Based on laser fragmentation in the biocompatible surfactant solution, our results have opened up a novel paradigm to obtain stable metal QDs directly from bulk targets. This is a breakthrough in the toxicity problems that arise from standard chemical fabrication. Project supported by the National Natural Science Foundation of China (Grant Nos. 11575102, 11105085, 11275116, and 11375108) and the Fundamental Research Funds of Shandong University, China (Grant No. 2015JC007).

  12. Deep ultraviolet photoluminescence of Tm-doped AlGaN alloys

    SciTech Connect

    Nepal, N.; Zavada, J. M.; Lee, D. S.; Steckl, A. J.; Sedhain, A.; Lin, J. Y.; Jiang, H. X.

    2009-03-16

    The ultraviolet (UV) photoluminescence (PL) properties of Tm-doped Al{sub x}Ga{sub 1-x}N (0.39{<=}x{<=}1) alloys grown by solid-source molecular beam epitaxy were probed using above-bandgap excitation from a laser source at 197 nm. The PL spectra show dominant UV emissions at 298 and 358 nm only for samples with x=1 and 0.81. Temperature dependence of the PL intensities of these emission lines reveals exciton binding energies of 150 and 57 meV, respectively. The quenching of these UV emissions appears related to the thermal activation of the excitons bound to rare-earth structured isovalent (RESI) charge traps, which transfer excitonic energy to Tm{sup 3+} ions resulting in the UV emissions. A model of the RESI trap levels in AlGaN alloys is presented.

  13. Facile route to highly photoluminescent carbon nanodots for ion detection, pH sensors and bioimaging

    NASA Astrophysics Data System (ADS)

    Shen, Chen; Sun, Yupeng; Wang, Jing; Lu, Yun

    2014-07-01

    Carbon nanodots (CDs) of uniform size were prepared simply by the hydrothermal decomposition of folic acid (FA) precursor at various reaction temperatures. The CDs formed via dehydration of FA at 260 °C contributed the strongest photoluminescence (PL) signal and the highest quantum yield at about 68%, without assistance of any passivation agent. The effects of preparation conditions on PL behavior of CDs have been investigated in detail, and the quantum yield of the CDs was found to be associated strongly with sample crystallinity. Moreover, because the obtained CDs also exhibited high luminescence stability, abundant surface functional groups and good biocompatibility, there are many promising applications in printing ink, ion detection, pH sensors and cell imaging.Carbon nanodots (CDs) of uniform size were prepared simply by the hydrothermal decomposition of folic acid (FA) precursor at various reaction temperatures. The CDs formed via dehydration of FA at 260 °C contributed the strongest photoluminescence (PL) signal and the highest quantum yield at about 68%, without assistance of any passivation agent. The effects of preparation conditions on PL behavior of CDs have been investigated in detail, and the quantum yield of the CDs was found to be associated strongly with sample crystallinity. Moreover, because the obtained CDs also exhibited high luminescence stability, abundant surface functional groups and good biocompatibility, there are many promising applications in printing ink, ion detection, pH sensors and cell imaging. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr02154a

  14. Fluorescence and visual detection of fluoride ions using a photoluminescent graphene oxide paper sensor

    NASA Astrophysics Data System (ADS)

    Chen, Xiaochun; Yu, Shaoming; Yang, Liang; Wang, Jianping; Jiang, Changlong

    2016-07-01

    The instant and on-site detection of trace aqueous fluoride ions is still a challenge for environmental monitoring and protection. This work demonstrates a new analytical method and its utility of a paper sensor for visual detection of F- on the basis of the fluorescence resonance energy transfer (FRET) between photoluminescent graphene oxide (GO) and silver nanoparticles (AgNPs) through the formation of cyclic esters between phenylborinic acid and diol. The fluorescence of GO was quenched by the AgNPs, and trace F- can recover the fluorescence of the quenched photoluminescent GO. The increase in fluorescence intensity is proportional to the concentration of F- in the range of 0.05-0.55 nM, along with a limit of detection (LOD) as low as 9.07 pM. Following the sensing mechanism, a paper-based sensor for the visual detection of aqueous F- has been successfully developed. The paper sensor showed high sensitivity for aqueous F-, and the LOD could reach as low as 0.1 μM as observed by the naked eye. The very simple and effective strategy reported here could be extended to the visual detection of a wide range of analytes in the environment by the construction of highly efficient FRET nanoprobes.The instant and on-site detection of trace aqueous fluoride ions is still a challenge for environmental monitoring and protection. This work demonstrates a new analytical method and its utility of a paper sensor for visual detection of F- on the basis of the fluorescence resonance energy transfer (FRET) between photoluminescent graphene oxide (GO) and silver nanoparticles (AgNPs) through the formation of cyclic esters between phenylborinic acid and diol. The fluorescence of GO was quenched by the AgNPs, and trace F- can recover the fluorescence of the quenched photoluminescent GO. The increase in fluorescence intensity is proportional to the concentration of F- in the range of 0.05-0.55 nM, along with a limit of detection (LOD) as low as 9.07 pM. Following the sensing mechanism

  15. Single-cell photonic nanocavity probes

    PubMed Central

    Shambat, Gary; Kothapalli, Sri-Rajasekhar; Provine, J; Sarmiento, Tomas; Harris, James; Gambhir, Sanjiv Sam; Vučković, Jelena

    2013-01-01

    Single-cell interrogation at the nanoscale can take on many forms—namely, pillars1, tubes2–5, and wires6–8 as probes for gentle insertion into a cell’s interior, allowing for studies on single-cell cargo delivery4, electrochemistry3 or electrophysiology1, and optical signaling9–10. However, optical probes such as nanowires9 or tapered fibers10 are passive in nature and have only served as conduits to guide light into and out of a cell. Here we demonstrate a nanobeam photonic crystal (PC) cavity as an advanced cellular nanoprobe, active in nature, and configurable to provide a multitude of actions for both intracellular sensing and control. Our semiconductor nanocavity probes emit photoluminescence (PL) from embedded quantum dots (QD) and sustain high quality resonant photonic modes inside cells. The beams can be loaded in cells and tracked for days at a time, with cells undergoing regular division with the beams. Furthermore, we present in vitro label-free protein sensing with our probes as a path towards real-time biomarker detection in single cells. PMID:23387382

  16. Effects of thickness layer on the photoluminescence properties of InAlAs/GaAlAs quantum dots

    NASA Astrophysics Data System (ADS)

    Daly, A. Ben; Bernardot, F.; Barisien, T.; Galopin, E.; Lemaître, A.; Maaref, M. A.; Testelin, C.

    2016-09-01

    We investigated the effect of InAlAs layer thickness on exciton-spin relaxation and optical properties of In0.62Al0.38As/Al0.67Ga0.33As QDs. The luminescence properties and carrier dynamics of QDs were studied by the temperature-dependent photoluminescence (PL) and pump-probe measurements. As the total amount of deposited In0.62Al0.38As alloy increased, the central position of the low-energy PL signal decreases, while its full width at half maximum (FWHM) increases. A monotonous redshift of the PL peak was observed with increasing temperature due to the electron-phonon scattering. From the pump-probe measurement, the spin relaxation time decreases with the monolayers at higher temperatures, in agreement with the phonon energy determinate by PL measurements.

  17. Origin of the Avalanche-Like Photoluminescence from Metallic Nanowires

    PubMed Central

    Ma, Zongwei; Yu, Ying; Shen, Shaoxin; Dai, Hongwei; Yao, Linhua; Han, Yibo; Wang, Xia; Han, Jun-Bo; Li, Liang

    2016-01-01

    Surface plasmonic systems provide extremely efficient ways to modulate light-matter interaction in photon emission, light harvesting, energy conversion and transferring, etc. Various surface plasmon enhanced luminescent behaviors have been observed and investigated in these systems. But the origin of an avalanche-like photoluminescence, which was firstly reported in 2007 from Au and subsequently from Ag nanowire arrays/monomers, is still not clear. Here we show, based on systematic investigations including the excitation power/time related photoluminescent measurements as well as calculations, that this avalanche-like photoluminescence is in fact a result of surface plasmon assisted thermal radiation. Nearly all of the related observations could be perfectly interpreted with this concept. Our finding is crucial for understanding the surface plasmon mediated thermal and photoemission behaviors in plasmonic structures, which is of great importance in designing functional plasmonic devices. PMID:26728439

  18. Steady-state photoluminescent excitation characterization of semiconductor carrier recombination.

    PubMed

    Bhosale, J S; Moore, J E; Wang, X; Bermel, P; Lundstrom, M S

    2016-01-01

    Photoluminescence excitation spectroscopy is a contactless characterization technique that can provide valuable information about the surface and bulk recombination parameters of a semiconductor device, distinct from other sorts of photoluminescent measurements. For this technique, a temperature-tuned light emitting diode (LED) has several advantages over other light sources. The large radiation density offered by LEDs from near-infrared to ultraviolet region at a low cost enables efficient and fast photoluminescence measurements. A simple and inexpensive LED-based setup facilitates measurement of surface recombination velocity and bulk Shockley-Read-Hall lifetime, which are key parameters to assess device performance. Under the right conditions, this technique can also provide a contactless way to measure the external quantum efficiency of a solar cell. PMID:26827306

  19. Steady-state photoluminescent excitation characterization of semiconductor carrier recombination

    NASA Astrophysics Data System (ADS)

    Bhosale, J. S.; Moore, J. E.; Wang, X.; Bermel, P.; Lundstrom, M. S.

    2016-01-01

    Photoluminescence excitation spectroscopy is a contactless characterization technique that can provide valuable information about the surface and bulk recombination parameters of a semiconductor device, distinct from other sorts of photoluminescent measurements. For this technique, a temperature-tuned light emitting diode (LED) has several advantages over other light sources. The large radiation density offered by LEDs from near-infrared to ultraviolet region at a low cost enables efficient and fast photoluminescence measurements. A simple and inexpensive LED-based setup facilitates measurement of surface recombination velocity and bulk Shockley-Read-Hall lifetime, which are key parameters to assess device performance. Under the right conditions, this technique can also provide a contactless way to measure the external quantum efficiency of a solar cell.

  20. Direct observation of the cyclic dimer in liquid acetic acid by probing the C=O vibration with ultrafast coherent Raman spectroscopy.

    PubMed

    Lütgens, Matthias; Friedriszik, Frank; Lochbrunner, Stefan

    2014-09-01

    We present a comparison of spontaneous Raman and ultrafast coherent anti-Stokes Raman scattering (CARS) spectra of the C=O vibration of liquid acetic acid. The former technique cannot clearly reveal the number of contributions in the spectrum. However, the additional time and spectrally resolved CARS experiment supports strictly the existence of four modes, which proves the coexistence of more than one H-bonded configuration in liquid acetic acid. A comparably slowly dephasing mode which is obscured by a broad band in the linear Raman spectrum is assigned to the cyclic dimer and can be observed freed from all other contributions by ultrafast CARS.

  1. A probe on the intermolecular forces in diisopropyl ether-n-butyric acid mixture by dielectric, FTIR studies and quantum chemical calculations.

    PubMed

    Arivazhagan, G; Shanmugam, R; Elangovan, A

    2013-03-15

    The results of FTIR spectral measurement on equimolar diisopropyl ether-butyric acid binary mixture and quantum chemical calculations on the complex molecule have been presented. Dielectric studies have been carried out on the binary mixture over the entire composition range and at four different temperatures 303 K, 308 K, 313 K and 318 K. n-Butyric acid seems to prefer less polar ether to interact with it. It appears that the usual interpretation of variation of static dielectric constant and positive deviation of excess permittivity from ideal mixture behavior needs to be relooked.

  2. Photoluminescence quantum yield of PbS nanocrystals in colloidal suspensions

    SciTech Connect

    Greben, M.; Fucikova, A.; Valenta, J.

    2015-04-14

    The absolute photoluminescence (PL) quantum yield (QY) of oleic acid-capped colloidal PbS quantum dots (QDs) in toluene is thoroughly investigated as function of QD size, concentration, excitation photon energy, and conditions of storage. We observed anomalous decrease of QY with decreasing concentration for highly diluted suspensions. The ligand desorption and QD-oxidation are demonstrated to be responsible for this phenomenon. Excess of oleic acid in suspensions makes the QY values concentration-independent over the entire reabsorption-free range. The PL emission is shown to be dominated by surface-related recombinations with some contribution from QD-core transitions. We demonstrate that QD colloidal suspension stability improves with increasing the concentration and size of PbS QDs.

  3. In situ etching WO{sub 3} nanoplates: Hydrothermal synthesis, photoluminescence and gas sensor properties

    SciTech Connect

    Su, Xintai; Li, Yani; Jian, Jikang; Wang, Jide

    2010-12-15

    A novel hydrothermal process using p-nitrobenzoic acid as structure-directing agent has been employed to synthesize plate-shaped WO{sub 3} nanostructures containing holes. The p-nitrobenzoic acid plays a critical role in the synthesis of such novel WO{sub 3} nanoplates. The morphology, structure and optical property of the WO{sub 3} nanoplates have been characterized by transmission electron microcopy (TEM), scanning electron microcopy (SEM), X-ray diffraction (XRD) and photoluminescence (PL). The lateral size of the nanoplates is 500-1000 nm, and the thickness is about 80 nm. The formation mechanism of WO{sub 3} nanoplates is discussed briefly. The gas sensitivity of WO{sub 3} nanoplates was studied to ethanol and acetone at different operation temperatures and concentrations. Furthermore, the WO{sub 3} nanoplate-based gas sensor exhibits high sensitivity for ethanol and acetone as well as quick response and recovery time at low temperature.

  4. Use of H2S to Probe the Active Sites in FeNC Catalysts for the Oxygen Reduction Reaction (ORR) in Acidic Media

    SciTech Connect

    Singh, Deepika; Mamtani, Kuldeep; Bruening, Christopher R.; Miller, Jeffrey T.; Ozkan, Umit S.

    2014-10-01

    H2S has been used as a probe molecule both in an “in situ” poisoning experiment and in intermediate-temperature heat-treatment steps during and after the preparation of FeNC catalysts in an attempt to analyze its effect on their ORR activity. The heat treatments were employed either on the ball-milled precursor of FeNC or after the Ar-NH3 high temperature heat treatments. ORR activity of the H2S-treated catalysts was seen to be significantly lower than the sulfur-free catalysts, whether the sulfur exposure was during a half-cell testing, or as an intermediate-temperature exposure to H2S. The incorporation of sulfur species and interaction of Fe with sulfur were confirmed by characterization using XPS, EXAFS, TPO, and TPD. This study provides crucial evidence regarding differences in active sites in FeNC versus nitrogen-containing carbon nanostructured (CNx) catalysts.

  5. A novel sandwich assay with molecular beacon as report probe for nucleic acids detection on one-dimensional microfluidic beads array.

    PubMed

    Zuo, Xinbing; Yang, Xiaohai; Wang, Kemin; Tan, Weihong; Wen, Jianhui

    2007-03-21

    A novel sandwich assay with molecular beacons as report probes has been developed and integrated into one-dimensional microfluidic beads array (1-D chip) to pursue a label-free and elution-free detection of DNA/mRNA targets. In contrast with the immobilized molecular beacons, this sandwich assay can offer lower fluorescence background and correspondingly higher sensitivity. Furthermore, this sandwich assay on 1-D chip operating in conjunction with molecular beacon technique allows multiple targets detection without the need of laborious and time-consuming elution, which makes the experiment process simple, easy to handle, and reproducible results. In the experiment, the synthesized DNA targets with different concentrations were detected with a detection limit of approximately 0.05 nM. Moreover, the mRNA expression changes in A549 cells before and after anticancer drug 5-flouorouracil treatments were detected and the results were validated by the conventional RT-PCR method.

  6. Molecular beacon-based junction probes for efficient detection of nucleic acids via a true target-triggered enzymatic recycling amplification.

    PubMed

    Kong, Rong-Mei; Zhang, Xiao-Bing; Zhang, Liang-Liang; Huang, Yan; Lu, Dan-Qing; Tan, Weihong; Shen, Guo-Li; Yu, Ru-Qin

    2011-01-01

    This work reports the development of a new molecular beacon-based junction sensing system with highly sensitive DNA detection and a strong capability to identify SNPs. The single linear probe typically labels the midsection of the oligonucleotide, but our next-generation junction sensing system uses a hairpin-structured MB with labels on each end of the oligonucleotide to maintain the cleaving activity of our newly designed ssDNA-cleaved endonuclease, Nt.BbvCI, rather than the typical dsDNA-cleaved endonuclease. These design improvements guarantee a true and efficient target-triggered enzymatic recycling amplification process in our sensing system. They also afford a faster and more sensitive response toward target DNA than the first-generation junction sensing system.

  7. Photoluminescent carbon quantum dots as a directly film-forming phosphor towards white LEDs.

    PubMed

    Zhang, Feng; Feng, Xiaoting; Zhang, Yi; Yan, Lingpeng; Yang, Yongzhen; Liu, Xuguang

    2016-04-28

    Photoluminescent organosilane-functionalized carbon quantum dots (CQDs), 3.0-3.5 nm in diameter, were synthesized via a facile hydrothermal method using citric acid monohydrate as a precursor and N-(3-(trimethoxysilyl) propyl) ethylenediamine as a coordinating and passivation agent. The optical properties of the as-obtained CQDs were investigated in detail. The CQD aqueous solution emits bright blue-white light under ultraviolet (UV) illumination with a quantum yield of 57.3% and high red-green-blue (RGB) spectral composition of 60.1%, and in particular the CQDs exhibit excitation-independent photoluminescence. The CQDs have a narrow size distribution around 3.1 nm and good film-forming ability through simple heat-treatment. By virtue of these excellent optical characteristics and good film-forming ability, a white light-emitting device (LED) was fabricated by combining a UV-LED chip with a single CQD phosphor film, which exhibited cool white light with a CIE coordinate of (0.31, 0.36), a color rendering index of 84 and a correlated color temperature of 6282 K. In addition, the white LED exhibits good optical stability under various working currents and for different working time intervals. Moreover, the interaction between the carbogenic core and surface groups was discussed using the DMol(3) program based on density functional theory. This research suggests the great potential of CQDs for solid-state lighting systems and reveals the effect of the surface state on the photoluminescent mechanism of CQDs. PMID:27049931

  8. Photoluminescent carbon quantum dots as a directly film-forming phosphor towards white LEDs

    NASA Astrophysics Data System (ADS)

    Zhang, Feng; Feng, Xiaoting; Zhang, Yi; Yan, Lingpeng; Yang, Yongzhen; Liu, Xuguang

    2016-04-01

    Photoluminescent organosilane-functionalized carbon quantum dots (CQDs), 3.0-3.5 nm in diameter, were synthesized via a facile hydrothermal method using citric acid monohydrate as a precursor and N-(3-(trimethoxysilyl) propyl) ethylenediamine as a coordinating and passivation agent. The optical properties of the as-obtained CQDs were investigated in detail. The CQD aqueous solution emits bright blue-white light under ultraviolet (UV) illumination with a quantum yield of 57.3% and high red-green-blue (RGB) spectral composition of 60.1%, and in particular the CQDs exhibit excitation-independent photoluminescence. The CQDs have a narrow size distribution around 3.1 nm and good film-forming ability through simple heat-treatment. By virtue of these excellent optical characteristics and good film-forming ability, a white light-emitting device (LED) was fabricated by combining a UV-LED chip with a single CQD phosphor film, which exhibited cool white light with a CIE coordinate of (0.31, 0.36), a color rendering index of 84 and a correlated color temperature of 6282 K. In addition, the white LED exhibits good optical stability under various working currents and for different working time intervals. Moreover, the interaction between the carbogenic core and surface groups was discussed using the DMol3 program based on density functional theory. This research suggests the great potential of CQDs for solid-state lighting systems and reveals the effect of the surface state on the photoluminescent mechanism of CQDs.

  9. Constrained photophysics of partially and fully encapsulated charge transfer probe (E)-3-(4-Methylaminophenyl) acrylic acid methyl ester inside cyclodextrin nano-cavities: Evidence of cyclodextrins cavity dependent complex stoichiometry

    NASA Astrophysics Data System (ADS)

    Ghosh, Shalini; Jana, Sankar; Guchhait, Nikhil

    2011-12-01

    The polarity sensitive intra-molecular charge transfer (ICT) emission from (E)-3-(4-Methylaminophenyl) acrylic acid methyl ester (MAPAME) is found to show distinct changes once introduced into the nano-cavities of cyclodextrins in aqueous environment. Movement of the molecule from the more polar aqueous environment to the less polar, hydrophobic cyclodextrin interior is marked by the blue shift of the CT emission band with simultaneous fluorescence intensity enhancement. The emission spectral changes on complexation with the α- and β-CD show different stoichiometries as observed from the Benesi-Hildebrand plots. Fluorescence anisotropy and lifetime measurements were performed to probe the different behaviors of MAPAME in aqueous α- and β-CD solutions.

  10. THE APPLICATION OF PEPTIDE NUCLEIC ACID PROBES FOR RAPID DETECTION AND ENUMERATION OF EUBACTERIA, STAPHYLOCOCCUS AUREUS AND PSEUDOMONAS AERUGINOSA IN RECREATIONAL BEACHES OF S. FLORIDA. (R828830)

    EPA Science Inventory

    A novel chemiluminescent in situ hybridization technique using peptide nucleic acids (PNA) was adapted for the detection of bacteria in beach sand and recreational waters in South Florida. The simultaneous detection and enumeration of eubacteria and the novel indicators, S...

  11. Electrospray ionization mass spectrometric investigations of [alpha]-dicarbonyl compounds--Probing intermediates formed in the course of the nonenzymatic browning reaction of l-ascorbic acid

    NASA Astrophysics Data System (ADS)

    Schulz, Anke; Trage, Claudia; Schwarz, Helmut; Kroh, Lothar W.

    2007-05-01

    A new method is presented which allows the simultaneous detection of various [alpha]-dicarbonyl compounds generated in the course of the nonenzymatic browning reaction initiated by thermal treatment of l-ascorbic acid, namely: glyoxal, methylglyoxal, diacetyl, 3-deoxy-l-pentosone, and l-threosoneE 3-Deoxy-l-threosone was successfully identified as a new C4-[alpha]-dicarbonyl structure for the first time in the degradation of Vitamin C by application of this non-chromatographic mass spectrometric approach. Moreover, a more detailed elucidation of the mechanistic scenario with respect to the oxidative and nonoxidative pathways is presented by using dehydro-l-ascorbic acid and 2,3-diketo-l-gulonic acid instead of l-ascorbic acid as a starting material. Furthermore, the postulated pathways are corroborated with the aid of 13C-isotopic labeling studies. The investigations were extended to baby food, and the successful detection of [alpha]-dicarbonyl compounds characteristic for Vitamin C degradation proved the matrix tolerance of the introduced method.

  12. Low-temperature photoluminescence studies of mercuric-iodide photodetectors

    NASA Astrophysics Data System (ADS)

    James, R. B.; Bao, X. J.; Schlesinger, T. E.; Markakis, J. M.; Cheng, A. Y.; Ortale, C.

    1989-09-01

    Mercuric-iodide (HgI2 ) photodetectors with sputtered indium-tin-oxide (ITO) entrance electrodes were studied using low-temperature photoluminescence spectroscopy. The photoluminescence spectrum obtained on each photodetector was found to differ for points beneath the ITO contact and points adjacent to it, indicating that the contact fabrication process introduces new carrier traps and radiative recombination centers within the ITO-HgI2 interfacial region. In particular, a new broad band was observed in the spectra taken from points beneath the ITO electrode. Photocurrent-versus-position measurements showed that the intensity of this broad band was enhanced in regions having relatively poor photoresponse.

  13. Optical enhancement of photoluminescence with colloidal quantum dots

    NASA Astrophysics Data System (ADS)

    Abraham, Gabrielle; French, David A.; Bajwa, Pooja; Heyes, Colin D.; Herzog, Joseph B.

    2015-08-01

    This work investigates colloidal, semiconductor Cadmium Selenide (CdSe) QDs with optical spectroscopy measurements. A custom-built microscope has been used for photoluminescence spectroscopy and has collected images, videos, and spectra of samples to study the effects of substrates, sample density, uniformity, and QD aging with time. This set up will be used to detect single to a few molecules, shown by fluorescent intermittency, or QD blinking. Differences in the spectrum will be noted as related to the age of samples, the density of the quantum dots, and the concentration of samples. Further experiments include the potential plasmonic enhancement of QD photoluminescence by gold nanoparticles or nanostructures.

  14. Photoluminescence lifetime measurements in InP wafers

    NASA Technical Reports Server (NTRS)

    Landis, Geoffrey A.; Jenkins, Phillip; Weinberg, Irving

    1991-01-01

    A simple apparatus to measure the minority carrier lifetime in InP has been developed. The technique stimulates the sample with a short pulse of light from a diode laser and measures the photoluminescence decay to extract the minority carrier lifetime. The photoluminescence lifetime in InP as a function of doping on both n- and p-type material is examined. The results also show a marked difference in the lifetime of n-type InP and p-type InP of similar doping levels. N-type InP shows a lifetime considerably longer than the expected radiative limited lifetime.

  15. Photoluminescence spectroscopy of YVO{sub 4}:Eu{sup 3+} nanoparticles with aromatic linker molecules: A precursor to biomedical functionalization

    SciTech Connect

    Senty, T. R.; Yalamanchi, M.; Cushing, S. K.; Seehra, M. S.; Bristow, A. D.; Zhang, Y.; Shi, X.

    2014-04-28

    Photoluminescence spectra of YVO{sub 4}:Eu{sup 3+} nanoparticles are presented, with and without the attachment of organic molecules that are proposed for linking to biomolecules. YVO{sub 4}:Eu{sup 3+} nanoparticles with 5% dopant concentration were synthesized via wet chemical synthesis. X-ray diffraction and transmission electron microscopy show the expected wakefieldite structure of tetragonal particles with an average size of 17 nm. Fourier-transform infrared spectroscopy determines that metal-carboxylate coordination is successful in replacing native metal-hydroxyl bonds with three organic linkers, namely, benzoic acid, 3-nitro 4-chloro-benzoic acid, and 3,4-dihydroxybenzoic acid, in separate treatments. UV-excitation photoluminescence spectra show that the position and intensity of the dominant {sup 5}D{sub 0} – {sup 7}F{sub 2} electric-dipole transition at 619 nm are unaffected by the benzoic acid and 3-nitro 4-chloro-benzoic acid treatments. Attachment of 3,4-dihydroxybenzoic acid produces an order-of-magnitude quenching in the photoluminescence, due to the presence of high-frequency vibrational modes in the linker. Ratios of the dominant electric- and magnetic-dipole transitions confirm infrared measurements, which indicate that the bulk crystal of the nanoparticle is unchanged by all three treatments.

  16. Nine New Fluorescent Probes

    NASA Astrophysics Data System (ADS)

    Lin, Tsung-I.; Jovanovic, Misa V.; Dowben, Robert M.

    1989-06-01

    Absorption and fluorescence spectroscopic studies are reported here for nine new fluorescent probes recently synthesized in our laboratories: four pyrene derivatives with substituents of (i) 1,3-diacetoxy-6,8-dichlorosulfonyl, (ii) 1,3-dihydroxy-6,8-disodiumsulfonate, (iii) 1,3-disodiumsulfonate, and (iv) l-ethoxy-3,6,8-trisodiumsulfonate groups, and five [7-julolidino] coumarin derivatives with substituents of (v) 3-carboxylate-4-methyl, (vi) 3- methylcarboxylate, (vii) 3-acetate-4-methyl, (viii) 3-propionate-4-methyl, and (ix) 3-sulfonate-4-methyl groups. Pyrene compounds i and ii and coumarin compounds v and vi exhibit interesting absorbance and fluorescence properties: their absorption maxima are red shifted compared to the parent compound to the blue-green region, and the band width broadens considerably. All four blue-absorbing dyes fluoresce intensely in the green region, and the two pyrene compounds emit at such long wavelengths without formation of excimers. The fluorescence properties of these compounds are quite environment-sensitive: considerable spectral shifts and fluorescence intensity changes have been observed in the pH range from 3 to 10 and in a wide variety of polar and hydrophobic solvents with vastly different dielectric constants. The high extinction and fluorescence quantum yield of these probes make them ideal fluorescent labeling reagents for proteins, antibodies, nucleic acids, and cellular organelles. The pH and hydrophobicity-dependent fluorescence changes can be utilized as optical pH and/or hydrophobicity indicators for mapping environmental difference in various cellular components in a single cell. Since all nine probes absorb in the UV, but emit at different wavelengths in the visible, these two groups of compounds offer an advantage of utilizing a single monochromatic light source (e.g., a nitrogen laser) to achieve multi-wavelength detection for flow cytometry application. As a first step to explore potential application in

  17. In vivo incorporation of unnatural amino acids to probe structure, dynamics and ligand binding in a large protein by Nuclear Magnetic Resonance spectroscopy

    PubMed Central

    Cellitti, Susan E.; Jones, David H.; Lagpacan, Leanna; Hao, Xueshi; Zhang, Qiong; Hu, Huiyong; Brittain, Scott M.; Brinker, Achim; Caldwell, Jeremy; Bursulaya, Badry; Spraggon, Glen; Brock, Ansgar; Ryu, Youngha; Uno, Tetsuo; Schultz, Peter G.; Geierstanger, Bernhard H.

    2008-01-01

    In vivo incorporation of isotopically labeled unnatural amino acids into large proteins drastically reduces the complexity of nuclear magnetic resonance (NMR) spectra. Incorporation is accomplished by co-expressing an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid added to the media and the protein of interest with a TAG amber codon at the desired incorporation site. To demonstrate the utility of this approach for NMR studies, 2-amino-3-(4-(trifluoromethoxy) phenyl) propanoic acid (OCF3Phe), 13C/15N-labeled p-methoxyphenylalanine (OMePhe), and 15N-labeled o-nitrobenzyl-tyrosine (oNBTyr) were incorporated individually into 11 positions around the active site of the 33 kDa thioesterase domain of human fatty acid synthase (FAS-TE). In the process, a novel tRNA synthetase was evolved for OCF3Phe. Incorporation efficiencies and FAS-TE yields were improved by including an inducible copy of the respective aminoacyl-tRNA synthetase gene on each incorporation plasmid. Using only between 8 and 25 mg of unnatural amino acid, typically 2 mg of FAS-TE, sufficient for one 0.1 mM NMR sample, were produced from 50 mL of E. coli culture grown in rich media. Singly labeled protein samples were then used to study the binding of a tool compound. Chemical shift changes in 1H-15N, 1H-13C HSQC and 19F NMR spectra of the different single site mutants consistently identified the binding site and the effect of ligand binding on conformational exchange of some of the residues. OMePhe or OCF3Phe mutants of an active site tyrosine inhibited binding; incorporating 15N-Tyr at this site through UV-cleavage of the nitrobenzyl-photocage from oNBTyr re-established binding. These data suggest not only robust methods for using unnatural amino acids to study large proteins by NMR but also establish a new avenue for the site-specific labeling of proteins at individual residues without altering the protein sequence, a feat that can currently not be accomplished with

  18. Acid-base interactions and secondary structures of poly-L-lysine probed by 15N and 13C solid state NMR and Ab initio model calculations.

    PubMed

    Dos, Alexandra; Schimming, Volkmar; Tosoni, Sergio; Limbach, Hans-Heinrich

    2008-12-11

    The interactions of the 15N-labeled amino groups of dry solid poly-L-lysine (PLL) with various halogen and oxygen acids HX and the relation to the secondary structure have been studied using solid-state 15N and 13C CPMAS NMR spectroscopy (CP = cross polarization and MAS = magic angle spinning). For comparison, 15N NMR spectra of an aqueous solution of PLL were measured as a function of pH. In order to understand the effects of protonation and hydration on the 15N chemical shifts of the amino groups, DFT and chemical shielding calculations were performed on isolated methylamine-acid complexes and on periodic halide clusters of the type (CH3NH3(+)X(-))n. The combined experimental and computational results reveal low-field shifts of the amino nitrogens upon interaction with the oxygen acids HX = HF, H2SO4, CH3COOH, (CH3)2POOH, H3PO4, HNO3, and internal carbamic acid formed by reaction of the amino groups with gaseous CO2. Evidence is obtained that only hydrogen-bonded species of the type (Lys-NH2***H-X)n are formed in the absence of water. 15N chemical shifts are maximum when H is located in the hydrogen bond center and then decrease again upon full protonation, as found for aqueous solution at low pH. By contrast, halogen acids interact in a different way. They form internal salts of the type (Lys-NH3(+)X(-))n via the interaction of many acid-base pairs. This salt formation is possible only in the beta-sheet conformation. By contrast, the formation of hydrogen-bonded complexes can occur both in beta-sheet domains as well as in alpha-helical domains. The 15N chemical shifts of the protonated ammonium groups increase when the size of the interacting halogen anions is increased from chloride to iodide and when the number of the interacting anions is increased. Thus, the observed high-field 15N shift of ammonium groups upon hydration is the consequence of replacing interacting halogen atoms by oxygen atoms.

  19. A new general model for predicting melting thermodynamics of complementary and mismatched B-form duplexes containing locked nucleic acids: application to probe design for digital PCR detection of somatic mutations.

    PubMed

    Hughesman, Curtis; Fakhfakh, Kareem; Bidshahri, Roza; Lund, H Louise; Haynes, Charles

    2015-02-17

    Advances in real-time polymerase chain reaction (PCR), as well as the emergence of digital PCR (dPCR) and useful modified nucleotide chemistries, including locked nucleic acids (LNAs), have created the potential to improve and expand clinical applications of PCR through their ability to better quantify and differentiate amplification products, but fully realizing this potential will require robust methods for designing dual-labeled hydrolysis probes and predicting their hybridization thermodynamics as a function of their sequence, chemistry, and template complementarity. We present here a nearest-neighbor thermodynamic model that accurately predicts the melting thermodynamics of a short oligonucleotide duplexed either to its perfect complement or to a template containing mismatched base pairs. The model may be applied to pure-DNA duplexes or to duplexes for which one strand contains any number and pattern of LNA substitutions. Perturbations to duplex stability arising from mismatched DNA:DNA or LNA:DNA base pairs are treated at the Gibbs energy level to maintain statistical significance in the regressed model parameters. This approach, when combined with the model's accounting of the temperature dependencies of the melting enthalpy and entropy, permits accurate prediction of T(m) values for pure-DNA homoduplexes or LNA-substituted heteroduplexes containing one or two independent mismatched base pairs. Terms accounting for changes in solution conditions and terminal addition of fluorescent dyes and quenchers are then introduced so that the model may be used to accurately predict and thereby tailor the T(m) of a pure-DNA or LNA-substituted hydrolysis probe when duplexed either to its perfect-match template or to a template harboring a noncomplementary base. The model, which builds on classic nearest-neighbor thermodynamics, should therefore be of use to clinicians and biologists who require probes that distinguish and quantify two closely related alleles in either a

  20. What Is a pH Probe Study?

    MedlinePlus

    What is a pH Probe Study ? What is pH a probe study? M easuring the pH in the esophagus helps determine whether or not acid is coming up from the stomach. A pH probe study is usually done in patients where ...

  1. Probing the Lewis acidity and catalytic activity of the metal-organic framework [Cu3(btc)2] (BTC=benzene-1,3,5-tricarboxylate).

    PubMed

    Alaerts, Luc; Séguin, Etienne; Poelman, Hilde; Thibault-Starzyk, Frédéric; Jacobs, Pierre A; De Vos, Dirk E

    2006-09-25

    An optimized procedure was designed for the preparation of the microporous metal-organic framework (MOF) [Cu3(btc)2] (BTC=benzene-1,3,5-tricarboxylate). The crystalline material was characterized by X-ray diffraction, optical microscopy, SEM, X-ray photoelectron spectroscopy, N2 sorption, thermogravimetry, and IR spectroscopy of adsorbed CO. CO adsorbs on a small number of Cu2O impurities, and particularly on the free CuII coordination sites in the framework. [Cu3(btc)2] is a highly selective Lewis acid catalyst for the isomerization of terpene derivatives, such as the rearrangement of alpha-pinene oxide to campholenic aldehyde and the cyclization of citronellal to isopulegol. By using the ethylene ketal of 2-bromopropiophenone as a test substrate, it was demonstrated that the active sites in [Cu3(btc)2] are hard Lewis acids. Catalyst stability, re-usability, and heterogeneity are critically assessed. PMID:16881030

  2. A DFT study of the acid-base properties of anatase TiO2 and tetragonal ZrO2 by adsorption of CO and CO2 probe molecules

    NASA Astrophysics Data System (ADS)

    Chen, Hsin-Yi Tiffany; Tosoni, Sergio; Pacchioni, Gianfranco

    2016-10-01

    We have performed a comparative study of the acid-base characteristics of the surfaces of anatase TiO2 and tetragonal ZrO2. To this end we performed DFT + U calculations on CO and CO2 probe molecules adsorbed both on terraces and steps of the two oxides. For titania, CO adsorption results in a moderate adsorption energy (about - 0.3 eV) and in a positive shift of the Csbnd O stretching frequency (about + 40 cm- 1), typical of Lewis acid sites, with no clear difference in the acidity between terraces or steps. For zirconia we found a similar CO binding energy as for titania, and a CO vibrational shift that depends on the location of the Zr cation: negligible on terraces, similar to TiO2 on steps. We conclude that the acidic properties are similar in the two oxide surfaces. Things are different for CO2 adsorption. On titania the interaction is weak and surface carbonates compete with physisorbed CO2, indicating a weak basic character. On the contrary, on zirconia three types of stable carbonates have been identified. Their vibrational frequencies are consistent with IR measurements reported in the literature. The most stable species forms on steps of the t-ZrO2 surface and consists of a CO32 - unit which lies flat on the surface with the O atoms pointing towards three Zr ions. The species forms spontaneously by extraction of a lattice oxygen by an incoming CO2 molecule. The different reactivity points towards a much more pronounced basic character of zirconia compared to titania, at least if measured by CO2 adsorption.

  3. A dinuclear ruthenium(II) complex as turn-on luminescent probe for hypochlorous acid and its application for in vivo imaging

    PubMed Central

    Liu, Zonglun; Gao, Kuo; Wang, Beng; Yan, Hui; Xing, Panfei; Zhong, Chongmin; Xu, Yongqian; Li, Hongjuan; Chen, Jianxin; Wang, Wei; Sun, Shiguo

    2016-01-01

    A dinuclear ruthenium(II) complex Ruazo was designed and synthesized, in which oxidative cyclization of the azo and o-amino group was employed for the detection of hypochlorous acid (HClO) in aqueous solution. The non-emissive Ruazo formed highly luminescent triazole-ruthenium(II) complex in presence of HClO and successfully imaged HClO in living cell and living mouse. PMID:27356618

  4. A dinuclear ruthenium(II) complex as turn-on luminescent probe for hypochlorous acid and its application for in vivo imaging

    NASA Astrophysics Data System (ADS)

    Liu, Zonglun; Gao, Kuo; Wang, Beng; Yan, Hui; Xing, Panfei; Zhong, Chongmin; Xu, Yongqian; Li, Hongjuan; Chen, Jianxin; Wang, Wei; Sun, Shiguo

    2016-06-01

    A dinuclear ruthenium(II) complex Ruazo was designed and synthesized, in which oxidative cyclization of the azo and o-amino group was employed for the detection of hypochlorous acid (HClO) in aqueous solution. The non-emissive Ruazo formed highly luminescent triazole-ruthenium(II) complex in presence of HClO and successfully imaged HClO in living cell and living mouse.

  5. Excitation correlation photoluminescence in the presence of Shockley-Read-Hall recombination

    SciTech Connect

    Borgwardt, M.; Sippel, P.; Eichberger, R.; Semtsiv, M. P.; Masselink, W. T.; Schwarzburg, K.

    2015-06-07

    Excitation correlation photoluminescence (ECPL) measurements are often analyzed in the approximation of a cross correlation of charge carrier populations generated by the two delayed pulses. In semiconductors, this approach is valid for a linear non-radiative recombination path, but not for a non-linear recombination rate as in the general Shockley-Read-Hall recombination scenario. Here, the evolution of the ECPL signal was studied for deep trap recombination following Shockley-Read-Hall statistics. Analytic solutions can be obtained for a fast minority trapping regime and steady state recombination. For the steady state case, our results show that the quadratic radiative term plays only a minor role, and that the shape of the measured signal is mostly determined by the non-linearity of the recombination itself. We find that measurements with unbalanced intense pump and probe pulses can directly provide information about the dominant non-radiative recombination mechanism. The signal traces follow the charge carrier concentrations, despite the complex origins of the signal, thus showing that ECPL can be applied to study charge carrier dynamics in semiconductors without requiring elaborate calculations. The model is compared with measurements on a reference sample with alternating layers of InGaAs/InAlAs that were additionally cross-checked with time resolved optical pump terahertz probe measurements and found to be in excellent agreement.

  6. Photoaffinity analogues of methotrexate as folate antagonist binding probes. 1. Photoaffinity labeling of murine L1210 dihydrofolate reductase and amino acid sequence of the binding region

    SciTech Connect

    Price, E.M.; Smith, P.L.; Klein, T.E.; Freisheim, J.H.

    1987-07-28

    N/sup ..cap alpha../-(4-Amino-4-deoxy-10-methylpteroyl)-N/sup epsilon/-(4-azido-5-(/sup 125/I)iodosalicylyl)-L-lysine, a photoaffinity analogue of methotrexate, is only 2-fold less potent than methotrexate in the inhibition of murine L1210 dihydrofolate reductase. Irradiation of the enzyme in the presence of an equimolar concentration of the /sup 125/I-labeled analogue ultimately leads to an 8% incorporation of the photoprobe. A 100-fold molar excess of methotrexate essentially blocks this incorporation. Cyanogen bromide digestion of the labeled enzyme, followed by high-pressure liquid chromatography purification of the generated peptides, indicates that greater than 85% of the total radioactivity is incorporated into a single cyanogen bromide peptide. Sequence analysis revealed this peptide to be residues 53-111, with a majority of the radioactivity centered around residues 63-65 (Lys-Asn-Arg). These data demonstrate that the photoaffinity analogue specifically binds to dihydrofolate reductase and covalently modifies the enzyme following irradiation and is therefore a photolabeling agent useful for probing the inhibitor binding domain of the enzyme.

  7. Fluorescence and visual detection of fluoride ions using a photoluminescent graphene oxide paper sensor.

    PubMed

    Chen, Xiaochun; Yu, Shaoming; Yang, Liang; Wang, Jianping; Jiang, Changlong

    2016-07-14

    The instant and on-site detection of trace aqueous fluoride ions is still a challenge for environmental monitoring and protection. This work demonstrates a new analytical method and its utility of a paper sensor for visual detection of F(-) on the basis of the fluorescence resonance energy transfer (FRET) between photoluminescent graphene oxide (GO) and silver nanoparticles (AgNPs) through the formation of cyclic esters between phenylborinic acid and diol. The fluorescence of GO was quenched by the AgNPs, and trace F(-) can recover the fluorescence of the quenched photoluminescent GO. The increase in fluorescence intensity is proportional to the concentration of F(-) in the range of 0.05-0.55 nM, along with a limit of detection (LOD) as low as 9.07 pM. Following the sensing mechanism, a paper-based sensor for the visual detection of aqueous F(-) has been successfully developed. The paper sensor showed high sensitivity for aqueous F(-), and the LOD could reach as low as 0.1 μM as observed by the naked eye. The very simple and effective strategy reported here could be extended to the visual detection of a wide range of analytes in the environment by the construction of highly efficient FRET nanoprobes. PMID:27376510

  8. Photoluminescent PEG based comacromers as excitation dependent fluorophores for biomedical applications.

    PubMed

    Vijayan, Vineeth M; Komeri, Remya; Victor, Sunita P; Muthu, Jayabalan

    2015-11-01

    We report a novel multi-modal biodegradable photoluminescent comacromer [poly(propylene fumarate)-PEG-glycine] (PLM) having excitation-dependent fluorescence (EDF) for biomedical applications. The photoluminescence of the synthesized PLM in aqueous and solid state condition, fluorescence life time and photo stability were evaluated. Hydrogels and nanogels were prepared from the PLM by cross linking with acrylic acid. Nanogels exhibited spherical morphology with a particle size of 100 nm as evaluated by transmission electron microscopy (TEM). In vitro cytotoxic and hemolytic studies revealed cytocompatibility. Furthermore, cellular imaging of nanogels on L929 fibroblast and Hela cell lines revealed EDF characteristics. We hypothesize that the EDF characteristics of the synthesized PLM may be attributed to the presence of n-π* interactions of the hydroxyl oxygen atoms of PEG with carbonyl groups of the ester linkages. Taken together, our results indicate that the synthesized PEG-based comacromer can serve as biocompatible fluorophores for various biomedical applications. More importantly, the facile way of synthesizing fluorescent polymers based on PEG with EDF characteristics demonstrated in this work can pave the way for developing more novel biocompatible fluorophores with wide range of biomedical applications.

  9. Biomimetic Taste Receptors with Chiral Recognition by Photoluminescent Metal-Organic Frameworks Chelated with Polyaniline Helices.

    PubMed

    Lee, Tu; Lin, Tsung Yan; Lee, Hung Lin; Chang, Yun Hsuan; Tsai, Yee Chen

    2016-01-22

    The adsorption of phenylaniline (Phe) enantiomers on (+)-polyaniline (PAN)-chelated [In(OH)(bdc)]n microcrystals was carefully designed and studied by using the Job titration, circular dichroism, X-ray photoelectron spectroscopy, and photoluminescence to mimic heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors in selective, but not specific, ligand binding with chiral recognition and signal transduction. Six essential working principles across different length scales are unraveled: 1) a chiral (+)-PAN (host), 2) specific sites for Phe-(+)/PAN (guest-host) binding, 3) a conformational change of (+)-PAN after binding with Phe enantiomers, 4) different degrees of packing for (+)-PAN, 5) interactions between (+)-PAN and the underlying signal-generating framework (i.e., [In(OH)(bdc)]n microcrystals), and 6) a systematic photoluminescent signal combination by using principal-component analysis from the other three polymer-chelated metal-organic frameworkds (MOFs), such as poly(acrylic acid) (PAA), sodium alginate (SA), and polyvinylpyrrolidone (PVP) to enhance the selectivity and discrimination capabilities.

  10. Dynamics of four-photon photoluminescence in gold nanoantennas.

    PubMed

    Biagioni, Paolo; Brida, Daniele; Huang, Jer-Shing; Kern, Johannes; Duò, Lamberto; Hecht, Bert; Finazzi, Marco; Cerullo, Giulio

    2012-06-13

    Two-pulse correlation is employed to investigate the temporal dynamics of both two-photon photoluminescence (2PPL) and four-photon photoluminescence (4PPL) in resonant and nonresonant nanoantennas excited at a wavelength of 800 nm. Both 2PPL and 4PPL data are consistent with the same two-step model already established for 2PPL, implying that the first excitation step in 4PPL is a three-photon sp → sp direct interband transition. Considering energy and parity conservation, we also explain why 4PPL behavior is favored over, for example, three- and five-photon photoluminescence in the power range below the damage threshold of our antennas. Since sizable 4PPL requires larger peak intensities of the local field, we are able to select either 2PPL or 4PPL in the same gold nanoantennas by choosing a suitable laser pulse duration. We thus provide a first consistent model for the understanding of multiphoton photoluminescence generation in gold nanoantennas, opening new perspectives for applications ranging from the characterization of plasmonic resonances to biomedical imaging. PMID:22551099

  11. Thermally enhanced photoluminescence for heat harvesting in photovoltaics

    PubMed Central

    Manor, Assaf; Kruger, Nimrod; Sabapathy, Tamilarasan; Rotschild, Carmel

    2016-01-01

    The maximal Shockley–Queisser efficiency limit of 41% for single-junction photovoltaics is primarily caused by heat dissipation following energetic-photon absorption. Solar-thermophotovoltaics concepts attempt to harvest this heat loss, but the required high temperatures (T>2,000 K) hinder device realization. Conversely, we have recently demonstrated how thermally enhanced photoluminescence is an efficient optical heat-pump that operates in comparably low temperatures. Here we theoretically and experimentally demonstrate such a thermally enhanced photoluminescence based solar-energy converter. Here heat is harvested by a low bandgap photoluminescent absorber that emits thermally enhanced photoluminescence towards a higher bandgap photovoltaic cell, resulting in a maximum theoretical efficiency of 70% at a temperature of 1,140 K. We experimentally demonstrate the key feature of sub-bandgap photon thermal upconversion with an efficiency of 1.4% at only 600 K. Experiments on white light excitation of a tailored Cr:Nd:Yb glass absorber suggest that conversion efficiencies as high as 48% at 1,500 K are in reach. PMID:27762271

  12. Photoluminescence of spray pyrolysis deposited ZnO nanorods

    PubMed Central

    2011-01-01

    Photoluminescence of highly structured ZnO layers comprising well-shaped hexagonal rods is presented. The ZnO rods (length 500-1,000 nm, diameter 100-300 nm) were grown in air onto a preheated soda-lime glass (SGL) or ITO/SGL substrate by low-cost chemical spray pyrolysis method using zinc chloride precursor solutions and growth temperatures in the range of 450-550°C. We report the effect of the variation in deposition parameters (substrate type, growth temperature, spray rate, solvent type) on the photoluminescence properties of the spray-deposited ZnO nanorods. A dominant near band edge (NBE) emission is observed at 300 K and at 10 K. High-resolution photoluminescence measurements at 10 K reveal fine structure of the NBE band with the dominant peaks related to the bound exciton transitions. It is found that all studied technological parameters affect the excitonic photoluminescence in ZnO nanorods. PACS: 78.55.Et, 81.15.Rs, 61.46.Km PMID:21711895

  13. Hybrid microtubes of polyoxometalate and fluorescence dye with tunable photoluminescence.

    PubMed

    Zhang, Huanqiu; Peng, Jun; Shen, Yan; Yu, Xia; Zhang, Fang; Mei, Jilan; Li, Bin; Zhang, Liming

    2012-05-11

    Fluorescent microtubes based on α-Keggin tungstosilicate and fluorescein (SiW(12)-F) have been obtained by using a simple method, which present tunable photoluminescence from sky blue to green to red by variation of excitation light. The SiW(12) component can inhibit photobleaching of fluorescein.

  14. Photoluminescence of Zn-implanted GaN

    NASA Technical Reports Server (NTRS)

    Pankove, J. I.; Hutchby, J. A.

    1974-01-01

    The photoluminescence spectrum of Zn-implanted GaN peaks at 2.87 eV at room temperature. The emission efficiency decreases linearly with the logarithm of the Zn concentration in the range from 1 x 10 to the 18th to 20 x 10 to the 18th Zn/cu cm.

  15. Photoluminescent polymer nanoparticles for label-free cellular imaging.

    PubMed

    Lee, Kyung Jin; Oh, Wan-Kyu; Song, Jooyoung; Kim, Sojin; Lee, Jiwoon; Jang, Jyongsik

    2010-08-01

    Novel polymer based photoluminescent nanoparticles were fabricated by ultra-sound induced emulsion polymerization and applied to bioimaging of human breast cancer SK-BR-3 cells after ethylenediamine treatment and conjugation with anti-ErbB2 antibody. PMID:20567782

  16. Hydrothermal synthesis, crystal structures and photoluminescence properties of mixed europium-yttrium organic frameworks

    SciTech Connect

    Han Yinfeng; Fu Lianshe; Mafra, Luis; Shi, Fa-Nian

    2012-02-15

    Three mixed europium-yttrium organic frameworks: Eu{sub 2-x}Y{sub x}(Mel)(H{sub 2}O){sub 6} (Mel=mellitic acid or benzene-1,2,3,4,5,6-hexacarboxylic acid, x=0.38 1, 0.74 2, and 0.86 3) have been synthesized and characterized. All the compounds contain a 3-D net with (4, 8)-flu topology. The study indicates that the photoluminescence properties are effectively affected by the different ratios of europium and yttrium ions, the quantum efficiency is increased and the Eu{sup 3+} lifetime becomes longer in these MOFs than those of the Eu analog. - Graphical abstract: Three mixed europium and yttrium organic frameworks: Eu{sub 2-x}Y{sub x}(Mel)(H{sub 2}O){sub 6} (Mel=mellitic acid) have been synthesized and characterized. All the compounds contain a 3-D net with (4, 8)-flu topology. The study indicates that the photoluminescence properties are effectively affected by the different ratios of europium and yttrium ions, the quantum efficiency is increased and the Eu{sup 3+} lifetime becomes longer in these MOFs than those of the Eu analog. Highlights: Black-Right-Pointing-Pointer Three (4, 8)-flu topological mixed Eu and Y MOFs were synthesized under mild conditions. Black-Right-Pointing-Pointer Metal ratios were refined by the single crystal data consistent with the EDS analysis. Black-Right-Pointing-Pointer Mixed Eu and Y MOFs show longer lifetime and higher quantum efficiency than the Eu analog. Black-Right-Pointing-Pointer Adding inert lanthanide into luminescent MOFs enlarges the field of luminescent MOFs.

  17. A novel DAD type and folic acid conjugated fluorescent monomer as a targeting probe for imaging of folate receptor overexpressed cells.

    PubMed

    Ekiz Kanik, Fulya; Ag, Didem; Seleci, Muharrem; Barlas, Firat Baris; Kesik, Melis; Hizalan, Gonul; Akpinar, Hava; Timur, Suna; Toppare, Levent

    2014-01-01

    We describe a modification and post-functionalization technique for a donor-acceptor-donor type monomer; 6-(4,7-bis(2,3-dihydrothieno[3,4-b][1,4]dioxin-5-yl)-2H-benzo[d][1,2, 3]triazol-2-yl)hexan-1-amine. Folic acid was attached to the fluorescent structure. The conjugation was confirmed via NMR and Fourier transform infrared analyses. Cytotoxicity was investigated and the comparison of association of targeted monomeric structures in tumor cells was monitored via fluorescence microscopy.

  18. Probing the molecular and electronic structure of norhipposudoric and hipposudoric acids from the red sweat of Hippopotamus amphibius: a DFT investigation.

    PubMed

    Galasso, Vinicio; Pichierri, Fabio

    2009-03-19

    Molecular structure and tautomeric/conformational preferences of norhipposudoric and hipposudoric acids, the recently isolated pigments of the Hippopotamus amphibius' sweat, were investigated using the density functional theory (DFT) PBE0 formalism. Among a large variety of possible structures, two similar keto-enol tautomer/conformers are nearly isoenergetic and markedly more stable than the others both in the gas phase and aqueous solution. The bulk solvent effect was accounted for with the polarizable continuum model (PCM). A distinctive structural feature is the strong intramolecular hydrogen bonding in the keto-enol O-H...O bridge, as shown by analysis of the atoms-in-molecules topological properties of the electron density. To elucidate the claimed strong acidity of these pigments, the site-specific microscopic dissociation constants were also calculated using the cluster-continuum model, a hybrid approach based on inclusion of explicit solvent molecules and solvation of the cluster by the dielectric continuum. Notably, the first deprotonation should occur predominantly from the enolic group with a remarkably low pk(i) value. This factor could play an important role in the potent antibiotic activity of the pigments. The absorption spectra of the undissociated and dissociated compounds in aqueous solution were interpreted with time-dependent DFT/PCM calculations. The pi-pi* diquinoid excitations, mainly occurring in the fluorenoid nucleus, are the major contributors to the color and strong absorption bands in the UVA and UVB regions, which are closely related to the efficient sunscreen activity exerted by the pigments.

  19. Ethylene Diamine Tetraacetic Acid Etched Quantum Dots as a "Turn-On" Fluorescence Probe for Detection of Trace Zinc in Food.

    PubMed

    Liu, Wei; Wei, Fangdi; Xu, Guanhong; Wu, Yanzi; Hu, Chunting; Song, Quan; Yang, Jing; Hu, Qin

    2016-06-01

    In the present paper, a simple and rapid "turn-on" fluorescence sensor for Zn2+ based on ethylene diamine tetraacetic acid (EDTA) etched CdTe quantum dots (QDs) was developed. First, the initial bright fluorescence of mercaptopropionic acid (MPA) capped CdTe QDs was effectively quenched by EDTA, and then the presence of Zn2+ could "turn on" the weak fluorescence of QDs quenched by EDTA due to the formation of ZnS passivation shell. The increase of fluorescence intensity of EDTA etched QDs was found to be linear with the concentration of Zn2+ added. Under the optimum conditions, the calibration curve of this method showed good linearity in the concentration range of 9.1-1 09.1 μM of Zn2+ with the correlation coefficient R2 = 0.998. The limit of detection (3σ/K) was 2 μM. The developed QDs-based sensor was successfully applied to detect trace zinc in zinc fortified table salts and energy drinks with satisfactory results. PMID:27427745

  20. Hydrodynamic ultrasonic probe

    DOEpatents

    Day, Robert A.; Conti, Armond E.

    1980-01-01

    An improved probe for in-service ultrasonic inspection of long lengths of a workpiece, such as small diameter tubing from the interior. The improved probe utilizes a conventional transducer or transducers configured to inspect the tubing for flaws and/or wall thickness variations. The probe utilizes a hydraulic technique, in place of the conventional mechanical guides or bushings, which allows the probe to move rectilinearly or rotationally while preventing cocking thereof in the tube and provides damping vibration of the probe. The probe thus has lower friction and higher inspection speed than presently known probes.

  1. Laser excited novel near-infrared photoluminescence bands in fast neutron-irradiated MgO·nAl2O3

    NASA Astrophysics Data System (ADS)

    Rahman, Abu Zayed Mohammad Saliqur; Haseeb, A. S. M. A.; Xu, Qiu; Evslin, Jarah; Cinausero, Marco

    2016-08-01

    New near-infrared photoluminescence bands were observed in neutron-irradiated spinel single crystal upon excitation by a 532 nm laser. The surface morphology of the unirradiated and fast neutron-irradiated samples was investigated using atomic force microscopy and scanning probe microscopy. Fast neutron-irradiated samples show a strong emission peak at 1685 nm along with weak bands at 1065 and 2365 nm. The temperature dependence of the photoluminescence intensity was also measured. At lower temperatures, the dominant peak at 1685 nm shifts toward lower energy whereas the other peaks remain fixed. Activation energies of luminescence quenching were estimated to be 5.7 and 54.6 meV for the lower and higher temperature regions respectively.

  2. Stealth CD44-targeted hyaluronic acid supramolecular nanoassemblies for doxorubicin delivery: probing the effect of uncovalent pegylation degree on cellular uptake and blood long circulation.

    PubMed

    Han, Xiaopeng; Li, Zhenbao; Sun, Jin; Luo, Cong; Li, Lin; Liu, Yuhai; Du, Yuqian; Qiu, Shuhong; Ai, Xiaoyu; Wu, Chunnuan; Lian, He; He, Zhonggui

    2015-01-10

    Stealth active targeting nanoparticles (NPs) usually include two types of ligand sites: ligand anchored on distal ends of the polyethylene glycol (PEG) and ligand buried under pegylated layer. The latter typical case is hyaluronic acid (HA)-based NPs; however, there is little information available for the latter NPs about effect of the optimal density of surface PEG coating on the blood circulation time, cellular uptake and in vivo anticancer activity. Thus, in this study, in order to optimize the anticancer effects of HA-based NPs, we focus on how uncovalent pegylation degree modulates blood circulation time and cellular uptake of HA-based NPs. We firstly designed a new double-hydrophilic copolymer by conjugating HP-β-cyclodextrin with HA, and this carrier was further pegylated with adamantyl-peg (ADA-PEG) to form inclusion complex HA-HPCD/ADA-PEG, termed as HCPs. The supramolecular nanoassemblies were fabricated by host-guest and polar interactions between HCPs and doxorubicin (Dox), with vitamin E succinate (VES) being a nanobridge. Despite the active recognition between HA and CD44 receptor, the cellular uptake and targeting efficiency of HA-NPs decreased with the increasing peg density, demonstrating HA was partly buried by high density peg coating. However, the high density of peg coating was beneficial to long circulation time, tumor biodistribution and anticancer activity in vivo. NPs with 5% peg coating had the optimal cellular targeting efficiency in vitro and anticancer effects in vivo. The findings suggest that balancing long circulation property and cellular uptake is important to achieve the optimal antitumor efficacy for pegylated HA-based NPs, and that PEG coating densities cannot be extended beyond a certain density for shielding effect without compromising the efficacy of hyaluronic acid targeted delivery.

  3. Probing polymorphism and reactivity in the organic solid state using 13C NMR spectroscopy: Studies of p-Formyl- trans-cinnamic acid

    NASA Astrophysics Data System (ADS)

    Harris, Kenneth D. M.; Thomas, John M.

    1991-09-01

    p-Formyl- trans-cinnamic acid (p-FCA) is known to exist in two different crystal phases (denoted β and γ). When crystals of the β phase of p-FCA are exposed to UV radiation, a solid state dimerization reaction occurs to produce 4,4'-diformyl-β-truxinic acid. In contrast, crystals of the γ phase of p-FCA are photostable. It is shown in this paper that high resolution solid state 13C NMR spectroscopy is a sensitive technique for distinguishing the β and γ phases of p-FCA, and can be used to investigate, in detail, the chemical transformation that occurs upon UV irradiation of the β phase. Specifically, the 13C NMR spectra presented here were recorded using the TOSS (total suppression of sidebands) pulse sequence; this is based upon the standard 13C CPMAS (cross polarization/magic angle sample spinning/high power 1H decoupling) method, but has the additional feature that all orders of spinning sidebands are eliminated from the spectrum. The photoproduct obtained from UV irradiation of β-p-FCA contains a significant noncrystalline component (assessed via powder X-ray diffraction), and our NMR studies suggest that this noncrystalline component of the photoproduct contains some amount of the γ phase of the monomer p-FCA. A mechanism is proposed to explain the fact that UV irradiation of β-p-FCA can generate, in addition to the expected photodimer, an impurity amount of the γ phase of p-FCA.

  4. Probing the molecular and electronic structure of norhipposudoric and hipposudoric acids from the red sweat of Hippopotamus amphibius: a DFT investigation.

    PubMed

    Galasso, Vinicio; Pichierri, Fabio

    2009-03-19

    Molecular structure and tautomeric/conformational preferences of norhipposudoric and hipposudoric acids, the recently isolated pigments of the Hippopotamus amphibius' sweat, were investigated using the density functional theory (DFT) PBE0 formalism. Among a large variety of possible structures, two similar keto-enol tautomer/conformers are nearly isoenergetic and markedly more stable than the others both in the gas phase and aqueous solution. The bulk solvent effect was accounted for with the polarizable continuum model (PCM). A distinctive structural feature is the strong intramolecular hydrogen bonding in the keto-enol O-H...O bridge, as shown by analysis of the atoms-in-molecules topological properties of the electron density. To elucidate the claimed strong acidity of these pigments, the site-specific microscopic dissociation constants were also calculated using the cluster-continuum model, a hybrid approach based on inclusion of explicit solvent molecules and solvation of the cluster by the dielectric continuum. Notably, the first deprotonation should occur predominantly from the enolic group with a remarkably low pk(i) value. This factor could play an important role in the potent antibiotic activity of the pigments. The absorption spectra of the undissociated and dissociated compounds in aqueous solution were interpreted with time-dependent DFT/PCM calculations. The pi-pi* diquinoid excitations, mainly occurring in the fluorenoid nucleus, are the major contributors to the color and strong absorption bands in the UVA and UVB regions, which are closely related to the efficient sunscreen activity exerted by the pigments. PMID:19239216

  5. Core/Shell NaGdF4:Nd3+/NaGdF4 Nanocrystals with Efficient Near-Infrared to Near-Infrared Downconversion Photoluminescence for Bioimaging Applications

    PubMed Central

    Chen, Guanying; Ohulchanskyy, Tymish Y.; Liu, Sha; Law, Wing-Cheung; Wu, Fang; Swihart, Mark T.; Ågren, Hans; Prasad, Paras N.

    2012-01-01

    We have synthesized core/shell NaGdF4:Nd3+/NaGdF4 nanocrystals with an average size of 15 nm and exceptionally high photoluminescence (PL) quantum yield. When excited at 740 nm, the nanocrystals manifest spectrally distinguished, near infrared to near infrared (NIR-to-NIR) downconversion PL peaked at ~900, ~1050, and ~1300 nm. The absolute quantum yield of NIR-to-NIR PL reached 40% for core-shell nanoparticles dispersed in hexane. Time-resolved PL measurements revealed that this high quantum yield was achieved through suppression of nonradiative recombination originating from surface states and cross relaxations between dopants. NaGdF4:Nd3+/NaGdF4 nanocrystals, synthesized in organic media, were further converted to be water-dispersible by eliminating the capping ligand of oleic acid. NIR-to-NIR PL bioimaging was demonstrated both in vitro and in vivo through visualization of the NIR-to-NIR PL at ~900 nm under incoherent lamp light excitation. The fact that both excitation and the PL of these nanocrystals are in the biological window of optical transparency, combined with their high quantum efficiency, spectral sharpness and photostability, makes these nanocrystals extremely promising as optical biomaging probes. PMID:22401578

  6. High Performance Photoluminescent Carbon Dots for In Vitro and In Vivo Bioimaging: Effect of Nitrogen Doping Ratios.

    PubMed

    Wang, Junqing; Zhang, Pengfei; Huang, Chao; Liu, Gang; Leung, Ken Cham-Fai; Wáng, Yì Xiáng J

    2015-07-28

    Photoluminescent carbon dots (CDs) have received ever-increasing attention in the application of optical bioimaging because of their low toxicity, tunable fluorescent properties, and ultracompact size. We report for the first time on enhanced photoluminescence (PL) performance influenced by structure effects among the various types of nitrogen doped (N-doped) PL CDs. These CDs were facilely synthesized from condensation carbonization of linear polyethylenic amine (PEA) analogues and citric acid (CA) of different ratios. Detailed structural and property studies demonstrated that either the structures or the molar ratio of PEAs altered the PL properties of the CDs. The content of conjugated π-domains with C═N in the carbon backbone was correlated with their PL Quantum Yield (QY) (up to 69%). The hybridization between the surface/molecule state and the carbon backbone synergistically affected the chemical/physical properties. Also, long-chain polyethylenic amine (PEA) molecule-doped CDs exhibit increasing photostability, but at the expense of PL efficiency, proving that the PL emission of high QY CDs arise not only from the sp(2)/sp(3) carbon core and surface passivation of CDs, but also from the molecular fluorophores integrated in the CDs. In vitro and in vivo bioimaging of these N-doped CDs showed strong photoluminescence signals. Good biocompatibility demonstrates their potential feasibility for bioimaging applications. In addition, the overall size profile of the as-prepared CDs is comparable to the average size of capillary pores in normal living tissues (∼5 nm). Our study provides valuable insights into the effects of the PEA doping ratios on photoluminescence efficiency, biocompatibility, cellular uptake, and optical bioimaging of CDs. PMID:26135003

  7. 5 prime -Azido-(3,6- sup 3 H sub 2 )-1-naphthylphthalamic acid, a photoactivatable probe for naphthylphthalamic acid receptor proteins from higher plants: Identification of a 23-kDa protein from maize coleoptile plasma membranes

    SciTech Connect

    Zettl, R.; Feldwisch, J.; Schell, J.; Palme, K. ); Boland, W. )

    1992-01-15

    1-Naphthylphthalamic acid (NPA) is a specific inhibitor of polar auxin transport that blocks carrier mediated auxin efflux from plant cells. To allow identification of the NPA receptor thought to be part of the auxin efflux carrier, the authors have synthesized a tritiated, photolabile NPA analogue, 5{prime}-azido-(3,6-{sup 3}H{sub 2})NPA (({sup 3}H{sub 2})N{sub 3}NPA). This analogue was used to identify NPA-binding proteins in fractions highly enriched for plasma membrane vesicles isolated from maize coleoptiles (Zea mays L.). Competition studies showed that binding of ({sup 3}H{sub 2})N{sub 3}NPA to maize plasma membrane vesicles was blocked by nonradioactive NPA but not by benzoic acid. After incubation of plasma membrane vesicles with ({sup 3}H{sub 2})N{sub 3}NPA and exposure to UV light, they observed specific photoaffinity labeling of a protein with an apparent molecular mass of 23 kDa. Pretreatment of the plasma membrane vesicles with indole-3-acetic acid or with the auxin-transport inhibitors NPA and 2,3,5-triiodobenzoic acid strongly reduced specific labeling of this protein. This 23-kDa protein was also labeled by addition of 5-azido-(7-{sup 3}H)indole-3-acetic acid to plasma membranes prior to exposure to UV light. The 23-kDa protein was solubilized from plasma membranes by 1% Triton X-100. The possibility that this 23-kDa polypeptide is part of the auxin efflux carrier system is discussed.

  8. A family of uranyl-aromatic dicarboxylate (pht-, ipa-, tpa-) framework hybrid materials: photoluminescence, surface photovoltage and dye adsorption.

    PubMed

    Gao, Xue; Wang, Che; Shi, Zhong-Feng; Song, Jian; Bai, Feng-Ying; Wang, Ji-Xiao; Xing, Yong-Heng

    2015-07-01

    Four uranyl complexes [(UO2)(pht)H2O]·H2O (pht = phthalic acid) (1), (UO2)2(Hipa)4(H2O)2 (Hipa = isophthalic acid) (2), (UO2)(tpa)(DMF)2 (tpa = terephthalic acid) (3) and (UO2)(box)2 (box = benzoic acid) (4) were synthesized by the reaction of UO2(CH3COO)2·2H2O as the metal source and phthalic acid, isophthalic acid, terephthalic acid or benzoic acid as the ligand. They were characterized by elemental analyses, IR, UV-Vis, XRD, single crystal X-ray diffraction analysis and thermal gravimetric analysis. The structural analysis reveals that complex 1 exhibits a one-dimensional chain structure constructed by the building unit [(UO2)2(pht)4(H2O)2] and further extends the chain into a 2D supramolecular architecture by hydrogen bonding interactions. Complex 2 is a discrete [(UO2)2(Hipa)4(H2O)2] structure, and by the hydrogen bonding interaction, forms a 3D supramolecular structure. In complexes 3 and 4, adjacent uranyl polyhedra form a 1D chain through bridging terephthalic acid and benzoic acid, respectively. In order to extend their functional properties, their photoluminescence, surface photovoltage and dye adsorption properties have been studied. PMID:26038888

  9. Spectroscopic system for direct lanthanide photoluminescence spectroscopy with nanomolar detection limits.

    PubMed

    Andolina, Christopher M; Holthoff, William G; Page, Phillip M; Mathews, Ryan A; Morrow, Janet R; Bright, Frank V

    2009-05-01

    A new spectroscopic system for direct photoluminescence of lanthanide ions (Ln(III)) through electronic transitions within the 4f(n) manifold is described. The system is based on an injection seeded frequency tripled (lambda = 355 nm) Nd:YAG pump laser coupled with a master oscillator power oscillator (MOPO). The MOPO delivers an average pulse energy of approximately 60 mJ/pulse, is continuously tunable from 425 to 690 nm (Signal) and 735 to 1800 nm (Idler) with a linewidth of <0.2 cm(-1), and has a pulse duration of 10-12 ns. Aqueous solutions containing two polyaminocarboxylate complexes, ethylenediaminetetraacetic acid (EDTA) and diethylenetriaminepentaacetic acid (DTPA), and Ln(3+) aqua ion for several lanthanides including Eu(III), Tb(III), Dy(III), and Sm(III)) are used as steady-state and time-resolved photoluminescence standards. The versatility of the instrument is demonstrated by excitation scans over a broad visible range for aqueous solutions of complexes of Eu(III), Dy(III), Sm(III), and Tb(III). The Eu(III) excitation band ((7)F(o)-->(5)D(o)) is recorded over a range of complex concentrations that are 1000-fold less than reported previously, including Eu(EDTA) (1.00 nM), Eu(DTPA) (1.00 nM), and Eu(III) aqua ion (50.0 nM). Emission spectra are recorded in the visible range for Ln(III) complexes at pH 6.5 and 1.00 mM. Excited-state lifetimes for the standards were constant as a function of concentration from 10.0 nM to 1.00 mM for Eu(EDTA) and Eu(DTPA) and from 100 nM to 1.00 mM for Eu(III) aqua ion. Photoluminescence lifetimes in H(2)O and D(2)O are recorded and used to calculate the number of bound water molecules for all complexes.

  10. Probing the Efficacy of Peptide-Based Inhibitors against Acid- and Zinc-Promoted Oligomerization of Amyloid-β Peptide via Single-Oligomer Spectroscopy

    PubMed Central

    Powell, Lyndsey R.; Dukes, Kyle D.; Lammi, Robin K.

    2011-01-01

    One avenue for prevention and treatment of Alzheimer's disease involves inhibiting the aggregation of amyloid-β peptide (Aβ). Given the deleterious effects reported for Aβ dimers and trimers, it is important to investigate inhibition of the earliest association steps. We have employed quantized photobleaching of dye-labeled Aβ peptides to characterize four peptide-based inhibitors of fibrillogenesis and/or cytotoxicity, assessing their ability to inhibit association in the smallest oligomers (n = 2–5). Inhibitors were tested at acidic pH and in the presence of zinc, conditions that may promote oligomerization in vivo. Distributions of peptide species were constructed by examining dozens of surface-tethered monomers and oligomers, one at a time. Results show that all four inhibitors shift the distribution of Aβ species toward monomers; however, efficacies vary for each compound and sample environment. Collectively, these studies highlight promising design strategies for future oligomerization inhibitors, affording insight into oligomer structures and inhibition mechanisms in two physiologically significant environments. PMID:21945664

  11. Triacontanol and jasmonic acid differentially modulate the lipid organization as evidenced by the fluorescent probe behavior and 31P nuclear magnetic resonance shifts in model membranes.

    PubMed

    Sivakumar Swamy, G; Swamy, Sivakumar G; Ramanarayan, K; Inamdar, Laxmi S; Inamdar, Sanjeev R

    2009-04-01

    Fluorescence resonance energy transfer (FRET), time-resolved fluorescence and anisotropy decays were determined in large unilamellar vesicles (LUVs) of egg phosphatidylcholine with the FRET pair N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)-1,2-dipalmitoyl-sn-glycero-3-phospho-ethanolamine as donor and lissamine rhodamine B 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine as acceptor, using 2-ps pulses from a Ti:sapphire laser on LUVs with incorporated plant growth regulators: triacontanol (TRIA) and jasmonic acid (JA). FRET efficiency, energy transfer rate, rotation correlation time, microviscosity, and diffusion coefficient of lateral diffusion of lipids were calculated from these results. It was observed that TRIA and JA differentially modulated all parameters studied. The effect of JA in such modulations was always partially reversed by TRIA. Also, the generalized polarization of laurdan fluorescence indicated that JA enhances the degree of hydration in lipid bilayers to a larger extent than does TRIA. Solid-state (31)P magic-angle spinning nuclear magnetic resonance spectra of LUVs showed two chemical shifts, at 0.009 and -11.988 ppm, at low temperatures (20 degrees C), while at increasing temperatures (20-60 degrees C) only one (at -11.988 ppm) was prominent and the other (0.009 ppm) gradually became obscure. However, LUVs with TRIA exhibited only one of the shifts at 0.353 ppm even at lower temperatures and JA did not affect the chemical shifts.

  12. Sensitive fluorescence response of ZnSe(S) quantum dots: an efficient fluorescence probe

    NASA Astrophysics Data System (ADS)

    Saikia, K.; Deb, P.; Kalita, E.

    2013-06-01

    An efficient fluorescence probe based on ZnSe(S) alloyed quantum dots (QDs) has been reported here. The alloyed QDs were prepared through an aqueous route, where 3-mercaptopropionic acid (MPA) was employed as the effective precursor for both the sulfur source and stabilizer in the development of the alloyed system. Five-fold quantum yield (QY) enhancement was obtained for the ZnSe(S) QDs compared to the ZnSe QDs, formed in the initial stage of the refluxing process. The ultimate alloyed systems retained their high biocompatibility characteristics similar to the conventional ZnSe QDs. The photoluminescence of the ZnSe(S) QDs showed pH dependence, which was also evidenced in mammalian lymphocyte cells suspended in biological buffer over a wide pH range of 4.00-12.00. These characteristics make our prepared ZnSe(S) an efficient system for development of cell tracking, monitoring and sensing intracellular nanoprobes and devices.

  13. Probing local coordination and oxidation state of uranium in ThO2: U nanostructured

    NASA Astrophysics Data System (ADS)

    Gupta, Santosh K.; Pathak, N.; Kadam, R. M.

    2015-12-01

    Uranium doped thorium oxide nanoparticle (UDT) was synthesized using citric acid assisted combustion method. The concentration of uranium was varied from 0.5 to 5.0 mol % to investigate the effect of doping concentration on its optical properties. The synthesised UDT powder were characterized systematically using X-ray diffraction (XRD), transmission electron microscopy (TEM) and selected area electron diffraction (SAED) respectively for phase purity, morphology and crystallinity. Pertaining to nuclear industry, UDT is an important material and investigating the local structure of uranium in UDT is interesting as well as challenging because of complexity involved in synthesis of such ceramic powder. We have used time resolved photoluminescence spectroscopy (TRPLS) to probe the local coordination and oxidation state of uranium in UDT. Based on PL emission spectroscopy it was confirmed that uranium stabilizes as UO22+ ion in UDT. Lifetime spectroscopy shows that uranyl ion is not homogenously distributed in UDT lattice; rather it has two different chemical environments. Effect of concentration on PL behaviour shows that, concentration quenching takes place beyond 2.0 mol %; and based on critical distance calculation multipolar interaction was found to be responsible for such non-radiative quenching. As far as application in luminescence industry is concerned PL measurement shows that UDT gives intense green emission under UV excitation.

  14. Probing the roles of Ca(2+) and Mg(2+) in humic acids-induced ultrafiltration membrane fouling using an integrated approach.

    PubMed

    Wang, Long-Fei; He, Dong-Qin; Chen, Wei; Yu, Han-Qing

    2015-09-15

    Membrane fouling induced by natural organic matter (NOM) negatively affects the performance of ultrafiltration (UF) technology in producing drinking water. Divalent cation is found to be an important factor that affects the NOM-induced membrane fouling process. In this work, attenuated total reflection-Fourier transformation infrared spectroscopy (ATR-FTIR) coupled with quartz crystal microbalance (QCM), assisted by isothermal titration calorimetry (ITC), is used to explore the contribution of Mg(2+) and Ca(2+), the two abundant divalent cations in natural water, to the UF membrane fouling caused by humic acid (HA) at a molecular level. The results show that Ca(2+) exhibited superior performance in accelerating fouling compared to Mg(2+). The hydrophobic polyethersulfone (PES) membrane exhibited greater complexation with HA in the presence of Mg(2+) and Ca(2+), compared to the hydrophilic cellulose membrane, as evidenced by the more intense polysaccharide C-O, aromatic C=C and carboxylic C=O bands in the FTIR spectra. The QCM and ITC measurements provide quantitative evidence to support that Ca(2+) was more effective than Mg(2+) in binding with HA and accumulating foulants on the membrane surfaces. The higher charge neutralization capacity and more favorable binding ability of Ca(2+) were found to be responsible for its greater contribution to the NOM-induced membrane fouling than Mg(2+). This work offers a new insight into the mechanism of cation-mediated NOM-induced membrane fouling process, and demonstrates that such an integrated ATR-FTIR/QCM/ITC approach could be a useful tool to explore other complicated interaction processes in natural and engineered environments. PMID:26094086

  15. Validation of a Fluorescence In Situ Hybridization Method Using Peptide Nucleic Acid Probes for Detection of Helicobacter pylori Clarithromycin Resistance in Gastric Biopsy Specimens

    PubMed Central

    Cerqueira, Laura; Fernandes, Ricardo M.; Ferreira, Rui M.; Oleastro, Mónica; Carneiro, Fátima; Brandão, Catarina; Pimentel-Nunes, Pedro; Dinis-Ribeiro, Mário; Figueiredo, Céu; Keevil, Charles W.; Vieira, Maria J.

    2013-01-01

    Here, we evaluated a previously established peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH) method as a new diagnostic test for Helicobacter pylori clarithromycin resistance detection in paraffin-embedded gastric biopsy specimens. Both a retrospective study and a prospective cohort study were conducted to evaluate the specificity and sensitivity of a PNA-FISH method to determine H. pylori clarithromycin resistance. In the retrospective study (n = 30 patients), full agreement between PNA-FISH and PCR-sequencing was observed. Compared to the reference method (culture followed by Etest), the specificity and sensitivity of PNA-FISH were 90.9% (95% confidence interval [CI], 57.1% to 99.5%) and 84.2% (95% CI, 59.5% to 95.8%), respectively. In the prospective cohort (n = 93 patients), 21 cases were positive by culture. For the patients harboring clarithromycin-resistant H. pylori, the method showed sensitivity of 80.0% (95% CI, 29.9% to 98.9%) and specificity of 93.8% (95% CI, 67.7% to 99.7%). These values likely represent underestimations, as some of the discrepant results corresponded to patients infected by more than one strain. PNA-FISH appears to be a simple, quick, and accurate method for detecting H. pylori clarithromycin resistance in paraffin-embedded biopsy specimens. It is also the only one of the methods assessed here that allows direct and specific visualization of this microorganism within the biopsy specimens, a characteristic that allowed the observation that cells of different H. pylori strains can subsist in very close proximity in the stomach. PMID:23596234

  16. Developing an Acidic Residue Reactive and Sulfoxide-Containing MS-Cleavable Homobifunctional Cross-Linker for Probing Protein–Protein Interactions

    PubMed Central

    2016-01-01

    Cross-linking mass spectrometry (XL-MS) has become a powerful strategy for defining protein–protein interactions and elucidating architectures of large protein complexes. However, one of the inherent challenges in MS analysis of cross-linked peptides is their unambiguous identification. To facilitate this process, we have previously developed a series of amine-reactive sulfoxide-containing MS-cleavable cross-linkers. These MS-cleavable reagents have allowed us to establish a common robust XL-MS workflow that enables fast and accurate identification of cross-linked peptides using multistage tandem mass spectrometry (MSn). Although amine-reactive reagents targeting lysine residues have been successful, it remains difficult to characterize protein interaction interfaces with little or no lysine residues. To expand the coverage of protein interaction regions, we present here the development of a new acidic residue-targeting sulfoxide-containing MS-cleavable homobifunctional cross-linker, dihydrazide sulfoxide (DHSO). We demonstrate that DHSO cross-linked peptides display the same predictable and characteristic fragmentation pattern during collision induced dissociation as amine-reactive sulfoxide-containing MS-cleavable cross-linked peptides, thus permitting their simplified analysis and unambiguous identification by MSn. Additionally, we show that DHSO can provide complementary data to amine-reactive reagents. Collectively, this work not only enlarges the range of the application of XL-MS approaches but also further demonstrates the robustness and applicability of sulfoxide-based MS-cleavability in conjunction with various cross-linking chemistries. PMID:27417384

  17. Photoluminescence characterization of single heterojunction quantum well structures

    NASA Astrophysics Data System (ADS)

    Aina, O.; Mattingly, M.; Juan, F. Y.; Bhattacharya, P. K.

    1987-01-01

    A photoluminescence emission band at 830 nm has been detected in single heterojunction quantum well structures (modulation-doped structures) in the range of 250-400 K. This emission band is observed neither in heterojunction structures without a two-dimensional electron gas (2DEG), nor in n(+) AlGaAs and GaAs. The intensity of the emission band increases as the mobility of the samples with 2DEG and shows excitonic behavior in its variation with incident laser excitation intensity. This photoluminescence emission was observed in samples grown by both molecular beam epitaxy and by organometallic vapor phase epitaxy. This effect may be useful as a rough identification of high quality, modulation-doped heterostructures.

  18. Photoluminescence from chemically exfoliated MoS2.

    PubMed

    Eda, Goki; Yamaguchi, Hisato; Voiry, Damien; Fujita, Takeshi; Chen, Mingwei; Chhowalla, Manish

    2011-12-14

    A two-dimensional crystal of molybdenum disulfide (MoS2) monolayer is a photoluminescent direct gap semiconductor in striking contrast to its bulk counterpart. Exfoliation of bulk MoS2 via Li intercalation is an attractive route to large-scale synthesis of monolayer crystals. However, this method results in loss of pristine semiconducting properties of MoS2 due to structural changes that occur during Li intercalation. Here, we report structural and electronic properties of chemically exfoliated MoS2. The metastable metallic phase that emerges from Li intercalation was found to dominate the properties of as-exfoliated material, but mild annealing leads to gradual restoration of the semiconducting phase. Above an annealing temperature of 300 °C, chemically exfoliated MoS2 exhibit prominent band gap photoluminescence, similar to mechanically exfoliated monolayers, indicating that their semiconducting properties are largely restored.

  19. Spatially resolved micro-photoluminescence imaging of porphyrin single crystals

    NASA Astrophysics Data System (ADS)

    Marin, Dawn M.; Castaneda, Jose; Kaushal, Meesha; Kaouk, Ghallia; Jones, Daniel S.; Walter, Michael G.

    2016-08-01

    We describe the collection of both time-resolved and steady-state micro-photoluminescence data from solution-grown single crystals of 5,15-bis(4-carbomethoxyphenyl)porphyrin (BCM2PP). Linking molecular orientation and structure with excited-state dynamics is crucial for engineering efficient organic solar cells, light-emitting diodes, and related molecular electronics. Photoluminescence features of single porphyrin crystals were imaged using a laser scanning confocal microscope equipped with time-correlated single photon counting (TCSPC). We show enhanced exciton lifetimes (τs1 = 2.6 ns) and stronger steady-state emission in crystalline BCM2PP samples relative to semicrystalline thin films (τs1 = 1.8 ns).

  20. Modulation of mixed-phase titania photoluminescence by oxygen adsorption

    SciTech Connect

    Pallotti, D.; Orabona, E.; Amoruso, S.; Maddalena, P.; Lettieri, S.

    2014-07-21

    We investigate the effect of oxygen (O{sub 2}) adsorption on photoluminescence properties of mixed-phase titania nanoparticle films deposited by femtosecond pulsed laser deposition, aiming to assess preliminary conclusions about the feasibility of opto-chemical sensing based on titania. We evidence that O{sub 2} produces opposite responses in rutile and anatase photoluminescence efficiency, highlighting interesting potentialities for future double-parametric optical sensing based on titania. The results evidence an important role of lattice oxygen atoms, suggesting that the standard Schottky barrier mechanism driving the response toward gas species in most used metal-oxide sensors (e.g., tin dioxide) is not the only active mechanism in titania.

  1. Supercollision cooling effects on the hot photoluminescence emission of graphene

    NASA Astrophysics Data System (ADS)

    Alencar, Thonimar V.; Malard, Leandro M.; de Paula, Ana M.

    2016-11-01

    We report on hot photoluminescence measurements that show the effects of acoustic phonon supercollision processes in the intensity of graphene light emission. We use a simple optical method to induce defects on single layer graphene in a controlled manner to study in detail the light emission dependence on the sample defect density. It is now well accepted that the graphene photoluminescence is due to black-body thermal emission from the quasi-equilibrium electrons at a temperature well above the lattice temperature. Our results show that as the sample defect density is increased the electrons relax energy more efficiently via acoustic phonon supercollision processes leading to lower electron temperatures and thus lower emission intensities. The calculated intensity decrease due to supercollision energy relaxation agrees well with the experimental data.

  2. Photoluminescence Imaging Characterization of Thin-Film InP

    SciTech Connect

    Johnston, Steve; Allende Motz, Alyssa; Moore, James; Zheng, Maxwell; Javey, Ali; Bermel, Peter

    2015-06-14

    Indium phosphide grown using a novel vapor-liquid-solid method is a promising low-cost material for III-V single-junction photovoltaics. In this work, we characterize the properties of these materials using photoluminescence (PL) imaging, time-resolved photoluminescence (TRPL), and microwave-reflection photoconductive decay (u-PCD). PL image data clearly shows the emergence of a self-similar dendritic growth network from nucleation sites, while zoomed-in images show grain structure and grain boundaries. Single photon TRPL data shows initial surface-dominated recombination, while two-photon excitation TRPL shows a lifetime of 10 ns. Bulk carrier lifetime may be as long as 35 ns as measured by u-PCD, which can be less sensitive to surface recombination.

  3. Preparation and photoluminescence study of mesoporous indium hydroxide nanorods

    SciTech Connect

    Li, Changyu; Lian, Suoyuan; Liu, Yang; Liu, Shouxin; Kang, Zhenhui

    2010-02-15

    Mesoporous indium hydroxide nanorods were successfully synthesized by a mild one-step one-pot method. The obtained samples were characterized by X-ray diffraction, transmission electron microscopy with selected area electron diffraction, N{sub 2} adsorption, ultraviolet-visible absorption and photoluminescence, respectively. Transmission electron microscopy showed that there were some pores in the samples, which were mainly composed of rod-like shapes with length of 300 nm and diameter of 90 nm. N{sub 2} adsorption/desorption measurements confirmed that the prepared powder was mesoporous with average pore diameter of 3.1 nm. The ultraviolet-visible absorption spectroscopy analysis indicated that the band gap energy of the samples was 5.15 eV. Photoluminescence spectrum showed that there were two strong emissions under ultraviolet light irradiation. The growth mechanism of indium hydroxide nanorods and the role of cetyltrimethyl ammonium bromide were also discussed.

  4. Photoluminescence from stain-etched polycrystalline Si thin films

    NASA Astrophysics Data System (ADS)

    Steckl, A. J.; Xu, J.; Mogul, H. C.

    1993-04-01

    Visible room-temperature photoluminescence has been observed from stain-etched polycrystalline Si thin films. Poly-Si thin films deposited on oxidized Si and quartz substrates became porous (PoSi) after stain-etching in a 1:3:5 solution of HF:HNO3:H2O. Under UV excitation, the stain-etched doped and undoped poly-Si films produce uniform orange-red (about 650 nm) luminescence very similar to that obtained from stain-etched crystalline Si substrates. Stained amorphous thin films did not exhibit photoluminescence. Luminescent patterns with sub-micrometer (about 0.6 micron) dimensions have been obtained for the first time from PoSi produced from poly-Si films.

  5. Recombination Behaviour at the Ultrathin Polypyrrole Film/Silicon Interface Investigated by In-situ Pulsed Photoluminescence

    NASA Astrophysics Data System (ADS)

    Intelmann, Carl Matthias; Hinrichs, Karsten; Syritski, Vitali; Yang, Florent; Rappich, Jörg

    2008-01-01

    We investigated the change in Si surface recombination behaviour during the electrodeposition of ultrathin polypyrrole (PPy) films onto Si surfaces by means of in-situ pulsed photoluminescence (PL) spectroscopy. The quenching of the band-gap related PL is lower (better passivation) when the electrodeposition is performed in a less acidic solution by use of potential pulse sequences. In-situ infrared spectroscopic ellipsometry (IR-SE) was applied for the first time to PPy electrodeposition. IR-SE and PL measurements confirm negligible formation of SiOx species at the Si/PPy interface although aqueous electrolytes were used.

  6. Nonlinear broadband photoluminescence of graphene induced by femtosecond laser irradiation

    SciTech Connect

    Liu, Wei-Tao; Wu, S.W.; Schuck, P.J.; Salmeron, Miquel; Shen, Y.R.; Wang, F.

    2010-07-01

    Upon femtosecond laser irradiation, a bright, broadband photoluminescence is observed from graphene at frequencies well above the excitation frequency. Analyses show that it arises from radiative recombination of a broad distribution of nonequilibrium electrons and holes, generated by rapid scattering between photoexcited carriers within tens of femtoseconds after the optical excitation. Its highly unusual characteristics come from the unique electronic and structural properties of graphene.

  7. Photoluminescence polarization of single InP quantum dots

    SciTech Connect

    Zwiller, Valery; Jarlskog, Linda; Pistol, Mats-Erik; Pryor, Craig; Castrillo, Pedro; Seifert, Werner; Samuelson, Lars

    2001-06-15

    The linear polarization dependence of photoluminescence emission was measured on single self-assembled InP quantum dots. The dots were obtained by Stranski-Krastanow growth on Ga{sub 0.5}In{sub 0.5}P. The highest-intensity emission occurred for light polarized parallel to the elongation of the dots in agreement with theoretical calculations. The excitation intensity was varied to obtain the polarization dependence of higher (state-filled) levels.

  8. Photoluminescence of ion-implanted GaN

    NASA Technical Reports Server (NTRS)

    Pankove, J. I.; Hutchby, J. A.

    1976-01-01

    Thirty-five elements were implanted in GaN. Their photoluminescence spectra were measured and compared to those of an unimplanted control sample. Most impurities emit a peak at about 2.15 eV. Mg, Zn, Cd, Ca, As, Hg, and Ag have more characteristic emissions. Zn provides the most efficient recombination center. A set of midgap states is generated during the damage-annealing treatment.

  9. Properties of Zn-doped GaN. I - Photoluminescence

    NASA Technical Reports Server (NTRS)

    Pankove, J. I.; Berkeyheiser, J. E.; Miller, E. A.

    1974-01-01

    It is shown that zinc in gallium nitride forms an efficient radiative center emitting blue light at 2.86 plus or minus 0.02 eV and acts as a deep acceptor that can render the crystal insulating. A systematic variation of growth conditions indicates that an optimization of the photoluminescence efficiency is possible. Under nonoptimal conditions lower photon energy emission is obtained.

  10. Enhanced Photoluminescence Properties of Carbon Dots by Doping with Europium.

    PubMed

    Chen, Yuan; Xu, Jiafu; Liu, Bitao; Li, Jiyun; Fang, Xiaomei; Xiong, Liqiong; Peng, Lingling; Han, Tao; Tu, Mingjing

    2016-04-01

    Europium (Eu) doped carbon dots (CDs) were synthesized via a rapid and simple microwave medi- ated method using polyethylene glycol (PEG) as a precursor, and characterized in detail. The results were that these as-prepared CDs showed a uniform and small particle size, and exhibit good pho- tostability and high photoluminescence quantum yields. Additionally, it also found that the doped Eu would change the fluorescence properties, which indicates potential applications in the field of biolabeling. PMID:27451699

  11. The unique probe selector: a comprehensive web service for probe design and oligonucleotide arrays

    PubMed Central

    Chen, Shu-Hwa; Lo, Chen-Zen; Tsai, Ming-Chi; Hsiung, Chao A; Lin, Chung-Yen

    2008-01-01

    Background Nucleic acid hybridization, a fundamental technique in molecular biology, can be modified into very effective and sensitive methods for detecting particular targets mixed with millions of non-target sequences. Therefore, avoiding cross-hybridization is the most crucial issue for developing diagnostic methods based on hybridization. Results To develop a probe with a high discriminating power, this study constructed a web service, the Unique Probe Selector (UPS), for customized probe design. The UPS service integrates a probe design mechanism and a scoring system for evaluating the performance of probe annealing and the uniqueness of a probe in a user-defined genetic background. Starting from an intuitive web interface, the UPS accepts a query with single or multiple sequences in fasta format. The best probe(s) for each sequence can be downloaded from result pages in a fasta or .csv format with a summary of probe characteristics. The option "Unique probe within group" selects the most unique probe for each target sequence with low probability to hybridize to the other sequences in the same submitted query. The option "Unique probe in the specific organism" devises probes for each submitted sequence to identify its target among selected genetic backgrounds based on Unigene. Conclusion The UPS evaluates probe-to-target hybridization under a user-defined condition in silico to ensure high-performance hybridization and minimizes the possibility of non-specific reactions. UPS has been applied to design human arrays for gene expression studies and to develop several small arrays of gene families that were inferred as molecular signatures of cancer typing/staging or pathogen signatures. Notably, UPS is freely accessible at . PMID:18315861

  12. Photoluminescence properties of S2 molecule trapped in Melanophlogite

    NASA Astrophysics Data System (ADS)

    Messina, Fabrizio; Todaro, Michela; Buscarino, Gianpiero; Vaccaro, Lavinia; Cannas, Marco; Gelardi, Franco M.

    2016-03-01

    We studied the photoluminescence properties of a sample of SiO2-clathrate Melanophlogite, a crystalline microporous material which is found in nature as a rare mineral. Upon β irradiation, the material displays an intense light emission under near-UV illumination. We studied in detail this optical activity by steady-state and time-resolved photoluminescence measurements as a function of temperature. The spectroscopic properties we find can be ascribed to a population of quasi-free molecules trapped within each of the two different types of cage available in the structure of this clathrate, although the spectroscopic properties of the guest molecules are affected by their interactions with the host matrix. Based on the available data, we attribute the observed photoluminescence to trapped S2 molecules, emitting from their excited 3Σ u - or 3Π u electronic states, depending on the cage they are trapped in and on temperature. Our results have an impact on the fundamental understanding of host-guest interactions characteristic of microporous systems such as clathrates. Indeed, the data highlight that even a relatively weak coupling between quasi-free S2 molecules and the two types of cages provided by the Melanophlogite host has a surprisingly complex influence on the optical properties of the guest.

  13. Mechanoresponsive change in photoluminescent color of rod-like liquid-crystalline compounds and control of molecular orientation on photoaligned layer

    NASA Astrophysics Data System (ADS)

    Kondo, Mizuho; Miura, Seiya; Okumoto, Kentaro; Hashimoto, Mayuko; Fukae, Ryohei; Kawatsuki, Nobuhiro

    2014-10-01

    In this paper, we reported novel liquid-crystalline luminophore that switches its photoluminescent color by mechanically grinding. Mechanochromic luminescence (MCL) is expected for mechanical sensor, cellular imaging, detection of microenvironmental changes, and optical memory. In this work, we focused on liquid-crystalline MCL compounds on alignment layer. Controlling the molecular alignment of MCL compounds with photoalignment layer have potential to succeed in functional MCL film such as polarized micropatterned MCL and directional detection of mechanical stimuli. Herein, we prepared asymmetric rodlike MCL compounds containing cyano- and pyridyl molecular terminal and explored their photoluminescence behavior under mechanical stimulus. The cyano terminated compound showed a nematic phase and tuned its photoluminescent color from green to yellow upon grinding, while the pyridyl-terminated compounds that show no mesophase changed its photoluminescent color from blue to green and reverted to its initial color by heating above its melting point. The cyano-terminated MCL was aligned along the orientation direction of photoalignment layer and pyridyl-terminated MCL exhibited uniaxial alignment when it coated on photoaligned film containing carboxylic acid.

  14. Development of a quantitative real-time nucleic acid sequence-based amplification assay with an internal control using molecular beacon probes for selective and sensitive detection of human rhinovirus serotypes.

    PubMed

    Sidoti, Francesca; Bergallo, Massimiliano; Terlizzi, Maria Elena; Piasentin Alessio, Elsa; Astegiano, Sara; Gasparini, Giorgio; Cavallo, Rossana

    2012-03-01

    Evidence demonstrating that human rhinovirus (HRV) disease is not exclusively limited to the upper airways and may cause lower respiratory complications, together with the frequency of HRV infections and the increasing number of immunocompromised patients underline the need for rapid and accurate diagnosis of HRV infections. In this study, we developed the first quantitative real-time nucleic acid sequence-based amplification assay with an internal control using molecular beacon probes for selective and sensitive detection of human rhinovirus serotypes. We described a simple method to accurately quantify RNA target by computing the time to positivity (TTP) values for HRV RNA. Quantification capacity was assessed by plotting these TTP values against the starting number of target molecules. By using this simple method, we have significantly increased the diagnostic accuracy, precision, and trueness of real-time NASBA assay. Specificity of the method was verified in both in silico and experimental studies. Moreover, for assessment of clinical reactivity of the assay, NASBA has been validated on bronchoalveolar lavage (BAL) specimens. Our quantitative NASBA assay was found to be very specific, accurate, and precise with high repeatability and reproducibility.

  15. Transformation of 17β-estradiol in humic acid solution by ε-MnO2 nanorods as probed by high-resolution mass spectrometry combined with (13)C labeling.

    PubMed

    Sun, Kai; Liang, Shangtao; Kang, Fuxing; Gao, Yanzheng; Huang, Qingguo

    2016-07-01

    Steroidal estrogens (SEs), widespread in aquatic systems, have a potential to disrupt the endocrine system of wildlife species and humans. In our experiments, the performance of ε-MnO2 nanorods in transforming 17β-estradiol (E2) was investigated, and the effect of humic acid (HA) on the reaction behaviors was systematically characterized. Reconfiguration of humic molecules was also investigated by high-performance size exclusion chromatography (HPSEC). Results indicated that ε-MnO2 nanomaterials ensured efficient removal of E2 from the aqueous solution. The presence of HA hindered the transformation of E2, while enhanced the cross-coupling between E2 and humic molecules. In particular, we used a mixture of un-labeled E2 and (13)C3-labeled E2 at a 1: 1 set ratio (w/w) to probe the reaction products via high-resolution mass spectrometry (HRMS). The combination of HRMS and (13)C3-labeling revealed the intermediate products including estrone (E1), and hydroxylated, quinone-like, and ring-opened species, as well as E2 dimer and trimer. More importantly, possible cross-coupling products between E2 and HA were also identified. A reaction mechanism including two-electron oxidation and single-electron oxidation was proposed. The applied analytical approach using HRMS along with (13)C3-labeling for reaction-product identification is crucial to understanding the role of HA in the transformation of SEs.

  16. Transformation of 17β-estradiol in humic acid solution by ε-MnO2 nanorods as probed by high-resolution mass spectrometry combined with (13)C labeling.

    PubMed

    Sun, Kai; Liang, Shangtao; Kang, Fuxing; Gao, Yanzheng; Huang, Qingguo

    2016-07-01

    Steroidal estrogens (SEs), widespread in aquatic systems, have a potential to disrupt the endocrine system of wildlife species and humans. In our experiments, the performance of ε-MnO2 nanorods in transforming 17β-estradiol (E2) was investigated, and the effect of humic acid (HA) on the reaction behaviors was systematically characterized. Reconfiguration of humic molecules was also investigated by high-performance size exclusion chromatography (HPSEC). Results indicated that ε-MnO2 nanomaterials ensured efficient removal of E2 from the aqueous solution. The presence of HA hindered the transformation of E2, while enhanced the cross-coupling between E2 and humic molecules. In particular, we used a mixture of un-labeled E2 and (13)C3-labeled E2 at a 1: 1 set ratio (w/w) to probe the reaction products via high-resolution mass spectrometry (HRMS). The combination of HRMS and (13)C3-labeling revealed the intermediate products including estrone (E1), and hydroxylated, quinone-like, and ring-opened species, as well as E2 dimer and trimer. More importantly, possible cross-coupling products between E2 and HA were also identified. A reaction mechanism including two-electron oxidation and single-electron oxidation was proposed. The applied analytical approach using HRMS along with (13)C3-labeling for reaction-product identification is crucial to understanding the role of HA in the transformation of SEs. PMID:27086077

  17. Raman and photoluminescence properties of type II GaSb/GaAs quantum dots on (001) Ge substrate

    NASA Astrophysics Data System (ADS)

    Zon; Poempool, Thanavorn; Kiravittaya, Suwit; Nuntawong, Noppadon; Sopitpan, Suwat; Thainoi, Supachok; Kanjanachuchai, Songphol; Ratanathammaphan, Somchai; Panyakeow, Somsak

    2016-07-01

    We investigate structural Raman and photoluminescence properties of type II GaSb/GaAs quantum dots (QDs) grown on (001) Ge substrate by molecular beam epitaxy. Array of self-assembled GaSb QDs having an areal density of ˜1.66 × 1010 dots/cm2 is obtained by a growth at relatively low substrate temperature (450 °C) on a GaAs surface segmented into anti-phase domains (APDs). Most of QDs form in one APD area. However, a few QDs can be observed at the APD boundaries. Raman spectroscopy is used to probe the strain in GaAs layer. Slight redshift of both LO and TO GaAs peaks are observed when GaSb QDs are buried into GaAs matrix. Optical properties of capped QDs are characterized by photoluminescence measurement at low temperatures (20 K and 30 K). Emission peaks of GaSb/GaAs QDs are found in the range of 1.0-1.3 eV at both temperatures. Slight redshift is observed when the laser excitation power is increased at 20 K while blueshift of QD peak is observed at 30 K. We attribute this abnormal behavior to the contribution of overlapped GaSb wetting layer peak in the PL emission as well as the feature of type II band structure. [Figure not available: see fulltext.

  18. Galileo Probe Battery System

    NASA Technical Reports Server (NTRS)

    Dagarin, B. P.; Taenaka, R. K.; Stofel, E. J.

    1997-01-01

    The conclusions of the Galileo probe battery system are: the battery performance met mission requirements with margin; extensive ground-based and flight tests of batteries prior to probe separation from orbiter provided good prediction of actual entry performance at Jupiter; and the Li-SO2 battery was an important choice for the probe's main power.

  19. Phenylboronic acid functionalized reduced graphene oxide based fluorescence nano sensor for glucose sensing.

    PubMed

    Basiruddin, S K; Swain, Sarat K

    2016-01-01

    Reduced graphene has emerged as promising tools for detection based application of biomolecules as it has high surface area with strong fluorescence quenching property. We have used the concept of fluorescent quenching property of reduced graphene oxide to the fluorescent probes which are close vicinity of its surface. In present work, we have synthesized fluorescent based nano-sensor consist of phenylboronic acid functionalized reduced graphene oxide (rGO-PBA) and di-ol modified fluorescent probe for detection of biologically important glucose molecules. This fluorescent graphene based nano-probe has been characterized by high resolution transmission electron microscope (HRTEM), Atomic force microscope (AFM), UV-visible, Photo-luminescence (PL) and Fourier transformed infrared (FT-IR) spectroscopy. Finally, using this PBA functionalized reduced GO based nano-sensor, we were able to detect glucose molecule in the range of 2 mg/mL to 75 mg/mL in aqueous solution of pH7.4.

  20. Use of a fiber optic probe for organic species determination

    DOEpatents

    Ekechukwu, Amy A.

    1996-01-01

    A fiber optic probe for remotely detecting the presence and concentration organic species in aqueous solutions. The probe includes a cylindrical housing with an organic species indicator, preferably diaminonaphthyl sulfonic acid adsorbed in a silica gel (DANS-modified gel), contained in the probe's distal end. The probe admits aqueous solutions to the probe interior for mixing within the DANS-modified gel. An optical fiber transmits light through the DANS-modified gel while the indicator reacts with organic species present in the solution, thereby shifting the location of the fluorescent peak. The altered light is reflected to a receiving fiber that carries the light to a spectrophotometer or other analysis device.