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Sample records for nucleobase analogue fret

  1. Studying Z-DNA and B- to Z-DNA transitions using a cytosine analogue FRET-pair.

    PubMed

    Dumat, Blaise; Larsen, Anders Foller; Wilhelmsson, L Marcus

    2016-06-20

    Herein, we report on the use of a tricyclic cytosine FRET pair, incorporated into DNA with different base pair separations, to study Z-DNA and B-Z DNA junctions. With its position inside the DNA structure, the FRET pair responds to a B- to Z-DNA transition with a distinct change in FRET efficiency for each donor/acceptor configuration allowing reliable structural probing. Moreover, we show how fluorescence spectroscopy and our cytosine analogues can be used to determine rate constants for the B- to Z-DNA transition mechanism. The modified cytosines have little influence on the transition and the FRET pair is thus an easily implemented and virtually non-perturbing fluorescence tool to study Z-DNA. This nucleobase analogue FRET pair represents a valuable addition to the limited number of fluorescence methods available to study Z-DNA and we suggest it will facilitate, for example, deciphering the B- to Z-DNA transition mechanism and investigating the interaction of DNA with Z-DNA binding proteins. PMID:26896804

  2. Studying Z-DNA and B- to Z-DNA transitions using a cytosine analogue FRET-pair

    PubMed Central

    Dumat, Blaise; Larsen, Anders Foller; Wilhelmsson, L. Marcus

    2016-01-01

    Herein, we report on the use of a tricyclic cytosine FRET pair, incorporated into DNA with different base pair separations, to study Z-DNA and B-Z DNA junctions. With its position inside the DNA structure, the FRET pair responds to a B- to Z-DNA transition with a distinct change in FRET efficiency for each donor/acceptor configuration allowing reliable structural probing. Moreover, we show how fluorescence spectroscopy and our cytosine analogues can be used to determine rate constants for the B- to Z-DNA transition mechanism. The modified cytosines have little influence on the transition and the FRET pair is thus an easily implemented and virtually non-perturbing fluorescence tool to study Z-DNA. This nucleobase analogue FRET pair represents a valuable addition to the limited number of fluorescence methods available to study Z-DNA and we suggest it will facilitate, for example, deciphering the B- to Z-DNA transition mechanism and investigating the interaction of DNA with Z-DNA binding proteins. PMID:26896804

  3. Gas-phase lifetimes of nucleobase analogues by picosecond pumpionization and streak techniques.

    PubMed

    Blaser, Susan; Frey, Hans-Martin; Heid, Cornelia G; Leutwyler, Samuel

    2014-01-01

    The picosecond (ps) timescale is relevant for the investigation of many molecular dynamical processes such as fluorescence, nonradiative relaxation, intramolecular vibrational relaxation, molecular rotation and intermolecular energy transfer, to name a few. While investigations of ultrafast (femtosecond) processes of biological molecules, e.g. nucleobases and their analogues in the gas phase are available, there are few investigations on the ps time scale. We have constructed a ps pump-ionization setup and a ps streak camera fluorescence apparatus for the determination of lifetimes of supersonic jet-cooled and isolated molecules and clusters. The ps pump-ionization setup was used to determine the lifetimes of the nucleobase analogue 2-aminopurine (2AP) and of two 2AP˙(H2O)n water cluster isomers with n=1 and 2. Their lifetimes lie between 150 ps and 3 ns and are strongly cluster-size dependent. The ps streak camera setup was used to determine accurate fluorescence lifetimes of the uracil analogue 2-pyridone (2PY), its self-dimer (2PY)2, two isomers of its trimer (2PY)3 and its tetramer (2PY)4, which lie in the 7-12 ns range. PMID:24983611

  4. Reactions of β-Propiolactone with Nucleobase Analogues, Nucleosides, and Peptides

    PubMed Central

    Uittenbogaard, Joost P.; Zomer, Bert; Hoogerhout, Peter; Metz, Bernard

    2011-01-01

    β-Propiolactone is often applied for inactivation of viruses and preparation of viral vaccines. However, the exact nature of the reactions of β-propiolactone with viral components is largely unknown. The purpose of the current study was to elucidate the chemical modifications occurring on nucleotides and amino acid residues caused by β-propiolactone. Therefore, a set of nucleobase analogues was treated with β-propiolactone, and reaction products were identified and quantified. NMR revealed at least one modification in either deoxyguanosine, deoxyadenosine, or cytidine after treatment with β-propiolactone. However, no reaction products were found from thymidine and uracil. The most reactive sides of the nucleobase analogues and nucleosides were identified by NMR. Furthermore, a series of synthetic peptides was used to determine the conversion of reactive amino acid residues by liquid chromatography-mass spectrometry. β-Propiolactone was shown to react with nine different amino acid residues. The most reactive residues are cysteine, methionine, and histidine and, to a lesser degree, aspartic acid, glutamic acid, tyrosine, lysine, serine, and threonine. Remarkably, cystine residues (disulfide groups) do not react with β-propiolactone. In addition, no reaction was observed for β-propiolactone with asparagine, glutamine, and tryptophan residues. β-Propiolactone modifies proteins to a larger extent than expected from current literature. In conclusion, the study determined the reactivity of β-propiolactone with nucleobase analogues, nucleosides, and amino acid residues and elucidated the chemical structures of the reaction products. The study provides detailed knowledge on the chemistry of β-propiolactone inactivation of viruses. PMID:21868382

  5. Asymmetric Hydrogenation of α-Purine Nucleobase-Substituted Acrylates with Rhodium Diphosphine Complexes: Access to Tenofovir Analogues.

    PubMed

    Sun, Huan-Li; Chen, Fei; Xie, Ming-Sheng; Guo, Hai-Ming; Qu, Gui-Rong; He, Yan-Mei; Fan, Qing-Hua

    2016-05-01

    The first asymmetric hydrogenation of α-purine nucleobase-substituted α,β-unsaturated esters, catalyzed by a chiral rhodium (R)-Synphos catalyst, has been developed. A wide range of mono- and disubstituted acrylates were successfully hydrogenated under very mild conditions in high yields with good to excellent enantioselectivities (up to 99% ee). This method provides a convenient approach to the synthesis of a new kind of optically pure acyclic nucleoside and Tenofovir analogues. PMID:27112983

  6. A straightforward entry to chiral carbocyclic nucleoside analogues via the enantioselective [3+2] cycloaddition of α-nucleobase substituted acrylates.

    PubMed

    Xie, Ming-Sheng; Wang, Yong; Li, Jian-Ping; Du, Cong; Zhang, Yan-Yan; Hao, Er-Jun; Zhang, Yi-Ming; Qu, Gui-Rong; Guo, Hai-Ming

    2015-08-11

    A straightforward entry to chiral carbocyclic nucleoside analogues has been realized via the enantioselective [3+2] cycloaddition of α-nucleobase substituted acrylates to vinyl cyclopropanes for the first time. With Pd2(dba)3-L5 as the catalyst, carbocyclic purine, uracil, and thymine nucleoside analogues with quaternary stereocenters were obtained in excellent yields (up to 99% yield) and good enantioselectivities (up to 92% ee). PMID:26145719

  7. Ultrafast Dynamics of a Nucleobase Analogue Illuminated by a Short Intense X-ray Free Electron Laser Pulse

    NASA Astrophysics Data System (ADS)

    Nagaya, K.; Motomura, K.; Kukk, E.; Fukuzawa, H.; Wada, S.; Tachibana, T.; Ito, Y.; Mondal, S.; Sakai, T.; Matsunami, K.; Koga, R.; Ohmura, S.; Takahashi, Y.; Kanno, M.; Rudenko, A.; Nicolas, C.; Liu, X.-J.; Zhang, Y.; Chen, J.; Anand, M.; Jiang, Y. H.; Kim, D.-E.; Tono, K.; Yabashi, M.; Kono, H.; Miron, C.; Yao, M.; Ueda, K.

    2016-04-01

    Understanding x-ray radiation damage is a crucial issue for both medical applications of x rays and x-ray free-electron-laser (XFEL) science aimed at molecular imaging. Decrypting the charge and fragmentation dynamics of nucleobases, the smallest units of a macro-biomolecule, contributes to a bottom-up understanding of the damage via cascades of phenomena following x-ray exposure. We investigate experimentally and by numerical simulations the ultrafast radiation damage induced on a nucleobase analogue (5-iodouracil) by an ultrashort (10 fs) high-intensity radiation pulse generated by XFEL at SPring-8 Angstrom Compact free electron Laser (SACLA). The present study elucidates a plausible underlying radiosensitizing mechanism of 5-iodouracil. This mechanism is independent of the exact composition of 5-iodouracil and thus relevant to other such radiosensitizers. Furthermore, we found that despite a rapid increase of the net molecular charge in the presence of iodine, and of the ultrafast release of hydrogen, the other atoms are almost frozen within the 10-fs duration of the exposure. This validates single-shot molecular imaging as a consistent approach, provided the radiation pulse used is brief enough.

  8. Functionalized Solid Electrodes for Electrochemical Biosensing of Purine Nucleobases and Their Analogues: A Review

    PubMed Central

    Sharma, Vimal Kumar; Jelen, Frantisek; Trnkova, Libuse

    2015-01-01

    Interest in electrochemical analysis of purine nucleobases and few other important purine derivatives has been growing rapidly. Over the period of the past decade, the design of electrochemical biosensors has been focused on achieving high sensitivity and efficiency. The range of existing electrochemical methods with carbon electrode displays the highest rate in the development of biosensors. Moreover, modification of electrode surfaces based on nanomaterials is frequently used due to their extraordinary conductivity and surface to volume ratio. Different strategies for modifying electrode surfaces facilitate electron transport between the electrode surface and biomolecules, including DNA, oligonucleotides and their components. This review aims to summarize recent developments in the electrochemical analysis of purine derivatives, as well as discuss different applications. PMID:25594595

  9. Bicyclic and Tricyclic "Expanded" Nucleobase Analogues of Sofosbuvir: New Scaffolds for Hepatitis C Therapies.

    PubMed

    Chen, Zhe; Jochmans, Dirk; Ku, Therese; Paeshuyse, Jan; Neyts, Johan; Seley-Radtke, Katherine L

    2015-08-14

    Given the impressive success of Gilead's Sofosbuvir, many laboratories, including ours, have explored the unique 2'-sugar modification (2'-Me, 2'-F) of nucleoside analogues in the hopes of exploiting the biological activity that this unique modification has imparted to the nucleoside scaffold. In that regard, we have combined our tricyclic "expanded" purine base motif with the 2'-Me, 2'-F sugar modification. Although the synthesis of these complex molecules proved to be nontrivial, with the best results coming from a linear approach, the overall strategy resulted in highly promising biological results for several of the target compounds, including their corresponding McGuigan ProTides. Modest activity against HCV was observed with inhibitory concentrations of as low as 20 μM. PMID:27624884

  10. Inhibition of Siderophore Biosynthesis in Mycobacterium tuberculosis with Nucleoside Bisubstrate Analogues: Structure–Activity Relationships of the Nucleobase Domain of 5′-O-[N-(Salicyl)sulfamoyl]adenosine

    PubMed Central

    Neres, João; Labello, Nicholas P.; Somu, Ravindranadh V.; Boshoff, Helena I.; Wilson, Daniel J.; Vannada, Jagadeshwar; Chen, Liqiang; Barry, Clifton E.; Bennett, Eric M.; Aldrich, Courtney C.

    2009-01-01

    5′-O-[N-(salicyl)sulfamoyl]adenosine (Sal-AMS) is a prototype for a new class of antitubercular agents that inhibit the aryl acid adenylating enzyme (AAAE) known as MbtA involved in biosynthesis of the mycobactins. Herein, we report the structure-based design, synthesis, biochemical, and biological evaluation of a comprehensive and systematic series of analogues, exploring the structure–activity relationship of the purine nucleobase domain of Sal-AMS. Significantly, 2-phenyl-Sal-AMS derivative 26 exhibited exceptionally potent antitubercular activity with an MIC99 under iron-deficient conditions of 0.049 µM while the N-6-cyclopropyl-Sal-AMS 16 led to improved potency and to a 64-enhancement in activity under iron-deficient conditions relative to iron-replete conditions, a phenotype concordant with the designed mechanism of action. The most potent MbtA inhibitors disclosed here display in vitro antitubercular activity superior to most current first line TB drugs, and these compounds are also expected to be useful against a wide range of pathogens that require aryl-capped siderphores for virulence. PMID:18690677

  11. Microhydration of Deprotonated Nucleobases

    NASA Astrophysics Data System (ADS)

    Wincel, Henryk

    2016-05-01

    Hydration reactions of deprotonated nucleobases (uracil, thymine, 5-fluorouracil,2-thiouracil, cytosine, adenine, and hypoxanthine) produced by electrospray have been experimentally studied in the gas phase at 10 mbar using a pulsed ion-beam high-pressure mass spectrometer. The thermochemical data, ΔH o , ΔS o , and ΔG o , for the monohydrated systems were determined. The hydration enthalpies were found to be similar for all studied systems and varied between 39.4 and 44.8 kJ/mol. A linear correlation was found between water binding energies in the hydrated complexes and the corresponding acidities of the most acidic site of nucleobases. The structural and energetic aspects of the precursors for the hydrated complexes are discussed in conjunction with available literature data.

  12. Microhydration of Deprotonated Nucleobases

    NASA Astrophysics Data System (ADS)

    Wincel, Henryk

    2016-08-01

    Hydration reactions of deprotonated nucleobases (uracil, thymine, 5-fluorouracil,2-thiouracil, cytosine, adenine, and hypoxanthine) produced by electrospray have been experimentally studied in the gas phase at 10 mbar using a pulsed ion-beam high-pressure mass spectrometer. The thermochemical data, ΔH o , ΔS o , and ΔG o , for the monohydrated systems were determined. The hydration enthalpies were found to be similar for all studied systems and varied between 39.4 and 44.8 kJ/mol. A linear correlation was found between water binding energies in the hydrated complexes and the corresponding acidities of the most acidic site of nucleobases. The structural and energetic aspects of the precursors for the hydrated complexes are discussed in conjunction with available literature data.

  13. Fretting in aircraft turbine engines

    NASA Technical Reports Server (NTRS)

    Johnson, R. L.; Bill, R. C.

    1974-01-01

    The problem of fretting in aircraft turbine engines is discussed. Critical fretting can occur on fan, compressor, and turbine blade mountings, as well as on splines, rolling element bearing races, and secondary sealing elements of face type seals. Structural fatigue failures have been shown to occur at fretted areas on component parts. Methods used by designers to reduce the effects of fretting are given.

  14. Extraterrestrial Nucleobases in Carbonaceous Chondrites

    NASA Astrophysics Data System (ADS)

    Martins, Z.; Botta, O.; Fogel, M.; Sephton, M.; Glavin, D.; Watson, J.; Dworkin, J.; Schwartz, A.; Ehrenfreund, P.

    Nucleobases in Carbonaceous Chondrites Z. Martins (1), O. Botta (2), M. L. Fogel (3), M. A. Sephton (4), D. P. Glavin (2), J. S. Watson (5), J. P. Dworkin (2), A. W. Schwartz (6) and P. Ehrenfreund (1,6). (1) Astrobiology Laboratory, Leiden Institute of Chemistry, Leiden, The Netherlands, (2) NASA Goddard Space Flight Center, Goddard Center for Astrobiology, Greenbelt, MD, USA, (3) GL, Carnegie Institution of Washington, Washington DC, USA, (4) Impacts and Astromaterials Research Centre, Department of Earth Science and Engineering, South Kensington Campus, Imperial College, London, UK, (5) Planetary and Space Sciences Research Institute, The Open University, Walton Hall, Milton Keynes, UK, (6) Radboud University Nijmegen, Nijmegen, The Netherlands. E-mail: z.martins@chem.leidenuniv.nl/Phone:+31715274440 Nucleobases are crucial compounds in terrestrial biochemistry, because they are key components of DNA and RNA. Carbonaceous meteorites have been analyzed for nucleobases by different research groups [1-5]. However, significant quantitative and qualitative differences were observed, leading to the controversial about the origin of these nucleobases. In order to establish the origin of these compounds in carbonaceous chondrites and to assess the plausibility of their exogenous delivery to the early Earth, we have performed formic acid extraction of samples of the Murchison meteorite [6], followed by an extensive purification procedure, analysis and quantification by high-performance liquid chromatography with UV absorption detection and gas chromatography-mass spectrometry. Our results were qualitatively consistent with previous results [3, 4], but showed significant quantitative differences. Compound specific carbon isotope values were obtained, using gas chromatography-combustion- isotope ratio mass spectrometry. A soil sample collected in the proximity of the Murchison meteorite fall site was subjected to the same extraction, purification and analysis procedure

  15. Synthesis and fluorescence characteristics of ATP-based FRET probes.

    PubMed

    Hardt, Norman; Hacker, Stephan M; Marx, Andreas

    2013-12-28

    Adenosine triphosphate (ATP) analogues labelled with two dyes suitable for undergoing Förster Resonance Energy Transfer (FRET) have the potential to be valuable tools to continuously study the enzymatic activity of ATP consuming enzymes. Here, we present a synthesis strategy that allows obtaining these ATP analogues in a straight-forward manner. Earlier studies indicate that modifying ATP at the O2'- and the γ-position is a very promising starting point for the design of these probes. We synthesized probes modified with five different combinations of dyes attached to these positions and investigated their fluorescence characteristics in the non-cleaved state as well as after enzymatic hydrolysis. All presented probes largely change their fluorescence characteristics upon cleavage. They include ratiometric FRET probes as well as dark quenched analogues. For typical in vitro applications a combination of the sulfonated polymethine dyes Sulfo-Cy3 and Sulfo-Cy5 seems to be most promising due to their excellent solubility in aqueous buffer and a large change of fluorescence characteristics upon cleavage. For this combination of dyes we also synthesized analogues modified at the γ- and the C2- or the O3'-position, respectively, as these attachment sites are also well accepted by certain ATP consuming enzymes. These analogues show comparably large changes in fluorescence characteristics. Overall, we present new ATP-based FRET probes that have the potential to enable monitoring the enzymatic activity of ATP consuming enzymes. PMID:24173528

  16. Fretting of AISI 9310 and selected fretting resistant surface treatments

    NASA Technical Reports Server (NTRS)

    Bill, R. C.

    1977-01-01

    Fretting wear experiments were conducted with uncoated AISI 9310 mating surfaces, and with combinations incorporating a selected coating to one of the mating surfaces. Wear measurements and SEM observations indicated that surface fatigue, as made evident by spallation and surface crack formation, is an important mechanism in promoting fretting wear to uncoated 9310. Increasing humidity resulted in accelerated fretting, and a very noticeable difference in nature of the fretting debris. Of the coatings evaluated, aluminum bronze with a polyester additive was most effective at reducing wear and minimizing fretting damage to the mating uncoated surface, by means of a selflubricating film that developed on the fretting surfaces. Chromium plate performed as an effective protective coating, itself resisting fretting and not accelerating damage to the uncoated surface.

  17. Fretting of AISI 9310 and selected fretting resistant surface treatments

    NASA Technical Reports Server (NTRS)

    Bill, R. C.

    1977-01-01

    Fretting wear experiments were conducted with uncoated AISI 9310 mating surfaces, and with combinations incorporating a selected coating to one of the mating surfaces. Wear measurements and SEM observations indicated that surface fatigue, as made evident by spallation and surface crack formation, is an important mechanism in promoting fretting wear to uncoated 9310. Increasing humidity resulted in accelerated fretting, and a very noticeable difference in nature of the fretting debris. Of the coatings evaluated, alumimum bronze with a polyester additive was most effective at reducing wear and minimizing fretting damage to the mating uncoated surface, by means of a self-lubricating film that developed on the fretting surfaces. Chromium plate performed as an effective protective coating, itself resisting fretting and not accelerating damage to the uncoated surface.

  18. Spectroscopy of Isolated Prebiotic Nucleobases

    NASA Technical Reports Server (NTRS)

    Svadlenak, Nathan; Callahan, Michael P.; Ligare, Marshall; Gulian, Lisa; Gengeliczki, Zsolt; Nachtigallova, Dana; Hobza, Pavel; deVries, Mattanjah

    2011-01-01

    We use multiphoton ionization and double resonance spectroscopy to study the excited state dynamics of biologically relevant molecules as well as prebiotic nucleobases, isolated in the gas phase. Molecules that are biologically relevant to life today tend to exhibit short excited state lifetimes compared to similar but non-biologically relevant analogs. The mechanism is internal conversion, which may help protect the biologically active molecules from UV damage. This process is governed by conical intersections that depend very strongly on molecular structure. Therefore we have studied purines and pyrimidines with systematic variations of structure, including substitutions, tautomeric forms, and cluster structures that represent different base pair binding motifs. These structural variations also include possible alternate base pairs that may shed light on prebiotic chemistry. With this in mind we have begun to probe the ultrafast dynamics of molecules that exhibit very short excited states and search for evidence of internal conversions.

  19. FRET and mechanobiology

    PubMed Central

    2009-01-01

    Since the development of green fluorescent protein (GFP) and other fluorescent proteins (FPs) with distinct colors, genetically-encoded probes and biosensors have been widely applied to visualize the molecular localization and activities in live cells. In particular, biosensors based on fluorescence resonance energy transfer (FRET) have significantly advanced our understanding of the dynamic molecular hierarchy at subcellular levels. These biosensors have also been extensively applied in recent years to study how cells perceive the mechanical environment and transmit it into intracellular molecular signals (i.e. mechanotransduction). In this review, we will first provide a brief introduction of the recent development of FPs. Different FRET biosensors based on FPs will then be described. The last part of the review will be dedicated to the introduction of examples applying FRET biosensors to visualize mechanotransduction in live cells. In summary, the integration of FRET technology and the different cutting-edge mechanical stimulation systems can provide powerful tools to allow the elucidation of the mechanisms regulating mechanobiology at cellular and molecular levels in normal and pathophysiological conditions. PMID:20016756

  20. Depolarized FRET (depolFRET) on the cell surface: FRET control by photoselection.

    PubMed

    Bene, László; Gogolák, Péter; Ungvári, Tamás; Bagdány, Miklós; Nagy, István; Damjanovich, László

    2016-02-01

    Sensitivity of FRET in hetero- and homo-FRET systems on the photoselected orientation distribution of donors has been proven by using polarized and depolarized light for excitation. FRET as well as donor and acceptor anisotropies have been simultaneously measured in a dual emission-polarization scheme realized in a conventional flow cytometer by using single laser excitation and applying fluorophore-conjugated mAbs against the MHCI and MHCII cell surface receptors. Depolarization of the originally polarized light have been achieved by using crystal depolarizers based on Cornu's principle, a quarter-wave plate for circular polarization, and a parallel beam splitter acting as a diagonal-polarizer for dual-polarization excitation. Simultaneous analysis of intensity-based FRET efficiency and acceptor depolarization equivocally report that depolarization of light may increase FRET in an amount depending on the acceptor-to-donor concentration ratio. Acceptor depolarization turned to be more sensitive to FRET than donor hyper-polarization and even than intensity-based FRET efficiency. It can be used as a sensitive tool for monitoring changes in the dynamics of the donor-acceptor pairs. The basic observations of FRET enhancement and increased acceptor depolarization obtained for hetero-FRET are paralleled by analog observations of homo-FRET enhancements under depolarized excitation. In terms of the orientation factor for FRET, the FRET enhancements on depolarization in the condition of the macroscopically isotropic orientation distributions such as those of the cell surface bound fluorophores report on the presence of local orientation mismatches of the donor and acceptor preventing the optimal FRET in the polarized case, which may be eliminated by the excitation depolarization. A theory of fluorescence anisotropy for depolarized excitation is also presented. PMID:26657258

  1. Photoelectron Spectroscopy of Hexachloroplatinate-Nucleobase Complexes: Nucleobase Excited State Decay Observed via Delayed Electron Emission

    SciTech Connect

    Sen, Ananya; Matthews, Edward M.; Hou, Gao-Lei; Wang, Xue B.; Dessent, Caroline

    2015-11-14

    We report low-temperature photoelectron spectra of isolated gas-phase complexes of the hexachloroplatinate dianion bound to the nucleobases uracil, thymine, cytosine and adenine. The spectra display well-resolved, distinct peaks that are consistent with complexes where the hexachloroplatinate dianion is largely intact. Adiabatic electron detachment energies for the hexachloroplatinate-nucleobase complexes are measured as 2.26-2.36 eV. The magnitudes of the repulsive Coulomb barriers (RCBs) of the complexes are all ~1.7 eV, values that are lower than the RCB of the uncomplexed PtCl6 2- dianion as a result of charge solvation by the nucleobases. In addition to the resolved spectral features, broad featureless bands indicative of delayed electron detachment are observed in the 193 nm photoelectron spectra of the four clusters. The 266 nm spectra of the PtCl6 2-∙thymine and PtCl6 2-∙adenine complexes also display very prominent delayed electron emission bands. These results mirror recent results on the related Pt(CN)4 2-∙nucleobase complexes [Sen et al, J. Phys. Chem. B, 119, 11626, 2015]. The observation of delayed electron emission bands in the PtCl6 2-∙nucleobase spectra obtained in this work, as for the previously studied Pt(CN)4 2-∙nucleobase complexes, is attributed to onephoton excitation of nucleobase-centred excited states that can effectively couple to the electron detachment continuum, producing strong electron detachment. Moreover, the selective, strong excitation of the delayed emission bands in the 266 nm spectra is linked to fundamental differences in the individual nucleobase photophysics at this excitation energy. This strongly supports our previous suggestion that the dianion within these clusters can be viewed as a “dynamic tag” which has the propensity to emit electrons when the attached nucleobase decays over a timescale long enough to allow autodetachment.

  2. Mechanics of fretting fatigue

    NASA Astrophysics Data System (ADS)

    Hills, D. A.

    1994-06-01

    Several aspects of the mechanics of cracks originating at sites of fretting are considered. It is argued that the problem may be distilled into three separate parts: the contact problem itself in full or partial slip, the initiation of a crack from a surface suffering severe distress, and the propagation of a crack under combined contact and bulk loading. The first of these may be solved by either a classical or numerical means, while the last merely requires the careful use of fracture mechanics. However, it is the second element which remains elusive to quantify, and the influence of the intrinsic length scales in the problem, including contact length, surface roughness and amplitude of relative tangential displacement on initiation conditions, is discussed and explored.

  3. Engineering Genetically Encoded FRET Sensors

    PubMed Central

    Lindenburg, Laurens; Merkx, Maarten

    2014-01-01

    Förster Resonance Energy Transfer (FRET) between two fluorescent proteins can be exploited to create fully genetically encoded and thus subcellularly targetable sensors. FRET sensors report changes in energy transfer between a donor and an acceptor fluorescent protein that occur when an attached sensor domain undergoes a change in conformation in response to ligand binding. The design of sensitive FRET sensors remains challenging as there are few generally applicable design rules and each sensor must be optimized anew. In this review we discuss various strategies that address this shortcoming, including rational design approaches that exploit self-associating fluorescent domains and the directed evolution of FRET sensors using high-throughput screening. PMID:24991940

  4. Photoelectron spectroscopy of hexachloroplatinate-nucleobase complexes: Nucleobase excited state decay observed via delayed electron emission

    SciTech Connect

    Sen, Ananya; Matthews, Edward M.; Dessent, Caroline E. H. E-mail: xuebin.wang@pnnl.gov; Hou, Gao-Lei; Wang, Xue-Bin E-mail: xuebin.wang@pnnl.gov

    2015-11-14

    We report low-temperature photoelectron spectra of isolated gas-phase complexes of the hexachloroplatinate dianion bound to the nucleobases uracil, thymine, cytosine, and adenine. The spectra display well-resolved, distinct peaks that are consistent with complexes where the hexachloroplatinate dianion is largely intact. Adiabatic electron detachment energies for the hexachloroplatinate-nucleobase complexes are measured as 2.26-2.36 eV. The magnitudes of the repulsive Coulomb barriers (RCBs) of the complexes are all ∼1.7 eV, values that are lower than the RCB of the uncomplexed PtCl{sub 6}{sup 2−} dianion as a result of charge solvation by the nucleobases. In addition to the resolved spectral features, broad featureless bands indicative of delayed electron detachment are observed in the 193 nm photoelectron spectra of the four clusters. The 266 nm spectra of the PtCl{sub 6}{sup 2−} ⋅ thymine and PtCl{sub 6}{sup 2−} ⋅ adenine complexes also display very prominent delayed electron emission bands. These results mirror recent results on the related Pt(CN){sub 4}{sup 2−} ⋅ nucleobase complexes [A. Sen et al., J. Phys. Chem. B 119, 11626 (2015)]. The observation of delayed electron emission bands in the PtCl{sub 6}{sup 2−} ⋅ nucleobase spectra obtained in this work, as for the previously studied Pt(CN){sub 4}{sup 2−} ⋅ nucleobase complexes, is attributed to one-photon excitation of nucleobase-centred excited states that can effectively couple to the electron detachment continuum, producing strong electron detachment. Moreover, the selective, strong excitation of the delayed emission bands in the 266 nm spectra is linked to fundamental differences in the individual nucleobase photophysics at this excitation energy. This strongly supports our previous suggestion that the dianion within these clusters can be viewed as a “dynamic tag” which has the propensity to emit electrons when the attached nucleobase decays over a time scale long enough to

  5. Communication: Photoactivation of nucleobase bound platinum(II) metal complexes: probing the influence of the nucleobase.

    PubMed

    Sen, Ananya; Dessent, Caroline E H

    2014-12-28

    We present UV laser action spectra (220-300 nm) of isolated nucleobase-bound Pt(II)(CN)4(2-) complexes, i.e., Pt(CN)4(2-)⋅M, where M = uracil, thymine, cytosine, and adenine. These metal complex-nucleobase clusters represent model systems for identifying the fundamental photophysical and photochemical processes occurring in photodynamic platinum (II) drug therapies that target DNA. This is the first study to explore the specific role of the nucleobase in the photophysics of the aggregate complex. Each of the complexes studied displays a broadly similar absorption spectra, with a strong λmax ∼ 4.7 eV absorption band (nucleobase localized chromophore) and a subsequent increase in the absorption intensity towards higher spectral-energy (Pt(CN)4(2-) localized chromophore). However, strikingly different band widths are observed across the series of complexes, decreasing in the order Pt(CN)4(2-)⋅Thymine > Pt(CN)4(2-)⋅Uracil > Pt(CN)4(2-)⋅Adenine > Pt(CN)4(2-)⋅Cytosine. Changes in the bandwidth of the ∼4.7 eV band are accompanied by distinctive changes in the photofragment product ions observed following photoexcitation, with the narrower-bandwidth complexes showing a greater propensity to decay via electron detachment decay. We discuss these observations in the context of the distinctive nucleobase-dependent excited state lifetimes. PMID:25554122

  6. Carbonaceous Meteorites Contain a Wide Range of Extraterrestrial Nucleobases

    NASA Technical Reports Server (NTRS)

    Callahan, Michael P.; Smith, Karen E.; Cleaves, H. James, II; Ruzicka, Josef; Stern, Jennifer C.; Glavin, Daniel P.; House, Christopher H.; Dworkin, Jason P.

    2011-01-01

    All terrestrial organisms depend on nucleic acids (RNA and DNA), which use pyrimidine and purine nucleobases to encode genetic information. Carbon-rich meteorites may have been important sources of organic compounds required for the emergence of life on the early Earth; however, the origin and formation of nuc1eobases in meteorites has been debated for over 50 y. So far, the few nuc1eobases reported in meteorites are biologically common and lacked the structural diversity typical of other indigenous meteoritic organics. Here, we investigated the abundance and distribution of nucleobases and nucleobase analogs in formic acid extracts of 12 different meteorites by liquid chromatography-mass spectrometry. The Murchison and Lonewolf Nunataks 94102 meteorites contained a diverse suite of nucleobases, which included three unusual and terrestrially rare nucleobase analogs; purine, 2,6-diminopurine, and 6,8-diaminopurine. In a parallel experiment, we found an identical suite of nucleobases and nucleobase analogs generated in reactions of ammonium cyanide. Additionally, these nucleobase analoge were not detected above our parts-per-billion detection limits in any of the procedural blanks, control samples, a terrestrial soil sample, and an Antarctic ice sample. Our results demonstrate that the purines detected in meteorites are consistent with products of ammonium cyanide chemistry, which provides a plausible mechanism for their synthesis in the asteroid parent bodies, and strongly supports an extraterrestrial origin. The discovery of new nucleobase analogs in meteorites also expands the prebiotic molecular inventory available for constructing the first genetic molecules.

  7. FRET enhanced fluorescent nanodiamonds.

    PubMed

    Fudala, Rafal; Raut, Sangram; Maliwal, Badri P; Zerda, T W; Gryczynski, Ignacy; Simanek, Eric; Borejdo, Julian; Rich, Ryan; Akopova, Irina; Gryczynski, Zygmunt

    2014-01-01

    Fluorescent nanodiamonds (FNDs) are one of the new and very promising biocompatible nanomaterials that can be used both as a fluorescence imaging agent and a highly versatile platform for controlled functionalization to target and deliver a wide spectrum of therapeutic agents. Among the remarkable fluorescence properties are excellent photostability, emission between 600-700nm, quantum yield of 1 and moderately long fluorescence lifetimes. However the low absorption cross section of fluorescent (N-V)(-) centers limits FNDs' brightness. In this work we show that an approach based on the Forster resonance energy transfer (FRET) may significantly enhance the fluorescence signal observed from a single ND. We demonstrate that organic dyes (fluorophores) attached to the FND surface can efficiently transfer the excitation energy to (N-V)(-) centers. Multiple dyes positioned in close proximity to the ND facile surface may serve as harvesting antennas transferring excitation energy to the fluorescent centers. We propose that, with the help of some of the functional groups present on the FND surface, we can either directly link flurophores or use scalable dendrimer chemistry to position many organic dyes at a calibrated distance. Also, the remaining multiple functional groups will be still available for particle targeting and drug delivery. This opens a new way for designing a new type of theranostics particles of ultrahigh brightness, high photostability, specific targeting, and high capacity for drug delivery. PMID:22394126

  8. Oxidation of DNA: damage to nucleobases.

    PubMed

    Kanvah, Sriram; Joseph, Joshy; Schuster, Gary B; Barnett, Robert N; Cleveland, Charles L; Landman, Uzi

    2010-02-16

    All organisms store the information necessary to maintain life in their DNA. Any process that damages DNA, causing a loss or corruption of that information, jeopardizes the viability of the organism. One-electron oxidation is such a process. In this Account, we address three of the central features of one-electron oxidation of DNA: (i) the migration of the radical cation away from the site of its formation; (ii) the electronic and structural factors that determine the nucleobases at which irreversible reactions most readily occur; (iii) the mechanism of reaction for nucleobase radical cations. The loss of an electron (ionization) from DNA generates an electron "hole" (a radical cation), located most often on its nucleobases, that migrates reversibly through duplex DNA by hopping until it is trapped in an irreversible chemical reaction. The particular sequence of nucleobases in a DNA oligomer determines both the efficiency of hopping and the specific location and nature of the damaging chemical reaction. In aqueous solution, DNA is a polyanion because of the negative charge carried by its phosphate groups. Counterions to the phosphate groups (typically Na(+)) play an important role in facilitating both hopping and the eventual reaction of the radical cation with H(2)O. Irreversible reaction of a radical cation with H(2)O in duplex DNA occurs preferentially at the most reactive site. In normal DNA, comprising the four common DNA nucleobases G, C, A, and T, reaction occurs most commonly at a guanine, resulting in its conversion primarily to 8-oxo-7,8-dihydroguanine (8-OxoG). Both electronic and steric effects control the outcome of this process. If the DNA oligomer does not contain a suitable guanine, then reaction of the radical cation occurs at the thymine of a TT step, primarily by a tandem process. The oxidative damage of DNA is a complex process, influenced by charge transport and reactions that are controlled by a combination of enthalpic, entropic, steric, and

  9. Correlation of nucleoside and nucleobase transporter gene expression with antimetabolite drug cytotoxicity.

    PubMed

    Lu, Xin; Gong, Shimei; Monks, Anne; Zaharevitz, Daniel; Moscow, Jeffrey A

    2002-01-01

    Antimetabolite drugs that inhibit nucleic acid metabolism are widely used in cancer chemotherapy. Nucleoside and nucleobase transporters are important for the cellular uptake of nucleic acids and their corresponding anticancer analogue drugs. Thus, these transporters may play a role both in antimetabolite drug sensitivity, by mediating the uptake of nucleoside analogues, and in antimetabolite drug resistance, by mediating the uptake of endogenous nucleosides that may rescue cells from toxicity. Therefore, we examined the relation of the expression of nucleoside and nucleobase transporters to antimetabolite cytotoxicity. We measured the RNA levels of all eight known nucleoside and nucleobase transporters in 50 cell lines included in the National Cancer Institute's Anticancer Drug Screen panel. RNA levels of concentrative nucleoside transporters (CNTs), equilibrative nucleoside transporters (ENTs) and nucleobase transporters (NCBTs) were determined by quantitative RT-PCR using real-time fluorescence acquisition. This method was validated by measuring the expression of the MDR1 gene, and correlating our results with independently determined measurements of MDR1 RNA levels and protein function in these cell lines. We then correlated the pattern of RNA levels to the pattern of cytotoxicity of anticancer drugs in the NCI drug screen database using the COMPARE analysis. Several hypothesized relations between transporter gene expression and cytotoxicity, based upon known interactions between certain nucleoside analogues and transporter proteins, were not observed, suggesting that expression of individual transporters may not be a significant determinant of the cytotoxicity of these drugs. The most closely correlated drug cytotoxicity patterns to transporter gene expression patterns (where increased expression corresponds to increase sensitivity) included those between CNT1 and O6-methylguanine and between ENT2 and hydroxyurea. We also observed that p53 status influenced

  10. Demonstration of FRET in solutions

    NASA Astrophysics Data System (ADS)

    Shah, Sunil; Gryczynski, Zygmunt; Chib, Rahul; Fudala, Rafal; Baxi, Aatmun; Borejdo, Julian; Synak, Anna; Gryczynski, Ignacy

    2016-03-01

    We measured the Förster resonance energy transfer (FRET) from Uranin (U) donor to Rhodamine 101 (R101) acceptor in propylene glycol. Steady-state fluorescence measurements show a significant difference between mixed and unmixed fluorophore solutions. In the solution with mixed fluorophores, fluorescence intensity of the U donor decreases and intensity of R101 fluorescence increases. This is visualized as a color change from green to orange. Fluorescence anisotropy of the mixture solution increases in the donor emission wavelength region and decreases in the acceptor emission wavelengths; which is consistent with FRET occurrence. Time-resolved (lifetime) measurements show a decrease of the U lifetime in the presence of R101 acceptor. In the intensity decay of R101 acceptor appears a negative component indicating excited state process. All these measurements prove the presence of FRET in U/R101 mixture fluorescence.

  11. Evaluation of RSRM case hardware fretting concerns

    NASA Technical Reports Server (NTRS)

    Swauger, Thomas R.

    1990-01-01

    Fretting corrosion was first noted on Shuttle flight STS-26. This flight was the first usage of the Redesigned Solid Rocket Motor (RSRM). The occurrence of fretting has since been observed on both the field and factory joints of the RSRM. Fretting is a form of corrosion that occurs at the interface between contacting, highly loaded, metal surfaces when exposed to slight relative vibratory motions. The engineering effort performed to evaluate the effect of fretting on the RSRM case hardware is summarized. Based on the results of this evaluation, several conclusions were made concerning flight safety. Also, recommendations were made concerning trending the effects of multiple generations of fretting damage.

  12. Latest advances in biomaterials: from deoxyribonucleic acid to nucleobases

    NASA Astrophysics Data System (ADS)

    Ouchen, Fahima; Gomez, Eliot; Joyce, Donna; Williams, Adrienne; Kim, Steve; Heckman, Emily; Johnson, Lewis; Yaney, Perry; Venkat, Narayanan; Steckl, Andrew; Kajzar, François; Rau, Ileana; Pawlicka, Agnieszka; Prasad, Paras; Grote, James

    2014-03-01

    This paper is a review of the recent research in bio-based materials for photonics and electronics applications. Materials that we have been working with include: deoxyribonucleic acid (DNA)-based biopolymers and nucleobases. We will highlight work on increasing the ionic conductivity of DNA-based membranes, enhancing the direct (DC) current and photoconductivity of DNA-based biopolymers, crosslinking of DNA-based biopolymers and promising applications for DNA nucleobases. Key

  13. Fretting about FRET: Failure of the Ideal Dipole Approximation

    PubMed Central

    Muñoz-Losa, Aurora; Curutchet, Carles; Krueger, Brent P.; Hartsell, Lydia R.; Mennucci, Benedetta

    2009-01-01

    Abstract With recent growth in the use of fluorescence-detected resonance energy transfer (FRET), it is being applied to complex systems in modern and diverse ways where it is not always clear that the common approximations required for analysis are applicable. For instance, the ideal dipole approximation (IDA), which is implicit in the Förster equation, is known to break down when molecules get “too close” to each other. Yet, no clear definition exists of what is meant by “too close”. Here we examine several common fluorescent probe molecules to determine boundaries for use of the IDA. We compare the Coulombic coupling determined essentially exactly with a linear response approach with the IDA coupling to find the distance regimes over which the IDA begins to fail. We find that the IDA performs well down to roughly 20 Å separation, provided the molecules sample an isotropic set of relative orientations. However, if molecular motions are restricted, the IDA performs poorly at separations beyond 50 Å. Thus, isotropic probe motions help mask poor performance of the IDA through cancellation of error. Therefore, if fluorescent probe motions are restricted, FRET practitioners should be concerned with not only the well-known κ2 approximation, but also possible failure of the IDA. PMID:19527638

  14. Fretting about FRET: failure of the ideal dipole approximation.

    PubMed

    Muñoz-Losa, Aurora; Curutchet, Carles; Krueger, Brent P; Hartsell, Lydia R; Mennucci, Benedetta

    2009-06-17

    With recent growth in the use of fluorescence-detected resonance energy transfer (FRET), it is being applied to complex systems in modern and diverse ways where it is not always clear that the common approximations required for analysis are applicable. For instance, the ideal dipole approximation (IDA), which is implicit in the Förster equation, is known to break down when molecules get "too close" to each other. Yet, no clear definition exists of what is meant by "too close". Here we examine several common fluorescent probe molecules to determine boundaries for use of the IDA. We compare the Coulombic coupling determined essentially exactly with a linear response approach with the IDA coupling to find the distance regimes over which the IDA begins to fail. We find that the IDA performs well down to roughly 20 A separation, provided the molecules sample an isotropic set of relative orientations. However, if molecular motions are restricted, the IDA performs poorly at separations beyond 50 A. Thus, isotropic probe motions help mask poor performance of the IDA through cancellation of error. Therefore, if fluorescent probe motions are restricted, FRET practitioners should be concerned with not only the well-known kappa2 approximation, but also possible failure of the IDA. PMID:19527638

  15. Excitation of nucleobases from a computational perspective I: reaction paths.

    PubMed

    Giussani, Angelo; Segarra-Martí, Javier; Roca-Sanjuán, Daniel; Merchán, Manuela

    2015-01-01

    The main intrinsic photochemical events in nucleobases can be described on theoretical grounds within the realm of non-adiabatic computational photochemistry. From a static standpoint, the photochemical reaction path approach (PRPA), through the computation of the respective minimum energy path (MEP), can be regarded as the most suitable strategy in order to explore the electronically excited isolated nucleobases. Unfortunately, the PRPA does not appear widely in the studies reported in the last decade. The main ultrafast decay observed experimentally for the gas-phase excited nucleobases is related to the computed barrierless MEPs from the bright excited state connecting the initial Franck-Condon region and a conical intersection involving the ground state. At the highest level of theory currently available (CASPT2//CASPT2), the lowest excited (1)(ππ*) hypersurface for cytosine has a shallow minimum along the MEP deactivation pathway. In any case, the internal conversion processes in all the natural nucleobases are attained by means of interstate crossings, a self-protection mechanism that prevents the occurrence of photoinduced damage of nucleobases by ultraviolet radiation. Many alternative and secondary paths have been proposed in the literature, which ultimately provide a rich and constructive interplay between experimentally and theoretically oriented research. PMID:24264958

  16. DNA-mediated excitonic upconversion FRET switching

    NASA Astrophysics Data System (ADS)

    Kellis, Donald L.; Rehn, Sarah M.; Cannon, Brittany L.; Davis, Paul H.; Graugnard, Elton; Lee, Jeunghoon; Yurke, Bernard; Knowlton, William B.

    2015-11-01

    Excitonics is a rapidly expanding field of nanophotonics in which the harvesting of photons, ensuing creation and transport of excitons via Förster resonant energy transfer (FRET), and subsequent charge separation or photon emission has led to the demonstration of excitonic wires, switches, Boolean logic and light harvesting antennas for many applications. FRET funnels excitons down an energy gradient resulting in energy loss with each step along the pathway. Conversely, excitonic energy upconversion via upconversion nanoparticles (UCNPs), although currently inefficient, serves as an energy ratchet to boost the exciton energy. Although FRET-based upconversion has been demonstrated, it suffers from low FRET efficiency and lacks the ability to modulate the FRET. We have engineered an upconversion FRET-based switch by combining lanthanide-doped UCNPs and fluorophores that demonstrates excitonic energy upconversion by nearly a factor of 2, an excited state donor to acceptor FRET efficiency of nearly 25%, and an acceptor fluorophore quantum efficiency that is close to unity. These findings offer a promising path for energy upconversion in nanophotonic applications including artificial light harvesting, excitonic circuits, photovoltaics, nanomedicine, and optoelectronics.

  17. DNA-mediated excitonic upconversion FRET switching

    SciTech Connect

    Kellis, Donald L.; Rehn, Sarah M.; Cannon, Brittany L.; Davis, Paul H.; Graugnard, Elton; Lee, Jeunghoon; Yurke, Bernard; Knowlton, William B.

    2015-11-17

    Excitonics is a rapidly expanding field of nanophotonics in which the harvesting of photons, ensuing creation and transport of excitons via Förster resonant energy transfer (FRET), and subsequent charge separation or photon emission has led to the demonstration of excitonic wires, switches, Boolean logic and light harvesting antennas for many applications. FRET funnels excitons down an energy gradient resulting in energy loss with each step along the pathway. Conversely, excitonic energy up conversion via up conversion nanoparticles (UCNPs), although currently inefficient, serves as an energy ratchet to boost the exciton energy. Although FRET-based up conversion has been demonstrated, it suffers from low FRET efficiency and lacks the ability to modulate the FRET. We have engineered an up conversion FRET-based switch by combining lanthanide-doped UCNPs and fluorophores that demonstrates excitonic energy up conversion by nearly a factor of 2, an excited state donor to acceptor FRET efficiency of nearly 25%, and an acceptor fluorophore quantum efficiency that is close to unity. These findings offer a promising path for energy up conversion in nanophotonic applications including artificial light harvesting, excitonic circuits, photovoltaics, nanomedicine, and optoelectronics.

  18. DNA-mediated excitonic upconversion FRET switching

    DOE PAGESBeta

    Kellis, Donald L.; Rehn, Sarah M.; Cannon, Brittany L.; Davis, Paul H.; Graugnard, Elton; Lee, Jeunghoon; Yurke, Bernard; Knowlton, William B.

    2015-11-17

    Excitonics is a rapidly expanding field of nanophotonics in which the harvesting of photons, ensuing creation and transport of excitons via Förster resonant energy transfer (FRET), and subsequent charge separation or photon emission has led to the demonstration of excitonic wires, switches, Boolean logic and light harvesting antennas for many applications. FRET funnels excitons down an energy gradient resulting in energy loss with each step along the pathway. Conversely, excitonic energy up conversion via up conversion nanoparticles (UCNPs), although currently inefficient, serves as an energy ratchet to boost the exciton energy. Although FRET-based up conversion has been demonstrated, it suffersmore » from low FRET efficiency and lacks the ability to modulate the FRET. We have engineered an up conversion FRET-based switch by combining lanthanide-doped UCNPs and fluorophores that demonstrates excitonic energy up conversion by nearly a factor of 2, an excited state donor to acceptor FRET efficiency of nearly 25%, and an acceptor fluorophore quantum efficiency that is close to unity. These findings offer a promising path for energy up conversion in nanophotonic applications including artificial light harvesting, excitonic circuits, photovoltaics, nanomedicine, and optoelectronics.« less

  19. Recognition of DNA sequencing through binding of nucleobases to graphene

    NASA Astrophysics Data System (ADS)

    Zaffino, Valentina

    Graphene is one of the most promising materials in nanotechnology. Its large surface to volume ratio, high conductivity and electron mobility at room temperature are outstanding properties for use in DNA sensors. For this study, we used Density Functional Theory (DFT), ?with and without the inclusion of van der Waals (vdW) interactions, ?to investigate the adsorption of nucleobases (cytosine, guanine, adenine, thymine, and uracil) on pristine graphene and graphene with defects (Divacancy and Stone-Wales). We investigated the performance of two types of vdW-DF functional (optB86b-vdW and rPW86-vdW), as well as the PBE functional, and their description of the adsorption geometry and electronic structure of the nucleobase-graphene systems.The inclusion of defects results in an increase in binding energy, closer adsorption of the molecule to graphene and greater buckling in both the graphene structure and nucleobase.

  20. Fretting fatigue of 2XXX series aerospace aluminum alloys

    NASA Astrophysics Data System (ADS)

    Giummarra, Cindie

    Fretting is a wear mechanism that occurs at the contact region between two materials subject to minute cyclic relative motion. Fretting causes the initiation of surface cracks within the first few thousand cycles, which in the presence of a fatigue stress, grow to cause material failure approximately 10 to 100 times earlier than expected under standard fatigue conditions. Examples of fretting fatigue have been seen in joints in aircraft, and the aerospace industry acknowledges the possibility of catastrophic failure from this mechanism. Improvements in a material's resistance to fretting would benefit aluminum alloys in aerospace applications. This research investigated the effect of microstructural properties on the fretting response in 2XXX series aerospace aluminum alloys. Fretting wear and fretting fatigue tests were conducted to determine the influence of slip characteristics, alloy purity, grain orientation and yield strength on fretting crack initiation and growth. Crack length measurements and micrographs of the fretting indicated there was no significant difference in the fretting response of these alloys based on their microstructural characteristics. Results showed that fretting initiated cracks in the first 1--8% of the life while standard fatigue initiation took around 90% of the life. This reduction in initiation resulted in a shorter life under fretting conditions. Additionally, fretting normalized the initiation time in all alloys which eliminated any intrinsic initiation resistance. The alloys with the highest stress-life (S-N) fatigue properties exhibiting a greater reduction in fatigue strength under fretting conditions. The fretting stresses appeared to influence the crack growth to a distance below the surface of approximately 17mum under fretting fatigue conditions, after which some cracks changed direction and propagated under the influence of the fatigue stress. Under fretting wear conditions, the cracks tended to arrest at a depth of 8

  1. 1'-Homonucleosides and their structural analogues: A review.

    PubMed

    Wróblewski, Andrzej E; Głowacka, Iwona E; Piotrowska, Dorota G

    2016-08-01

    Nucleoside analogues belong to an important class of antiviral and anticancer drugs. Insertion of a methylene fragment between the anomeric carbon and pyrimidine or purine bases transforms nucleosides into 1'-homonucleosides. When compared with nucleosides this modification lengthens the separation between HO-C5' of pentofuranoside fragments and nitrogen (N1 or N9) atoms of nucleobases, lowers the steric and electronic interactions between nucleobases and sugar rings, introduces greater flexibility around a CH2-Base bond and thus allows for more rotational freedom, and since the anomeric effect no longer operates any sugar or pseudosugar moiety exists in its unique conformation and experiences specific conformational mobility and hydrolysis of the C1'-CH2Base bond by cellular enzymes is no longer feasible. This review covers 1'-homonucleosides with a tetrahydrofuran ring and its nitrogen and sulfur analogues as well as those containing a cyclopentane moiety as a sugar replacer. Achievements in syntheses of sugar or pseudosugar scaffolds are of primary interest since pathways to install nucleobases are well recognized. Whenever possible, the biological activity, mostly antiviral and antitumor but sometimes as inhibitors of specific enzymes, will be presented and discussed to help identify structural features responsible for the particular mode of action and thus possible therapeutic significance. PMID:27128178

  2. Photoreponsive Hybrid Nanoparticles with Inherent FRET Activity.

    PubMed

    Achilleos, Demetra S; Hatton, T Alan; Vamvakaki, Maria

    2016-06-14

    The photoactivated inherent fluorescence resonance energy transfer (FRET) properties of a hard-and-soft hybrid nanosystem comprising poly(1'-(2-methacryloxyethyl)-3',3'-dimethyl-6-nitrospiro-(2H-1-benzopyran-2,2'-indoline))-co-poly[2-(dimethylamino)ethyl methacrylate] (PSPMA-co-PDMAEMA) random copolymer brushes on silica nanoparticles are described. This unique FRET process is switched on by the simultaneous generation of isomer X and merocyanine (MC), which are bipolar in nature and comprise donor-acceptor dyads, from a single spiropyran (SP) chromophore upon UV irradiation. These X-MC species exhibit sufficient lifetimes to allow the read-out of the FRET process. The phenomenon is gradually switched off because of the thermal relaxation of the bipolar chromophores. This inherent property of the nanoemitters is employed in the development of biosensors of high specificity by monitoring variations in the FRET efficiency and lifetime of the hybrids in the presence of biological substances. More specifically, bovine serum albumin (BSA) augments the formation of MC species and retards the MC photobleaching process, leading to the enhancement of the FRET efficiency and lifetime, respectively. On the other hand, amino acid l-histidine further retards the MC thermal relaxation and prolongs the FRET process. We envisage that this platform opens new perspectives in the development of novel, optical nanosensors for applications in various fields including healthcare products and environmental monitoring. PMID:27222922

  3. Isolation of Human Genomic DNA Sequences with Expanded Nucleobase Selectivity.

    PubMed

    Rathi, Preeti; Maurer, Sara; Kubik, Grzegorz; Summerer, Daniel

    2016-08-10

    We report the direct isolation of user-defined DNA sequences from the human genome with programmable selectivity for both canonical and epigenetic nucleobases. This is enabled by the use of engineered transcription-activator-like effectors (TALEs) as DNA major groove-binding probes in affinity enrichment. The approach provides the direct quantification of 5-methylcytosine (5mC) levels at single genomic nucleotide positions in a strand-specific manner. We demonstrate the simple, multiplexed typing of a variety of epigenetic cancer biomarker 5mC with custom TALE mixes. Compared to antibodies as the most widely used affinity probes for 5mC analysis, i.e., employed in the methylated DNA immunoprecipitation (MeDIP) protocol, TALEs provide superior sensitivity, resolution and technical ease. We engineer a range of size-reduced TALE repeats and establish full selectivity profiles for their binding to all five human cytosine nucleobases. These provide insights into their nucleobase recognition mechanisms and reveal the ability of TALEs to isolate genomic target sequences with selectivity for single 5-hydroxymethylcytosine and, in combination with sodium borohydride reduction, single 5-formylcytosine nucleobases. PMID:27429302

  4. Photochemical etiology of promising ancestors of the RNA nucleobases.

    PubMed

    Brister, M M; Pollum, M; Crespo-Hernández, C E

    2016-07-27

    RNA is a product of chemical and biological evolution and the identification of its heterocyclic ancestors is essential for understanding the molecular origins of life. Among a diverse array of selection pressures thought to have shaped the composition of the nucleobases on prebiotic Earth, protection against intense ultraviolet radiation must have been essential. In this contribution, a detailed spectroscopic and photophysical investigation of barbituric acid and 2,4,6-triaminopyrimidine, two promising candidates for the prebiotic ancestors of RNA nucleobases, is presented in aqueous solution. It is shown that although these pyrimidine derivatives absorb ultraviolet radiation strongly, both compounds possess efficient electronic relaxation mechanisms for dissipating most of the absorbed ultraviolet energy to their aqueous environment as heat within hundreds of femtoseconds, thus safeguarding their chemical integrity. In fact, these two heterocyclic compounds rival the photostability observed in the canonical nucleobases in aqueous solution, thus supporting the recent proposal that both barbituric acid and 2,4,6-triaminopyrimidine are promising ancestors of the RNA nucleobases. PMID:26898746

  5. The Renaissance of Metal-Pyrimidine Nucleobase Coordination Chemistry.

    PubMed

    Lippert, Bernhard; Sanz Miguel, Pablo J

    2016-08-16

    The significance of metal ions for the function and properties of DNA and RNA, long seen primarily under biological aspects and medicinal uses, has recently gained a renewed momentum. This is a consequence of the advent of novel applications in the fields of materials science, biotechnology, and analytical sensor chemistry that relate to the designed incorporation of transition metal ions into nucleic acid base pairs. Ag(+) and Hg(2+) ions, binding to pyrimidine (pym) nucleobases, represent major players in this development. Interestingly, these metal ions were the ones that some 60 years ago started the field! At the same time, the mentioned metal ions had demonstrated a "special relationship" with the pym nucleobases cytosine, thymine, and uracil! Parallel work conducted with oligonucleotides and model nucleobases fostered numerous significant details of these interactions, in particular when X-ray crystallography was involved, correcting earlier views occasionally. Our own activities during the past three to four decades have focused on, among others, the coordination chemistry of transition and main-group metal ions with pym model nucleobases, with an emphasis on Pt(II) and Pd(II). It has always been our goal to deduce, if possible, the potential relevance of our findings for biological processes. It is interesting to put our data, in particular for trans-a2Pt(II) (a = NH3 or amine), into perspective with those of other metal ions, notably Ag(+) and Hg(2+). Irrespective of major differences in kinetics and lability/inertness between d(8) and d(10) metal ions, there is also a lot of similarity in structural aspects as a result of the preferred linear coordination geometry of these species. Moreover, the apparent clustering of metal ions to the pym nucleobases, which is presumably essential for the formation of nanoclusters on oligonucleotide scaffolds, is impressively reflected in model systems, as are reasons for inter-nucleobase cross-links containing more

  6. Formation of a stable triplex incorporating a CG interrupting site by a new WNA derivative containing 3-aminopyrazole as a nucleobase.

    PubMed

    Uchida, Yuko; Taniguchi, Yosuke; Aoki, Eriko; Togo, Mieko; Sasaki, Shigeki

    2008-01-01

    Triplex-forming oligonucleotides (TFOs) bind within the major groove of duplex DNA in a sequence-specific manner, and have attracted much interest as genomic tools. However, as the triplex DNA is formed by the interaction between the TFOs and homopurine/homopyrimidine sequences of the target duplex DNA, the stable triplex formation is prevented by one pyrimidine base in the homopurine strand. Previously, we developed the nucleoside analogues (WNA: W-shaped nucleoside analogues) that furnish an aromatic ring as a stacking part and a nucleobase as a recognition part onto the bicyclic skeleton. Selective recognition of a TA and a CG interrupting site has been achieved by WNA-beta T and WNA-beta C, respectively. In the subsequent study, it was found that the triplex formation by the WNA analogues depend on its neighbouring bases within the TFO. In this paper, we describe the synthesis and the evaluation of the triplex forming ability of WNA-beta 3AP, having 3-aminopyrazole (3AP) as a nucleobase. It is remarkable that the TFO containing the WNA-beta 3AP recognizes the CG interrupting site with high selectivity in the TFO sequence of 3'-GZG-5', in which the previous WNA-beta C did not show the stabilizing effect. PMID:18776291

  7. Communication: Photoactivation of nucleobase bound platinum{sup II} metal complexes: Probing the influence of the nucleobase

    SciTech Connect

    Sen, Ananya; Dessent, Caroline E. H.

    2014-12-28

    We present UV laser action spectra (220-300 nm) of isolated nucleobase-bound Pt{sup II}(CN){sub 4}{sup 2−} complexes, i.e., Pt(CN){sub 4}{sup 2−}⋅M, where M = uracil, thymine, cytosine, and adenine. These metal complex-nucleobase clusters represent model systems for identifying the fundamental photophysical and photochemical processes occurring in photodynamic platinum (II) drug therapies that target DNA. This is the first study to explore the specific role of the nucleobase in the photophysics of the aggregate complex. Each of the complexes studied displays a broadly similar absorption spectra, with a strong λ{sub max} ∼ 4.7 eV absorption band (nucleobase localized chromophore) and a subsequent increase in the absorption intensity towards higher spectral-energy (Pt(CN){sub 4}{sup 2−} localized chromophore). However, strikingly different band widths are observed across the series of complexes, decreasing in the order Pt(CN){sub 4}{sup 2−}⋅Thymine > Pt(CN){sub 4}{sup 2−}⋅Uracil > Pt(CN){sub 4}{sup 2−}⋅Adenine > Pt(CN){sub 4}{sup 2−}⋅Cytosine. Changes in the bandwidth of the ∼4.7 eV band are accompanied by distinctive changes in the photofragment product ions observed following photoexcitation, with the narrower-bandwidth complexes showing a greater propensity to decay via electron detachment decay. We discuss these observations in the context of the distinctive nucleobase-dependent excited state lifetimes.

  8. Intracellular protein interaction mapping with FRET hybrids

    PubMed Central

    You, Xia; Nguyen, Annalee W.; Jabaiah, Abeer; Sheff, Mark A.; Thorn, Kurt S.; Daugherty, Patrick S.

    2006-01-01

    A quantitative methodology was developed to identify protein interactions in a broad range of cell types by using FRET between fluorescent proteins. Genetic fusions of a target receptor to a FRET acceptor and a large library of candidate peptide ligands to a FRET donor enabled high-throughput optical screening for optimal interaction partners in the cytoplasm of Escherichia coli. Flow cytometric screening identified a panel of peptide ligands capable of recognizing the target receptors in the intracellular environment. For both SH3 and PDZ domain-type target receptors, physiologically meaningful consensus sequences were apparent among the isolated ligands. The relative dissociation constants of interacting partners could be measured directly by using a dilution series of cell lysates containing FRET hybrids, providing a previously undescribed high-throughput approach to rank the affinity of many interaction partners. FRET hybrid interaction screening provides a powerful tool to discover protein ligands in the cellular context with potential applications to a wide variety of eukaryotic cell types. PMID:17130455

  9. Action-FRET of a Gaseous Protein

    NASA Astrophysics Data System (ADS)

    Daly, Steven; Knight, Geoffrey; Halim, Mohamed Abdul; Kulesza, Alexander; Choi, Chang Min; Chirot, Fabien; MacAleese, Luke; Antoine, Rodolphe; Dugourd, Philippe

    2016-08-01

    Mass spectrometry is an extremely powerful technique for analysis of biological molecules, in particular proteins. One aspect that has been contentious is how much native solution-phase structure is preserved upon transposition to the gas phase by soft ionization methods such as electrospray ionization. To address this question—and thus further develop mass spectrometry as a tool for structural biology—structure-sensitive techniques must be developed to probe the gas-phase conformations of proteins. Here, we report Förster resonance energy transfer (FRET) measurements on a ubiquitin mutant using specific photofragmentation as a reporter of the FRET efficiency. The FRET data is interpreted in the context of circular dichroism, molecular dynamics simulation, and ion mobility data. Both the dependence of the FRET efficiency on the charge state—where a systematic decrease is observed—and on methanol concentration are considered. In the latter case, a decrease in FRET efficiency with methanol concentration is taken as evidence that the conformational ensemble of gaseous protein cations retains a memory of the solution phase conformational ensemble upon electrospray ionization.

  10. FRET-based Molecular Tension Microscopy.

    PubMed

    Gayrard, Charlène; Borghi, Nicolas

    2016-02-01

    Cells generate and experience mechanical forces that may shape tissues and regulate signaling pathways in a variety of physiological or pathological situations. How forces propagate and transduce signals at the molecular level is poorly understood. The advent of FRET-based Molecular Tension Microscopy now allows to achieve mechanical force measurements at a molecular scale with molecular specificity in situ, and thereby better understand the mechanical architecture of cells and tissues, and mechanotransduction pathways. In this review, we will first expose the basic principles of FRET-based MTM and its various incarnations. We will describe different ways of measuring FRET, their advantages and drawbacks. Then, throughout the range of proteins of interest, cells and organisms to which it has been applied, we will review the tests developed to validate the approach, how molecular tension was related to cell functions, and conclude with possible developments and offshoots. PMID:26210398

  11. pH-Insensitive FRET voltage dyes.

    PubMed

    Maher, Michael P; Wu, Nyan-Tsz; Ao, Hong

    2007-08-01

    Many high-throughput ion channel assays require the use of voltage-sensitive dyes to detect channel activity in the presence of test compounds. Dye systems employing Förster resonance energy transfer (FRET) between 2 membrane-bound dyes are advantageous in combining high sensitivity, relatively fast response, and ratiometric output. The most widely used FRET voltage dye system employs a coumarin fluorescence donor whose excitation spectrum is pH dependent. The authors have validated a new class of voltage-sensitive FRET donors based on a pyrene moiety. These dyes are significantly brighter than CC2-DMPE and are not pH sensitive in the physiological range. With the new dye system, the authors demonstrate a new high-throughput assay for the acid-sensing ion channel (ASIC) family. They also introduce a novel method for absolute calibration of voltage-sensitive dyes, simultaneously determining the resting membrane potential of a cell. PMID:17517905

  12. Glucose-Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA.

    PubMed

    Vengut-Climent, Empar; Gómez-Pinto, Irene; Lucas, Ricardo; Peñalver, Pablo; Aviñó, Anna; Fonseca Guerra, Célia; Bickelhaupt, F Matthias; Eritja, Ramón; González, Carlos; Morales, Juan C

    2016-07-18

    Noncovalent forces rule the interactions between biomolecules. Inspired by a biomolecular interaction found in aminoglycoside-RNA recognition, glucose-nucleobase pairs have been examined. Deoxyoligonucleotides with a 6-deoxyglucose insertion are able to hybridize with their complementary strand, thus exhibiting a preference for purine nucleobases. Although the resulting double helices are less stable than natural ones, they present only minor local distortions. 6-Deoxyglucose stays fully integrated in the double helix and its OH groups form two hydrogen bonds with the opposing guanine. This 6-deoxyglucose-guanine pair closely resembles a purine-pyrimidine geometry. Quantum chemical calculations indicate that glucose-purine pairs are as stable as a natural T-A pair. PMID:27328804

  13. Nucleobase appended viologens: Building blocks for new optoelectronic materials

    NASA Astrophysics Data System (ADS)

    Ciobanu, Marius; Asaftei, Simona

    2015-04-01

    We describe here the fabrication, characterization and possible applications of a new type of optical material - consisting of 4,4‧-bipyridinium core ("viologen") and nucleobases i.e. adenine and/or thymine made by H-bonding. The viologen-nucleobase derivatives were used to construct supramolecular structures in a "biomimetic way" with complementary oligonucleotides (ssDNA) and peptide nucleic acids (ssPNA) as templates. The new nanostructured materials are expected to exhibit enhanced optical and optoelectronic properties with application in the field of supramolecular electronics. Such viologen derivatives could be significant in the design of new 2D and 3D materials with potentially application in optoelectronics, molecular electronics or sensoric.

  14. Supramolecular gels made from nucleobase, nucleoside and nucleotide analogs.

    PubMed

    Peters, Gretchen Marie; Davis, Jeffery T

    2016-06-01

    Supramolecular or molecular gels are attractive for various applications, including diagnostics, tissue scaffolding and targeted drug release. Gelators derived from natural products are of particular interest for biomedical purposes, as they are generally biocompatible and stimuli-responsive. The building blocks of nucleic acids (i.e. nucleobases, nucleosides, and nucleotides) are desirable candidates for supramolecular gelation as they readily engage in reversible, noncovalent interactions. In this review, we describe a number of organo- and hydrogels formed through the assembly of nucleosides, nucleotides, and their derivatives. While natural nucleosides and nucleotides generally require derivatization to induce gelation, guanosine and its corresponding nucleotides are well known gelators. This unique gelating ability is due to propensity of the guanine nucleobase to self-associate into stable higher-order assemblies, such as G-ribbons, G4-quartets, and G-quadruplexes. PMID:27146863

  15. Local piezoresponse and polarization switching in nucleobase thymine microcrystals

    NASA Astrophysics Data System (ADS)

    Bdikin, Igor; Heredia, Alejandro; Neumayer, Sabine M.; Bystrov, Vladimir S.; Gracio, José; Rodriguez, Brian J.; Kholkin, Andrei L.

    2015-08-01

    Thymine (2-oxy-4-oxy-5 methyl pyrimidine) is one of the four nucleobases of deoxyribonucleic acid (DNA). In the DNA molecule, thymine binds to adenine via two hydrogen bonds, thus stabilizing the nucleic acid structure and is involved in pairing and replication. Here, we show that synthetic thymine microcrystals grown from the solution exhibit local piezoelectricity and apparent ferroelectricity, as evidenced by nanoscale electromechanical measurements via Piezoresponse Force Microscopy. Our experimental results demonstrate significant electromechanical activity and polarization switchability of thymine, thus opening a pathway for piezoelectric and ferroelectric-based applications of thymine and, perhaps, of other DNA nucleobase materials. The results are supported by molecular modeling of polarization switching under an external electric field.

  16. Proton Transfer in Nucleobases is Mediated by Water

    SciTech Connect

    Khistyaev, Kirill; Golan, Amir; Bravaya, Ksenia B.; Orms, Natalie; Krylov, Anna I.; Ahmed, Musahid

    2013-08-08

    Water plays a central role in chemistry and biology by mediating the interactions between molecules, altering energy levels of solvated species, modifying potential energy proles along reaction coordinates, and facilitating ecient proton transport through ion channels and interfaces. This study investigates proton transfer in a model system comprising dry and microhydrated clusters of nucleobases. With mass spectrometry and tunable vacuum ultraviolet synchrotron radiation, we show that water shuts down ionization-induced proton transfer between nucleobases, which is very ecient in dry clusters. Instead, a new pathway opens up in which protonated nucleo bases are generated by proton transfer from the ionized water molecule and elimination of a hydroxyl radical. Electronic structure calculations reveal that the shape of the potential energy prole along the proton transfer coordinate depends strongly on the character of the molecular orbital from which the electron is removed, i.e., the proton transfer from water to nucleobases is barrierless when an ionized state localized on water is accessed. The computed energetics of proton transfer is in excellent agreement with the experimental appearance energies. Possible adiabatic passage on the ground electronic state of the ionized system, while energetically accessible at lower energies, is not ecient. Thus, proton transfer is controlled electronically, by the character of the ionized state, rather than statistically, by simple energy considerations.

  17. Nucleobase and nucleoside transport and integration into plant metabolism

    PubMed Central

    Girke, Christopher; Daumann, Manuel; Niopek-Witz, Sandra; Möhlmann, Torsten

    2014-01-01

    Nucleotide metabolism is an essential process in all living organisms. Besides newly synthesized nucleotides, the recycling (salvage) of partially degraded nucleotides, i.e., nucleosides and nucleobases serves to keep the homeostasis of the nucleotide pool. Both types of metabolites are substrates of at least six families of transport proteins in Arabidopsis thaliana (Arabidopsis) with a total of 49 members. In the last years several members of such transport proteins have been analyzed allowing to present a more detailed picture of nucleoside and nucleobase transport and the physiological function of these processes. Besides functioning in nucleotide metabolism it turned out that individual members of the before named transporters exhibit the capacity to transport a wide range of different substrates including vitamins and phytohormones. The aim of this review is to summarize the current knowledge on nucleobase and nucleoside transport processes in plants and integrate this into nucleotide metabolism in general. Thereby, we will focus on those proteins which have been characterized at the biochemical level. PMID:25250038

  18. Reliable measurement of the FRET sensitized-quenching transition factor for FRET quantification in living cells.

    PubMed

    Zhang, Jiang; Zhang, Lili; Chai, Liuying; Yang, Fangfang; Du, Mengyan; Chen, Tongsheng

    2016-09-01

    3-cube-based Förster resonance energy transfer (FRET) microscopy, a sensitized acceptor FRET quantification method, has been widely used to visualize dynamic protein-protein interaction in living cells. Determining the FRET sensitized-quenching transition factor (G factor) of a particular donor-acceptor pair and optical system is crucial for 3-cube FRET quantification. We here improved the acceptor photobleaching-based G factor determination method (termed as mPb-G) and the two-plasmid-based G factor determination method (termed as mTP-G) for rapid and reliable measurement of the G factor. mTP-G method determines G factor by simultaneously detecting three images of cells exclusively expressing each of two tandem constructs with multiple donors and multiple acceptors. This method circumvents switchover of the cells exclusively expressing each of the two constructs. mPb-G method images G factor by detecting three images of cells expressing a donor-acceptor tandem FRET construct before and after partially photobleaching acceptor. We performed the two methods on our dual-channel wide-field FRET microscope to obtain reliable G factor, and also measured the FRET efficiency and acceptor-to-donor concentration ratio of tandem constructs with different acceptor-donor stoichiometries in living HepG2 cells. mTP-G and mPb-G methods provide two simple and reliable tools for determining the G factor, in turn, quantitatively measuring FRET signal and monitoring dynamic biochemical processes in living cells. PMID:27239984

  19. Nonenzymatic template-directed reactions on altritol oligomers, preorganized analogues of oligonucleotides

    NASA Technical Reports Server (NTRS)

    Kozlov, I. A.; Zielinski, M.; Allart, B.; Kerremans, L.; Van Aerschot, A.; Busson, R.; Herdewijn, P.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

    2000-01-01

    Altritol nucleic acids (ANAs) are RNA analogues with a phosphorylated D-altritol backbone. The nucleobase is attached at the 2-(S)-position of the carbohydrate moiety. We report that ANA oligomers are superior to the corresponding DNA, RNA, and HNA (hexitol nucleic acid) in supporting efficient nonenzymatic template-directed synthesis of complementary RNAs from nucleoside-5'-phosphoro-2-methyl imidazolides. Activated ANA and HNA monomers do not oligomerize efficiently on DNA, RNA, HNA, or ANA templates.

  20. A Transition-State Interaction Shifts Nucleobase Ionization Toward Neutrality to Facilitate Small Ribozyme Catalysis

    PubMed Central

    Liberman, Joseph A.; Guo, Man; Jenkins, Jermaine L.; Krucinska, Jolanta; Chen, Yuanyuan; Carey, Paul R.; Wedekind, Joseph E.

    2012-01-01

    One mechanism by which ribozymes can accelerate biological reactions is by adopting folds that favorably perturb nucleobase ionization. Herein we used Raman crystallography to directly measure pKa values for the Ade38 N1-imino group of a hairpin ribozyme in distinct conformational states. A transition-state analogue gave a pKa value of 6.27 ± 0.05, which agrees strikingly well with values measured by pH-rate analyses. To identify the chemical attributes that contribute to the shifted pKa we determined crystal structures of hairpin ribozyme variants containing single-atom substitutions at the active site and measured their respective Ade38 N1 pKa values. This approach led to the identification of a single interaction in the transition-state conformation that elevates the base pKa >0.8 log units relative to the precatalytic state. The agreement of the microscopic and macroscopic pKa values and the accompanying structural analysis support a mechanism in which Ade38 N1(H)+ functions as a general acid in phosphodiester bond cleavage. Overall the results quantify the contribution of a single electrostatic interaction to base ionization, which has broad relevance for understanding how RNA structure can control chemical reactivity. PMID:22989273

  1. Bioinspired optofluidic FRET lasers via DNA scaffolds

    PubMed Central

    Sun, Yuze; Shopova, Siyka I.; Wu, Chung-Shieh; Arnold, Stephen; Fan, Xudong

    2010-01-01

    Optofluidic dye lasers hold great promise for adaptive photonic devices, compact and wavelength-tunable light sources, and micro total analysis systems. To date, however, nearly all those lasers are directly excited by tuning the pump laser into the gain medium absorption band. Here we demonstrate bioinspired optofluidic dye lasers excited by FRET, in which the donor-acceptor distance, ratio, and spatial configuration can be precisely controlled by DNA scaffolds. The characteristics of the FRET lasers such as spectrum, threshold, and energy conversion efficiency are reported. Through DNA scaffolds, nearly 100% energy transfer can be maintained regardless of the donor and acceptor concentration. As a result, efficient FRET lasing is achieved at an unusually low acceptor concentration of micromolar, over 1,000 times lower than that in conventional optofluidic dye lasers. The lasing threshold is on the order of μJ/mm2. Various DNA scaffold FRET lasers are demonstrated to illustrate vast possibilities in optofluidic laser designs. Our work opens a door to many researches and applications such as intracavity bio/chemical sensing, biocontrolled photonic devices, and biophysics. PMID:20798062

  2. CTAB enhancement of FRET in DNA structures.

    PubMed

    Oh, Taeseok; Takahashi, Tsukasa; Kim, Sejung; Heller, Michael J

    2016-01-01

    The effect of cetyl-trimethylammonium bromide (CTAB) on enhancing the fluorescence resonance energy transfer (FRET) between two dye-conjugated DNA strands was studied using fluorescence emission spectroscopy and dynamic light scattering (DLS). For hybridized DNA where one strand is conjugated with a TAMRA donor and the other with a TexasRed acceptor, increasing the concentration of CTAB changes the fluorescence emission properties and improves the FRET transfer efficiency through changes in the polarity of the solvent, neutralization of the DNA backbone and micelle formation. For the DNA FRET system without CTAB, the DNA hybridization leads to contact quenching between TAMRA donor and TexasRed acceptor producing reduced donor emission and only a small increase in acceptor emission. At 50 µM CTAB, however, the sheathing and neutralization of the dye-conjugated dsDNA structure significantly reduces quenching by DNA bases and dye interactions, producing a large increase in FRET efficiency, which is almost four fold higher than without CTAB. PMID:26530400

  3. FRET Enabled Real Time Detection of RNA-Small Molecule Binding

    PubMed Central

    Xie, Yun; Dix, Andrew V.; Tor, Yitzhak

    2011-01-01

    A robust analysis and discovery platform for antibiotics targeting the bacterial rRNA A-site has been developed by incorporating a new emissive U surrogate into the RNA and labeling the aminoglycosides with an appropriate fluorescence acceptor. Specifically, a 5-methoxyquinazoline-2,4(1H,3H)-dione-based emissive uracil analogue was identified to be an ideal donor for 7-diethylaminocoumarin-3-carboxylic acid. This donor/acceptor pair displays a critical Förster radius (R0) of 27 Å, a value suitable for an A-site-aminoglycoside assembly. Titrating the coumarin labeled aminoglycosides into the emissive A-site construct, labeled at position U1406, shows a decrease in donor emission (at 395 nm) and concurrent increase of the acceptor emission (at 473 nm). Titration curves, obtained by fitting the donor’s emission quenching or the augmentation of the acceptor’s sensitized emission, faithfully generate EC50 values. Titration of unlabeled ligands into the preformed FRET complex showed a continuous increase of the donor emission, with a concurrent decrease of the acceptor emission, yielding valuable data regarding competitive displacement of aminoglycosides by A-site binders. Detection of antibiotic binding is therefore not dependent on changes in the environment of a single fluorophore, but rather on the responsive interaction between two chromophores acting as a FRET pair, facilitating the determination of direct binding and competitive displacement events with FRET accuracy. PMID:19908830

  4. Efficient self-assembly in water of long noncovalent polymers by nucleobase analogues.

    PubMed

    Cafferty, Brian J; Gállego, Isaac; Chen, Michael C; Farley, Katherine I; Eritja, Ramon; Hud, Nicholas V

    2013-02-20

    Molecular self-assembly is widely appreciated to result from a delicate balance between several noncovalent interactions and solvation effects. However, current design approaches for achieving self-assembly in water with small, synthetic molecules do not consider all aspects of the hydrophobic effect, in particular the requirement of surface areas greater than 1 nm(2) for an appreciable free energy of hydration. With the concept of a minimum hydrophobic surface area in mind, we designed a system that achieves highly cooperative self-assembly in water. Two weakly interacting low-molecular-weight monomers (cyanuric acid and a modified triaminopyrimidine) are shown to form extremely long supramolecular polymer assemblies that retain water solubility. The complete absence of intermediate assemblies means that the observed equilibrium is between free monomers and supramolecular assemblies. These observations are in excellent agreement with literature values for the free energy of nucleic acid base interactions as well as the calculated free energy penalty for the exposure of hydrophobic structures in water. The results of our study have implications for the design of new self-assembling structures and hydrogel-forming molecules and may provide insights into the origin of the first RNA-like polymers. PMID:23394182

  5. A Re-Examination of Nucleobases in Carbonaceous Chondrites

    NASA Astrophysics Data System (ADS)

    Martins, Z.; Botta, O.; de Vries, M.; Becker, L.; Ehrenfreund, E.

    The biomolecular building blocks of life, as we know it, are amino acids, purines and pyrimidines. The latter two form the bases of DNA and RNA, molecules that are used in the storage, transcription and translation of genetic information in all terrestrial organisms. A dedicated search for these compounds in meteorites can shed light on the origins of life in two ways: (i) Results can help assess the plausibility of extraterrestrial formation of prebiotic molecules followed by their meteoritic delivery to the early Earth. (ii) Such studies can also provide insights into possible prebiotic synthetic routes. We will search for these compounds in selected carbonaceous chondrites using formic acid extraction and reverse phase high performance liquid chromatography (HPLC) to isolate specific nucleobases from the bulk meteorite material as previously reported [1,2,3]. We will also use a new technique, resonant two-photon ionization mass spectrometry (R2PI) that can, not only identify organic compounds by their mass, but at the same time by their vibronic spectroscopy [4]. R2PI dramatically enhances the specificity for certain compounds (e.g. amino acids, nucleobases) and allows for distinction of structural isomers, tautomers and enantiomers as well as providing additional information due to isotope shifts. The optical spectroscopy can thus help us to further discriminate between terrestrial and extraterrestrial nucleobases. References: [1] Van Der Velden, W. and Schwarts, A. W. (1977) Geochim. Cosmochim. Acta, 41, 961-968. [2] Stoks, P. G. and Schwartz, A. W. (1979a) Nature, 282, 709-10. [3] Glavin, D. P. and Bada, J. L. (2004) In Lunar and Planetary Science XXXV, Abstract # 1022, Houston. [4] Nir, E., Grace, L. I., Brauer, B. and de Vries, M. S. (1999) Journal of the American Chemical Society, 121, 4896-4897.

  6. Oxidative stress modulates nucleobase transport in microvascular endothelial cells.

    PubMed

    Bone, Derek B J; Antic, Milica; Vilas, Gonzalo; Hammond, James R

    2014-09-01

    Purine nucleosides and nucleobases play key roles in the physiological response to vascular ischemia/reperfusion events. The intra- and extracellular concentrations of these compounds are controlled, in part, by equilibrative nucleoside transporter subtype 1 (ENT1; SLC29A1) and by equilibrative nucleobase transporter subtype 1 (ENBT1). These transporters are expressed at the membranes of numerous cell types including microvascular endothelial cells. We studied the impact of reactive oxygen species on the function of ENT1 and ENBT1 in primary (CMVEC) and immortalized (HMEC-1) human microvascular endothelial cells. Both cell types displayed similar transporter expression profiles, with the majority (>90%) of 2-chloro[(3)H]adenosine (nucleoside) uptake mediated by ENT1 and [(3)H]hypoxanthine (nucleobase) uptake mediated by ENBT1. An in vitro mineral oil-overlay model of ischemia/reperfusion had no effect on ENT1 function, but significantly reduced ENBT1 Vmax in both cell types. This decrease in transport function was mimicked by the intracellular superoxide generator menadione and could be reversed by the superoxide dismutase mimetic MnTMPyP. In contrast, neither the extracellular peroxide donor TBHP nor the extracellular peroxynitrite donor 3-morpholinosydnonimine (SIN-1) affected ENBT1-mediated [(3)H]hypoxanthine uptake. SIN-1 did, however, enhance ENT1-mediated 2-chloro[(3)H]adenosine uptake. Our data establish HMEC-1 as an appropriate model for study of purine transport in CMVEC. Additionally, these data suggest that the generation of intracellular superoxide in ischemia/reperfusion leads to the down-regulation of ENBT1 function. Modification of purine transport by oxidant stress may contribute to ischemia/reperfusion induced vascular damage and should be considered in the development of therapeutic strategies. PMID:24976360

  7. Fluorescent 2-Aminopyridine Nucleobases for Triplex-Forming Peptide Nucleic Acids.

    PubMed

    Cheruiyot, Samwel K; Rozners, Eriks

    2016-08-17

    Development of new fluorescent peptide nucleic acids (PNAs) is important for fundamental research and practical applications. The goal of this study was the design of fluorogenic nucleobases for incorporation in triplex-forming PNAs. The underlying design principle was the use of a protonation event that accompanied binding of a 2-aminopyridine (M) nucleobase to a G-C base pair as an on switch for a fluorescence signal. Two fluorogenic nucleobases, 3-(1-phenylethynyl)-M and phenylpyrrolo-M, were designed, synthesized and studied. The new M derivatives provided modest enhancement of fluorescence upon protonation but showed reduced RNA binding affinity and quenching of fluorescence signal upon triple-helix formation with cognate double-stranded RNA. Our study illustrates the principal challenges of design and provides guidelines for future improvement of fluorogenic PNA nucleobases. The 3-(1-phenylethynyl)-M may be used as a fluorescent nucleobase to study PNA-RNA triple-helix formation. PMID:27223320

  8. Adeninealkylresorcinol, the first alkylresorcinol tethered with nucleobase from Lasiodiplodia sp.

    PubMed

    Gao, Yu-Meng; Sun, Tian-Yu; Ma, Min; Chen, Guo-Dong; Zhou, Zheng-Qun; Wang, Chuan-Xi; Hu, Dan; Chen, Li-Guo; Yao, Xin-Sheng; Gao, Hao

    2016-07-01

    Adeninealkylresorcinol (1), an unusual alkylresorcinol with adenine-alkylresorcinol conjoined skeleton, was isolated from an endophytic fungus Lasiodiplodia sp. obtained from a traditional Chinese medicine Houttuynia cordata Thunb., together with three new biogenetically related compounds (2-4). Their structures were elucidated by comprehensive spectroscopic analysis, and the absolute configuration of 4 was determined by the modified Mosher's method and quantum chemical calculation. Among them, adeninealkylresorcinol (1) is the first alkylresorcinol tethered with nucleobase. In addition, the antioxidant, cytotoxic, and antimicrobial activities of 1-3 were evaluated. PMID:27343368

  9. A Versatile Approach Towards Nucleobase-Modified Aptamers.

    PubMed

    Tolle, Fabian; Brändle, Gerhard M; Matzner, Daniel; Mayer, Günter

    2015-09-01

    A novel and versatile method has been developed for modular expansion of the chemical space of nucleic acid libraries, thus enabling the generation of nucleobase-modified aptamers with unprecedented recognition properties. Reintroduction of the modification after enzymatic replication gives broad access to many chemical modifications. This wide applicability, which is not limited to a single modification, will rapidly advance the application of in vitro selection approaches beyond what is currently feasible and enable the generation of aptamers to many targets that have so far not been addressable. PMID:26224087

  10. Probing nucleobase photo protection with soft x-rays

    NASA Astrophysics Data System (ADS)

    Gühr, Markus

    2013-05-01

    We [1] present a new method for ultrafast spectroscopy of molecular photoexcited dynamics. The technique uses a pair of femtosecond pulses: a photoexcitation pulse initiating excited state dynamics followed by a soft x-ray (SXR) probe pulse that core ionizes certain atoms inside the molecule. We observe the Auger decay of the core hole as a function of delay between the photoexcitation and SXR pulses. The core hole decay is particularly sensitive to the local valence electrons near the core and shows new types of propensity rules, compared to dipole selection rules in SXR absorption or emission spectroscopy. We apply the delayed ultrafast x-ray Auger probing (DUXAP) method to the specific problem of nucleobase photoprotection to demonstrate its potential. The ultraviolet photoexcited ππ * states of nucleobases are prone to chemical reactions with neighboring bases. To avoid this, the single molecules funnel the ππ * population to lower lying electronic states on an ultrafast timescale under violation of the Born-Oppenheimer approximation. The new type of propensity rule, which is confirmed by Auger decay simulations, allows us to have increased sensitivity on the direct relaxation from the ππ * state to the vibrationally hot electronic ground state. For the nucleobase thymine, we measure a decay of the ππ * state and a subsequent filling of the vibrationally hot ground state in 300 fs. This work was supported by the AMOS program within the Chemical Sciences, Geosciences, and Biosciences Division of the Office of Basic Energy Sciences, Office of Science, U.S. Department of Energy.Portions of this research were carried out at the Linac Coherent Light Source (LCLS) at the SLAC National Accelerator Laboratory. LCLS is an Office of Science User Facility operated for the U.S. Department of Energy Office of Science by Stanford University. Other portions of this research were carried out at the Advanced Light Source, which is supported by the Director, Office of

  11. Investigation of Fretting by Microscopic Observation

    NASA Technical Reports Server (NTRS)

    Godfrey, Douglas

    1951-01-01

    An experimental investigation, using microscopic observation and color motion photomicrographs of the action, was conducted to determine the cause of fretting. Glass and other noncorrosive materials, as well as metals, were used as specimens. A very simple apparatus vibrated convex surfaces in contact with stationary flat surfaces at frequencies of 120 cycles or less than l cycle per second, an amplitude of 0.0001 inch, and load of 0.2 pound.

  12. High-Frequency, High-Temperature Fretting Experiments

    NASA Technical Reports Server (NTRS)

    Matlik, J. F.; Farris, T. N.; Haake, F. K.; Swanson, G. R.; Duke, G. C.

    2005-01-01

    Fretting is a structural damage mechanism observed when two nominally clamped surfaces are subjected to an oscillatory loading. A critical location for fretting induced damage has been identified at the blade/disk and blade/damper interfaces of gas turbine engine turbomachinery and space propulsion components. The high-temperature, high-frequency loading environment seen by these components lead to severe stress gradients at the edge-of-contact. These contact stresses drive crack nucleation and propagation in fretting and are very sensitive to the geometry of the contacting bodies, the contact loads, materials, temperature, and contact surface tribology (friction). To diagnose the threat that small and relatively undetectable fretting cracks pose to damage tolerance and structural integrity of in-service components, the objective of this work is to develop a well-characterized experimental fretting rig capable of investigating fretting behavior of advanced aerospace alloys subjected to load and temperature conditions representative of such turbomachinery components.

  13. The role of oxidation in the fretting wear process

    NASA Technical Reports Server (NTRS)

    Bill, R. C.

    1980-01-01

    Fretting experiments were conducted on titanium, a series of Ni-Cr-Al alloys and on some high temperature turbine alloys at room temperature and at elevated temperatures in air and in various inert environments. It was found that, depending on temperature and environment, the fretting behavior of the materials examined could be classified according to four general types of behavior. Briefly, these types of behavior were: (1) the complete absence of oxidation, as in inert environments, generally leading to low rates of fretting wear but high fretting friction; (2) gradual attrition of surface oxide with each fretting stroke, found in these experiments to operate in concert with other dominating mechanisms; (3) rapid oxidation at surface fatigue damage sites, resulting in undermining and rapid disintegration of the load bearing surface; and (4) the formation of coherent, protective oxide film, resulting in low rates of fretting wear. An analytical model predicting conditions favorable to the fourth type of behavior was outlined.

  14. The effect of lubricant additives on fretting wear

    NASA Astrophysics Data System (ADS)

    Qiu, Y.; Roylance, B. J.

    1992-10-01

    The effect of lubricant additives on fretting wear has been investigated using a ball-on-plate machine. The test results confirm that the antiwear additives, e.g. phospho-sulphurized terpene, sulphurized esters and sulphurized paraffins, are effective in reducing friction and wear. Examination of worn surfaces by optical and electron microscope inspection indicated the presence of thin films which had been deposited under fretting action when using oils containing these additives. Unlubricated fretting wear occurred in the scuffing region. In contrast, the lubricated fretting wear with the lubricating oils containing the antiwear additives took place in the mixed lubrication region. In lubricated fretting wear, the size of the wear particles was smaller than with dry fretting wear.

  15. Coupled thermoelastic analysis of fretting contacts

    NASA Astrophysics Data System (ADS)

    Ganapathy, Harish

    Fretting fatigue is the contact phenomenon occurring when two bodies in contact experience oscillatory loads. The surface tribology and contact stress evolution in a fretting contact has been studied using coupled thermoelastic analysis. Both, an aluminum and titanium alloy have been studied. Full-field real-time in-situ temperature maps of the contact region and its vicinity have been obtained using a multi-element infrared camera. The distinguishing features of the contact including the sliding regime, partial slip contact, bulk stress effects, boundary conditions effects etc. have been successfully captured using temperature measurement of the order of millikelvin. The coupled thermoclastic response of aluminum and titanium alloy has been successfully characterized, including the mean stress effect. A full coupled thermoelastic finite element model with Coulomb friction, frictional heating and gap conductance, has been used to predict the experimental temperatures. Changes in loads and changes in the coefficient of friction produce changes in different areas of the temperature field. The coupled thermoelastic effect may be used as a powerful tool to guide the march towards the complete understanding of the phenomenon of fretting. The method has been successfully used to guide the finite element analysis of a lap joint specimen.

  16. FRET-based glucose monitoring for bioprocessing

    NASA Astrophysics Data System (ADS)

    Bartolome, Amelita; Smalls-Mantey, Lauren; Lin, Debora; Rao, Govind; Tolosa, Leah

    2006-02-01

    The glucose-mediated conformational changes in the glucose binding protein (GBP) have been exploited in the development of fluorescence based glucose sensors. The fluorescence response is generated by a polarity sensitive dye attached to a specific site. Such fluorescent sensors respond to submicromolar glucose at diffusion-controlled rates mimicking the wild type. However, such sensors have been limited to in vitro glucose sensing because of the preliminary dye-labeling step. In the study described here, the dye-labeling step is omitted by genetically encoding the GBP with two green fluorescent mutants namely, the green fluorescent protein (GFP) and the yellow fluorescent protein (YFP) in the N- and C-terminal ends, respectively. These two GFP mutants comprise a fluorescence resonance energy transfer (FRET) donor and acceptor pair. Thus, when glucose binds with GBP, the conformational changes affect the FRET efficiency yielding a dose-dependent response. A potential application for this FRET-based glucose biosensor is online glucose sensing in bioprocessing and cell culture. This was demonstrated by the measurement of glucose consumption in yeast fermentation. Further development of this system should yield in vivo measurement of glucose in bioprocesses.

  17. Two-Photon-Induced Fluorescence of Isomorphic Nucleobase Analogs

    PubMed Central

    Lane, Richard S. K.; Jones, Rosemary; Sinkeldam, Renatus W.

    2014-01-01

    Five isomorphic fluorescent uridine mimics have been subjected to two-photon (2P) excitation analysis to investigate their potential applicability as non-perturbing probes for the single-molecule detection of nucleic acids. We find that small structural differences can cause major changes in the two-photon excitation probability, with the 2P cross sections varying by over one order of magnitude. Two of the probes, both furan-modified uridine analogs, have the highest 2P cross sections (3.8 GM and 7.6 GM) reported for nucleobase analogs, using a conventional Ti:sapphire laser for excitation at 690 nm; they also have the lowest emission quantum yields. In contrast, the analogs with the highest reported quantum yields have the lowest 2P cross sections. The structure-photophysical property relationship presented here is a first step towards the rational design of emissive nucleobase analogs with controlled 2P characteristics. The results demonstrate the potential for major improvements through judicious structural modifications. PMID:24604669

  18. Distinction of nucleobases – a tip-enhanced Raman approach

    PubMed Central

    Treffer, Regina; Lin, Xiumei; Bailo, Elena; Deckert-Gaudig, Tanja

    2011-01-01

    Summary The development of novel DNA sequencing methods is one of the ongoing challenges in various fields of research seeking to address the demand for sequence information. However, many of these techniques rely on some kind of labeling or amplification steps. Here we investigate the intrinsic properties of tip-enhanced Raman scattering (TERS) towards the development of a novel, label-free, direct sequencing method. It is known that TERS allows the acquisition of spectral information with high lateral resolution and single-molecule sensitivity. In the presented experiments, single stranded adenine and uracil homopolymers were immobilized on different kinds of substrates (mica and gold nanoplates) and TERS experiments were conducted, which demonstrated the reproducibility of the technique. To elucidate the signal contributions from the specific nucleobases, TERS spectra were collected on single stranded calf thymus DNA with arbitrary sequence. The results show that, while the Raman signals with respect to the four nucleobases differ remarkably, specific markers can be determined for each respective base. The combination of sensitivity and reproducibility shows that the crucial demands for a sequencing procedure are met. PMID:22003468

  19. RNA fragment modeling with a nucleobase discrete-state model

    NASA Astrophysics Data System (ADS)

    Zhang, Jian; Bian, Yunqiang; Lin, Hui; Wang, Wei

    2012-02-01

    In this work we develop an approach for predicting the tertiary structures of RNA fragments by combining an RNA nucleobase discrete state (RNAnbds) model, a sequential Monte Carlo method, and a statistical potential. The RNAnbds model is designed for optimizing the configuration of nucleobases with respect to their preceding ones along the sequence and their spatial neighbors, in contrast to previous works that focus on RNA backbones. The tests of our approach with the fragments taken from a small RNA pseudoknot and a 23S ribosome RNA show that for short fragments (<10 nucleotides), the root mean square deviations (RMSDs) between the predicted and the experimental ones are generally smaller than 3 Å; for slightly longer fragments (10-15 nucleotides), most RMSDs are smaller than 4 Å. The comparison of our method with another physics-based predictor with a testing set containing nine loops shows that ours is superior in both accuracy and efficiency. Our approach is useful in facilitating RNA three-dimensional structure prediction as well as loop modeling. It also holds the promise of providing insight into the structural ensembles of RNA loops.

  20. Microstructural characterization of titanium alloys with fretting damage

    NASA Astrophysics Data System (ADS)

    Swalla, Dana Ray

    The primary focus of this work is to understand the role of microstructure in the fretting damage process and develop quantifying measures in fretting damage accumulation in a dual phase Ti-6Al-4V as well as two single phase materials: commercially pure titanium (CP-Ti), which consists of pure alpha-phase titanium, and a near alpha Ti-5Al-2.5Sn. The size and distribution of crystallographic orientation of the alpha-phase, which has an HCP crystalline structure, is significant in fretting crack formation. In particular, the effect of slip displacement amplitude and number of fretting cycles on the evolution of grain morphology, grain orientation, misorientation distribution, composition, and microhardness is investigated. The fretting behavior is also related to the macroscopic monotonic and cyclic deformation response. The research goals are accomplished using state-of-the-art surface characterization tools such as orientation image microscopy (OIM) using electron backscatter diffraction (EBSD), energy dispersive X-ray analysis (EDX) and nanoindentation. This study is the first of its kind to use OIM to characterize fretting damage and also makes contributions to the body of knowledge about deformation mechanisms in titanium alloys. The results provide a foundation for developing and validating computational crystal plasticity models and their application to fretting and sliding contact problems. New fretting assessment measures have also been identified and have application for components that suffer from fretting wear and/or fatigue related failures.

  1. Effect of humidity on fretting wear of several pure metals

    NASA Technical Reports Server (NTRS)

    Goto, H.; Buckley, D. H.

    1984-01-01

    Fretting wear experiments with several pure metals were conducted in air at various relative humidity levels. The materials used were iron, aluminum, copper, silver, chromium, titanium, and nickel. Each pure metal had a maximum fretting wear volume at a specific humidity level RH sub max that was not dependent on mechanical factors such as contact load, fretting amplitude, and frequency in the ranges studied. The weight loss due to fretting wear at RH sub max for each pure metal decreased with increasing heat of oxygen adsorption on the metal, indicating that adhesive wear dominated at RH sub max.

  2. In silico FRET from simulated dye dynamics

    NASA Astrophysics Data System (ADS)

    Hoefling, Martin; Grubmüller, Helmut

    2013-03-01

    Single molecule fluorescence resonance energy transfer (smFRET) experiments probe molecular distances on the nanometer scale. In such experiments, distances are recorded from FRET transfer efficiencies via the Förster formula, E=1/(1+(). The energy transfer however also depends on the mutual orientation of the two dyes used as distance reporter. Since this information is typically inaccessible in FRET experiments, one has to rely on approximations, which reduce the accuracy of these distance measurements. A common approximation is an isotropic and uncorrelated dye orientation distribution. To assess the impact of such approximations, we present the algorithms and implementation of a computational toolkit for the simulation of smFRET on the basis of molecular dynamics (MD) trajectory ensembles. In this study, the dye orientation dynamics, which are used to determine dynamic FRET efficiencies, are extracted from MD simulations. In a subsequent step, photons and bursts are generated using a Monte Carlo algorithm. The application of the developed toolkit on a poly-proline system demonstrated good agreement between smFRET simulations and experimental results and therefore confirms our computational method. Furthermore, it enabled the identification of the structural basis of measured heterogeneity. The presented computational toolkit is written in Python, available as open-source, applicable to arbitrary systems and can easily be extended and adapted to further problems. Catalogue identifier: AENV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPLv3, the bundled SIMD friendly Mersenne twister implementation [1] is provided under the SFMT-License. No. of lines in distributed program, including test data, etc.: 317880 No. of bytes in distributed program, including test data, etc.: 54774217 Distribution format: tar.gz Programming language

  3. Click Reaction on Solid Phase Enables High Fidelity Synthesis of Nucleobase-Modified DNA.

    PubMed

    Tolle, Fabian; Rosenthal, Malte; Pfeiffer, Franziska; Mayer, Günter

    2016-03-16

    The post-synthetic functionalization of nucleic acids via click chemistry (CuAAC) has seen tremendous implementation, extending the applicability of nucleobase-modified nucleic acids in fields like fluorescent labeling, nanotechnology, and in vitro selection. However, the production of large quantities of high-density functionalized material via solid phase synthesis has been hampered by oxidative by-product formation associated with the alkaline workup conditions. Herein, we describe a rapid and cost-effective protocol for the high fidelity large-scale production of nucleobase-modified nucleic acids, exemplified with a recently described nucleobase-modified aptamer. PMID:26850226

  4. Optofluidic FRET Lasers Using Aqueous Quantum Dots as Donors

    PubMed Central

    Chen, Qiushu; Kiraz, Alper; Fan, Xudong

    2015-01-01

    An optofluidic FRET (fluorescence resonance energy transfer) laser is formed by putting FRET pairs inside a microcavity acting as gain medium. This integration of optofluidic laser and FRET mechanism provides novel research frontiers, including sensitive biochemical analysis and novel photonic devices, such as on-chip coherent light sources and bio-tunable lasers. Here we investigated an optofluidic FRET laser using quantum dots (QDs) as FRET donors. We achieved lasing from Cy5 as the acceptor in the QD-Cy5 pair when excited at 450 nm where Cy5 has negligible absorption by itself. The threshold was approximately 14 µJ/mm2. The demonstrated capability of QDs as the donor in a FRET laser greatly improves the versatility of optofluidic laser operation due to the broad and large absorption cross section of QDs in the blue and UV spectral region. The excitation efficiency of the acceptor molecules through FRET channel was also analyzed, showing that the energy transfer rate and the non-radiative Auger recombination rate of QDs plays a significant role in FRET laser performance. PMID:26659274

  5. Influence of Fretting Wear on Lifetime of Tin Plated Connectors

    NASA Astrophysics Data System (ADS)

    Ikeda, Hirosaka; Ito, Tetsuya; Sawada, Shigeru; Hattori, Yasuhiro; Saitoh, Yasushi; Tamai, Terutaka; Iida, Kazuo

    Due to the recent increase in electronic devices mounted on automobiles, a large number of connectors, especially low-cost tin plated connectors are being used. As a result, their contact reliability has become problematic. Furthermore, for the connectors which are subjected to fretting wear caused by heat cycle and vibrations, the contact resistance increases because of wear of tin and deposition of oxides, which generates problems of poor contact. This study is intended to analyze the change in contact resistance of tin plated connectors from the start of fretting wear to the end of their lifetime from the viewpoint of practical reliability, and to observe the trace and the characteristics of fretting wear microscopically. This study found that wear and oxidation of tin plated connectors start immediately with fretting wear, and thus accumulation of abrasion powder on fretting areas causes connectors to reach to the end of their useful lifetime quickly. Especially, it was demonstrated that amplitude of fretting has a considerable influence on a connector's lifetime. It is made clear that air-tightness, so-called “gas-tight” of tin in a fretting area influences fretting wear considerably.

  6. Remote field eddy current inspection of support plate fretting wear

    SciTech Connect

    Shatat, A.; Atherton, D.L.

    1997-03-01

    This article demonstrates how the remote field eddy current technique might be extended to measure support plate fretting wear in heat exchanger tubes. A finite element analysis was used to examine the plate`s effect on the eddy current signal. Experimental data lend support to a suggested multifrequency method for sizing fretting grooves.

  7. BOBA FRET: Bootstrap-Based Analysis of Single-Molecule FRET Data

    PubMed Central

    König, Sebastian L. B.; Hadzic, Mélodie; Fiorini, Erica; Börner, Richard; Kowerko, Danny; Blanckenhorn, Wolf U.; Sigel, Roland K. O.

    2013-01-01

    Time-binned single-molecule Förster resonance energy transfer (smFRET) experiments with surface-tethered nucleic acids or proteins permit to follow folding and catalysis of single molecules in real-time. Due to the intrinsically low signal-to-noise ratio (SNR) in smFRET time traces, research over the past years has focused on the development of new methods to extract discrete states (conformations) from noisy data. However, limited observation time typically leads to pronounced cross-sample variability, i.e., single molecules display differences in the relative population of states and the corresponding conversion rates. Quantification of cross-sample variability is necessary to perform statistical testing in order to assess whether changes observed in response to an experimental parameter (metal ion concentration, the presence of a ligand, etc.) are significant. However, such hypothesis testing has been disregarded to date, precluding robust biological interpretation. Here, we address this problem by a bootstrap-based approach to estimate the experimental variability. Simulated time traces are presented to assess the robustness of the algorithm in conjunction with approaches commonly used in thermodynamic and kinetic analysis of time-binned smFRET data. Furthermore, a pair of functionally important sequences derived from the self-cleaving group II intron Sc.ai5γ (d3'EBS1*/IBS1*) is used as a model system. Through statistical hypothesis testing, divalent metal ions are shown to have a statistically significant effect on both thermodynamic and kinetic aspects of their interaction. The Matlab source code used for analysis (bootstrap-based analysis of smFRET data, BOBA FRET), as well as a graphical user interface, is available via http://www.aci.uzh.ch/rna/. PMID:24386343

  8. Metal ion mediated nucleobase recognition by the ZTP riboswitch

    PubMed Central

    Trausch, Jeremiah J.; Marcano-Velázquez, Joan G.; Matyjasik, Michal M.; Batey, Robert T.

    2015-01-01

    SUMMARY The ZTP riboswitch is a widespread family of regulatory RNAs that upregulate de novo purine synthesis in response to increased intracellular levels of ZTP or ZMP (AICAR). As an important intermediate in purine biosynthesis, ZMP also serves as a proxy for the concentration of 10-formyltetrahydrofolate, a key component of one carbon metabolism. Here we report the structure of the ZTP riboswitch bound to ZMP at a resolution of 1.80 Å. The RNA contains two subdomains brought together through a long-range pseudoknot further stabilized through helix-helix packing. ZMP is bound at the subdomain interface of the RNA through a set of interactions with the ligand's base, ribose sugar and phosphate moieties. Unique to nucleobase recognition by RNAs, the Z base is inner sphere coordinated to a magnesium cation bound by two backbone phosphates. This interaction, along with steric hindrance by the backbone, imparts specificity over related analogs such as ATP/AMP. PMID:26144884

  9. Large Scale Bacterial Colony Screening of Diversified FRET Biosensors

    PubMed Central

    Litzlbauer, Julia; Schifferer, Martina; Ng, David; Fabritius, Arne; Thestrup, Thomas; Griesbeck, Oliver

    2015-01-01

    Biosensors based on Förster Resonance Energy Transfer (FRET) between fluorescent protein mutants have started to revolutionize physiology and biochemistry. However, many types of FRET biosensors show relatively small FRET changes, making measurements with these probes challenging when used under sub-optimal experimental conditions. Thus, a major effort in the field currently lies in designing new optimization strategies for these types of sensors. Here we describe procedures for optimizing FRET changes by large scale screening of mutant biosensor libraries in bacterial colonies. We describe optimization of biosensor expression, permeabilization of bacteria, software tools for analysis, and screening conditions. The procedures reported here may help in improving FRET changes in multiple suitable classes of biosensors. PMID:26061878

  10. Anchoring of FRET Sensors—A Requirement for Spatiotemporal Resolution

    PubMed Central

    Ivanova, Elena V.; Figueroa, Ricardo A.; Gatsinzi, Tom; Hallberg, Einar; Iverfeldt, Kerstin

    2016-01-01

    FRET biosensors have become a routine tool for investigating mechanisms and components of cell signaling. Strategies for improving them for particular applications are continuously sought. One important aspect to consider when designing FRET probes is the dynamic distribution and propagation of signals within living cells. We have addressed this issue by directly comparing an anchored (taFS) to a non-anchored (naFS) cleavable FRET sensor. We chose a microtubule-associated protein tau as an anchor, as microtubules are abundant throughout the cytosol of cells. We show that tau-anchored FRET sensors are concentrated at the cytoskeleton and enriched in the neurite-like processes of cells, providing high intensity of the total signal. In addition, anchoring limits the diffusion of the sensor, enabling spatiotemporally resolved monitoring of subcellular variations in enzyme activity. Thus, anchoring is an important aspect to consider when designing FRET sensors for deeper understanding of cell signaling. PMID:27196902

  11. Anchoring of FRET Sensors-A Requirement for Spatiotemporal Resolution.

    PubMed

    Ivanova, Elena V; Figueroa, Ricardo A; Gatsinzi, Tom; Hallberg, Einar; Iverfeldt, Kerstin

    2016-01-01

    FRET biosensors have become a routine tool for investigating mechanisms and components of cell signaling. Strategies for improving them for particular applications are continuously sought. One important aspect to consider when designing FRET probes is the dynamic distribution and propagation of signals within living cells. We have addressed this issue by directly comparing an anchored (taFS) to a non-anchored (naFS) cleavable FRET sensor. We chose a microtubule-associated protein tau as an anchor, as microtubules are abundant throughout the cytosol of cells. We show that tau-anchored FRET sensors are concentrated at the cytoskeleton and enriched in the neurite-like processes of cells, providing high intensity of the total signal. In addition, anchoring limits the diffusion of the sensor, enabling spatiotemporally resolved monitoring of subcellular variations in enzyme activity. Thus, anchoring is an important aspect to consider when designing FRET sensors for deeper understanding of cell signaling. PMID:27196902

  12. X-Ray Photoelectron Spectroscopy (XPS) of Bacteriorhodopsin Analogues Synthesized from Fluorophenyl Retinals

    NASA Astrophysics Data System (ADS)

    Takahashi, Masae; Takahashi, Takashi; Tokunaga, Fumio; Murano, Kentaro; Tsujimoto, Kazuo; Sagawa, Takasi

    1984-04-01

    The two external point-charge (TEPC) model for bacteriorhodopsin (bR) has been examined by X-ray photoelectron spectroscopy (XPS) and CNDO/S molecular orbital calculations. A main concern was given to a point charge near the β-ionone ring. XPS measurements were carried out on fluorophenyl retinal (F-ret) and their derivatives (Schiff base, protonated Schiff base and bacteriorhodopsin analogues (F-bR)), paying close attention to the chemical shift of the F 1s core level. No meaningful differences were observed among these species although numerical calculations on an assumption of the TEPC model have predicted the chemical shift of about 3 eV between F-ret and F-bR. This fact has arisen a serious question to the validity of the TEPC model. The same conclusion has been reached by the present study of absorption maxima of F-ret and their derivatives.

  13. Photo-Irradiation of Pyrimidine in Interstellar Ice Analogs: Searching for Nucleobases

    NASA Astrophysics Data System (ADS)

    Milam, S. N.; Nuevo, M.; Sandford, S. A.; Elsila, J. E.; Dworkin, J. P.

    2009-03-01

    Nucleobases have been detected in meteorites and possibly form in space. The functionalization of PAHs from UV photons in mixed ices has proven effective in the lab. Here we investigate how irradiation affects pyrimidine in interstellar ice analogs.

  14. Nucleobases and Other Prebiotic Species from the Ultraviolet Irradiation of Pyrimidine in Astrophysical Ices

    NASA Astrophysics Data System (ADS)

    Sandford, S. A.; Nuevo, M.; Materese, C. K.; Milam, S. N.

    2012-03-01

    We discuss the results of UV irradiation of ices containing pyrimidine and show that such processing efficiently forms the nucleobases uracil and cytosine, but not thymine, a pattern similar to what is seen in carbonaceous meteorites.

  15. Formation of Nucleobases from the UV Photo-Irradiation of Pyrimidine in Astrophysical Ice Analogs

    NASA Astrophysics Data System (ADS)

    Milam, S. N.; Nuevo, M.; Sandford, S. A.; Elsila, J. E.; Dworkin, J. P.

    2010-04-01

    This work shows how pyrimidic nucleobases (uracil, cytosine, etc.) can be formed under abiotic conditions from the UV irradiation of pyrimidine in astrophysical ices. The formation mechanisms and the photo-stability of such compounds are discussed.

  16. Binding Strength of Nucleobases and Nucleosides on Silver Nanoparticles Probed by a Colorimetric Method.

    PubMed

    Yu, Lu; Li, Na

    2016-06-01

    Because of their unique and tunable properties, oligonucleotide-functionalized noble metal nanoparticles have provided a versatile platform for various engineering and biomedical applications. The vast majority of such applications were demonstrated with gold nanoparticles (AuNPs) while only a few were demonstrated with sliver nanoparticles (AgNPs). This is largely due to the lack of robust protocols to functionalize AgNPs with thiol-modified oligonucleotides. Previous studies have revealed strong interactions between nucleobases and AgNPs. This could enable an alternative way to functionalize AgNPs with non-thiolated oligonucleotides. However, there is no quantitative study on the interaction strengths between AgNPs and oligonucleotides. Several methods have been used for quantitative evaluation of the interaction strengths between AuNPs and oligonucleotides. These methods often require specialized equipment that might not be widely accessible or rely on labor-intensive procedures to obtain the adsorption isotherms. Herein, we developed a colorimetric method, as a simple and high-throughput alternative of existing methods, to quantify the binding strength between AgNPs and nucleobases/nucleosides. In this colorimetric method, concentration-dependent destabilizing effects of nucleobase/nucleoside adsorption on AgNPs are utilized to indirectly quantify the amount of nucleobases/nucleosides adsorbed on AgNPs, thus deriving the binding strength between AgNPs and nucleobases/nucleosides. First, the concentration-dependent AgNP aggregation kinetics in the presence of nucleobases/nucleosides were systematically investigated. Then, this colorimetric method was used to determine the binding strengths between AgNPs and various DNA/RNA nucleobases/nucleosides. It was found that the ranking of interaction strengths between AgNPs and DNA/RNA nucleosides (dC < dT < dA, rC < rU < rA) is generally agreed with that between AgNPs and corresponding nucleobases (C < T < U < A). This

  17. FLIM-FRET for Cancer Applications

    PubMed Central

    Rajoria, Shilpi; Zhao, Lingling; Intes, Xavier; Barroso, Margarida

    2015-01-01

    Optical imaging assays, especially fluorescence molecular assays, are minimally invasive if not completely noninvasive, and thus an ideal technique to be applied to live specimens. These fluorescence imaging assays are a powerful tool in biomedical sciences as they allow the study of a wide range of molecular and physiological events occurring in biological systems. Furthermore, optical imaging assays bridge the gap between the in vitro cell-based analysis of subcellular processes and in vivo study of disease mechanisms in small animal models. In particular, the application of Förster resonance energy transfer (FRET) and fluorescence lifetime imaging (FLIM), well-known techniques widely used in microscopy, to the optical imaging assay toolbox, will have a significant impact in the molecular study of protein-protein interactions during cancer progression. This review article describes the application of FLIM-FRET to the field of optical imaging and addresses their various applications, both current and potential, to anti-cancer drug delivery and cancer research. PMID:26023359

  18. Synthesis of alanyl nucleobase amino acids and their incorporation into proteins.

    PubMed

    Talukder, Poulami; Dedkova, Larisa M; Ellington, Andrew D; Yakovchuk, Petro; Lim, Jaebum; Anslyn, Eric V; Hecht, Sidney M

    2016-09-15

    Proteins which bind to nucleic acids and regulate their structure and functions are numerous and exceptionally important. Such proteins employ a variety of strategies for recognition of the relevant structural elements in their nucleic acid substrates, some of which have been shown to involve rather subtle interactions which might have been difficult to design from first principles. In the present study, we have explored the preparation of proteins containing unnatural amino acids having nucleobase side chains. In principle, the introduction of multiple nucleobase amino acids into the nucleic acid binding domain of a protein should enable these modified proteins to interact with their nucleic acid substrates using Watson-Crick and other base pairing interactions. We describe the synthesis of five alanyl nucleobase amino acids protected in a fashion which enabled their attachment to a suppressor tRNA, and their incorporation into each of two proteins with acceptable efficiencies. The nucleobases studied included cytosine, uracil, thymine, adenine and guanine, i.e. the major nucleobase constituents of DNA and RNA. Dihydrofolate reductase was chosen as one model protein to enable direct comparison of the facility of incorporation of the nucleobase amino acids with numerous other unnatural amino acids studied previously. The Klenow fragment of DNA polymerase I was chosen as a representative DNA binding protein whose mode of action has been studied in detail. PMID:27452282

  19. Adsorption of nucleobase pairs on hexagonal boron nitride sheet: hydrogen bonding versus stacking.

    PubMed

    Ding, Ning; Chen, Xiangfeng; Wu, Chi-Man Lawrence; Li, Hui

    2013-07-14

    The adsorption of hydrogen-bonded and stacked nucleobase pairs on the hexagonal boron nitride (h-BN) surface was studied by density functional theory and molecular dynamics methods. Eight types of nucleobase pairs (i.e., GG, AA, TT, CC, UU, AT, GC, and AU) were chosen as the adsorbates. The adsorption configurations, interaction energies, and electronic properties of the nucleobase pair on the h-BN surface were obtained and compared. The density of states analysis result shows that both the hydrogen-bonded and stacked nucleobase pairs were physisorbed on h-BN with minimal charge transfer. The hydrogen-bonded base pairs lying on the h-BN surface are significantly more stable than the stacked forms in both the gas and water phase. The molecular dynamics simulation result indicates that h-BN possessed high sensitivity for the nucleobases and the h-BN surface adsorption could revert the base pair interaction from stacking back to hydrogen bonding in aqueous environment. The h-BN surface could immobilize the nucleobases on its surface, which suggests the use of h-BN has good potential in DNA/RNA detection biosensors and self-assembly nanodevices. PMID:23689542

  20. Adsorption of DNA/RNA nucleobases on hexagonal boron nitride sheet: an ab initio study.

    PubMed

    Lin, Qing; Zou, Xiaolong; Zhou, Gang; Liu, Rui; Wu, Jian; Li, Jia; Duan, Wenhui

    2011-07-14

    Our ab initio calculations indicate that the interaction of deoxyribonucleic/ribonucleic acid (DNA/RNA) nucleobases [guanine (G), adenine (A), thymine (T), cytosine (C), and uracil (U)] with the hexagonal boron nitride (h-BN) sheet, a polar but chemically inert surface, is governed by mutual polarization. Unlike the case of graphene, all nucleobases exhibit the same stacking arrangement on the h-BN sheet due to polarization effects: the anions (N and O atoms) of nucleobases prefer to stay on top of cations (B) of the substrate as far as possible, regardless of the biological properties of nucleobases. The adsorption energies, ranging from 0.5 eV to 0.69 eV, increase in the order of U, C, T, A and G, which can be attributed to different side groups or atoms of nucleobases. The fundamental nature of DNA/RNA nucleobases and h-BN sheet remains unchanged upon adsorption, suggesting that the h-BN sheet is a promising template for DNA/RNA-related research, such as self-assembly. PMID:21637870

  1. Which Electronic and Structural Factors Control the Photostability of DNA and RNA Purine Nucleobases?

    NASA Astrophysics Data System (ADS)

    Pollum, Marvin; Reichardt, Christian; Crespo-Hernández, Carlos E.; Martínez-Fernández, Lara; Corral, Inés; Rauer, Clemens; Mai, Sebastian; Marquetand, Philipp; González, Leticia

    2015-06-01

    Following ultraviolet excitation, the canonical purine nucleobases, guanine and adenine, are able to efficiently dissipate the absorbed energy within hundreds of femtoseconds. This property affords these nucleobases with great photostability. Conversely, non-canonical purine nucleobases exhibit high fluorescence quantum yields or efficiently populate long-lived triplet excited states from which chemistry can occur. Using femtosecond broadband transient absorption spectroscopy in combination with ab initio static and surface hopping dynamics simulations we have determined the electronic and structural factors that regulate the excited state dynamics of the purine nucleobase derivatives. Importantly, we have uncovered that the photostability of the guanine and adenine nucleobases is not due to the structure of the purine core itself and that the substituent at the C6 position of the purine nucleobase plays a more important role than that at the C2 position in the ultrafast relaxation of deleterious electronic energy. [The authors acknowledge the CAREER program of the National Science Foundation (Grant No. CHE-1255084) for financial support.

  2. Quantitative tomographic imaging of intermolecular FRET in small animals

    PubMed Central

    Venugopal, Vivek; Chen, Jin; Barroso, Margarida; Intes, Xavier

    2012-01-01

    Forster resonance energy transfer (FRET) is a nonradiative transfer of energy between two fluorescent molecules (a donor and an acceptor) in nanometer range proximity. FRET imaging methods have been applied to proteomic studies and drug discovery applications based on intermolecular FRET efficiency measurements and stoichiometric measurements of FRET interaction as quantitative parameters of interest. Importantly, FRET provides information about biomolecular interactions at a molecular level, well beyond the diffraction limits of standard microscopy techniques. The application of FRET to small animal imaging will allow biomedical researchers to investigate physiological processes occurring at nanometer range in vivo as well as in situ. In this work a new method for the quantitative reconstruction of FRET measurements in small animals, incorporating a full-field tomographic acquisition system with a Monte Carlo based hierarchical reconstruction scheme, is described and validated in murine models. Our main objective is to estimate the relative concentration of two forms of donor species, i.e., a donor molecule involved in FRETing to an acceptor close by and a nonFRETing donor molecule. PMID:23243567

  3. Understanding FRET as a Research Tool for Cellular Studies

    PubMed Central

    Shrestha, Dilip; Jenei, Attila; Nagy, Péter; Vereb, György; Szöllősi, János

    2015-01-01

    Communication of molecular species through dynamic association and/or dissociation at various cellular sites governs biological functions. Understanding these physiological processes require delineation of molecular events occurring at the level of individual complexes in a living cell. Among the few non-invasive approaches with nanometer resolution are methods based on Förster Resonance Energy Transfer (FRET). FRET is effective at a distance of 1–10 nm which is equivalent to the size of macromolecules, thus providing an unprecedented level of detail on molecular interactions. The emergence of fluorescent proteins and SNAP- and CLIP- tag proteins provided FRET with the capability to monitor changes in a molecular complex in real-time making it possible to establish the functional significance of the studied molecules in a native environment. Now, FRET is widely used in biological sciences, including the field of proteomics, signal transduction, diagnostics and drug development to address questions almost unimaginable with biochemical methods and conventional microscopies. However, the underlying physics of FRET often scares biologists. Therefore, in this review, our goal is to introduce FRET to non-physicists in a lucid manner. We will also discuss our contributions to various FRET methodologies based on microscopy and flow cytometry, while describing its application for determining the molecular heterogeneity of the plasma membrane in various cell types. PMID:25815593

  4. Small-molecule FRET probes for protein kinase activity monitoring in living cells

    SciTech Connect

    Vaasa, Angela; Lust, Marje; Terrin, Anna; Uri, Asko; Zaccolo, Manuela

    2010-07-09

    In this study, the applicability of fluorescently labeled adenosine analogue-oligoarginine conjugates (ARC-Photo probes) for monitoring of protein kinase A (PKA) activity in living cells was demonstrated. ARC-Photo probes possessing subnanomolar affinity towards the catalytic subunit of PKA (PKAc) and competitive with the regulatory subunit (PKAr), penetrate cell plasma membrane and associate with PKAc fused with yellow fluorescent protein (PKAc-YFP). Detection of inter-molecular Foerster resonance energy transfer (FRET) efficiency between the fluorophores of the fusion protein and ARC-Photo probe can be used for both the evaluation of non-labeled inhibitors of PKAc and for monitoring of cAMP signaling via detection of changes in the activity of PKA as a cAMP downstream effector.

  5. IODINE MONOCHLORIDE FACILITATED DEGLYCOSYLATION, ANOMERIZATION, AND ISOMERIZATION OF 3-SUBSTITUTED THYMIDINE ANALOGUES

    PubMed Central

    Khalil, Ahmed; Ishita, Keisuke; Ali, Tehane; Tiwari, Rohit; Riachy, Ramy; Toppino, Antonio; Hasabelnaby, Sherifa; Sayfullin, Naum; Oliver, Allen G.; Gallucci, Judith; Huang, Zhenguo; Tjarks, Werner

    2014-01-01

    The reaction of thymidine, 3-mono-, and 3,3′,5′-trialkylsubstitued thymidine analogues with iodine monochloride (ICl) was investigated. Treatment with ICl resulted in rapid deglycosylation, anomerization, and isomerization of thymidine and 3-substituted thymidine analogues under various reaction conditions leading to the formation of the nucleobases as the major products accompanied by minor formation of α-furanosidic-, α-pyranosidic- and β-pyranosidic nucleosides. On the other hand, 3,3′,5′-trisubstitued thymidine analogues were only deglycosylated and anomerized. These results are similar to those observed for the acidic hydrolysis of the glycoside bond in nucleosides, but were presumably caused by the Lewis acid character of an iodine electrophile. PMID:25372994

  6. Friction and fretting wear characteristics of different diamond-like carbon coatings against alumina in water-lubricated fretting conditions.

    PubMed

    Watabe, Tsukasa; Amanov, Auezhan; Tsuboi, Ryo; Sasaki, Shinya

    2013-12-01

    Diamond-like carbon (DLC) coatings typically show low friction and high wear resistance. In this study, the friction and fretting wear characteristics of PVD, CVD and CVD-Si DLC coatings were investigated against an alumina (Al2O3) ball under water-lubricated fretting conditions. The objective of this study is to investigate and compare the friction and fretting wear characteristics of those DLC coatings at various fretting frequencies. The test results showed that the PVD DLC coating led to a lower friction coefficient and a higher resistance to fretting wear compared to those of the CVD and CVD-Si DLC coatings. However, the CVD DLC coating showed that the fretting wear resistance decreases with increasing frequency, while no significant difference in fretting wear resistances of the PVD and CVD-Si DLC coatings was observed. Quantitative surface analyses of the specimens were performed using an energy dispersive spectroscopy (EDS), a laser scanning microscope (LSM), a scanning electron microscope (SEM), an atomic force microscope (AFM) and the Raman spectroscopy. PMID:24266210

  7. Elevated temperature fretting fatigue of nickel based alloys

    NASA Astrophysics Data System (ADS)

    Gean, Matthew C.

    This document details the high temperature fretting fatigue of high temperature nickel based alloys common to turbine disk and blade applications. The research consists of three area of focus: Experiments are conducted to determine quantitatively the fretting fatigue lives of advanced nickel based alloys; Analytical tools are developed and used to investigate the fretting fatigue response of the material; Fractographic analysis of the experimental results is used to improve the analytical models employed in the analysis of the experiments. Sixty three fretting fatigue experiments were conducted at 649 °C using a polycrystalline Nickel specimen in contact with directionally solidified and single crystal Nickel pads. Various influences on the fretting fatigue life are investigated. Shot peened Rene' 95 had better fretting fatigue life compared to shot peened Rene' 88. Shot peening produced a 2x increase in life for Rene' 95, but only a marginal improvement in the fretting fatigue life for Rene' 88. Minor cycles in variable amplitude loading produces significant damage to the specimen. Addition of occasional overpeaks in load produces improvements in fretting fatigue life. Contact tractions and stresses are obtained through a variety of available tools. The contact tractions can be efficiently obtained for limited geometries, while FEM can provide the contact tractions for a broader class of problems, but with the cost of increased CPU requirements. Similarly, the subsurface contact stresses can be obtained using the contact tractions as a boundary condition with either a semi-analytical FFT method or FEM. It is found that to calculate contact stresses the FFT was only marginally faster than FEM. The experimental results are combined with the analysis to produce tools that are used to design against fretting fatigue. Fractographic analysis of the fracture surface indicates the nature of the fretting fatigue crack behavior. Interrupted tests were performed to analyze

  8. Intonation and compensation of fretted string instruments

    NASA Astrophysics Data System (ADS)

    Varieschi, Gabriele U.; Gower, Christina M.

    2010-01-01

    We discuss theoretical and physical models that are useful for analyzing the intonation of musical instruments such as guitars and mandolins and can be used to improve the tuning on these instruments. The placement of frets on the fingerboard is designed according to mathematical rules and the assumption of an ideal string. The analysis becomes more complicated when we include the effects of deformation of the string and inharmonicity due to other string characteristics. As a consequence, perfect intonation of all the notes on the instrument cannot be achieved, but complex compensation procedures can be introduced to minimize the problem. To test the validity of these procedures, we performed extensive measurements using standard monochord sonometers and other acoustical devices, confirming the correctness of our theoretical models. These experimental activities can be integrated into acoustics courses and laboratories and can become a more advanced version of basic experiments with monochords and sonometers.

  9. Unified reaction pathways for the prebiotic formation of RNA and DNA nucleobases.

    PubMed

    Jeilani, Yassin Aweis; Williams, Phoenix N; Walton, Sofia; Nguyen, Minh Tho

    2016-07-27

    The reaction pathways for the prebiotic formation of nucleobases are complex and lead to the formation of a mixture of products. In the past 50 years, there has been a concerted effort for identifying a unified mechanism for the abiotic origin of the biomolecules but with little success. In the present theoretical study, we identified two prominent precursors for the building up of RNA and DNA nucleobases under prebiotic conditions: (a) 1,2-diaminomaleonitrile (DAMN), which is a tetramer of hydrogen cyanide (HCN), and (b) formamide, a hydrolysis product of HCN; it is important to emphasize that HCN is the source of both precursors. We find that free radical pathways are potentially appropriate to account for the origin of nucleobases from HCN. The current study unites the formamide pathways with the DAMN pathways. The mechanisms for the formation of the RNA and DNA nucleobases (uracil, adenine, purine, cytosine) were studied by quantum chemical computations using density functional theory at the B3LYP/6-311G(d,p) level. All the routes involved proceed with relatively low energy barriers (within the error margin of DFT methods). We showed that the radical mechanisms for the formation of nucleobases could be unified through common precursors. The results demonstrated that 4-aminoimidazole-5-carbonitrile (AICN), which is a known precursor for nucleobases, is a product of DAMN. The overall mechanisms are internally consistent with the abiotic formation of the nucleobases, namely (a) under a meteoritic impact scenario on the early Earth's surface that generated high internal energy, and/or (b) in the (gas phase) interstellar regions without the presence of catalysts. PMID:27220279

  10. Seeding the Pregenetic Earth: Meteoritic Abundances of Nucleobases and Potential Reaction Pathways

    NASA Astrophysics Data System (ADS)

    Pearce, Ben K. D.; Pudritz, Ralph E.

    2015-07-01

    Carbonaceous chondrites are a class of meteorite known for having high contents of water and organics. In this study, the abundances of the nucleobases, i.e., the building blocks of RNA and DNA, found in carbonaceous chondrites are collated from a variety of published data and compared across various meteorite classes. An extensive review of abiotic chemical reactions producing nucleobases is then performed. These reactions are then reduced to a list of 15 individual reaction pathways that could potentially occur within meteorite parent bodies. The nucleobases guanine, adenine, and uracil are found in carbonaceous chondrites in amounts of 1–500 ppb. It is currently unknown which reaction is responsible for their synthesis within the meteorite parent bodies. One class of carbonaceous meteorite dominates the abundances of both amino acids and nucleobases—the so-called CM2 (e.g., Murchison meteorite). CR2 meteorites (e.g., Graves Nunataks) also dominate the abundances of amino acids, but are the least abundant in nucleobases. The abundances of total nucleobases in these two classes are 330 ± 250 and 16 ± 13 ppb, respectively. Guanine most often has the greatest abundances in carbonaceous chondrites with respect to the other nucleobases, but is 1–2 orders of magnitude less abundant in CM2 meteorites than glycine (the most abundant amino acid). Our survey of the reaction mechanisms for nucleobase formation suggests that Fischer–Tropsch synthesis (i.e., CO, H2, and NH3 gases reacting in the presence of a catalyst such as alumina or silica) is the most likely candidate for conditions that characterize the early states of planetesimals.

  11. Identification of a nucleoside/nucleobase transporter from Plasmodium falciparum, a novel target for anti-malarial chemotherapy.

    PubMed Central

    Parker, M D; Hyde, R J; Yao, S Y; McRobert, L; Cass, C E; Young, J D; McConkey, G A; Baldwin, S A

    2000-01-01

    Plasmodium, the aetiologic agent of malaria, cannot synthesize purines de novo, and hence depends upon salvage from the host. Here we describe the molecular cloning and functional expression in Xenopus oocytes of the first purine transporter to be identified in this parasite. This 422-residue protein, which we designate PfENT1, is predicted to contain 11 membrane-spanning segments and is a distantly related member of the widely distributed eukaryotic protein family the equilibrative nucleoside transporters (ENTs). However, it differs profoundly at the sequence and functional levels from its homologous counterparts in the human host. The parasite protein exhibits a broad substrate specificity for natural nucleosides, but transports the purine nucleoside adenosine with a considerably higher apparent affinity (K(m) 0.32+/-0.05 mM) than the pyrimidine nucleoside uridine (K(m) 3.5+/-1.1 mM). It also efficiently transports nucleobases such as adenine (K(m) 0.32+/-0.10 mM) and hypoxanthine (K(m) 0.41+/-0.1 mM), and anti-viral 3'-deoxynucleoside analogues. Moreover, it is not sensitive to classical inhibitors of mammalian ENTs, including NBMPR [6-[(4-nitrobenzyl)thio]-9-beta-D-ribofuranosylpurine, or nitrobenzylthioinosine] and the coronary vasoactive drugs, dipyridamole, dilazep and draflazine. These unique properties suggest that PfENT1 might be a viable target for the development of novel anti-malarial drugs. PMID:10861212

  12. Detecting Pyrolysis Products from Bacteria in a Mars Soil Analogue

    NASA Technical Reports Server (NTRS)

    Glavin, D. P.; Cleaves, H. J.; Schubert, M.; Aubrey, A.; Buch, A.; Mahaffy, P. R.; Bada, J. L.

    2004-01-01

    One of the primary objectives of the 1976 Viking missions was to determine whether organic compounds, possibly of biological origin, were present in the Martian surface soils. The Viking gas chromatography mass spectrometry (GCMS) instruments found no evidence for any organic compounds of Martian origin above a few parts per billion in the upper 10 cm of surface soil, suggesting the absence of a widely distributed Martian biota. However, it is now known that key organic compounds important to biology, such as amino acids, carboxylic acids and nucleobases, would likely have been missed by the Viking GCMS instruments. In this study, a Mars soil analogue that was inoculated with approx. 10 billion Escherichia coli cells was heated at 500 C under Martian ambient pressure to release volatile organic compounds from the sample. The pyrolysis products were then analyzed for amino acids and nucleobases using high performance liquid chromatography (HPLC) and GCMS. Our experimental results indicate that at the part per billion level, the degradation products generated from several million bacterial cells per gram of Martian soil would not have been detected by the Viking GCMS instruments. Upcoming strategies for Mars exploration will require in-situ analyses by instruments that can assess whether any organic compounds, especially those that might be associated with life, are present in Martian surface samples.

  13. Synthesis and characterization of nucleobase-carbon nanotube hybrids.

    PubMed

    Singh, Prabhpreet; Kumar, Jitendra; Toma, Francesca Maria; Raya, Jesus; Prato, Maurizio; Fabre, Bruno; Verma, Sandeep; Bianco, Alberto

    2009-09-23

    We report the synthesis and characterization of adenine-single-walled carbon nanotube (SWCNT) hybrid materials, where for the first time nucleobases are covalently attached to the exosurface of SWCNTs. The structural properties of all hybrids have been characterized using usual spectroscopic and microscopic techniques. The degree of functional groups for functionalized SWCNTs (f-SWCNTs) 2a and 2b is one adenine group for each 26 and 37 carbon atoms, respectively. Solid-state magic angle spinning (13)C NMR spectroscopy (MAS NMR) and electrochemistry have been also applied for the characterization of these f-SWCNTs. AFM images of f-SWCNT 2b showed an interesting feature of horizontally aligned nanotubes along the surface when deposited on highly oriented pyrolytic graphite surface. Furthermore, we evaluated the coordinating ability of these hybrid materials toward silver ions, and interestingly, we found a pattern of silver nanoparticles localized over the surface of the carbon nanotube network. The presence of aligned and randomly oriented CNTs and their ability to coordinate with metal ions make this class of materials very interesting for applications in the development of novel electronic devices and as new supports for different catalytic transformations. PMID:19673527

  14. Anharmonic IR Spectra of Biomolecules: Nucleobases and Their Oligomers

    NASA Astrophysics Data System (ADS)

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Carnimeo, Ivan; Fornaro, Teresa

    2014-06-01

    Computational spectroscopy techniques have become in the last years effective means to predict and characterize spectra, such as infrared, for molecular systems of increasing dimensions with account for different environments. We are actively developing a comprehensive and robust computational protocol, set within a perturbative vibrational framework [1], aimed at a quantitative reproduction of the spectra of biomolecules. In order to model the vibrational spectra of weakly bound molecular complexes, dispersion interactions should be taken into proper account. In this work, we present critical assessment of dispersion-corrected DFT approaches for anharmonic vibrational frequency calculations. It is shown that fully anharmonic IR spectra, simulated through full and reduced-dimensionality generalized second-order vibrational perturbation theory (GVPT2)[1] with the potential energy surfaces computed with the B3LYP-D3 approach, may be used to interpret experimental data of nucleobases and their complexes[2] by the direct comparison of experimental IR spectra with their theoretical anharmonic counterpart, taking into account also overtones and combination bands. [1] V. Barone, M. Biczysko, J. Bloino, Phys. Chem. Chem. Phys., 2014,16, 1759-1787 [2] T. Fornaro, M. Biczysko, S. Monti, V. Barone, Phys. Chem. Chem. Phys., 2014, DOI: 10.1039/C3CP54724H

  15. Metal Ion-Mediated Nucleobase Recognition by the ZTP Riboswitch.

    PubMed

    Trausch, Jeremiah J; Marcano-Velázquez, Joan G; Matyjasik, Michal M; Batey, Robert T

    2015-07-23

    The ZTP riboswitch is a widespread family of regulatory RNAs that upregulate de novo purine synthesis in response to increased intracellular levels of ZTP or ZMP. As an important intermediate in purine biosynthesis, ZMP also serves as a proxy for the concentration of N10-formyl-tetrahydrofolate, a key component of one-carbon metabolism. Here, we report the structure of the ZTP riboswitch bound to ZMP at a resolution of 1.80 Å. The RNA contains two subdomains brought together through a long-range pseudoknot further stabilized through helix-helix packing. ZMP is bound at the subdomain interface of the RNA through a set of interactions with the base, ribose sugar, and phosphate moieties of the ligand. Unique to nucleobase recognition by RNAs, the Z base is inner-sphere coordinated to a magnesium cation bound by two backbone phosphates. This interaction, along with steric hindrance by the backbone, imparts specificity over chemically similar compounds such as ATP/AMP. PMID:26144884

  16. Accumulation of formamide in hydrothermal pores to form prebiotic nucleobases.

    PubMed

    Niether, Doreen; Afanasenkau, Dzmitry; Dhont, Jan K G; Wiegand, Simone

    2016-04-19

    Formamide is one of the important compounds from which prebiotic molecules can be synthesized, provided that its concentration is sufficiently high. For nucleotides and short DNA strands, it has been shown that a high degree of accumulation in hydrothermal pores occurs, so that temperature gradients might play a role in the origin of life [Baaske P, et al. (2007)Proc Natl Acad Sci USA104(22):9346-9351]. We show that the same combination of thermophoresis and convection in hydrothermal pores leads to accumulation of formamide up to concentrations where nucleobases are formed. The thermophoretic properties of aqueous formamide solutions are studied by means of Infrared Thermal Diffusion Forced Rayleigh Scattering. These data are used in numerical finite element calculations in hydrothermal pores for various initial concentrations, ambient temperatures, and pore sizes. The high degree of formamide accumulation is due to an unusual temperature and concentration dependence of the thermophoretic behavior of formamide. The accumulation fold in part of the pores increases strongly with increasing aspect ratio of the pores, and saturates to highly concentrated aqueous formamide solutions of ∼85 wt% at large aspect ratios. Time-dependent studies show that these high concentrations are reached after 45-90 d, starting with an initial formamide weight fraction of[Formula: see text]wt % that is typical for concentrations in shallow lakes on early Earth. PMID:27044100

  17. Nucleobases in Space: Laboratory Studies of Polycyclic Aromatic Nitrogen Heterocycles

    NASA Technical Reports Server (NTRS)

    Elsila, Jamie; Mattioda, Andy; Bernstein, Max; Sandford, Scott; Hudgins, Doug

    2005-01-01

    Polycyclic Aromatic Nitrogen Heterocycles (PANHs) are heterocyclic aromatics Le., PAHs with carbon atoms replaced by a nitrogen atom. These molecules have been detected in meteorite extracts, and in general these nitrogen heterocycles are of astrobiological interest since this class of molecules include nucleobases, basic components of our nucleic acids. These compounds are predicted to be present in the interstellar medium and in Titan tholin, but have received relatively little attention. We will present spectra and reactions of PANHs, frozen in solid H2O at 12 K, conditions germane to astronomical observations. In contrast to simple PAHs, that do not interact strongly with solid H2O, the nitrogen atoms in PANHs are potentially capable of hydrogen bonding with H20 changing their spectra, complicating their remote detection on the surfaces of icy bodies. Moreover, we have studied the photo-chemistry of these interesting compounds under astrophysical conditions and will use our lab studies to assess a potential interstellar heritage of these compounds in carbonaceous chondrites.

  18. Wide and high resolution tension measurement using FRET in embryo

    PubMed Central

    Yamashita, Satoshi; Tsuboi, Takashi; Ishinabe, Nanako; Kitaguchi, Tetsuya; Michiue, Tatsuo

    2016-01-01

    During embryonic development, physical force plays an important role in morphogenesis and differentiation. Stretch sensitive fluorescence resonance energy transfer (FRET) has the potential to provide non-invasive tension measurements inside living tissue. In this study, we introduced a FRET-based actinin tension sensor into Xenopus laevis embryos and demonstrated that this sensor captures variation of tension across differentiating ectoderm. The actinin tension sensor, containing mCherry and EGFP connected by spider silk protein, was validated in human embryonic kidney (HEK) cells and embryos. It co-localized with actin filaments and changed FRET efficiencies in response to actin filament destruction, myosin deactivation, and osmotic perturbation. Time-lapse FRET analysis showed that the prospective neural ectoderm bears higher tension than the epidermal ectoderm during gastrulation and neurulation, and cells morphogenetic behavior correlated with the tension difference. These data confirmed that the sensor enables us to measure tension across tissues concurrently and with high resolution. PMID:27335157

  19. QD-Based FRET Probes at a Glance

    PubMed Central

    Shamirian, Armen; Ghai, Aashima; Snee, Preston T.

    2015-01-01

    The unique optoelectronic properties of quantum dots (QDs) give them significant advantages over traditional organic dyes, not only as fluorescent labels for bioimaging, but also as emissive sensing probes. QD sensors that function via manipulation of fluorescent resonance energy transfer (FRET) are of special interest due to the multiple response mechanisms that may be utilized, which in turn imparts enhanced flexibility in their design. They may also function as ratiometric, or “color-changing” probes. In this review, we describe the fundamentals of FRET and provide examples of QD-FRET sensors as grouped by their response mechanisms such as link cleavage and structural rearrangement. An overview of early works, recent advances, and various models of QD-FRET sensors for the measurement of pH and oxygen, as well as the presence of metal ions and proteins such as enzymes, are also provided. PMID:26053750

  20. Pulse-shaping based two-photon FRET stoichiometry

    PubMed Central

    Flynn, Daniel C.; Bhagwat, Amar R.; Brenner, Meredith H.; Núñez, Marcos F.; Mork, Briana E.; Cai, Dawen; Swanson, Joel A.; Ogilvie, Jennifer P.

    2015-01-01

    Förster Resonance Energy Transfer (FRET) based measurements that calculate the stoichiometry of intermolecular interactions in living cells have recently been demonstrated, where the technique utilizes selective one-photon excitation of donor and acceptor fluorophores to isolate the pure FRET signal. Here, we present work towards extending this FRET stoichiometry method to employ two-photon excitation using a pulse-shaping methodology. In pulse-shaping, frequency-dependent phases are applied to a broadband femtosecond laser pulse to tailor the two-photon excitation conditions to preferentially excite donor and acceptor fluorophores. We have also generalized the existing stoichiometry theory to account for additional cross-talk terms that are non-vanishing under two-photon excitation conditions. Using the generalized theory we demonstrate two-photon FRET stoichiometry in live COS-7 cells expressing fluorescent proteins mAmetrine as the donor and tdTomato as the acceptor. PMID:25836193

  1. An Experimental Study of Fretting of Gear Teeth

    NASA Technical Reports Server (NTRS)

    Krantz, Timothy L.

    2008-01-01

    Experiments were conducted to study fretting of gears. The gears were made from case-carburized AISI 9310 alloy to match the material of a flight actuator gearbox of interest. The objective of the testing was to produce damage representative of that observed on flight hardware. The following correlations and observations were noted. The amplitude of dithering motion very strongly influenced the type and magnitude of damage. Sliding amounts on the order of 30% of the width of the line contact were judged to most readily produce fretting damage. There was observed an incubation period on the order of tens-of-thousands of cycles, and the incubation period was influenced by surface roughness, torque, and the motion extent. Fretting damage could be produced for any of the torques tested, and the severity of damage increased slightly with torque. Gear teeth having surface roughness of 0.7-0.8 micrometer were somewhat more resistant to fretting than were smoother surfaces.

  2. Wide and high resolution tension measurement using FRET in embryo.

    PubMed

    Yamashita, Satoshi; Tsuboi, Takashi; Ishinabe, Nanako; Kitaguchi, Tetsuya; Michiue, Tatsuo

    2016-01-01

    During embryonic development, physical force plays an important role in morphogenesis and differentiation. Stretch sensitive fluorescence resonance energy transfer (FRET) has the potential to provide non-invasive tension measurements inside living tissue. In this study, we introduced a FRET-based actinin tension sensor into Xenopus laevis embryos and demonstrated that this sensor captures variation of tension across differentiating ectoderm. The actinin tension sensor, containing mCherry and EGFP connected by spider silk protein, was validated in human embryonic kidney (HEK) cells and embryos. It co-localized with actin filaments and changed FRET efficiencies in response to actin filament destruction, myosin deactivation, and osmotic perturbation. Time-lapse FRET analysis showed that the prospective neural ectoderm bears higher tension than the epidermal ectoderm during gastrulation and neurulation, and cells morphogenetic behavior correlated with the tension difference. These data confirmed that the sensor enables us to measure tension across tissues concurrently and with high resolution. PMID:27335157

  3. Intravital FRET: Probing Cellular and Tissue Function in Vivo.

    PubMed

    Radbruch, Helena; Bremer, Daniel; Mothes, Ronja; Günther, Robert; Rinnenthal, Jan Leo; Pohlan, Julian; Ulbricht, Carolin; Hauser, Anja E; Niesner, Raluca

    2015-01-01

    The development of intravital Förster Resonance Energy Transfer (FRET) is required to probe cellular and tissue function in the natural context: the living organism. Only in this way can biomedicine truly comprehend pathogenesis and develop effective therapeutic strategies. Here we demonstrate and discuss the advantages and pitfalls of two strategies to quantify FRET in vivo-ratiometrically and time-resolved by fluorescence lifetime imaging-and show their concrete application in the context of neuroinflammation in adult mice. PMID:26006244

  4. Fretting maps of glass fiber-reinforced composites

    SciTech Connect

    Turki, C.; Salvia, M.; Vincent, L.

    1993-12-31

    Industrial development of new materials are often limited due to an insufficient knowledge in their functional properties. The paper deals with fretting behavior of glass fiber reinforced epoxy/metal contacts. Fretting is a plague for all industries, especially in the case of quasi-static loadings. Furthermore friction testing under small displacements appeared well fitted to understand the effect of fiber orientations and to relate results to microstructure (fiber, matrix and interface).

  5. Fluorescent Proteins as Genetically Encoded FRET Biosensors in Life Sciences

    PubMed Central

    Hochreiter, Bernhard; Pardo Garcia, Alan; Schmid, Johannes A.

    2015-01-01

    Fluorescence- or Förster resonance energy transfer (FRET) is a measurable physical energy transfer phenomenon between appropriate chromophores, when they are in sufficient proximity, usually within 10 nm. This feature has made them incredibly useful tools for many biomedical studies on molecular interactions. Furthermore, this principle is increasingly exploited for the design of biosensors, where two chromophores are linked with a sensory domain controlling their distance and thus the degree of FRET. The versatility of these FRET-biosensors made it possible to assess a vast amount of biological variables in a fast and standardized manner, allowing not only high-throughput studies but also sub-cellular measurements of biological processes. In this review, we aim at giving an overview over the recent advances in genetically encoded, fluorescent-protein based FRET-biosensors, as these represent the largest and most vividly growing group of FRET-based sensors. For easy understanding, we are grouping them into four categories, depending on their molecular mechanism. These are based on: (a) cleavage; (b) conformational-change; (c) mechanical force and (d) changes in the micro-environment. We also address the many issues and considerations that come with the development of FRET-based biosensors, as well as the possibilities that are available to measure them. PMID:26501285

  6. FRET-based biosensors to detect infectious agents

    NASA Astrophysics Data System (ADS)

    Xu, Juntao; Grant, Sheila A.

    2002-02-01

    We report herein on the development of a FRET-based method to detect changes caused by viral protein-receptor binding. FRET fluorophore pairs (donor and acceptor fluorophores) were tagged to two specific receptors, both which bind to a viral protein. When the binding event occurs, the distance between the donor and acceptor FRET fluorophores is decreased, thus initiating the fluorescence resonance energy transfer (FRET). Since the binding event is unique to the viral protein, fluorescent change indicates the present of the virus. In this paper, the viral protein gp120, which is the featured protein on the surface of HIV-1, was detected. The receptors, CD4 and gp120-antibody which specifically bind to gp120, were conjugated to the FRET fluorophore pair, AMCA-NHS (succinimidyl-7-amino-4-methylcoumarin-3-acetic acid) and FITC (fluorescein isothiocyanate) respectively. Spectrofluorimetry was used to detect the fluorescent change between AMCA-NHS and FITC peak intensities when the receptors bind to the gp120. Specific binding gp120 and non-specific binding gp120 were used to test the selectivity of the sensor. The results indicated that FRET-conjugated receptors can efficiently detect the presence of gp120.

  7. Formation of Nucleobases and Other Prebiotic Species from the UV Irradiation of Pyrimidine in Astrophysical Ices

    NASA Astrophysics Data System (ADS)

    Nuevo, M.; Sandford, S. A.; Milam, S. N.; Materese, C. K.; Elsila, J. E.; Dworkin, J. P.

    2011-05-01

    Nucleobases are N-heterocycles which are the informational subunits of DNA and RNA. Biological nucleobases are divided in two types: pyrimidine bases (uracil, cytosine, and thymine) and purine bases (adenine and guanine). Nucleobases have been detected in meteorites and their extraterrestrial origin has been confirmed by isotope measurements, but no N-heterocycle has ever been observed in the ISM. Experiments showed that the UV irradiation of pyrimidine mixed in astrophysical ices such as H_2O, NH_3, CH_3OH, or any combination of these at low temperature (20-30 K) leads to the formation of multiple photo-products derived from pyrimidine including the nucleobases uracil and cytosine. Theoretical studies on the formation of uracil confirmed its experimental formation pathway and demonstrated that the H_2O matrix plays a key role in the chemistry [9]. Thymine, however, was not found in any of the samples, though other pyrimidine derivatives, as well as other species of prebiotic interest such as urea and the amino acid glycine, could be identified [8]. We will extend this study to the formation of nucleobases and other prebiotic species from the UV irradiation of pyrimidine in astrophysically relevant ice mixtures containing H_2O, NH_3, CH_3OH, CO, and CO_2.

  8. Characterization of poly(N-isopropylacrylamide)-nucleobase supramolecular complexes featuring bio-multiple hydrogen bonds.

    PubMed

    Yang, Hsiu-Wen; Lee, Ai-Wei; Huang, Chi-Hsien; Chen, Jem-Kun

    2014-11-01

    In this study we employed poly(N-isopropylacrylamide) (PNIPAAm) as a matrix that we hybridized with five different nucleobase units (adenine, thymine, uracil, guanine, cytosine) to generate PNIPAAm-nucleobase supramolecular complexes (PNSCs) stabilized through bio-multiple hydrogen bonds (BMHBs). These nucleobase units interacted with PNIPAAm through BMHBs of various strengths, leading to competition between the BMHBs and the intramolecular hydrogen bonds (HBs) of PNIPAAm. The changes in morphology, crystalline structure, and thermoresponsive behavior of PNIPAAm were related to the strength of its BMHBs with the nucleobases. The strengths of the BMHBs followed the order guanine > adenine > thymine > cytosine > uracil, as verified through analyses of Fourier transform infrared spectra, lower critical solution temperatures, and inter-association equilibrium constants. The PNSCs also exhibited remarkable improvements in conductivity upon the formation of BMHBs, which facilitated proton transport. The neat PNIPAAm film was an insulator, but it transformed into a semiconductor after hybridizing with the nucleobases. In particular, the resistivity of the PNIPAAm-guanine supramolecular complex decreased to 1.35 × 10(5) ohm cm. The resistivity of the PNIPAAm-cytosine supramolecular complex increased significantly from 5.83 × 10(6) to 3 × 10(8) ohm cm upon increasing the temperature from 40 to 50 °C, suggesting that this material might have applicability in thermo-sensing. The ability to significantly improve the conductivity of hydrogels through such a simple approach involving BMHBs might facilitate their use as novel materials in bioelectronics. PMID:25196131

  9. Identification of nucleobases using variable currents through graphene nanopores: A first principles study

    NASA Astrophysics Data System (ADS)

    Haraldsen, J. T.; McFarland, H.; Ahmed, T.; Zhu, J.-X.; Balatsky, A. V.

    2015-03-01

    Nanopore-based technology has the potential to be an efficient method for DNA/RNA base sequencing, as well as an identifier of other biomolecules. However, the thickness of the nanopore substrate is critical for the identification of individual nucleobases due to resulting noise and resolution problems. Recently, graphene has been suggested as a possible nanopore substrate due to its single atomic thickness and robust strength. In this study, we examine a possible device mechanism for the voltage dependence of nucleobases passing through a graphene nanopore. We utilize density functional theory with a generalized gradient approach on a graphene ribbon with a nucleobase in order to calculate the transmission spectra for each base. Transmission spectra for each base allows for the calculation of the ballistic current and differential current as a function of voltage. We show that applying various bias voltages across a graphene ribbon for the general, energy-minimized position of the translocated nucleobase, it is possible to distinguish individual bases using the resulting current. Overall, our goal is to improve nanopore device design by helping to further DNA/RNA nucleobase identification and sequencing.

  10. The Formation of Nucleobases from the Irradiation of Purine in Astophysical Ices and Comparisons with Meteorites.

    NASA Technical Reports Server (NTRS)

    Sandford, S. A.; Materese, C. K.; Nuevo, M.

    2016-01-01

    N-heterocycles have been identified in meteorites and their extraterrestrial origins are suggested by isotopic ratio measurements. Although small N- heterocycles have not been detected in the interstellar medium (ISM), recent experiments in our lab have shown that the irradiation of the aromatic molecules like benzene (C6H6) and naphthalene (C10H8) in mixed molecular ices leads to the formation of O- and N-heterocyclic molecules. Among the class of N-heterocycles are the nucleobases, which are of astrobiological interest because they are the information bearing units of DNA and RNA. Nucleobases have been detected in meteorites [3-5], with isotopic signatures that are also consistent with an extraterrestrial origin. Three of the biologically relevant nucleobases (uracil, cytosine, and guanine) have a pyrimidine core structure while the remaining two (adenine and guanine) possess a purine core. Previous experiments in our lab have demonstrated that all of the bio-logical nucleobases (and numerous other molecules) with a pyrimidine core structure can be produced by irradiating pyrimidine in mixed molecular ices of several compositions [6-8]. In this work, we study the formation of purine-based molecules, including the nucleobases adenine, and guanine, from the ultraviolet (UV) irradiation of purine in ices consisting mixtures of H2O and NH3 at low temperature. The experiments are designed to simulate the astrophysical conditions under which these species may be formed in dense molecular clouds, protoplanetary disks, or on the surfaces of icy bodies in planetary systems.

  11. A new trend to determine biochemical parameters by quantitative FRET assays

    PubMed Central

    Liao, Jia-yu; Song, Yang; Liu, Yan

    2015-01-01

    Förster resonance energy transfer (FRET) has been widely used in biological and biomedical research because it can determine molecule or particle interactions within a range of 1–10 nm. The sensitivity and efficiency of FRET strongly depend on the distance between the FRET donor and acceptor. Historically, FRET assays have been used to quantitatively deduce molecular distances. However, another major potential application of the FRET assay has not been fully exploited, that is, the use of FRET signals to quantitatively describe molecular interactive events. In this review, we discuss the use of quantitative FRET assays for the determination of biochemical parameters, such as the protein interaction dissociation constant (Kd), enzymatic velocity (kcat) and Km. We also describe fluorescent microscopy-based quantitative FRET assays for protein interaction affinity determination in cells as well as fluorimeter-based quantitative FRET assays for protein interaction and enzymatic parameter determination in solution. PMID:26567729

  12. Fluorescent Protein Based FRET Pairs with Improved Dynamic Range for Fluorescence Lifetime Measurements.

    PubMed

    George Abraham, Bobin; Sarkisyan, Karen S; Mishin, Alexander S; Santala, Ville; Tkachenko, Nikolai V; Karp, Matti

    2015-01-01

    Fluorescence Resonance Energy Transfer (FRET) using fluorescent protein variants is widely used to study biochemical processes in living cells. FRET detection by fluorescence lifetime measurements is the most direct and robust method to measure FRET. The traditional cyan-yellow fluorescent protein based FRET pairs are getting replaced by green-red fluorescent protein variants. The green-red pair enables excitation at a longer wavelength which reduces cellular autofluorescence and phototoxicity while monitoring FRET. Despite the advances in FRET based sensors, the low FRET efficiency and dynamic range still complicates their use in cell biology and high throughput screening. In this paper, we utilized the higher lifetime of NowGFP and screened red fluorescent protein variants to develop FRET pairs with high dynamic range and FRET efficiency. The FRET variations were analyzed by proteolytic activity and detected by steady-state and time-resolved measurements. Based on the results, NowGFP-tdTomato and NowGFP-mRuby2 have shown high potentials as FRET pairs with large fluorescence lifetime dynamic range. The in vitro measurements revealed that the NowGFP-tdTomato has the highest Förster radius for any fluorescent protein based FRET pairs yet used in biological studies. The developed FRET pairs will be useful for designing FRET based sensors and studies employing Fluorescence Lifetime Imaging Microscopy (FLIM). PMID:26237400

  13. In vivo dynamics of enterovirus protease revealed by fluorescence resonance emission transfer (FRET) based on a novel FRET pair

    SciTech Connect

    Hsu, Y.-Y.; Liu, Y.-N.; Wang Wenyen; Kao, Fu-Jen; Kung, S.-H. . E-mail: szkung@ym.edu.tw

    2007-02-23

    An in vivo protease assay suitable for analysis by fluorescence resonance energy transfer (FRET) was developed on the basis of a novel FRET pair. The specifically designed fusion substrate consists of green fluorescent protein 2 (GFP{sup 2})-peptide-red fluorescent protein 2 (DsRed2), with a cleavage motif for the enterovirus 2A protease (2A{sup pro}) embedded within the peptide region. FRET can be readily visualized in real-time from cells expressing the fusion substrate until a proteolytic cleavage by 2A{sup pro} from the input virus. The level of FRET decay is a function of the amount and infection duration of the inoculated virus as measured by a fluorometer assay. The FRET biosensor also responded well to other related enteroviruses but not to a phylogenetically distant virus. Western blot analysis confirmed the physical cleavage of the fusion substrate upon the infections. The study provides proof of principle for applying the FRET technology to diagnostics, screening procedures, and cell biological research.

  14. Evolving a polymerase for hydrophobic base analogues.

    PubMed

    Loakes, David; Gallego, José; Pinheiro, Vitor B; Kool, Eric T; Holliger, Philipp

    2009-10-21

    Hydrophobic base analogues (HBAs) have shown great promise for the expansion of the chemical and coding potential of nucleic acids but are generally poor polymerase substrates. While extensive synthetic efforts have yielded examples of HBAs with favorable substrate properties, their discovery has remained challenging. Here we describe a complementary strategy for improving HBA substrate properties by directed evolution of a dedicated polymerase using compartmentalized self-replication (CSR) with the archetypal HBA 5-nitroindole (d5NI) and its derivative 5-nitroindole-3-carboxamide (d5NIC) as selection substrates. Starting from a repertoire of chimeric polymerases generated by molecular breeding of DNA polymerase genes from the genus Thermus, we isolated a polymerase (5D4) with a generically enhanced ability to utilize HBAs. The selected polymerase. 5D4 was able to form and extend d5NI and d5NIC (d5NI(C)) self-pairs as well as d5NI(C) heteropairs with all four bases with efficiencies approaching, or exceeding, those of the cognate Watson-Crick pairs, despite significant distortions caused by the intercalation of the d5NI(C) heterocycles into the opposing strand base stack, as shown by nuclear magnetic resonance spectroscopy (NMR). Unlike Taq polymerase, 5D4 was also able to extend HBA pairs such as Pyrene: varphi (abasic site), d5NI: varphi, and isocarbostyril (ICS): 7-azaindole (7AI), allowed bypass of a chemically diverse spectrum of HBAs, and enabled PCR amplification with primers comprising multiple d5NI(C)-substitutions, while maintaining high levels of catalytic activity and fidelity. The selected polymerase 5D4 promises to expand the range of nucleobase analogues amenable to replication and should find numerous applications, including the synthesis and replication of nucleic acid polymers with expanded chemical and functional diversity. PMID:19778048

  15. Evaluation of Ti-48Al-2Nb Under Fretting Conditions

    NASA Technical Reports Server (NTRS)

    Miyoshi, Kazuhisa; Lerch, Bradley A.; Draper, Susan L.; Raj, Sai V.

    2001-01-01

    An investigation was conducted to examine the fretting behavior of lambda-TiAl (Ti-48Al-2Cr-2Nb) in contact with a nickel-base superalloy (Inconel 718) in air at temperatures from 23 to 550 C. Fretting wear experiments were conducted with 9.4-mm-diameter hemispherical Inconel (IN) 718 pins in contact with Ti-48Al-2Cr-2Nb flats (and the reverse) at loads from 1 to 40 N and fretting frequencies from 50 to 160 Hz with slip amplitudes from 50 to 200 microns for 1 to 20 million fretting cycles. The results were similar for both combinations of pin and flat. Reference fretting wear experiments were also conducted with 9.4-mm-diameter hemispherical Ti-6Al-4V pins in contact with IN718 flats. The interfacial adhesive bonds between Ti-48Al-2Cr-2Nb and IN718 in contact were generally stronger than the cohesive bonds in the cohesively weaker Ti-48Al-2Cr-2Nb. The failed Ti-48Al-2Cr-2Nb subsequently transferred to the IN718 surface at any fretting condition. The wear scars produced on Ti-48Al-2Cr-2Nb contained metallic and oxide wear debris, scratches, plastically deformed asperities, cracks, and fracture pits. Oxide layers readily formed on the Ti-48Al-2Cr-2Nb surface at 550 C, but cracks easily occurred in the oxide layers. Factors including fretting frequency, temperature, slip amplitude, and load influenced the fretting behavior of Ti-48Al-2Cr-2Nb in contact with IN718. The wear volume loss of Ti-48Al-2Cr-2Nb generally decreased with increasing fretting frequency. The increasing rate of oxidation at elevated temperatures up to 200 C led to a drop in wear volume loss at 200 C. However, the fretting wear increased as the temperature was increased from 200 to 550 C. The highest temperatures of 450 and 550 C resulted in oxide film disruption with generation of cracks, loose wear debris, and pits on the Ti-48Al-2Cr-2Nb wear surface. The wear volume loss generally increased as the slip amplitude increased. The wear volume loss also generally increased as the load increased

  16. A graphene field-effect transistor as a molecule-specific probe of DNA nucleobases.

    PubMed

    Dontschuk, Nikolai; Stacey, Alastair; Tadich, Anton; Rietwyk, Kevin J; Schenk, Alex; Edmonds, Mark T; Shimoni, Olga; Pakes, Chris I; Prawer, Steven; Cervenka, Jiri

    2015-01-01

    Fast and reliable DNA sequencing is a long-standing target in biomedical research. Recent advances in graphene-based electrical sensors have demonstrated their unprecedented sensitivity to adsorbed molecules, which holds great promise for label-free DNA sequencing technology. To date, the proposed sequencing approaches rely on the ability of graphene electric devices to probe molecular-specific interactions with a graphene surface. Here we experimentally demonstrate the use of graphene field-effect transistors (GFETs) as probes of the presence of a layer of individual DNA nucleobases adsorbed on the graphene surface. We show that GFETs are able to measure distinct coverage-dependent conductance signatures upon adsorption of the four different DNA nucleobases; a result that can be attributed to the formation of an interface dipole field. Comparison between experimental GFET results and synchrotron-based material analysis allowed prediction of the ultimate device sensitivity, and assessment of the feasibility of single nucleobase sensing with graphene. PMID:25800494

  17. Efficient enzyme-free copying of all four nucleobases templated by immobilized RNA

    NASA Astrophysics Data System (ADS)

    Deck, Christopher; Jauker, Mario; Richert, Clemens

    2011-08-01

    The transition from inanimate materials to the earliest forms of life must have involved multiplication of a catalytically active polymer that is able to replicate. The semiconservative replication that is characteristic of genetic information transfer requires strands that contain more than one type of nucleobase. Short strands of RNA can act as catalysts, but attempts to induce efficient self-copying of mixed sequences (containing four different nucleobases) have been unsuccessful with ribonucleotides. Here we show that inhibition by spent monomers, formed by the hydrolysis of the activated nucleotides, is the cause for incomplete extension of growing daughter strands on RNA templates. Immobilization of strands and periodic displacement of the solution containing the activated monomers overcome this inhibition. Any of the four nucleobases (A/C/G/U) is successfully copied in the absence of enzymes. We conclude therefore that in a prebiotic world, oligoribonucleotides may have formed and undergone self-copying on surfaces.

  18. Nucleobases and Other Prebiotic Species from the UV Irradiation of Pyrimidine in Astrophysical Ices

    NASA Technical Reports Server (NTRS)

    Sandford, Scott; Materese, Christopher; Nuevo, Michel

    2012-01-01

    Nucleobases are aromatic N-heterocycles that constitute the informational subunits of DNA and RNA and are divided into two families: pyrimidine bases (uracil, cytosine, and thymine) and purine bases (adenine and guanine). Nucleobases have been detected in meteorites and their extraterrestrial origin confirmed by isotope measurement. Although no N-heterocycles have been individually identified in the ISM, the 6.2-micron interstellar emission feature seen towards many astronomical objects suggests a population of such molecules is likely present. We report on a study of the formation of pyrimidine-based molecules, including nucleobases and other species of prebiotic interest, from the ultraviolet (UV) irradiation of pyrimidine in low temperature ices containing H2O, NH3, C3OH, and CH4, to simulate the astrophysical conditions under which prebiotic species may be formed in the Solar System.

  19. An application of the van der Waals density functional: Hydrogen bonding and stacking interactions between nucleobases.

    PubMed

    Cooper, Valentino R; Thonhauser, T; Langreth, David C

    2008-05-28

    We apply the van der Waals density functional (vdW-DF) to study hydrogen bonding and stacking interactions between nucleobases. The excellent agreement of our results with high level quantum chemical calculations highlights the value of the vdW-DF for first-principles investigations of biologically important molecules. Our results suggest that, in the case of hydrogen-bonded nucleobase pairs, dispersion interactions reduce the cost of propeller twists while having a negligible effect on buckling. Furthermore, the efficient scaling of DFT methods allowed for the easy optimization of separation distance between nucleobase stacks, indicating enhancements in the interaction energy of up to 3 kcalmol over previous fixed distance calculations. We anticipate that these results are significant for extending the vdW-DF method to model larger vdW complexes and biological molecules. PMID:18513005

  20. A graphene field-effect transistor as a molecule-specific probe of DNA nucleobases

    NASA Astrophysics Data System (ADS)

    Dontschuk, Nikolai; Stacey, Alastair; Tadich, Anton; Rietwyk, Kevin J.; Schenk, Alex; Edmonds, Mark T.; Shimoni, Olga; Pakes, Chris I.; Prawer, Steven; Cervenka, Jiri

    2015-03-01

    Fast and reliable DNA sequencing is a long-standing target in biomedical research. Recent advances in graphene-based electrical sensors have demonstrated their unprecedented sensitivity to adsorbed molecules, which holds great promise for label-free DNA sequencing technology. To date, the proposed sequencing approaches rely on the ability of graphene electric devices to probe molecular-specific interactions with a graphene surface. Here we experimentally demonstrate the use of graphene field-effect transistors (GFETs) as probes of the presence of a layer of individual DNA nucleobases adsorbed on the graphene surface. We show that GFETs are able to measure distinct coverage-dependent conductance signatures upon adsorption of the four different DNA nucleobases; a result that can be attributed to the formation of an interface dipole field. Comparison between experimental GFET results and synchrotron-based material analysis allowed prediction of the ultimate device sensitivity, and assessment of the feasibility of single nucleobase sensing with graphene.

  1. Understanding Stacking Interactions between an Aromatic Ring and Nucleobases in Aqueous Solution: Experimental and Theoretical Study.

    PubMed

    Kataev, Evgeny A; Shumilova, Tatiana A; Fiedler, Benjamin; Anacker, Tony; Friedrich, Joachim

    2016-08-01

    Stacking interactions between aromatic compounds and nucleobases are crucial in recognition of nucleotides and nucleic acids, but a comprehensive understanding of the strength and selectivity of these interactions in aqueous solution has been elusive. To this end, model complexes have been designed and analyzed by experiment and theory. For the first time, stacking free energies between five nucleobases and anthracene were determined experimentally from thermodynamic double mutant cycles. Three different experimental methods were proposed and evaluated. The dye prefers to bind nucleobases in the order (kcal/mol): G (1.3) > T (0.9) > U (0.8) > C (0.5) > A (0.3). The respective trend of interaction free energies extracted from DFT calculations correlates to that obtained experimentally. Analysis of the data suggests that stacking interactions dominate over hydrophobic effects in an aqueous solution and can be predicted with DFT calculations. PMID:27314892

  2. Accumulation of formamide in hydrothermal pores to form prebiotic nucleobases

    NASA Astrophysics Data System (ADS)

    Niether, Doreen; Afanasenkau, Dzmitry; Dhont, Jan K. G.

    2016-04-01

    Formamide is one of the important compounds from which prebiotic molecules can be synthesized, provided that its concentration is sufficiently high. For nucleotides and short DNA strands, it has been shown that a high degree of accumulation in hydrothermal pores occurs, so that temperature gradients might play a role in the origin of life [Baaske P, et al. (2007) Proc Natl Acad Sci USA 104(22):9346-9351]. We show that the same combination of thermophoresis and convection in hydrothermal pores leads to accumulation of formamide up to concentrations where nucleobases are formed. The thermophoretic properties of aqueous formamide solutions are studied by means of Infrared Thermal Diffusion Forced Rayleigh Scattering. These data are used in numerical finite element calculations in hydrothermal pores for various initial concentrations, ambient temperatures, and pore sizes. The high degree of formamide accumulation is due to an unusual temperature and concentration dependence of the thermophoretic behavior of formamide. The accumulation fold in part of the pores increases strongly with increasing aspect ratio of the pores, and saturates to highly concentrated aqueous formamide solutions of ˜85 wt% at large aspect ratios. Time-dependent studies show that these high concentrations are reached after 45-90 d, starting with an initial formamide weight fraction of 10-310-3 wt % that is typical for concentrations in shallow lakes on early Earth.

  3. Dissociative electron attachment to the gas-phase nucleobase hypoxanthine

    SciTech Connect

    Dawley, M. Michele; Tanzer, Katrin; Denifl, Stephan E-mail: Sylwia.Ptasinska.1@nd.edu; Carmichael, Ian; Ptasińska, Sylwia E-mail: Sylwia.Ptasinska.1@nd.edu

    2015-06-07

    We present high-resolution measurements of the dissociative electron attachment (DEA) to isolated gas-phase hypoxanthine (C{sub 5}H{sub 4}N{sub 4}O, Hyp), a tRNA purine base. The anion mass spectra and individual ion efficiency curves from Hyp were measured as a function of electron energy below 9 eV. The mass spectra at 1 and 6 eV exhibit the highest anion yields, indicating possible common precursor ions that decay into the detectable anionic fragments. The (Hyp − H) anion (C{sub 5}H{sub 3}N{sub 4}O{sup −}) exhibits a sharp resonant peak at 1 eV, which we tentatively assign to a dipole-bound state of the keto-N1H,N9H tautomer in which dehydrogenation occurs at either the N1 or N9 position based upon our quantum chemical computations (B3LYP/6-311+G(d,p) and U(MP2-aug-cc-pVDZ+)) and prior studies with adenine. This closed-shell dehydrogenated anion is the dominant fragment formed upon electron attachment, as with other nucleobases. Seven other anions were also observed including (Hyp − NH){sup −}, C{sub 4}H{sub 3}N{sub 4}{sup −}/C{sub 4}HN{sub 3}O{sup −}, C{sub 4}H{sub 2}N{sub 3}{sup −}, C{sub 3}NO{sup −}/HC(HCN)CN{sup −}, OCN{sup −}, CN{sup −}, and O{sup −}. Most of these anions exhibit broad but weak resonances between 4 and 8 eV similar to many analogous anions from adenine. The DEA to Hyp involves significant fragmentation, which is relevant to understanding radiation damage of biomolecules.

  4. Synthesis of novel conjugates of a saccharide, amino acids, nucleobase and the evaluation of their cell compatibility.

    PubMed

    Yuan, Dan; Du, Xuewen; Shi, Junfeng; Zhou, Ning; Baoum, Abdulgader Ahmed; Xu, Bing

    2014-01-01

    This article reports the synthesis of a novel type of conjugate of three fundamental biological build blocks (i.e., saccharide, amino acids, and nucleobase) and their cell compatibility. The facile synthesis starts with the synthesis of nucleobase and saccharide derivatives, then uses solid-phase peptide synthesis (SPPS) to build the peptide segment (Phe-Arg-Gly-Asp or naphthAla-Phe-Arg-Gly-Asp with fully protected groups), and later, an amidation reaction in liquid phase connects these three parts together. The overall yield of these multiple step synthesis is about 34%. Besides exhibiting excellent solubility, these conjugates of saccharide-amino acids-nucleobase (SAN), like the previously reported conjugates of nucleobase-amino acids-saccharide (NAS) and nucleobase-saccharide-amino acids (NSA), are mammalian cell compatible. PMID:25383110

  5. Intonation and compensation of fretted string instruments

    NASA Astrophysics Data System (ADS)

    Varieschi, Gabriele; Gower, Christina

    2011-04-01

    We discuss theoretical and physical models that are useful for analyzing the intonation of musical instruments such as guitars and mandolins and can be used to improve the tuning on these instruments. The placement of frets on the fingerboard is designed according to mathematical rules and the assumption of an ideal string. The analysis becomes more complicated when we include the effects of deformation of the string and inharmonicity due to other string characteristics. As a consequence, perfect intonation of all the notes on the instrument cannot be achieved, but complex compensation procedures can be introduced to minimize the problem. To test the validity of these procedures, we performed extensive measurements using standard monochord sonometers and other acoustical devices, confirming the correctness of our theoretical models. These experimental activities can be integrated into acoustics courses and laboratories and can become a more advanced version of basic experiments with monochords and sonometers. This work was supported by a grant from the Frank R. Seaver College of Science and Engineering, Loyola Marymount University.

  6. An examination of faying surface fretting in single lap splices

    NASA Astrophysics Data System (ADS)

    Brown, Adam

    While fretting damage in mechanically fastened joints is widely acknowledged as a common source of crack nucleation, little work is available in the open literature on the role that fretting damage plays in the fatigue life of a riveted joint. To expand on the limited knowledge available, a study was undertaken on fretting fatigue in thin-sheet riveted fuselage lap joints. In joints constructed out of 1 mm thick 2024-T3 aluminum sheet the rivet forming load was found to have a significant effect on the location of fretting damage and crack nucleation. This effect was observed for splices riveted with machine countersunk and with universal rivets. The shift in the location of peak fretting damage and crack nucleation with changing rivet forming loads was investigated through numerical and experimental methods. A predictive model based on the critical plane Smith-Watson-Topper strain life equation was applied to the complex geometry of the single lap splice and was shown to be effective in predicting the fretting fatigue life as well as the location of fretting-induced crack nucleation. Basing this model on an explicit finite element simulation allowed for the inclusion of compressive residual stresses generated during rivet forming. Key to the proper functionality of the predictive model was to have a validated finite element model from which results for the stress and strain field in the loaded component could be obtained. In addition to the predictive model, a series of splice coupon and simplified geometry fretting fatigue tests were performed. The tests showed that, at higher rivet forming loads, crack nucleation is on the faying surface away from the hole edge and that the type of surface condition is important to the fretting fatigue life of the splice. The discovery of this variation with surface treatment at high rivet forming loads is important as more research is showing the benefit of using load-controlled rivet forming and higher rivet forming loads in

  7. The development of FRET-based dual receptor optical biosensor

    NASA Astrophysics Data System (ADS)

    Xu, Juntao

    The focus of the research presented in this dissertation is the development of a new FRET-based dual receptor sensing method for detecting the human immunodeficiency virus (HIV). The new detection method presented in this dissertation imitates the way HIV infects cells. It utilizes the two receptor-binding event and integrates a chemical transducer system with two unique protein receptors, CD4 and mAb (HIV-1 gp120 monoclonal antibody), which both bind to gp120. The chemical transduction system is based on the distance-dependant principle of fluorescence resonance energy transfer (FRET). The work presented in this dissertation attempts to demonstrate the feasibility of this new sensing method both in solution and on an optical fiber. Appropriate FRET pairs which have high energy transfer efficiency as well as good conjugation properties with receptors were selected and optimized. The two receptors, CD4 and mAb which specifically bind to gp120, were conjugated to one of the optimized FRET fluorophore pairs, AMCA-NHS (succinimidyl-7-amino-4-methylcoumarin-3-acetic acid) and FITC (fluorescein isothiocyanate), respectively. For the solution test, the viral protein gp120, which is the featured protein on the surface of HIV-1, was detected by the mixed solution of the two FRET pair tagged receptors. A spectrofluorometer was used to detect the fluorescent change between AMCA-NHS and FITC peak intensities when the receptors bind to the gp120. Specific binding and non-specific binding gp120 were used to test the selectivity of this method. The results of the solution test indicated that FRET-conjugated receptors can efficiently distinguish the presence of specific and non-specific binding gp120 and proved the feasibility of the FRET-based dual receptor method in detecting the presence of gp120 with a limit of detection of 5ng/ml (0.5nM) in solution. For the optical fiber test, two FRET-conjugated receptors were immobilized onto an optical fiber silica core tip to detect the

  8. Fluorescent proteins for FRET microscopy: monitoring protein interactions in living cells

    PubMed Central

    Day, Richard N.; Davidson, Michael W.

    2012-01-01

    Summary The discovery and engineering of novel fluorescent proteins (FPs) from diverse organisms is yielding fluorophores with exceptional characteristics for live-cell imaging. In particular, the development of FPs for fluorescence (or Förster) resonance energy transfer (FRET) microscopy is providing important tools for monitoring dynamic protein interactions inside living cells. The increased interest in FRET microscopy has driven the development of many different methods to measure FRET. However, the interpretation of FRET measurements is complicated by several factors including the high fluorescence background, the potential for photoconversion artifacts, and the relatively low dynamic range afforded by this technique. Here, we describe the advantages and disadvantages of four methods commonly used in FRET microscopy. We then discuss the selection of FPs for the different FRET methods, identifying the most useful FP candidates for FRET microscopy. The recent success in expanding the FP color palette offers the opportunity to explore new FRET pairs. PMID:22396229

  9. Influence of fretting on flexural fatigue of 304 stainless steel and mild steel

    NASA Technical Reports Server (NTRS)

    Bill, R. C.; Rohn, D. A.

    1978-01-01

    Fretting fatigue experiments conducted on 304 stainless steel using a flexural fatigue test arrangement with bolted on fretting pads demonstrated that fatigue life is reduced by at least a factor of 10 in the 265 to 334 MPa (38,500 - to 48,500 psi) nominal flexural fatigue stress range. In addition, experiments in which the fretting pads were removed after selected numbers of cycles, followed by continued flexural fatigue without fretting show that continued fretting beyond 50,000 cycles does not significantly further reduce fatigue life of 304 stainless steel at 317 MPa (46,000 psi). Microscopic examination of the fretted contact areas revealed fracture initiation sites as well as numerous cracks that did not propagate to failure. Flexural fretting fatigue experiments performed on mild steel showed an insensitivity of fatigue life to the incidence of fretting under flexural stress conditions of from 162 to 217 MPa (23,500 to 31,500 psi).

  10. DNA Stains as Surrogate Nucleobases in Fluorogenic Hybridization Probes.

    PubMed

    Hövelmann, Felix; Seitz, Oliver

    2016-04-19

    The increasing importance assigned to RNA dynamics in cells and tissues calls for probe molecules that enable fluorescence microscopy imaging in live cells. To achieve this goal, fluorescence dyes are conjugated with oligonucleotides so as to provide strong emission upon hybridization with the target molecule. The impressive 10(3)-fold fluorescence intensification observed when DNA stains such as thiazole orange (TO) interact with double-stranded DNA is intriguing and prompted the exploration of oligonucleotide conjugates. However, nonspecific interactions of DNA stains with polynucleotides tend to increase background, which would affect the contrast achievable in live-cell imaging. This Account describes the development of DNA-stain-labeled hybridization probes that provide high signal-to-background. We focus on our contributions in context with related advances from other laboratories. The emphasis will be on the requirements of RNA imaging in live cells. To reduce background, intercalator dyes such as TO were appended to peptide nucleic acid (PNA), which is less avidly recognized by DNA stains than DNA/RNA. Constraining the TO dye as a nucleobase surrogate in "forced intercalation (FIT) probes" improved the target specificity, presumably by helping to prevent unspecific interactions. The enforcement of TO intercalation between predetermined base pairs upon formation of the probe-target duplex provided for high brightness and enabled match/mismatch selectivity beyond stringency of hybridization. We show examples that highlight the use of PNA FIT probes in the imaging of mRNA, miRNA, and lncRNA in living cells. The "FIT approach" was recently extended to DNA probes. Signal brightness can become limiting when low-abundance targets ought to be visualized over cellular autofluorescence. We discuss strategies that further the brightness of signaling by FIT probes. Multilabeling with identical dyes does not solve the brightness issue. To avoid self-quenching, we

  11. Interactions of the "piano-stool" [ruthenium(II) (eta6-arene)(en)CL]+ complexes with water and nucleobases; ab initio and DFT study.

    PubMed

    Futera, Zdenek; Klenko, Julia; Sponer, Judit E; Sponer, Jirí; Burda, Jaroslav V

    2009-09-01

    Piano stool ruthenium complexes of the composition [Ru(II)(eta6-arene)(en)Cl](+/2+) (en = ethylenediamine) represent an emerging class of cisplatin-analogue anticancer drug candidates. In this study, we use computational quantum chemistry to characterize the structure, stability and reactivity of these compounds. All these structures were optimized at DFT(B3LYP)/6-31G(d) level and their single point properties were determined by the MP2/6-31++G(2df,2pd) method. Thermodynamic parameters and rate constants were determined for the aquation process, as a replacement of the initial chloro ligand by water and subsequent exchange reaction of aqua ligand by nucleobases. The computations were carried out at several levels of DFT and ab initio theories (B3LYP, MP2 and CCSD) utilizing a range of bases sets (from 6-31G(d) to aug-cc-pVQZ). Excellent agreement with experimental results for aquation process was obtained at the CCSD level and reasonable match was achieved also with the B3LYP/6-31++G(2df,2pd) method. This level was used also for nucleobase-water exchange reaction where a smaller rate constant for guanine exchange was found in comparison with adenine. Although adenine follows a simple replacement mechanism, guanine complex passes by a two-step mechanism. At first, Ru-O6(G) adduct is formed, which is transformed through a chelate TS2 to the Ru-N7(G) final complex. In case of guanine, the exchange reaction is more favorable thermodynamically (releasing in total by about 8 kcal/mol) but according to our results, the rate constant for guanine substitution is slightly smaller than the analogous constant in adenine case when reaction course from local minimum is considered. PMID:19090568

  12. Synthesis and Evaluation of a Library of Fluorescent Dipeptidomimetic Analogues as Substrates for Modified Bacterial Ribosomes.

    PubMed

    Chowdhury, Sandipan Roy; Chauhan, Pradeep S; Dedkova, Larisa M; Bai, Xiaoguang; Chen, Shengxi; Talukder, Poulami; Hecht, Sidney M

    2016-05-01

    Described herein are the synthesis and photophysical characterization of a library of aryl-substituted oxazole- and thiazole-based dipeptidomimetic analogues, and their incorporation into position 66 of green fluorescent protein (GFP) in lieu of the natural fluorophore. These fluorescent analogues resemble the fluorophore formed naturally by GFP. As anticipated, the photophysical properties of the analogues varied as a function of the substituents at the para position of the phenyl ring. The fluorescence emission wavelength maxima of compounds in the library varied from ∼365 nm (near-UV region) to ∼490 nm (visible region). The compounds also exhibited a large range of quantum yields (0.01-0.92). The analogues were used to activate a suppressor tRNACUA and were incorporated into position 66 of GFP using an in vitro protein biosynthesizing system that employed engineered ribosomes selected for their ability to incorporate dipeptides. Four analogues with interesting photophysical properties and reasonable suppression yields were chosen, and the fluorescent proteins (FPs) containing these fluorophores were prepared on a larger scale for more detailed study. When the FPs were compared with the respective aminoacyl-tRNAs and the actual dipeptide analogues, the FPs exhibited significantly enhanced fluorescence intensities at the same concentrations. Part of this was shown to be due to the presence of the fluorophores as an intrinsic element of the protein backbone. There were also characteristic shifts in the emission maxima, indicating the environmental sensitivity of these probes. Acridon-2-ylalanine and oxazole 1a were incorporated into positions 39 and 66 of GFP, respectively, and were shown to form an efficient Förster resonance energy transfer (FRET) pair, demonstrating that the analogues can be used as FRET probes. PMID:27050631

  13. Borromean three-body FRET in frozen Rydberg gases

    NASA Astrophysics Data System (ADS)

    Faoro, R.; Pelle, B.; Zuliani, A.; Cheinet, P.; Arimondo, E.; Pillet, P.

    2015-09-01

    Controlling the interactions between ultracold atoms is crucial for quantum simulation and computation purposes. Highly excited Rydberg atoms are considered in this prospect for their strong and controllable interactions known in the dipole-dipole case to induce non-radiative energy transfers between atom pairs, similarly to fluorescence resonance energy transfer (FRET) in biological systems. Here we predict few-body FRET processes in Rydberg atoms and observe the first three-body resonance energy transfer in cold Rydberg atoms using cold caesium atoms. In these resonances, additional relay atoms carry away an energy excess preventing the two-body resonance, leading thus to a Borromean type of energy transfer. These few-body processes present strong similarities with multistep FRET between chromophores sometimes called donor-bridge-acceptor or superexchange. Most importantly, they generalize to any Rydberg atom and could lead to new implementations of few-body quantum gates or entanglement.

  14. Borromean three-body FRET in frozen Rydberg gases

    PubMed Central

    Faoro, R.; Pelle, B.; Zuliani, A.; Cheinet, P.; Arimondo, E.; Pillet, P.

    2015-01-01

    Controlling the interactions between ultracold atoms is crucial for quantum simulation and computation purposes. Highly excited Rydberg atoms are considered in this prospect for their strong and controllable interactions known in the dipole-dipole case to induce non-radiative energy transfers between atom pairs, similarly to fluorescence resonance energy transfer (FRET) in biological systems. Here we predict few-body FRET processes in Rydberg atoms and observe the first three-body resonance energy transfer in cold Rydberg atoms using cold caesium atoms. In these resonances, additional relay atoms carry away an energy excess preventing the two-body resonance, leading thus to a Borromean type of energy transfer. These few-body processes present strong similarities with multistep FRET between chromophores sometimes called donor-bridge-acceptor or superexchange. Most importantly, they generalize to any Rydberg atom and could lead to new implementations of few-body quantum gates or entanglement. PMID:26348821

  15. Riboswitch Structure and Dynamics by smFRET Microscopy

    PubMed Central

    Suddala, Krishna C.; Walter, Nils G.

    2016-01-01

    Riboswitches are structured non-coding RNA elements that control the expression of their embedding messenger RNAs by sensing the intracellular concentration of diverse metabolites. As the name suggests, riboswitches are dynamic in nature so that studying their inherent conformational dynamics and ligand-mediated folding is important for understanding their mechanism of action. Single molecule fluorescence energy transfer (smFRET) microscopy is a powerful and versatile technique for studying the folding pathways and intra- and intermolecular dynamics of biological macromolecules, especially RNA. The ability of smFRET to monitor intramolecular distances and their temporal evolution make it a particularly insightful tool for probing the structure and dynamics of riboswitches. Here, we detail the general steps for using prism-based total internal reflection fluorescence (TIRF) microscopy for smFRET studies of the structure, dynamics and ligand binding mechanisms of riboswitches. PMID:25432756

  16. The Photochemistry of Pyrimidine in Realistic Astrophysical Ices and the Production of Nucleobases

    NASA Astrophysics Data System (ADS)

    Nuevo, Michel; Materese, Christopher K.; Sandford, Scott A.

    2014-10-01

    Nucleobases, together with deoxyribose/ribose and phosphoric acid, are the building blocks of DNA and RNA for all known life. The presence of nucleobase-like compounds in carbonaceous chondrites delivered to the Earth raises the question of an extraterrestrial origin for the molecules that triggered life on our planet. Whether these molecules are formed in interstellar/protostellar environments, in small parent bodies in the solar system, or both, is currently unclear. Recent experiments show that the UV irradiation of pyrimidine (C4H4N2) in H2O-rich ice mixtures that contain NH3, CH3OH, or CH4 leads to the formation of the pyrimidine-based nucleobases uracil, cytosine, and thymine. In this work, we discuss the low-temperature UV irradiation of pyrimidine in realistic astrophysical ice mixtures containing H2O, CH3OH, and NH3, with or without CH4, to search for the production of nucleobases and other prebiotic compounds. These experiments show the presence of uracil, urea, glycerol, hexamethylenetetramine, small amino acids, and small carboxylic acids in all samples. Cytosine was only found in one sample produced from ices irradiated with a higher UV dose, while thymine was not found in any sample, even after irradiation with a higher UV dose. Results are discussed to evaluate the role of the photochemistry of pyrimidine in the inventory of organic molecules detected in meteorites and their astrophysical/astrobiological implications.

  17. 6-Pyrazolylpurine as an Artificial Nucleobase for Metal-Mediated Base Pairing in DNA Duplexes

    PubMed Central

    Léon, J. Christian; Sinha, Indranil; Müller, Jens

    2016-01-01

    The artificial nucleobase 6-pyrazol-1-yl-purine (6PP) has been investigated with respect to its usability in metal-mediated base pairing. As was shown by temperature-dependent UV spectroscopy, 6PP may form weakly stabilizing 6PP–Ag(I)–6PP homo base pairs. Interestingly, 6PP can be used to selectively recognize a complementary pyrimidine nucleobase. The addition of Ag(I) to a DNA duplex comprising a central 6PP:C mispair (C = cytosine) leads to a slight destabilization of the duplex. In contrast, a stabilizing 6PP–Ag(I)–T base pair is formed with a complementary thymine (T) residue. It is interesting to note that 6PP is capable of differentiating between the pyrimidine moieties despite the fact that it is not as sterically crowded as 6-(3,5-dimethylpyrazol-1-yl)purine, an artificial nucleobase that had previously been suggested for the recognition of nucleic acid sequences via the formation of a metal-mediated base pair. Hence, the additional methyl groups of 6-(3,5-dimethylpyrazol-1-yl)purine may not be required for the specific recognition of the complementary nucleobase. PMID:27089326

  18. Synthesis of carbocyclic nucleoside analogs with five-membered heterocyclic nucleobases

    PubMed Central

    Cho, Jong hyun; Coats, Steven J.; Schinazi, Raymond F.

    2015-01-01

    New carbocyclic nucleoside analogs with five-membered heterocyclic nucleobases were synthesized and evaluated as potential anti-HIV and anti-HCV agents. Among the synthesized carbocyclic nucleoside analogs, the pyrazole amide 15f exhibited modest selective anti-HIV-1 activity (EC50 = 24 µM). PMID:26028788

  19. Nucleobase-functionalized ABC triblock copolymers: self-assembly of supramolecular architectures.

    PubMed

    Zhang, Keren; Fahs, Gregory B; Aiba, Motohiro; Moore, Robert B; Long, Timothy E

    2014-08-21

    RAFT polymerization afforded acrylic ABC triblock copolymers with self-complementary nucleobase-functionalized external blocks and a low-Tg soft central block. ABC triblock copolymers self-assembled into well-defined lamellar microphase-separated morphologies for potential applications as thermoplastic elastomers. Complementary hydrogen bonding within the hard phase facilitated self-assembly and enhanced mechanical performance. PMID:24984613

  20. Chemoenzymatic synthesis and utilization of a SAM analog with an isomorphic nucleobase.

    PubMed

    Vranken, C; Fin, A; Tufar, P; Hofkens, J; Burkart, M D; Tor, Y

    2016-07-14

    SalL, an enzyme that catalyzes the synthesis of SAM from l-methionine and 5'-chloro-5'-deoxyoadenosine, is shown to accept 5'-chloro-5'-deoxythienoadenosine as a substrate and facilitate the synthesis of a synthetic SAM analog with an unnatural nucleobase. This synthetic cofactor is demonstrated to replace SAM in the DNA methylation reaction with M.TaqI. PMID:27270873

  1. Characterizing 3D RNA structure by single molecule FRET.

    PubMed

    Stephenson, James D; Kenyon, Julia C; Symmons, Martyn F; Lever, Andrew M L

    2016-07-01

    The importance of elucidating the three dimensional structures of RNA molecules is becoming increasingly clear. However, traditional protein structural techniques such as NMR and X-ray crystallography have several important drawbacks when probing long RNA molecules. Single molecule Förster resonance energy transfer (smFRET) has emerged as a useful alternative as it allows native sequences to be probed in physiological conditions and allows multiple conformations to be probed simultaneously. This review serves to describe the method of generating a three dimensional RNA structure from smFRET data from the biochemical probing of the secondary structure to the computational refinement of the final model. PMID:26853327

  2. Fretting Stresses in Single Crystal Superalloy Turbine Blade Attachments

    NASA Technical Reports Server (NTRS)

    Arakere, Nagaraj K.; Swanson, Gregory

    2000-01-01

    Single crystal nickel base superalloy turbine blades are being utilized in rocket engine turbopumps and turbine engines because of their superior creep, stress rupture, melt resistance and thermomechanical fatigue capabilities over polycrystalline alloys. Currently the most widely used single crystal nickel base turbine blade superalloys are PWA 1480/1493 and PWA 1484. These alloys play an important role in commercial, military and space propulsion systems. High Cycle Fatigue (HCF) induced failures in aircraft gas turbine and rocket engine turbopump blades is a pervasive problem. Blade attachment regions are prone to fretting fatigue failures. Single crystal nickel base superalloy turbine blades are especially prone to fretting damage because the subsurface shear stresses induced by fretting action at the attachment regions can result in crystallographic initiation and crack growth along octahedral planes. Furthermore, crystallographic crack growth on octahedral planes under fretting induced mixed mode loading can be an order of magnitude faster than under pure mode I loading. This paper presents contact stress evaluation in the attachment region for single crystal turbine blades used in the NASA alternate Advanced High Pressure Fuel Turbo Pump (HPFTP/AT) for the Space Shuttle Main Engine (SSME). Single crystal materials have highly orthotropic properties making the position of the crystal lattice relative to the part geometry a significant factor in the overall analysis. Blades and the attachment region are modeled using a large-scale 3D finite element (FE) model capable of accounting for contact friction, material orthotrophy, and variation in primary and secondary crystal orientation. Contact stress analysis in the blade attachment regions is presented as a function of coefficient of friction and primary and secondary crystal orientation, Stress results are used to discuss fretting fatigue failure analysis of SSME blades. Attachment stresses are seen to reach

  3. Identification and Functional Characterization of the First Nucleobase Transporter in Mammals

    PubMed Central

    Yamamoto, Syunsuke; Inoue, Katsuhisa; Murata, Tomoaki; Kamigaso, Syunsuke; Yasujima, Tomoya; Maeda, Jun-ya; Yoshida, Yukihiro; Ohta, Kin-ya; Yuasa, Hiroaki

    2010-01-01

    Nucleobases are important compounds that constitute nucleosides and nucleic acids. Although it has long been suggested that specific transporters are involved in their intestinal absorption and uptake in other tissues, none of their molecular entities have been identified in mammals to date. Here we describe identification of rat Slc23a4 as the first sodium-dependent nucleobase transporter (rSNBT1). The mRNA of rSNBT1 was expressed highly and only in the small intestine. When transiently expressed in HEK293 cells, rSNBT1 could transport uracil most efficiently. The transport of uracil mediated by rSNBT1 was sodium-dependent and saturable with a Michaelis constant of 21.2 μm. Thymine, guanine, hypoxanthine, and xanthine were also transported, but adenine was not. It was also suggested by studies of the inhibitory effect on rSNBT1-mediated uracil transport that several nucleobase analogs such as 5-fluorouracil are recognized by rSNBT1, but cytosine and nucleosides are not or only poorly recognized. Furthermore, rSNBT1 fused with green fluorescent protein was mainly localized at the apical membrane, when stably expressed in polarized Madin-Darby canine kidney II cells. These characteristics of rSNBT1 were almost fully in agreement with those of the carrier-mediated transport system involved in intestinal uracil uptake. Therefore, it is likely that rSNBT1 is its molecular entity or at least in part responsible for that. It was also found that the gene orthologous to the rSNBT1 gene is genetically defective in humans. This may have a biological and evolutional meaning in the transport and metabolism of nucleobases. The present study provides novel insights into the specific transport and metabolism of nucleobases and their analogs for therapeutic use. PMID:20042597

  4. Photochemistry of Pyrimidine in Astrophysical Ices: Formation of Nucleobases and Other Prebiotic Species

    NASA Technical Reports Server (NTRS)

    Nuevo, Michel; Sandford, Scott A.; Materese, Christopher K.; Milam, Stefanie N.

    2012-01-01

    Nucleobases are N-heterocycles that are the informational subunits of DNA and RNA. They are divided into two molecular groups: pyrimidine bases (uracil, cytosine, and thymine) and purine bases (adenine and guanine). Nucleobases have been detected in meteorites, and their extraterrestrial origin confirmed by isotopic measurements. Although no N-heterocycles have ever been observed in the ISM, the positions of the 6.2- m interstellar emission features suggest a population of such molecules is likely to be present. However, laboratory experiments have shown that the ultraviolet (UV) irradiation of pyrimidine in ices of astrophysical relevance such as H2O, NH3, CH3OH, CH4, CO, or combinations of these at low temperature (less than or equal to 20 K) leads to the formation of several pyrimidine derivatives including the nucleobases uracil and cytosine, as well as precursors such as 4(3H)-pyrimidone and 4-aminopyrimidine. Quantum calculations on the formation of 4(3H)-pyrimidone and uracil from the irradiation of pyrimidine in pure H2O ices are in agreement with their experimental formation pathways.10 In those residues, other species of prebiotic interest such as urea as well as the amino acids glycine and alanine could also be identified. However, only very small amounts of pyrimidine derivatives containing CH3 groups could be detected, suggesting that the addition of methyl groups to pyrimidine is not an efficient process. For this reason, the nucleobase thymine was not observed in any of the samples. In this work, we study the formation of nucleobases and other photo-products of prebiotic interest from the UV irradiation of pyrimidine in ices containing H2O, NH3, CH3OH, and CO, mixed in astrophysical proportions.

  5. Solution structures of purine base analogues 9-deazaguanine and 9-deazahypoxanthine.

    PubMed

    Karnawat, Vishakha; Puranik, Mrinalini

    2016-03-01

    Deaza analogues of nucleobases are potential drugs against infectious diseases caused by parasites. A caveat is that apart from binding their target parasite enzymes, they also bind and inhibit enzymes of the host. In order to design derivatives of deaza analogues which specifically bind target enzymes, knowledge of their molecular structure, protonation state, and predominant tautomers at physiological conditions is essential. We have employed resonance Raman spectroscopy at an excitation wavelength of 260 nm, to decipher solution structure of 9-deazaguanine (9DAG) and 9-deazahypoxanthine (9DAH). These are analogues of guanine and hypoxanthine, respectively, and have been exploited to study static complexes of nucleobase binding enzymes. Such enzymes are known to perturb pKa of their ligands, and thus, we also determined solution structures of these analogues at two, acidic and alkaline, pH. Structure of each possible protonation state and tautomer was computed using density functional theoretical calculations. Species at various pHs were identified based on isotopic shifts in experimental wavenumbers and by comparing these shifts with corresponding computed isotopic shifts. Our results show that at physiological pH, N1 of pyrimidine ring in 9DAG and 9DAH bears a proton. At lower pH, N3 is place of protonation, and at higher pH, deprotonation occurs at N1 position. The proton at N7 of purine ring remains intact even at pH 12.5. We have further compared these results with naturally occurring nucleotides. Our results identify key vibrational modes which can report on hydrogen bonding interactions, protonation and deprotonation in purine rings upon binding to the active site of enzymes. PMID:25894214

  6. Fretting of Nickel-Chromium-Aluminum Alloys at Temperatures to 816 C

    NASA Technical Reports Server (NTRS)

    Bill, R. C.

    1974-01-01

    A series of four nickel-based alloys containing 10 percent and 20 percent chromium in combination with 2 percent and 5 percent aluminum were fretted in dry air at temperatures to 816 C. At all temperatures, the alloys showed far less fretting wear than did high-purity nickel. This was attributed to the formation of protective oxide films on the alloys, the result of the selective oxidation of the alloy constituents. Increasing the aluminum concentration reduced fretting wear at all temperatures. Increasing the chromium concentration from 10 percent to 20 percent resulted in decreased fretting wear at 23 and 540 C, but increased fretting wear at 650 and 816 C.

  7. Chromophoric Nucleoside Analogues: Synthesis and Characterization of 6-Aminouracil-Based Nucleodyes.

    PubMed

    Freeman, Noam S; Moore, Curtis E; Wilhelmsson, L Marcus; Tor, Yitzhak

    2016-06-01

    Nucleodyes, visibly colored chromophoric nucleoside analogues, are reported. Design criteria are outlined and the syntheses of cytidine and uridine azo dye analogues derived from 6-aminouracil are described. Structural analysis shows that the nucleodyes are sound structural analogues of their native nucleoside counterparts, and photophysical studies demonstrate that the nucleodyes are sensitive to microenvironmental changes. Quantum chemical calculations are presented as a valuable complementary tool for the design of strongly absorbing nucleodyes, which overlap with the emission of known fluorophores. Förster critical distance (R0) calculations determine that the nucleodyes make good FRET pairs with both 2-aminopurine (2AP) and pyrrolocytosine (PyC). Additionally, unique tautomerization features exhibited by 5-(4-nitrophenylazo)-6-oxocytidine (8) are visualized by an extraordinary crystal structure. PMID:27128151

  8. Uncovering aberrant mutant PKA function with flow cytometric FRET

    PubMed Central

    Lee, Shin-Rong; Sang, Lingjie; Yue, David T.

    2016-01-01

    SUMMARY Biology has been revolutionized by tools that allow the detection and characterization of protein-protein interactions (PPI). Förster resonance energy transfer (FRET)-based methods have become particularly attractive as they allow quantitative studies of PPIs within the convenient and relevant context of living cells. We describe here an approach that allows the rapid construction of live-cell, FRET-based binding curves using a commercially-available flow cytometer. We illustrate a simple method for absolutely calibrating the cytometer, validate our binding assay against the gold-standard isothermal calorimetry (ITC), and use flow cytometric FRET to uncover the structural and functional effects of the Cushing syndrome-causing mutation (L206R) on PKA’s catalytic subunit. We discover that this mutation not only differentially affects PKAcat’s binding to its multiple partners, but also impacts its rate of catalysis. These findings improve our mechanistic understanding of this disease-causing mutation, while illustrating the simplicity, general applicability and power of flow cytometric FRET. PMID:26997269

  9. Fretting Fatigue of Gamma TiAl Studied

    NASA Technical Reports Server (NTRS)

    Miyoshi, Kazuhisa; Lerch, Bradley A.; Draper, Susan L.

    2003-01-01

    Gamma titanium-aluminum alloy (g-TiAl) is an attractive new material for aerospace applications because of its low density and high specific strength in comparison to currently used titanium and nickel-base alloys. Potential applications for this material are compressor and low-pressure turbine blades. These blades are fitted into either the compressor or turbine disks via a dovetail connection. The dovetail region experiences a complex stress state due to the alternating centrifugal force and the natural high-frequency vibration of the blade. Because of the dovetail configuration and the complex stress state, fretting is often a problem in this area. Furthermore, the local stress state becomes more complex when the influence of the metal-metal contact and the edge of the contact is evaluated. Titanium and titanium-based alloys in the clean state exhibit strong adhesive bonds when in contact with themselves and other materials (refs. 1 and 2). This adhesion causes heavy surface damage and high friction in practical cases. Although the wear produced by fretting may be mild, the reduction in fatigue life can be substantial. Thus, there is the potential for fretting problems with these TiAl applications. Since TiAl is an emerging material, there has been limited information about its fretting behavior.

  10. A FRET-based probe with a chemically deactivatable quencher.

    PubMed

    Leriche, Geoffray; Budin, Ghyslain; Darwich, Zeinab; Weltin, Denis; Mély, Yves; Klymchenko, Andrey S; Wagner, Alain

    2012-03-28

    A new concept of a chemically deactivatable quencher is proposed for a FRET-based probe that turns-on its fluorescence by either an enzymatic cleavage or a chemical reagent (sodium dithionite). This concept allowed us to quantify the caspase-3 cleavage activity in solution and to reveal unreacted probes in cell experiments. PMID:22327268

  11. Uncovering Aberrant Mutant PKA Function with Flow Cytometric FRET.

    PubMed

    Lee, Shin-Rong; Sang, Lingjie; Yue, David T

    2016-03-29

    Biology has been revolutionized by tools that allow the detection and characterization of protein-protein interactions (PPIs). Förster resonance energy transfer (FRET)-based methods have become particularly attractive as they allow quantitative studies of PPIs within the convenient and relevant context of living cells. We describe here an approach that allows the rapid construction of live-cell FRET-based binding curves using a commercially available flow cytometer. We illustrate a simple method for absolutely calibrating the cytometer, validating our binding assay against the gold standard isothermal calorimetry (ITC), and using flow cytometric FRET to uncover the structural and functional effects of the Cushing-syndrome-causing mutation (L206R) on PKA's catalytic subunit. We discover that this mutation not only differentially affects PKAcat's binding to its multiple partners but also impacts its rate of catalysis. These findings improve our mechanistic understanding of this disease-causing mutation, while illustrating the simplicity, general applicability, and power of flow cytometric FRET. PMID:26997269

  12. Plant-based FRET biosensor discriminates enviornmental zinc levels

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Heavy metal accumulation in the environment poses great risks to flora and fauna. However, monitoring sites prone to accumulation poses scale and economic challenges. In this study, we present and test a method for monitoring these sites using fluorescent resonance energy transfer (FRET) change in r...

  13. Application of FRET probes in the analysis of neuronal plasticity

    PubMed Central

    Ueda, Yoshibumi; Kwok, Showming; Hayashi, Yasunori

    2013-01-01

    Breakthroughs in imaging techniques and optical probes in recent years have revolutionized the field of life sciences in ways that traditional methods could never match. The spatial and temporal regulation of molecular events can now be studied with great precision. There have been several key discoveries that have made this possible. Since green fluorescent protein (GFP) was cloned in 1992, it has become the dominant tracer of proteins in living cells. Then the evolution of color variants of GFP opened the door to the application of Förster resonance energy transfer (FRET), which is now widely recognized as a powerful tool to study complicated signal transduction events and interactions between molecules. Employment of fluorescent lifetime imaging microscopy (FLIM) allows the precise detection of FRET in small subcellular structures such as dendritic spines. In this review, we provide an overview of the basic and practical aspects of FRET imaging and discuss how different FRET probes have revealed insights into the molecular mechanisms of synaptic plasticity and enabled visualization of neuronal network activity both in vitro and in vivo. PMID:24133415

  14. Accurate single-molecule FRET studies using multiparameter fluorescence detection.

    PubMed

    Sisamakis, Evangelos; Valeri, Alessandro; Kalinin, Stanislav; Rothwell, Paul J; Seidel, Claus A M

    2010-01-01

    In the recent decade, single-molecule (sm) spectroscopy has come of age and is providing important insight into how biological molecules function. So far our view of protein function is formed, to a significant extent, by traditional structure determination showing many beautiful static protein structures. Recent experiments by single-molecule and other techniques have questioned the idea that proteins and other biomolecules are static structures. In particular, Förster resonance energy transfer (FRET) studies of single molecules have shown that biomolecules may adopt many conformations as they perform their function. Despite the success of sm-studies, interpretation of smFRET data are challenging since they can be complicated due to many artifacts arising from the complex photophysical behavior of fluorophores, dynamics, and motion of fluorophores, as well as from small amounts of contaminants. We demonstrate that the simultaneous acquisition of a maximum of fluorescence parameters by multiparameter fluorescence detection (MFD) allows for a robust assessment of all possible artifacts arising from smFRET and offers unsurpassed capabilities regarding the identification and analysis of individual species present in a population of molecules. After a short introduction, the data analysis procedure is described in detail together with some experimental considerations. The merits of MFD are highlighted further with the presentation of some applications to proteins and nucleic acids, including accurate structure determination based on FRET. A toolbox is introduced in order to demonstrate how complications originating from orientation, mobility, and position of fluorophores have to be taken into account when determining FRET-related distances with high accuracy. Furthermore, the broad time resolution (picoseconds to hours) of MFD allows for kinetic studies that resolve interconversion events between various subpopulations as a biomolecule of interest explores its

  15. Single-Molecule Pull-down FRET (SiMPull-FRET) to dissect the mechanisms of biomolecular machines

    PubMed Central

    Kahlscheuer, Matthew L.; Widom, Julia; Walter, Nils G.

    2016-01-01

    Spliceosomes are multi-megadalton RNA-protein complexes responsible for the faithful removal of non-coding segments (introns) from pre-messenger RNAs (pre-mRNAs), a process critical for the maturation of eukaryotic mRNAs for subsequent translation by the ribosome. Both the spliceosome and ribosome, as well as many other RNA and DNA processing machineries, contain central RNA components that endow biomolecular complexes with precise, sequence-specific nucleic acid recognition and versatile structural dynamics. Single molecule fluorescence (or Förster) resonance energy transfer (smFRET) microscopy is a powerful tool for the study of local and global conformational changes of both simple and complex biomolecular systems involving RNA. The integration of biochemical tools such as immunoprecipitation with advanced methods in smFRET microscopy and data analysis has opened up entirely new avenues towards studying the mechanisms of biomolecular machines isolated directly from complex biological specimens such as cell extracts. Here we detail the general steps for using prism-based total internal reflection fluorescence (TIRF) microscopy in exemplary single molecule pull-down FRET (SiMPull-FRET) studies of the yeast spliceosome and discuss the broad application potential of this technique. PMID:26068753

  16. Functional identification of SLC43A3 as an equilibrative nucleobase transporter involved in purine salvage in mammals

    PubMed Central

    Furukawa, Junji; Inoue, Katsuhisa; Maeda, Junya; Yasujima, Tomoya; Ohta, Kinya; Kanai, Yoshikatsu; Takada, Tappei; Matsuo, Hirotaka; Yuasa, Hiroaki

    2015-01-01

    The purine salvage pathway plays a major role in the nucleotide production, relying on the supply of nucleobases and nucleosides from extracellular sources. Although specific transporters have been suggested to be involved in facilitating their transport across the plasma membrane in mammals, those which are specifically responsible for utilization of extracellular nucleobases remain unknown. Here we present the molecular and functional characterization of SLC43A3, an orphan transporter belonging to an amino acid transporter family, as a purine-selective nucleobase transporter. SLC43A3 was highly expressed in the liver, where it was localized to the sinusoidal membrane of hepatocytes, and the lung. In addition, SLC43A3 expressed in MDCKII cells mediated the uptake of purine nucleobases such as adenine, guanine, and hypoxanthine without requiring typical driving ions such as Na+ and H+, but it did not mediate the uptake of nucleosides. When SLC43A3 was expressed in APRT/HPRT1-deficient A9 cells, adenine uptake was found to be low. However, it was markedly enhanced by the introduction of SLC43A3 with APRT. In HeLa cells, knock-down of SLC43A3 markedly decreased adenine uptake. These data suggest that SLC43A3 is a facilitative and purine-selective nucleobase transporter that mediates the cellular uptake of extracellular purine nucleobases in cooperation with salvage enzymes. PMID:26455426

  17. Functional identification of SLC43A3 as an equilibrative nucleobase transporter involved in purine salvage in mammals.

    PubMed

    Furukawa, Junji; Inoue, Katsuhisa; Maeda, Junya; Yasujima, Tomoya; Ohta, Kinya; Kanai, Yoshikatsu; Takada, Tappei; Matsuo, Hirotaka; Yuasa, Hiroaki

    2015-01-01

    The purine salvage pathway plays a major role in the nucleotide production, relying on the supply of nucleobases and nucleosides from extracellular sources. Although specific transporters have been suggested to be involved in facilitating their transport across the plasma membrane in mammals, those which are specifically responsible for utilization of extracellular nucleobases remain unknown. Here we present the molecular and functional characterization of SLC43A3, an orphan transporter belonging to an amino acid transporter family, as a purine-selective nucleobase transporter. SLC43A3 was highly expressed in the liver, where it was localized to the sinusoidal membrane of hepatocytes, and the lung. In addition, SLC43A3 expressed in MDCKII cells mediated the uptake of purine nucleobases such as adenine, guanine, and hypoxanthine without requiring typical driving ions such as Na(+) and H(+), but it did not mediate the uptake of nucleosides. When SLC43A3 was expressed in APRT/HPRT1-deficient A9 cells, adenine uptake was found to be low. However, it was markedly enhanced by the introduction of SLC43A3 with APRT. In HeLa cells, knock-down of SLC43A3 markedly decreased adenine uptake. These data suggest that SLC43A3 is a facilitative and purine-selective nucleobase transporter that mediates the cellular uptake of extracellular purine nucleobases in cooperation with salvage enzymes. PMID:26455426

  18. Detecting Organic Compounds in Martian Soil Analogues Using Gas Chromatography Mass Spectrometry

    NASA Technical Reports Server (NTRS)

    Glavin, D. P.; Buch, A.; Mahaffy, P. R.

    2004-01-01

    One of the primary objectives of the 1976 Viking missions was to determine whether organic compounds, possibly of biological origin, were present in the Martian surface soils. The Viking gas chromatography mass spectrometry (GCMS) instruments found no evidence for any organic compounds of Martian origin above a few parts per billion in the upper 10 cm of surface soil [l], suggesting the absence of a widely distributed Martian biota. However, Benner et d. have suggested that significant amounts of non-volatile organic compounds, possibly including oxidation products of bioorganic molecules (e.g. carboxylic acids) would not have been detected by the Viking GCMS [2]. Moreover, other key organic compounds important to biology, such as amino acids and nucleobases, would also likely have been missed by the Viking GCMS as these compounds require chemical derivatization to be stable in a GC column [3]. Recent pyrolysis experiments with a Mars soil analogue that had been innoculated with Escherichia coli bacteria have shown that amino acid decomposition products (amines) and nucleobases are among the most abundant products generated after pyrolysis of the bacterial cells [4,5]. At the part per billion level (Viking GCMS detection limit), these pyrolysis products generated from several million bacterial cells per gram of Martian soil would not have been detected by the Viking GCMS instruments [4]. Analytical protocols are under development for upcoming in situ lander opportunities to target several important biological compounds including amino acids and nucleobases. For example, extraction and chemical derivatization techniques [3] are being adapted for space flight use to transform reactive or fragile molecules that would not have been detected by the Viking GCMS instruments, into species that are sufficiently volatile to be detected by GCMS. Recent experiments carried out at NASA Goddard have shown that using this derivatization technique all of the targeted compounds

  19. Perrin and Förster unified: Dual-laser triple-polarization FRET (3polFRET) for interactions at the Förster-distance and beyond.

    PubMed

    Ungvári, Tamás; Gogolák, Péter; Bagdány, Miklós; Damjanovich, László; Bene, László

    2016-04-01

    Dual laser flow cytometric energy transfer (FCET)--elaborated by Trón et al. in 1984--is an efficient and rapid way of measuring FRET on large cell populations. FRET efficiency and the donor and acceptor concentrations are determined from one donor and two acceptor signals. In this communication this method is extended towards the domain of receptor dynamics by the detection of polarized components of the three intensities. By enabling a complete description of the proximity and dynamics of FRET-systems, the new measuring scheme allows a more refined description of both the structure and dynamics of cell surface receptor clusters at the nano-scale and beyond. Associated donor fraction, limiting anisotropy and rotational correlation time of the donor, acceptor anisotropy and cell-by-cell estimation of the orientation factor for FRET (κ2) are available in the steady state on a single FRET sample in a very rapid and statistically efficient way offered by flow cytometry. For a more sensitive detection of conformational changes the "polarized FRET indices"--quantities composed from FRET efficiency and anisotropies--are proposed. The method is illustrated by measurements on a FRET system with changing FRET-fraction and on a two donor-one acceptor-system, when the existence of receptor trimers are proven by the detection of "hetero-FRET induced homo-FRET relief", i.e. the diminishing of homo-FRET between the two donors in the presence of a donor quencher. The method also offers higher sensitivity for assessing conformational changes at the nano-scale, due to its capability for the simultaneous detection of changes of proximity and relative orientations of the FRET donor and acceptor. Although the method has been introduced in the context of FRET, it is more general: It can be used for monitoring triple-anisotropy correlations also in those cases when FRET actually does not occur, e.g. for interactions occuring beyond the Förster-distance R0. Interpretation of κ2 has

  20. rFRET: A comprehensive, Matlab-based program for analyzing intensity-based ratiometric microscopic FRET experiments.

    PubMed

    Nagy, Peter; Szabó, Ágnes; Váradi, Tímea; Kovács, Tamás; Batta, Gyula; Szöllősi, János

    2016-04-01

    Fluorescence or Förster resonance energy transfer (FRET) remains one of the most widely used methods for assessing protein clustering and conformation. Although it is a method with solid physical foundations, many applications of FRET fall short of providing quantitative results due to inappropriate calibration and controls. This shortcoming is especially valid for microscopy where currently available tools have limited or no capability at all to display parameter distributions or to perform gating. Since users of multiparameter flow cytometry usually apply these tools, the absence of these features in applications developed for microscopic FRET analysis is a significant limitation. Therefore, we developed a graphical user interface-controlled Matlab application for the evaluation of ratiometric, intensity-based microscopic FRET measurements. The program can calculate all the necessary overspill and spectroscopic correction factors and the FRET efficiency and it displays the results on histograms and dot plots. Gating on plots and mask images can be used to limit the calculation to certain parts of the image. It is an important feature of the program that the calculated parameters can be determined by regression methods, maximum likelihood estimation (MLE) and from summed intensities in addition to pixel-by-pixel evaluation. The confidence interval of calculated parameters can be estimated using parameter simulations if the approximate average number of detected photons is known. The program is not only user-friendly, but it provides rich output, it gives the user freedom to choose from different calculation modes and it gives insight into the reliability and distribution of the calculated parameters. © 2016 International Society for Advancement of Cytometry. PMID:27003481

  1. First-Principles Photoemission Spectroscopy of DNA and RNA Nucleobases from Koopmans-Compliant Functionals.

    PubMed

    Nguyen, Ngoc Linh; Borghi, Giovanni; Ferretti, Andrea; Marzari, Nicola

    2016-08-01

    The need to interpret ultraviolet photoemission data strongly motivates the refinement of first-principles techniques that are able to accurately predict spectral properties. In this work, we employ Koopmans-compliant functionals, constructed to enforce piecewise linearity in approximate density functionals, to calculate the structural and electronic properties of DNA and RNA nucleobases. Our results show that not only ionization potentials and electron affinities are accurately predicted with mean absolute errors of <0.1 eV, but also that calculated photoemission spectra are in excellent agreement with experimental ultraviolet photoemission spectra. In particular, the role and contribution of different tautomers to the photoemission spectra are highlighted and discussed in detail. The structural properties of nucleobases are also investigated, showing an improved description with respect to local and semilocal density-functional theory. Methodologically, our results further consolidate the role of Koopmans-compliant functionals in providing, through orbital-density-dependent potentials, accurate electronic and spectral properties. PMID:27267665

  2. Formation of Nucleobases from the UV Irradiation of Pyrimidine in Interstellar Ice Analogs

    NASA Technical Reports Server (NTRS)

    Milam, Stefanie N.; Nuevo, Michel; Sandford, Scott A.; Elsila, Jamie E.; Dworkin, Jason P.

    2010-01-01

    Previous laboratory simulations showed that complex molecules, including prebiotic compounds/can be formed under interstellar conditions from the vacuum UV irradiation of interstellar ice analogs containing H2O, CO, NH3 etc. Although some complex prebiotic species have not been confirmed In the interstellar medium, they are known to be present in meteorites. Nucleobases, the building blocks of DNA and RNA, have also been detected in meteorites. Here, we present a study of the formation of pyrimidine-based compounds from the UV irradiation of pyrimidine in H2O- and/or NH3-ices at 20-30 K, Our results show that various derivatives, induding the nucleobases uracil and cytosine, are formed under these conditions.

  3. Binding of nucleobases with graphene and carbon nanotube: a review of computational studies.

    PubMed

    Chehel Amirani, Morteza; Tang, Tian

    2015-01-01

    Functionalized carbon nanotubes (CNTs) constitute a new class of nanostructured materials that have vast applications in CNT purification and separation, biosensing, drug delivery, etc. Hybrids formed from the functionalization of CNT with biological molecules have shown interesting properties and have attracted great attention in recent years. Of particular interest is the hybridization of single- or double-stranded nucleic acid (NA) with CNT. Nucleobases, as the building blocks of NA, interact with CNT and contribute strongly to the stability of the NA-CNT hybrids and their properties. In this work, we present a thorough review of previous studies on the binding of nucleobases with graphene and CNT, with a focus on the simulation works that attempted to evaluate the structure and strength of binding. Discrepancies among these works are identified, and factors that might contribute to such discrepancies are discussed. PMID:25118044

  4. Time-resolved homo-FRET studies of biotin-streptavidin complexes.

    PubMed

    Andreoni, Alessandra; Nardo, Luca; Rigler, Rudolf

    2016-09-01

    Förster resonance energy transfer is a mechanism of fluorescence quenching that is notably useful for characterizing properties of biomolecules and/or their interactions. Here we study water-solutions of Biotin-Streptavidin complexes, in which Biotin is labeled with a rigidly-bound fluorophore that can interact by Förster resonance energy transfer with the fluorophores labeling the other, up to three, Biotins of the same complex. The fluorophore, Atto550, is a Rhodamine analogue. We detect the time-resolved fluorescence decay of the fluorophores with an apparatus endowed with single-photon sensitivity and temporal resolution of ~30ps. The decay profiles we observe for samples containing constant Biotin-Atto550 conjugates and varying Streptavidin concentrations are multi-exponential. Each decay component can be associated with the rate of quenching exerted on each donor by each of the acceptors that label the other Biotin molecules, depending on the binding site they occupy. The main features that lead to this result are that (i) the transition dipole moments of the up-to-four Atto550 fluorophores that label the complexes are fixed as to both relative positions and mutual orientations; (ii) the fluorophores are identical and the role of donor in each Biotin-Streptavidin complex is randomly attributed to the one that has absorbed the excitation light (homo-FRET). Obviously the high-temporal resolution of the excitation-detection apparatus is necessary to discriminate among the fluorescence decay components. PMID:27494295

  5. Site Covalent Modification of Methionyl Peptides for the Production of FRET Complexes.

    PubMed

    Jadhav, Pramodkumar D; Shen, Jianheng; Sammynaiken, Ramaswami; Reaney, Martin J T

    2015-11-16

    Flax cyclic peptides (orbitides, linusorbs (LOs)) [1-8-NαC],[1-MetO2]-linusorb B1 ([MetO2]-LO1) and [1-9-NαC],[1-MetO2]-linusorb B2 ([MetO2]-LO2) are biologically active. These LOs lack active nuclei commonly used in peptide modification. We have developed reactions to activate methionine methyl sulphide to produce stable derivatives. In these reactions, LOs are converted to sulfonium intermediates and subsequently to derivatives containing active nuclei while preserving their fundamental structures. The reaction conditions preserved cyclic peptide fundamental structure and organic solvent solubility. [Met]-LO1 and [Met]-LO2 analogues containing activated groups (-CN, -COOEt, and -NH2 ) in the form of methionine, methionine (S)-oxide, and methionine (S,S)-dioxide amino acids were synthesized and characterized by LCMS and 1D and 2D NMR spectroscopy. Coumarin orbitide complexes produced in this manner bind Eu(3+) yielding FRET compounds that absorb energy through coumarin antennae and emit photons at lanthanide wavelengths. PMID:26434760

  6. Multifunctional, Biocompatible Supramolecular Hydrogelators Consist Only of Nucleobase, Amino Acid, and Glycoside

    PubMed Central

    Li, Xinming; Kuang, Yi; Shi, Junfeng; Gao, Yuan; Lin, Hsin-Chieh; Xu, Bing

    2011-01-01

    The integration of nucleobase, amino acid, and glycoside into a single molecule results in a novel class of supramolecular hydrogelators, which not only exhibit biocompatibility and biostability, but also facilitate the entry of nucleic acids into cytosol and nuclei of cells. This work illustrates a simple way to generate an unprecedented molecular architecture from the basic biological building blocks for the development of sophisticated soft nanomaterials, including supramolecular hydrogels. PMID:21928792

  7. The photochemistry of pyrimidine in realistic astrophysical ices and the production of nucleobases

    SciTech Connect

    Nuevo, Michel; Materese, Christopher K.; Sandford, Scott A.

    2014-10-01

    Nucleobases, together with deoxyribose/ribose and phosphoric acid, are the building blocks of DNA and RNA for all known life. The presence of nucleobase-like compounds in carbonaceous chondrites delivered to the Earth raises the question of an extraterrestrial origin for the molecules that triggered life on our planet. Whether these molecules are formed in interstellar/protostellar environments, in small parent bodies in the solar system, or both, is currently unclear. Recent experiments show that the UV irradiation of pyrimidine (C{sub 4}H{sub 4}N{sub 2}) in H{sub 2}O-rich ice mixtures that contain NH{sub 3}, CH{sub 3}OH, or CH{sub 4} leads to the formation of the pyrimidine-based nucleobases uracil, cytosine, and thymine. In this work, we discuss the low-temperature UV irradiation of pyrimidine in realistic astrophysical ice mixtures containing H{sub 2}O, CH{sub 3}OH, and NH{sub 3}, with or without CH{sub 4}, to search for the production of nucleobases and other prebiotic compounds. These experiments show the presence of uracil, urea, glycerol, hexamethylenetetramine, small amino acids, and small carboxylic acids in all samples. Cytosine was only found in one sample produced from ices irradiated with a higher UV dose, while thymine was not found in any sample, even after irradiation with a higher UV dose. Results are discussed to evaluate the role of the photochemistry of pyrimidine in the inventory of organic molecules detected in meteorites and their astrophysical/astrobiological implications.

  8. Crystal Structures of Non-Natural Nucleobase Pairs in A- and B-DNA†

    PubMed Central

    Georgiadis, Millie M.; Singh, Isha; Kellett, Whitney F.; Hoshika, Shuichi; Benner, Steven A.; Richards, Nigel G. J.

    2015-01-01

    The extent to which synthetic biology can be used to expand genetic information systems compatible with natural enzymes and cells will depend on the extent to which multiple and contiguous non-natural nucleobase pairs fit within the standard double helical conformations of DNA. Toward this goal, two non-standard nucleobases (Z, 6-amino-5-nitro-2(1H)-pyridone and P, 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)one) were designed to form a Z:P pair with a standard “edge on” Watson-Crick geometry, but with rearranged hydrogen bond donor and acceptor groups. Here, we present the crystal structures of two self-complementary 16-mer oligonucleotides containing Z:P pairs. The first contained two consecutive Z:P nucleobase pairs and was found to crystallize within a host-guest complex in B-form. The second contained six consecutive Z:P pairs; it was found to crystallize as an A-form DNA duplex, although it can adopt B-form in solution as inferred from circular dichroism spectra. Although Z:P pairs have some structural properties that are similar to those of G:C pairs, unique features include stacking of the nitro group on Z with the adjacent heterocyclic nucleobase ring in A-DNA. In both B-and A-DNA, major groove widths associated with the Z:P pairs are approximately 1 Å wider than those of comparable G:C pairs potentially due to the presence of the nitro group in Z. Thus, our structural studies suggest that multiple and consecutive Z:P pairs are readily accommodated in DNA duplex structures recognized by natural polymerases, and therefore the GACTZP synthetic genetic system has the requisite properties to expand sequence space. PMID:25961938

  9. Time-gated FRET nanoassemblies for rapid and sensitive intra- and extracellular fluorescence imaging.

    PubMed

    Afsari, Hamid Samareh; Cardoso Dos Santos, Marcelina; Lindén, Stina; Chen, Ting; Qiu, Xue; van Bergen En Henegouwen, Paul M P; Jennings, Travis L; Susumu, Kimihiro; Medintz, Igor L; Hildebrandt, Niko; Miller, Lawrence W

    2016-06-01

    Time-gated Förster resonance energy transfer (FRET) using the unique material combination of long-lifetime terbium complexes (Tb) and semiconductor quantum dots (QDs) provides many advantages for highly sensitive and multiplexed biosensing. Although time-gated detection can efficiently suppress sample autofluorescence and background fluorescence from directly excited FRET acceptors, Tb-to-QD FRET has rarely been exploited for biomolecular imaging. We demonstrate Tb-to-QD time-gated FRET nanoassemblies that can be applied for intra- and extracellular imaging. Immunostaining of different epitopes of the epidermal growth factor receptor (EGFR) with Tb- and QD-conjugated antibodies and nanobodies allowed for efficient Tb-to-QD FRET on A431 cell membranes. The broad usability of Tb-to-QD FRET was further demonstrated by intracellular Tb-to-QD FRET and Tb-to-QD-to-dye FRET using microinjection as well as cell-penetrating peptide-mediated endocytosis with HeLa cells. Effective brightness enhancement by FRET from several Tb to the same QD, the use of low nanomolar concentrations, and the quick and sensitive detection void of FRET acceptor background fluorescence are important advantages for advanced intra- and extracellular imaging of biomolecular interactions. PMID:27386579

  10. Time-gated FRET nanoassemblies for rapid and sensitive intra- and extracellular fluorescence imaging

    PubMed Central

    Afsari, Hamid Samareh; Cardoso Dos Santos, Marcelina; Lindén, Stina; Chen, Ting; Qiu, Xue; van Bergen en Henegouwen, Paul M. P.; Jennings, Travis L.; Susumu, Kimihiro; Medintz, Igor L.; Hildebrandt, Niko; Miller, Lawrence W.

    2016-01-01

    Time-gated Förster resonance energy transfer (FRET) using the unique material combination of long-lifetime terbium complexes (Tb) and semiconductor quantum dots (QDs) provides many advantages for highly sensitive and multiplexed biosensing. Although time-gated detection can efficiently suppress sample autofluorescence and background fluorescence from directly excited FRET acceptors, Tb-to-QD FRET has rarely been exploited for biomolecular imaging. We demonstrate Tb-to-QD time-gated FRET nanoassemblies that can be applied for intra- and extracellular imaging. Immunostaining of different epitopes of the epidermal growth factor receptor (EGFR) with Tb- and QD-conjugated antibodies and nanobodies allowed for efficient Tb-to-QD FRET on A431 cell membranes. The broad usability of Tb-to-QD FRET was further demonstrated by intracellular Tb-to-QD FRET and Tb-to-QD-to-dye FRET using microinjection as well as cell-penetrating peptide–mediated endocytosis with HeLa cells. Effective brightness enhancement by FRET from several Tb to the same QD, the use of low nanomolar concentrations, and the quick and sensitive detection void of FRET acceptor background fluorescence are important advantages for advanced intra- and extracellular imaging of biomolecular interactions. PMID:27386579

  11. Nucleobase and amino acid formation through impacts of meteorites on the early ocean

    NASA Astrophysics Data System (ADS)

    Furukawa, Yoshihiro; Nakazawa, Hiromoto; Sekine, Toshimori; Kobayashi, Takamichi; Kakegawa, Takeshi

    2015-11-01

    The emergence of life's building blocks on the prebiotic Earth was the first crucial step for the origins of life. Extraterrestrial delivery of intact amino acids and nucleobases is the prevailing hypothesis for their availability on prebiotic Earth because of the difficulties associated with the production of these organics from terrestrial carbon and nitrogen sources under plausible prebiotic conditions. However, the variety and amounts of these intact organics delivered by meteorites would have been limited. Previous shock-recovery experiments have demonstrated that meteorite impact reactions could have generated organics on the prebiotic Earth. Here, we report on the simultaneous formation of nucleobases (cytosine and uracil) found in DNA and/or RNA, various proteinogenic amino acids (glycine, alanine, serine, aspartic acid, glutamic acid, valine, leucine, isoleucine, and proline), non-proteinogenic amino acids, and aliphatic amines in experiments simulating reactions induced by extraterrestrial objects impacting on the early oceans. To the best of our knowledge, this is the first report of the formation of nucleobases from inorganic materials by shock conditions. In these experiments, bicarbonate was used as the carbon source. Bicarbonate, which is a common dissolved carbon species in CO2-rich atmospheric conditions, was presumably the most abundant carbon species in the early oceans and in post-impact plumes. Thus, the present results expand the possibility that impact-induced reactions generated various building blocks for life on prebiotic Earth in large quantities through the use of terrestrial carbon reservoirs.

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

    PubMed

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

    2016-05-01

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

  13. Determination of HDV ribozyme N(-1) nucleobase and functional group specificity using internal competition kinetics

    PubMed Central

    Kellerman, Daniel L; Simmons, Kandice S; Pedraza, Mayra; Piccirilli, Joseph A; York, Darrin M; Harris, Michael E

    2015-01-01

    Biological catalysis involves interactions distant from the site of chemistry that can position the substrate for reaction. Catalysis of RNA 2′-O-transphosphorylation by the HDV ribozyme is sensitive to the identity of the N(-1) nucleotide flanking the reactive phosphoryl group. However, the interactions that affect the conformation of this position, and in turn the 2′O nucleophile, are unclear. Here, we describe the application of multiple substrate internal competition kinetic analyses to understand how the N(-1) nucleobase contributes to HDV catalysis, and to test the utility of this approach for RNA structure-function studies. Internal competition reactions containing all four substrate sequence variants at the N(-1) position in reactions using ribozyme active site mutations at A77 and A78 were used to test a proposed basepairing interaction. Mutants A78U, A78G and A79G retain significant catalytic activity, but do not alter the specificity for the N(-1) nucleobase. Effects of nucleobase analog substitutions at N(-1) indicate that U is preferred due to the ability to donate an H-bond in the Watson-Crick face and avoid minor groove steric clash. The results provide information essential for evaluating models of the HDV active site, and illustrate multiple-substrate kinetic analyses as a practical approach for characterizing structure-function relationships in RNA reactions. PMID:25937290

  14. Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone

    PubMed Central

    Sheng, Jia; Zhang, Wen; Hassan, Abdalla E. A.; Gan, Jianhua; Soares, Alexei S.; Geng, Song; Ren, Yi; Huang, Zhen

    2012-01-01

    Natural RNAs, especially tRNAs, are extensively modified to tailor structure and function diversities. Uracil is the most modified nucleobase among all natural nucleobases. Interestingly, >76% of uracil modifications are located on its 5-position. We have investigated the natural 5-methoxy (5-O-CH3) modification of uracil in the context of A-form oligonucleotide duplex. Our X-ray crystal structure indicates first a H-bond formation between the uracil 5-O-CH3 and its 5′-phosphate. This novel H-bond is not observed when the oxygen of 5-O-CH3 is replaced with a larger atom (selenium or sulfur). The 5-O-CH3 modification does not cause significant structure and stability alterations. Moreover, our computational study is consistent with the experimental observation. The investigation on the uracil 5-position demonstrates the importance of this RNA modification at the atomic level. Our finding suggests a general interaction between the nucleobase and backbone and reveals a plausible function of the tRNA 5-O-CH3 modification, which might potentially rigidify the local conformation and facilitates translation. PMID:22641848

  15. Understanding the interaction of DNA-RNA nucleobases with different ZnO nanomaterials.

    PubMed

    Saha, Supriya; Sarkar, Pranab

    2014-08-01

    Due to the potential application of different nanostructure materials in biomedical nanotechnologies, understanding the interaction between the inorganic nanoparticles and biological molecules at the atomic level is of paramount importance. We present here the results of our theoretical investigation of the interaction of different nucleotide bases--adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U) of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)--with different ZnO nanoparticles, such as ZnO nanowires (NWs), nanotubes (NTs), surfaces and quantum dots (QDs). As the size of the systems we studied is relatively large, we have used the self-consistent-charge density-functional tight-binding (SCC-DFTB) method to optimize the complex systems. We have studied in detail the site-specific binding nature and the adsorption strength of these nucleobases with different ZnO nanoparticles. The calculated binding energy order and the interaction strength of nucleobases are very much dependent on the nature of the nanoparticle surfaces and are different for different nanostructures. In most of the cases ZnO prefers to bind either through the top site of the nucleobases or with the ring nitrogen atom having a lone pair relative to other binding sites of the bases. PMID:24942064

  16. Formation of Nucleobases from the UV Irradiation of Pyrimidine in Astrophysical Ice Analogs

    NASA Technical Reports Server (NTRS)

    Sandford, Scott A.; Nuevo, Michel; Materese, Christopher K.

    2014-01-01

    Nucleobases are the informational subunits of DNA and RNA. They consist of Nheterocycles that belong to either the pyrimidine-base group (uracil, cytosine, and thymine) or the purinebase group (adenine and guanine). Several nucleobases, mostly purine bases, have been detected in meteorites [1-3], with isotopic signatures consistent with an extraterrestrial origin [4]. Uracil is the only pyrimidine-base compound formally reported in meteorites [2], though the presence of cytosine cannot be ruled out [5,6]. However, the actual process by which the uracil was made and the reasons for the non-detection of thymine in meteorites have yet to be fully explained. Although no N-heterocycles have ever been observed in the ISM [7,8], the positions of the 6.2-µm interstellar emission features suggest a population of such molecules is likely to be present [9]. In this work we study the formation of pyrimidine-based molecules, including the three nucleobases uracil, cytosine, and thymine from the ultraviolet (UV) irradiation of pyrimidine in ices consisting of several combinations of H(sub2)O, NH(sub3), CH(sub3)OH, and CH(sub4) at low temperature, in order to simulate the astrophysical conditions under which prebiotic species may be formed in the interstellar medium, in the protosolar nebula, and on icy bodies of the Solar System.

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

    PubMed Central

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

    2016-01-01

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

  18. DNA STRETCHING AND OPTIMISATION OF NUCLEOBASE RECOGNITION FOR ENZYMATIC NANOPORE SEQUENCING

    PubMed Central

    Stoddart, David; Franceschini, Lorenzo; Heron, Andrew; Bayley, Hagan; Maglia, Giovanni

    2015-01-01

    In nanopore sequencing, where single DNA strands are electrophoretically translocated through a nanopore and the resulting ionic signal is used to identify the four DNA bases, an enzyme has been used to ratchet the nucleic acid stepwise through the pore at a controlled speed. In this work, we investigated the ability of αHL nanopores to distinguish the four DNA bases under conditions that are compatible with the activity of DNA-handling enzymes. Our findings suggest that in immobilised strands, the applied potential exerts a force on DNA (~ 10 pN at +160 mV) that increases the distance between nucleobases by about 2.2 Å/V. The four nucleobases can be resolved over wide ranges of applied potentials (from +60 mV to +220 mV in 1 m KCl) and ionic strengths (from 200 mM KCl to 1 M KCl at +160 mV) and nucleobase recognition can be improved when the ionic strength on the side of the DNA-handling enzyme is low, while the ionic strength on the opposite side is high. PMID:25648138

  19. Single Cell FRET Analysis for the Identification of Optimal FRET-Pairs in Bacillus subtilis Using a Prototype MEM-FLIM System

    PubMed Central

    Detert Oude Weme, Ruud G. J.; Kovács, Ákos T.; de Jong, Sander J. G.; Veening, Jan-Willem; Siebring, Jeroen; Kuipers, Oscar P.

    2015-01-01

    Protein-protein interactions can be studied in vitro, e.g. with bacterial or yeast two-hybrid systems or surface plasmon resonance. In contrast to in vitro techniques, in vivo studies of protein-protein interactions allow examination of spatial and temporal behavior of such interactions in their native environment. One approach to study protein-protein interactions in vivo is via Förster Resonance Energy Transfer (FRET). Here, FRET efficiency of selected FRET-pairs was studied at the single cell level using sensitized emission and Frequency Domain-Fluorescence Lifetime Imaging Microscopy (FD-FLIM). For FRET-FLIM, a prototype Modulated Electron-Multiplied FLIM system was used, which is, to the best of our knowledge, the first account of Frequency Domain FLIM to analyze FRET in single bacterial cells. To perform FRET-FLIM, we first determined and benchmarked the best fluorescent protein-pair for FRET in Bacillus subtilis using a novel BglBrick-compatible integration vector. We show that GFP-tagRFP is an excellent donor-acceptor pair for B. subtilis in vivo FRET studies. As a proof of concept, selected donor and acceptor fluorescent proteins were fused using a linker that contained a tobacco etch virus (TEV)-protease recognition sequence. Induction of TEV-protease results in loss of FRET efficiency and increase in fluorescence lifetime. The loss of FRET efficiency after TEV induction can be followed in time in single cells via time-lapse microscopy. This work will facilitate future studies of in vivo dynamics of protein complexes in single B. subtilis cells. PMID:25886351

  20. Nucleobases and other Prebiotic Species from the Ultraviolet Irradiation of Pyrimidine in Astrophysical Ices

    NASA Technical Reports Server (NTRS)

    Sandford, S. A.; Nuevo, M.; Materese, C. K.; Milam, S. N.

    2012-01-01

    Nucleobases are N-heterocycles that are the informational subunits of DNA and RNA, and are divided into two families: pyrimidine bases (uracil, cytosine, and thymine) and purine bases (adenine and guanine). Nucleobases have been detected in meteorites and their extraterrestrial origin confirmed by isotope measurement. Although no Nheterocycles have ever been observed in the ISM, the positions of the 6.2-m interstellar emission features suggest a population of such molecules is likely to be present. In this work we study the formation of pyrimidine-based molecules, including nucleobases, as well as other species of prebiotic interest, from the ultraviolet (UV) irradiation of pyrimidine in combinations of H2O, NH3, CH3OH, and CH4 ices at low temperature, in order to simulate the astrophysical conditions under which prebiotic species may be formed in the interstellar medium and icy bodies of the Solar System. Experimental: Gas mixtures are prepared in a glass mixing line (background pressure approx. 10(exp -6)-10(exp -5) mbar). Relative proportions between mixture components are determined by their partial pressures. Gas mixtures are then deposited on an aluminum foil attached to a cold finger (15-20 K) and simultaneously irradiated with an H2 lamp emitting UV photons (Lyman and a continuum at approx.160 nm). After irradiation samples are warmed to room temperature, at which time the remaining residues are recovered to be analyzed with liquid and gas chromatographies. Results: These experiments showed that the UV irradiation of pyrimidine mixed in these ices at low temperature leads to the formation of several photoproducts derived from pyrimidine, including the nucleobases uracil and cytosine, as well as their precursors 4(3H)-pyrimidone and 4-aminopyrimidine (Fig. 1). Theoretical quantum calculations on the formation of 4(3H)-pyrimidone and uracil from the irradiation of pyrimidine in pure H2O ices are in agreement with their experimental formation pathways. In

  1. Fretting wear of iron, nickel, and titanium under varied environmental conditions

    NASA Technical Reports Server (NTRS)

    Bill, R. C.

    1978-01-01

    Fretting wear experiments were conducted on high purity iron, nickel and titanium in air under conditions of varied humidity and temperature, and in nitrogen. For iron and titanium, maximum fretting occurred at 10 and 30 percent relative humidity respectively. Nickel showed a minimum in fretting wear at about 10 percent relative humidity. With increasing temperature, all three metals initially showed reduced fretting wear, with increasing wear observed as temperatures increased beyond 200-300 C. For titanium, dramatically reduced fretting wear was observed at temperatures above 500 C, relatable to a change in oxidation kinetics. All three metals showed much less fretting wear in N2 with the presence of moisture in N2 having a proportionally stronger effect than in air.

  2. Multiphoton FLIM: a reliable FRET detection tool in cell biological applications

    NASA Astrophysics Data System (ADS)

    Krishnan, Ramanujan V.; Biener, Eva; Centonze, Victoria E.; Gertler, Arieh; Herman, Brian A.

    2004-06-01

    Fluorescence lifetime imaging microscopy (FLIM) using multiphoton excitation is emerging as a reliable quantitative tool for measuring fluorescence resonance energy transfer (FRET) in living cells. By virtue of being free from spectroscopic artifacts encountered in conventional FRET detection methods, multiphoton FLIM methods offer the advantages of high spatial and temporal resolution, faster data acquisition and data analysis. We compare the FRET results obtained by two different methods namely (i) multiphoton excitation lifetime-based FRET and (ii) single photon excitation intensity-based acceptor photobleaching FRET. Using the same biological samples, we apply these two different methods in understanding the growth hormone receptor dimerization kinetics at the cell surface of human embryonic kidney cells. We conclude that the multiphoton FLIM using the streak-camera approach provides the best ability to monitor FRET in dynamic situations where high temporal and spatial resolution are required with minimal photodamage/phototoxicity.

  3. Quantitative structural information from single-molecule FRET.

    PubMed

    Beckers, M; Drechsler, F; Eilert, T; Nagy, J; Michaelis, J

    2015-01-01

    Single-molecule studies can be used to study biological processes directly and in real-time. In particular, the fluorescence energy transfer between reporter dye molecules attached to specific sites on macromolecular complexes can be used to infer distance information. When several measurements are combined, the information can be used to determine the position and conformation of certain domains with respect to the complex. However, data analysis schemes that include all experimental uncertainties are highly complex, and the outcome depends on assumptions about the state of the dye molecules. Here, we present a new analysis algorithm using Bayesian parameter estimation based on Markov Chain Monte Carlo sampling and parallel tempering termed Fast-NPS that can analyse large smFRET networks in a relatively short time and yields the position of the dye molecules together with their respective uncertainties. Moreover, we show what effects different assumptions about the dye molecules have on the outcome. We discuss the possibilities and pitfalls in structure determination based on smFRET using experimental data for an archaeal transcription pre-initiation complex, whose architecture has recently been unravelled by smFRET measurements. PMID:26407323

  4. Fretting Wear of Ti-48Al-2Cr-2Nb

    NASA Technical Reports Server (NTRS)

    Miyoshi, Kazuhisa; Lerch, Bradley A.; Draper, Susan L.

    2001-01-01

    An investigation was conducted to examine the wear behavior of gamma titanium aluminide (Ti-48Al-2Cr-2Nb in atomic percent) in contact with a typical nickel-base superalloy under repeated microscopic vibratory motion in air at temperatures from 296-823 K. The surface damage observed on the interacting surfaces of both Ti-48Al-2Cr-2Nb and superalloy consisted of fracture pits, oxides, metallic debris, scratches, craters, plastic deformation, and cracks. The Ti-48Al-2Cr-2Nb transferred to the superalloy at all fretting conditions and caused scuffing or galling. The increasing rate of oxidation at elevated temperatures led to a drop in Ti-48Al-2Cr-2Nb wear at 473 K. Mild oxidative wear was observed at 473 K. However, fretting wear increased as the temperature was increased from 473-823 K. At 723 and 823 K, oxide disruption generated cracks, loose wear debris, and pits on the Ti-48Al-2Cr-2Nb wear surface. Ti-48Al-2Cr-2Nb wear generally decreased with increasing fretting frequency. Both increasing slip amplitude and increasing load tended to produce more metallic wear debris, causing severe abrasive wear in the contacting metals. Keywords

  5. Developing Fast Fluorescent Protein Voltage Sensors by Optimizing FRET Interactions

    PubMed Central

    Sung, Uhna; Sepehri-Rad, Masoud; Piao, Hong Hua; Jin, Lei; Hughes, Thomas; Cohen, Lawrence B.; Baker, Bradley J.

    2015-01-01

    FRET (Förster Resonance Energy Transfer)-based protein voltage sensors can be useful for monitoring neuronal activity in vivo because the ratio of signals between the donor and acceptor pair reduces common sources of noise such as heart beat artifacts. We improved the performance of FRET based genetically encoded Fluorescent Protein (FP) voltage sensors by optimizing the location of donor and acceptor FPs flanking the voltage sensitive domain of the Ciona intestinalis voltage sensitive phosphatase. First, we created 39 different “Nabi1” constructs by positioning the donor FP, UKG, at 8 different locations downstream of the voltage-sensing domain and the acceptor FP, mKO, at 6 positions upstream. Several of these combinations resulted in large voltage dependent signals and relatively fast kinetics. Nabi1 probes responded with signal size up to 11% ΔF/F for a 100 mV depolarization and fast response time constants both for signal activation (~2 ms) and signal decay (~3 ms). We improved expression in neuronal cells by replacing the mKO and UKG FRET pair with Clover (donor FP) and mRuby2 (acceptor FP) to create Nabi2 probes. Nabi2 probes also had large signals and relatively fast time constants in HEK293 cells. In primary neuronal culture, a Nabi2 probe was able to differentiate individual action potentials at 45 Hz. PMID:26587834

  6. Developing Fast Fluorescent Protein Voltage Sensors by Optimizing FRET Interactions.

    PubMed

    Sung, Uhna; Sepehri-Rad, Masoud; Piao, Hong Hua; Jin, Lei; Hughes, Thomas; Cohen, Lawrence B; Baker, Bradley J

    2015-01-01

    FRET (Förster Resonance Energy Transfer)-based protein voltage sensors can be useful for monitoring neuronal activity in vivo because the ratio of signals between the donor and acceptor pair reduces common sources of noise such as heart beat artifacts. We improved the performance of FRET based genetically encoded Fluorescent Protein (FP) voltage sensors by optimizing the location of donor and acceptor FPs flanking the voltage sensitive domain of the Ciona intestinalis voltage sensitive phosphatase. First, we created 39 different "Nabi1" constructs by positioning the donor FP, UKG, at 8 different locations downstream of the voltage-sensing domain and the acceptor FP, mKO, at 6 positions upstream. Several of these combinations resulted in large voltage dependent signals and relatively fast kinetics. Nabi1 probes responded with signal size up to 11% ΔF/F for a 100 mV depolarization and fast response time constants both for signal activation (~2 ms) and signal decay (~3 ms). We improved expression in neuronal cells by replacing the mKO and UKG FRET pair with Clover (donor FP) and mRuby2 (acceptor FP) to create Nabi2 probes. Nabi2 probes also had large signals and relatively fast time constants in HEK293 cells. In primary neuronal culture, a Nabi2 probe was able to differentiate individual action potentials at 45 Hz. PMID:26587834

  7. An improved cyan fluorescent protein variant useful for FRET.

    PubMed

    Rizzo, Mark A; Springer, Gerald H; Granada, Butch; Piston, David W

    2004-04-01

    Many genetically encoded biosensors use Förster resonance energy transfer (FRET) between fluorescent proteins to report biochemical phenomena in living cells. Most commonly, the enhanced cyan fluorescent protein (ECFP) is used as the donor fluorophore, coupled with one of several yellow fluorescent protein (YFP) variants as the acceptor. ECFP is used despite several spectroscopic disadvantages, namely a low quantum yield, a low extinction coefficient and a fluorescence lifetime that is best fit by a double exponential. To improve the characteristics of ECFP for FRET measurements, we used a site-directed mutagenesis approach to overcome these disadvantages. The resulting variant, which we named Cerulean (ECFP/S72A/Y145A/H148D), has a greatly improved quantum yield, a higher extinction coefficient and a fluorescence lifetime that is best fit by a single exponential. Cerulean is 2.5-fold brighter than ECFP and replacement of ECFP with Cerulean substantially improves the signal-to-noise ratio of a FRET-based sensor for glucokinase activation. PMID:14990965

  8. Quantum dots and fluorescent protein FRET-based biosensors.

    PubMed

    Boeneman, Kelly; Delehanty, James B; Susumu, Kimihiro; Stewart, Michael H; Deschamps, Jeffrey R; Medintz, Igor L

    2012-01-01

    There has been considerable recent interest in the creation of nanoparticle-biomolecule hybrid materials for uses such as in vitro and in vivo biosensing, biological imaging, and drug -delivery. Nanoparticles have a high surface to volume ratio, making them capable of being decorated with -various biomolecules on their surface which retain their biological activity. Techniques to bind these biomolecules to nanoparticle surfaces are also advancing rapidly. Here we demonstrate hybrid materials assembled around CdSe/ZnS core/shell semiconductor quantum dots (QDs). These intrinsically fluorescent materials are conjugated to the fluorescent proteins YFP, mCherry and the light harvesting complex b-phycoerythrin (b-PE). QDs have fluorescent properties that make them ideal as donor fluorophores for Förster resonance energy transfer (FRET) while the fluorescent proteins are able to act as FRET acceptors displaying many advantages over organic dyes. We examine FRET interactions between QDs and all three fluorescent proteins. Furthermore, we show QD-mCherry hybrid materials can be utilized for in vitro biosensing of caspase-3 enzymatic activity. We further show that QDs and fluorescent proteins can be conjugated together intracellularly with strong potential for live-cell imaging and biosensing applications. PMID:22101713

  9. Conformational Dynamics of Titin PEVK Explored with FRET Spectroscopy

    PubMed Central

    Huber, Tamás; Grama, László; Hetényi, Csaba; Schay, Gusztáv; Fülöp, Lívia; Penke, Botond; Kellermayer, Miklós S.Z.

    2012-01-01

    The proline-, glutamate-, valine-, and lysine-rich (PEVK) domain of the giant muscle protein titin is thought to be an intrinsically unstructured random-coil segment. Various observations suggest, however, that the domain may not be completely devoid of internal interactions and structural features. To test the validity of random polymer models for PEVK, we determined the mean end-to-end distances of an 11- and a 21-residue synthetic PEVK peptide, calculated from the efficiency of the fluorescence resonance energy transfer (FRET) between an N-terminal intrinsic tryptophan donor and a synthetically added C-terminal IAEDANS acceptor obtained in steady-state and time-resolved experiments. We find that the contour-length scaling of mean end-to-end distance deviates from predictions of a purely statistical polymer chain. Furthermore, the addition of guanidine hydrochloride decreased, whereas the addition of salt increased the FRET efficiency, pointing at the disruption of structure-stabilizing interactions. Increasing temperature between 10 and 50°C increased the normalized FRET efficiency in both peptides but with different trajectories, indicating that their elasticity and conformational stability are different. Simulations suggest that whereas the short PEVK peptide displays an overall random structure, the long PEVK peptide retains residual, loose helical configurations. Transitions in the local structure and dynamics of the PEVK domain may play a role in the modulation of passive muscle mechanics. PMID:23062340

  10. Considerations for sensitivity analysis, uncertainty quantification, and data assimilation for grid-to-rod fretting

    SciTech Connect

    Michael Pernice

    2012-10-01

    Grid-to-rod fretting is the leading cause of fuel failures in pressurized water reactors, and is one of the challenge problems being addressed by the Consortium for Advanced Simulation of Light Water Reactors to guide its efforts to develop a virtual reactor environment. Prior and current efforts in modeling and simulation of grid-to-rod fretting are discussed. Sources of uncertainty in grid-to-rod fretting are also described.

  11. Functionalized Tricyclic Cytosine Analogues Provide Nucleoside Fluorophores with Improved Photophysical Properties and a Range of Solvent Sensitivities

    PubMed Central

    Rodgers, Brittney J.; Elsharif, Nada A.; Vashisht, Nisha; Mingus, Macy M.; Mulvahill, Mark A.; Stengel, Gudrun; Kuchta, Robert D.

    2014-01-01

    Tricyclic cytosines (tC and tCO frameworks) have emerged as a unique class of fluorescent nucleobase analogues that minimally perturb the structure of B-form DNA and that are not quenched in duplex nucleic acids. Systematic derivatization of these frameworks is a likely approach to improve on and diversify photophysical properties, but has not so far been examined. Synthetic methods were refined to improve on tolerance for electron donating and electron withdrawing groups, resulting in a series of eight new, fluorescent cytidine analogues. Photophysical studies show that substitution of the framework results in a pattern of effects largely consistent across tC and tCO and provides nucleoside fluorophores that are brighter than either parent. Moreover, a range of solvent sensitivities is observed, offering promise that this family of probes can be extended to new applications that require reporting on the local environment. PMID:24311229

  12. Fretting Wear Mechanisms in A216 Plain Carbon Steel

    NASA Astrophysics Data System (ADS)

    Maich, Alyssa Anne

    The subsurface and surface microstructures during pin-on-disk fretting wear of A216 steel disks under various loading conditions and times are investigated. The corresponding pins are fabricated from 410 stainless steel to simulate in-service conditions found in such engineering components as the Siemens W501FD engine row-2 diaphragm of a Siemens turbine engine, which is known to be prone to failure by fretting wear. Loading conditions range from 2N to 15N and times from 1 hour to a maximum of 69 hours, when steady state is confirmed. Wear track depth is quantitatively determined by optical profilometry, and found to range from 3 to 11 microns dependent upon load. Wear depth increases from 2N to 10N load, but decreases when increased to 15N load, due to heavier transfer of pin material to disk, as can be seen by EDS images of chromium transfer on A216 disk. Microstructures are evaluated by transmission electron microscopy of samples prepared by focused ion beam machining to pinpoint wear tracks and expose them in cross-section. EDS is used, in conjunction with TEM, to elucidate primary wear mechanisms at each stage of fretting wear. Microstructures in the subsurface of wear tracks are found to be heavily dislocated and layered, features that vary with both applied load and time. The microstructure eventually evolves into stable dislocation cells with cell walls aligned parallel to the surface. Penetration depth of the damaged layers increases with applied load, associated with a non-uniform maximum shear stress distribution that varies with depth. Primary oxide appears to evolve from Fe2O3 to Fe3O4, with increasing fretting time, leading to a uniform oxide on the surface of the A216 disk. Oxidation rate may be increased with the evolution of this subsurface dislocation cell structure. It is concluded that fretting wear failure is likely associated with a synergy between oxidative wear and crack initiation and propagation along dislocation cell walls under high

  13. Probing Nucleobase Interactions and Predicting Mechanisms of Synthetic Interest Using Computational Chemistry, and Furthering the Development of BVI Education in Chemistry

    ERIC Educational Resources Information Center

    Harrison, Jason Gordon

    2013-01-01

    Quantum mechanical (QM) and molecular docking methods are used to probe systems of biological and synthetic interest. Probing interactions of nucleobases within proteins, and properly modeling said interactions toward novel nucleobase development, is extremely difficult, and of great utility in RNA interference (RNAi) therapeutics. The issues in…

  14. Aspartame and Its Analogues

    NASA Astrophysics Data System (ADS)

    Pavlova, L. A.; Komarova, T. V.; Davidovich, Yurii A.; Rogozhin, S. V.

    1981-04-01

    The results of studies on the biochemistry of the sweet taste are briefly reviewed. The methods of synthesis of "aspartame" — a sweet dipeptide — are considered, its structural analogues are described, and quantitative estimates are made of the degree of sweetness relative to sucrose. Attention is concentrated mainly on problems of the relation between the structure of the substance and its taste in the series of aspartyl derivatives. The bibliography includes 118 references.

  15. The mechanics and tribology of fretting fatigue with application to riveted lap joints

    NASA Astrophysics Data System (ADS)

    Szolwinski, Matthew Paul

    Fretting is the synergistic combination of wear, corrosion, and fatigue damage mechanisms driven by the partial slip of contacting surfaces. The surface microslip and near-surface contact stresses associated with fretting can lead to severe reduction in service lifetimes of contacting components as diversified as bearings, turbine blades and mechanically-fastened joints, both structural and biological. This tribologically induced degradation has come under close scrutiny by those responsible for maintaining aging fleets of both commercial and military aircraft. Thus a critical need exists for predicting fretting crack nucleation in riveted aluminum. aircraft joints. Fulfilling this need requires characterizing both the near-surface mechanics and intimately-related tribology of fretting. To this end, a well characterized experimental setup has been developed to generate carefully controlled and monitored fretting contacts to investigate the nature of the near-surface conditions. Included in this investigation were in-situ observations of the fretting contact stress field via a non-invasive thermal imaging technique and a characterization of the evolution of friction under partial slip conditions. With specific qualitative and quantitative understanding of these near-surface conditions, a series of fretting fatigue experiments have been conducted to validate a mechanics-based model for predicting fretting fatigue crack nucleation. Finally, efforts have been directed toward extending this understanding of fretting crack nucleation to riveted aircraft structure through modeling of the riveting process and a related experimental program designed to link riveting process parameters and fretting damage in single-lap joint structures. This work focuses specifically on determination of the residual stresses induced during rivet installation and the morphological characterization of fretting fatigue damage in the riveted test specimens manufactured under controlled

  16. Ab Initio Inverstagation of the Excited States of Nucleobases and Nucleosides

    NASA Astrophysics Data System (ADS)

    Szalay, Péter G.; Fogarasi, Géza; Watson, Thomas; Perera, Ajith; Lotrich, Victor; Bartlett, Rod J.

    2011-06-01

    Most living bodies are exposed to sunlight, essential life sustaining processes are using this natural radiation. Sunlight has, however, several components (has a broad "spectrum") and in particular the invisible component (UV, ultraviolet) is harmful for living organisms. Scientists around the word are busy to understand what happens in the cell when it is exposed to light: it seems that the building blocks of cells and in particular those carrying the genetic information (DNA and RNA) are highly protected against this exposition. Our research focuses on the spectral properties of the building blocks of DNA and RNA, the so called nucleobases and nucleosides, in order to understand this mechanism. Due to improvement in computer technology both at hardware and software side we are now able to use the most accurate methods of ab initio quantum chemistry to investigate the spectroscopic properties of these building blocks. These calculations provide direct information on the properties of these molecules but also provide important benchmarks for cheaper methods which can be used for even larger systems. We have calculated the excited state properties for the nucleobases (cytosine, guanine and adenine), their complexes with water and with each other (Watson-Crick base pairs and stacks) as well as corresponding nucleosides at the EOM-CCSD(T)/aug-cc-pVDZ level of theory and try to answer the following questions: (1) how the order of excited states varies in different nucleobases; (2) how hydration influences the excitation energy and order of excited states; (3) is there any effect of the sugar substituent; (4) how do close lying other bases change the spectrum. The calculations involve over hundred correlated electrons and up to thousand basis functions. Such calculations are now routinely available with the recently developed ACESIII code and can make use of hundreds or even several thousand of processors. V. Lotrich, N. Flocke, M. Ponton, A. Yau, A. Perera, E. Deumens

  17. Supramolecular hydrogels formed by the conjugates of nucleobases, Arg-Gly-Asp (RGD) peptides, and glucosamine

    PubMed Central

    Li, Xinming; Du, Xuewen; Gao, Yuan; Shi, Junfeng; Kuang, Yi

    2012-01-01

    Here we report the generation of a novel class of supramolecular hydrogelators based on the integration of nucleobase, Arg-Gly-Asp (RGD) peptides, and glucosamine in a single molecule. These novel small molecule hydrogelators self-assemble in water to form stable supramolecular nanofibers/hydrogels and exhibit useful biostability. This approach provides a new opportunity for systematic exploration of the self-assembly of small biomolecules by varying any individual segment to generate a large array of supramolecular hydrogels for biological functions and for biomedical applications. PMID:22844343

  18. Ice world: the origin of nucleobases in ice-liquid water coexistence conditions.

    NASA Astrophysics Data System (ADS)

    Menor Salvan, C.

    2013-09-01

    We could define the ice world as the chemical evolution in the range between freezing point of water and the limit of stability of liquid brines, ≈273 to 210 K. In this environment, the synthesis of nitrogen heterocycles using urea as nitrogen source and methane as precursor of active intermediates is favorable from a prebiotic chemistry standpoint, leading to a mixture dominated by pyrimidines and hydantoins. Hence, the synthesis in ice matrix constitutes an experimental model for the study of origin of nucleobases in Solar System bodies.

  19. Fretting induced plasticity in blade/disk contacts

    NASA Astrophysics Data System (ADS)

    Gao, Guofeng

    Finite element analyses of fretting contacts were developed for different pad geometries and material combinations. A better understanding of the surface tractions and life predictions for crack nucleation and propagation is achieved by including the effects of plasticity and the representative crack in the finite element modeling. Pure elastic finite element results were validated with the existing elastic solution suite based on Singular Integral Equations (SIEs). The elastic-perfectly-plastic analysis of a rigid cylindrical pad on an isotropic half-space was compared with the results in the literature. Different shapes of rigid indenters were examined and the results were compared with those from the SIEs. Fretting contacts with similar and dissimilar isotropic materials were studied. The effects of plasticity on fretting life were highlighted by comparing the results from pure elastic analyses and elastic-plastic analyses. Finite element modelings involving SCN materials with different rotations of material principle axes were also investigated. The crack nucleation life was calculated with the Modified Manson-McKnight model. This model, modified by stressed area approach, usually generates significantly conservative estimates when pure elastic stress results are used. When plasticity is taken into account, the life prediction accuracy for crack nucleation was proven to be improved tremendously. A representative crack was incorporated into the FEM model at the trailing edge of contact to study its effects on surface tractions and crack propagation life. The originally smooth pressure distribution has a singularity at the edge of contact and the contact size expands due to the crack growth. The crack propagation life was evaluated by using the modified crack closure method and the Paris law.

  20. The effect of surface roughness on the fretting corrosion of 316L stainless steel biomaterial surfaces

    NASA Astrophysics Data System (ADS)

    Shenoy, Aarti

    The medical device industry is still seeking answers to the mechanically-assisted corrosion (MAC) problem, which becomes increasingly important due to modularity in design. MAC manifests in various forms, some of which are fretting corrosion, crevice corrosion and stress corrosion. Several studies have been conducted to understand the causes and the factors that affect fretting corrosion. Some of the factors are the applied load, surface potential, oxide film characteristics and solution chemistry near the interface. Surface properties such as surface roughness determine the topography of the surface and the nature of asperity-asperity contact, which is a factor that would determine the mechanically assisted corrosion behavior of the interface, like the stem-neck and head-neck taper junctions in modular hip replacement devices. This study aims to understand the correlation between surface roughness of 316L stainless steel samples and fretting corrosion behavior using a variable load pin-on-disc test. It was found that the smoother surfaces are associated with lower fretting currents. However, smoother surfaces also created the conditions for fretting initiated crevice corrosion to occur more readily. Fretting corrosion regimes and the severity are thus dependent upon the surface roughness. A possible explanation could be due to the inverse relationship between the interasperity distance parameter, Delta, and fretting currents. The coefficient of friction between the two surfaces in contact however remained unaffected by surface roughness, but decreased with increasing load. Smoother surfaces, while lowering fretting corrosion reactions can enhance crevice corrosion reactions in 316L stainless steel interfaces.

  1. Lateral diffusion contributes to FRET from lanthanide-tagged membrane proteins

    SciTech Connect

    Lan, Tien-Hung; Wu, Guangyu; Lambert, Nevin A.

    2015-08-14

    Diffusion can enhance Förster resonance energy transfer (FRET) when donors or acceptors diffuse distances that are similar to the distances separating them during the donor's excited state lifetime. Lanthanide donors remain in the excited state for milliseconds, which makes them useful for time-resolved FRET applications but also allows time for diffusion to enhance energy transfer. Here we show that diffusion dramatically enhances FRET between membrane proteins labeled with lanthanide donors. This phenomenon complicates interpretation of experiments that use long-lived donors to infer association or proximity of mobile membrane proteins, but also offers a method of monitoring diffusion in membrane domains in real time in living cells. - Highlights: • Diffusion enhances TR-FRET from membrane proteins labeled with lanthanide donors. • Diffusion-dependent FRET can overshadow FRET due to oligomerization or clustering. • FRET studies using lanthanide-tagged membrane proteins should consider diffusion. • FRET from lanthanide donors can be used to monitor membrane protein diffusion.

  2. Prediction of Fretting Crack Location and Orientation in a Single Crystal Nickel Alloy

    NASA Technical Reports Server (NTRS)

    Matlik, J. F.; Farris, T. N.; Haynes, J.; Swanson, G. R.; Ham-Battista, G.

    2005-01-01

    Fretting is a structural damage mechanism arising between two nominally clamped surfaces subjected to an oscillatory loading. A critical location for fretting induced damage has been identified at the blade/disk and blade/damper interfaces of gas turbine engine turbomachinery and space propulsion components. The high- temperature, high-frequency loading environment seen by these components lead to severe stress gradients at the edge-of-contact that could potentially foster crack growth leading to component failure. These contact stresses drive crack nucleation in fretting and are very sensitive to the geometry of the contacting bodies, the contact loads, materials, temperature, and contact surface tribology (friction). Recently, a high-frequency, high-temperature load frame has been designed for experimentally investigating fretting damage of single crystal nickel materials employed in aircraft and spacecraft turbomachinery. A modeling method for characterizing the fretting stresses of the spherical fretting contact stress behavior in this experiment is developed and described. The calculated fretting stresses for a series of experiments are then correlated to the observed fretting damage. Results show that knowledge of the normal stresses and resolved shear stresses on each crystal plane can aid in predicting crack locations and orientations.

  3. Evaluating the Relationship between FRET Changes and Distance Changes Using DNA Length and Restriction Enzyme Specificity

    ERIC Educational Resources Information Center

    Pazhani, Yogitha; Horn, Abigail E.; Grado, Lizbeth; Kugel, Jennifer F.

    2016-01-01

    FRET (Fo¨rster resonance energy transfer) involves the transfer of energy from an excited donor fluorophore to an acceptor molecule in a manner that is dependent on the distance between the two. A biochemistry laboratory experiment is described that teaches students how to use FRET to evaluate distance changes in biological molecules. Students…

  4. Photophysical properties of pyrrolocytosine, a cytosine fluorescent base analogue.

    PubMed

    Nguyen, Quynh L; Spata, Vincent A; Matsika, Spiridoula

    2016-07-27

    The photophysical behavior of pyrrolocytosine (PC), a fluorescent base analogue of cytosine, has been investigated using theoretical approaches. The similarities between the PC and cytosine structures allow PC to maintain the pseudo-Watson-Crick base-pairing arrangement with guanine. Cytosine, similar to the other natural nucleobases, is practically non-fluorescent, because of ultrafast radiationless decay occurring through conical intersections. PC displays a much higher fluorescence quantum yield than cytosine, making it an effective fluorescent marker to study the structure, function, and dynamics of DNA/RNA complexes. Similar to 2-aminopurine, a constitutional isomer of adenine that base-pairs with thymine, PC's fluorescence is quenched when it is incorporated into a dinucleotide or a trinucleotide. In this work we examine the photophysical properties of isolated PC, microhydrated PC, as well as, complexes where PC is either base-stacked or hydrogen-bonded with guanine. Our results indicate that hydration affects the radiationless decay pathways in PC by destabilizing conical intersections. The calculations of dimers and trimers show that the radiative decay is affected by π stacking, while the presence of charge transfer states between PC and guanine may contribute to radiationless decay. PMID:27251599

  5. Polyfluorophore Excimers and Exciplexes as FRET Donors in DNA

    PubMed Central

    Teo, Yin Nah; Kool, Eric T.

    2009-01-01

    We describe studies aimed at testing whether oligomeric exciplex- and excimer fluorophores conjugated to DNA have the potential to act as donors for energy transfer by the Förster mechanism. Oligodeoxyfluorosides (ODFs) are composed of stacked, electronically interacting fluorophores replacing the bases on a DNA scaffold. The monomer chromophores in the twenty tetramer-length ODFs studied here include pyrene (Y), benzopyrene (B), perylene (E), dimethylaminostilbene (D), and a nonfluorescent spacer (S); these are conjugated in varied combinations at the 3’ end of a 14mer DNA probe sequence. In the absence of an acceptor chromophore, many of the ODF-DNAs show broad, unstructured long-wavelength emission peaks characteristic of excimer and exciplex excited states, similar to what has been observed for unconjugated ODFs. Although such delocalized excited states have been widely studied, we know of no prior report of their use in FRET. We tested the ability of the twenty ODFs to donate energy to Cy5 and TAMRA dyes conjugated to a complementary strand of DNA, with these acceptors oriented either at the near or far end of the ODF-conjugated probes. Results showed that a number of the ODF fluorophores exhibited relatively efficient energy transfer characteristic of the Förster mechanism, as judged by drops in donor emission quantum yield and fluorescence lifetime, accompanied by increases in intensity of acceptor emission bands. Excimer/exciplex bands in the donors were selectively quenched while shorter-wavelength monomer emission stayed relatively constant, consistent with the notion that the delocalized excited states, rather than individual fluorophores, are the donors. Interestingly, only specific sequences of ODFs were able to act as donors, while others did not, even though their emission wavelengths were similar. The new FRET donors possess large Stokes shifts, which can be beneficial for multiple applications. In addition, all ODFs can be excited at a single

  6. Tumor specific lung cancer diagnostics with multiplexed FRET immunoassays

    NASA Astrophysics Data System (ADS)

    Geißler, D.; Hill, D.; Löhmannsröben, H.-G.; Thomas, E.; Lavigne, A.; Darbouret, B.; Bois, E.; Charbonnière, L. J.; Ziessel, R. F.; Hildebrandt, N.

    2010-02-01

    An optical multiplexed homogeneous (liquid phase) immunoassay based on FRET from a terbium complex to eight different fluorescent dyes is presented. We achieved highly sensitive parallel detection of four different lung cancer specific tumor markers (CEA, NSE, SCC and CYFRA21-1) within a single assay and show a proof-of-principle for 5- fold multiplexing. The method is well suited for fast and low-cost miniaturized point-of-care testing as well as for highthroughput screening in a broad range of in-vitro diagnostic applications.

  7. Application of FRET Technology to the In Vivo Evaluation of Therapeutic Nucleic Acids (ANTs)

    NASA Astrophysics Data System (ADS)

    Benítez-Hess, María Luisa; Alvarez-Salas, Luis Marat

    2007-02-01

    Developing applications for therapeutic nucleic acids (TNAs) (i.e. ribozymes, antisense oligodeoxynucleotides (AS-ODNs), siRNA and aptamers) requires a reporter system designed to rapidly evaluate their in vivo effect. To this end we designed a reporter system based on the fluorescence resonance energy transfer (FRET) engineered to release the FRET effect produced by two green fluorescent protein (GFP) variants linked by a TNA target site. Because the FRET effect occurs instantaneously when two fluorophores are very close to each other (>100nm) stimulating emission of the acceptor fluorophore by the excitation of the donor fluorophore it has been widely use to reveal interactions between molecules. The present system (FRET2) correlates the FRET effect with the in vivo activity of distinct types of TNAs based on a model consisting of RNA from human papillomavirus type 16 (HPV-16) previously shown accessible to TNAs. HPV-16 is the most common papillomavirus associated with cervical cancer, the leading cause of death by cancer in México. The FRET2 system was first tested in vitro and then used in bacteria in which transcription is linked to translation allowing controlled expression and rapid evaluation of the FRET2 protein. To assure accessibility of the target mRNA to TNAs, the FRET2 mRNA was probed by RNaseH assays prior FRET testing. The fluorescence features of the FRET2 system was tested with different FRET-producing GFP donor-acceptor pairs leading to selection of green (donor) and yellow (acceptor) variants of GFP as the most efficient. Modifications in aminoacid composition and linker length of the target sequence did not affect FRET efficiency. In vivo AS-ODN-mediated destruction of the chimerical FRET2 reporter mRNA resulted in the recovery of GFP fluorescent spectrum in a concentration and time dependent manner. Reported anti-HPV ribozymes were also tested with similar results. Therefore, we conclude that the FRET effect can be a useful tool in the

  8. A Versatile Multiple Target Detection System Based on DNA Nano-assembled Linear FRET Arrays

    NASA Astrophysics Data System (ADS)

    Li, Yansheng; Du, Hongwu; Wang, Wenqian; Zhang, Peixun; Xu, Liping; Wen, Yongqiang; Zhang, Xueji

    2016-05-01

    DNA molecules have been utilized both as powerful synthetic building blocks to create nanoscale architectures and as inconstant programmable templates for assembly of biosensors. In this paper, a versatile, scalable and multiplex detection system is reported based on an extending fluorescent resonance energy transfer (FRET) cascades on a linear DNA assemblies. Seven combinations of three kinds of targets are successfully detected through the changes of fluorescence spectra because of the three-steps FRET or non-FRET continuity mechanisms. This nano-assembled FRET-based nanowire is extremely significant for the development of rapid, simple and sensitive detection system. The method used here could be extended to a general platform for multiplex detection through more-step FRET process.

  9. A Study on Fretting Fatigue Life in Elevated Temperature for Incoloy 800

    NASA Astrophysics Data System (ADS)

    Kwon, Jae Do; Woo, Seung Wan; Chung, Il Sup; Yoon, Dong Hwan; Park, Dae Kyu

    Incoloy 800, which is used within steam generator tubes, is a heat resistant material since it is an iron-nickel-chromium alloy. However, construction of a systematic database is needed to receive integrity data defecting insurance of specific data about room and elevated temperature fretting fatigue behavior for Incoloy 800. Accordingly, this study investigates the specific change in fatigue limitations under the condition of the fretting fatigue as compared to that under the condition of the plain fatigue by performing plain and fretting fatigue tests on Incoloy 800 at 320°C, real operating temperature and at room-temperature, respectively. The change in the frictional force is measured during the fretting fatigue testing against the repeated cycle, and the mechanism of fretting fatigue is investigated through the observation of the fatigue-fracture surface.

  10. A Versatile Multiple Target Detection System Based on DNA Nano-assembled Linear FRET Arrays

    PubMed Central

    Li, Yansheng; Du, Hongwu; Wang, Wenqian; Zhang, Peixun; Xu, Liping; Wen, Yongqiang; Zhang, Xueji

    2016-01-01

    DNA molecules have been utilized both as powerful synthetic building blocks to create nanoscale architectures and as inconstant programmable templates for assembly of biosensors. In this paper, a versatile, scalable and multiplex detection system is reported based on an extending fluorescent resonance energy transfer (FRET) cascades on a linear DNA assemblies. Seven combinations of three kinds of targets are successfully detected through the changes of fluorescence spectra because of the three-steps FRET or non-FRET continuity mechanisms. This nano-assembled FRET-based nanowire is extremely significant for the development of rapid, simple and sensitive detection system. The method used here could be extended to a general platform for multiplex detection through more-step FRET process. PMID:27230484

  11. Imaging of Metabolic Status in 3D Cultures with an Improved AMPK FRET Biosensor for FLIM.

    PubMed

    Chennell, George; Willows, Robin J W; Warren, Sean C; Carling, David; French, Paul M W; Dunsby, Chris; Sardini, Alessandro

    2016-01-01

    We describe an approach to non-invasively map spatiotemporal biochemical and physiological changes in 3D cell culture using Forster Resonance Energy Transfer (FRET) biosensors expressed in tumour spheroids. In particular, we present an improved Adenosine Monophosphate (AMP) Activated Protein Kinase (AMPK) FRET biosensor, mTurquoise2 AMPK Activity Reporter (T2AMPKAR), for fluorescence lifetime imaging (FLIM) readouts that we have evaluated in 2D and 3D cultures. Our results in 2D cell culture indicate that replacing the FRET donor, enhanced Cyan Fluorescent Protein (ECFP), in the original FRET biosensor, AMPK activity reporter (AMPKAR), with mTurquoise2 (mTq2FP), increases the dynamic range of the response to activation of AMPK, as demonstrated using the direct AMPK activator, 991. We demonstrated 3D FLIM of this T2AMPKAR FRET biosensor expressed in tumour spheroids using two-photon excitation. PMID:27548185

  12. Aggregation-Induced-Emissive Molecule Incorporated into Polymeric Nanoparticulate as FRET Donor for Observing Doxorubicin Delivery.

    PubMed

    Han, Xiongqi; Liu, De-E; Wang, Tieyan; Lu, Hongguang; Ma, Jianbiao; Chen, Qixian; Gao, Hui

    2015-10-28

    Tetraphenylethene (TPE) derivatives characterized with distinct aggregation-induced-emission, attempted to aggregate with doxorubicin (Dox) to formulate the interior compartment of polymeric nanoparticulate, served as fluorescence resonance energy transfer (FRET) donor to promote emission of acceptor Dox. Accordingly, this FRET formulation allowed identification of Dox in complexed form by detecting FRET. Important insight into the Dox releasing can be subsequently explored by extracting complexed Dox (FRET) from the overall Dox via direct single-photon excitation of Dox. Of note, functional catiomers were used to complex with FRET partners for a template formulation, which was verified to induce pH-responsive release in the targeted subcellular compartment. Hence, this well-defined multifunctional system entitles in situ observation of the drug releasing profile and insight on drug delivery journey from the tip of injection vein to the subcellular organelle of the targeted cells. PMID:26448180

  13. A Versatile Multiple Target Detection System Based on DNA Nano-assembled Linear FRET Arrays.

    PubMed

    Li, Yansheng; Du, Hongwu; Wang, Wenqian; Zhang, Peixun; Xu, Liping; Wen, Yongqiang; Zhang, Xueji

    2016-01-01

    DNA molecules have been utilized both as powerful synthetic building blocks to create nanoscale architectures and as inconstant programmable templates for assembly of biosensors. In this paper, a versatile, scalable and multiplex detection system is reported based on an extending fluorescent resonance energy transfer (FRET) cascades on a linear DNA assemblies. Seven combinations of three kinds of targets are successfully detected through the changes of fluorescence spectra because of the three-steps FRET or non-FRET continuity mechanisms. This nano-assembled FRET-based nanowire is extremely significant for the development of rapid, simple and sensitive detection system. The method used here could be extended to a general platform for multiplex detection through more-step FRET process. PMID:27230484

  14. Structural Analogues of Selfotel.

    PubMed

    Dziuganowska, Zofia A; Ślepokura, Katarzyna; Volle, Jean-Noël; Virieux, David; Pirat, Jean-Luc; Kafarski, Paweł

    2016-06-17

    A small library of phosphonopiperidylcarboxylic acids, analogues of NMDA antagonist selfotel (CGS 19755), was synthesized. First, the series of aromatic esters was obtained via a palladium-catalyzed cross-coupling reaction (Hirao coupling) of dialkyl phosphites with bromopyridinecarboxylates, followed by their hydrolysis. Then, hydrogenation of the resulting phosphonopyridylcarboxylic acids over PtO2 yielded the desired phosphonopiperidylcarboxylic acids. NMR studies indicated that the hydrogenation reaction proceeds predominantly by cis addition. Several compounds were obtained as monocrystal structures. Preliminary biological studies performed on cultures of neurons suggest that the obtained compounds possess promising activity toward NMDA receptors. PMID:27187758

  15. Catalytic Role of Manganese Oxides in Prebiotic Nucleobases Synthesis from Formamide.

    PubMed

    Bhushan, Brij; Nayak, Arunima; Kamaluddin

    2016-06-01

    Origin of life processes might have begun with the formation of important biomonomers, such as amino acids and nucleotides, from simple molecules present in the prebiotic environment and their subsequent condensation to biopolymers. While studying the prebiotic synthesis of naturally occurring purine and pyrimidine derivatives from formamide, the manganese oxides demonstrated not only good binding for formamide but demonstrated novel catalytic activity. A novel one pot manganese oxide catalyzed synthesis of pyrimidine nucleobases like thymine is reported along with the formation of other nucleobases like purine, 9-(hydroxyacetyl) purine, cytosine, 4(3 H)-pyrimidinone and adenine in acceptable amounts. The work reported is significant in the sense that the synthesis of thymine has exhibited difficulties especially under one pot conditions and also such has been reported only under the catalytic activity of TiO2. The lower oxides of manganese were reported to show higher potential as catalysts and their existence were favored by the reducing atmospheric conditions prevalent on early Earth; thereby confirming the hypothesis that mineral having metals in reduced form might have been more active during the course of chemical evolution. Our results further confirm the role of formamide as a probable precursor for the formation of purine and pyrimidine bases during the course of chemical evolution and origin of life. PMID:26758444

  16. The search for and identification of amino acids, nucleobases and nucleosides in samples returned from Mars

    NASA Technical Reports Server (NTRS)

    Gehrke, Charles W.; Ponnamperuma, Cyril; Kuo, Kenneth C.; Stalling, David L.; Zumwalt, Robert W.

    1989-01-01

    An investigation of the returned Mars samples for biologically important organic compounds, with emphasis on amino acid, the puring and pyrimidine bases, and nucleosides is proposed. These studies would be conducted on subsurface samples obtained by drilling past the surface oxidizing layer with emphasis on samples containing the larges quantities of organic carbon as determined by the rover gas chromatographic mass spectrometer (GCMS). Extraction of these molecules from the returned samples will be performed using the hydrothermal extraction technique described by Cheng and Ponnamperuma. More rigorous extraction methods will be developed and evaluated. For analysis of the extract for free amino acids or amino acids present in a bound or peptidic form, aliquots will be analyzed by capillary GCMS both before and after hydrolysis with 6N hydrochloric acid. Establishment of the presence of amino acids would then lead to the next logical step which would be the use of chiral stationary gas chromatography phases to determine the enatiomeic composition of the amino acids present, and thus potentially establish their biotic or abiotic origin. Confirmational analyses for amino acids would include ion-exchange and reversed-phase liquid chromatographic analysis. For analyses of the returned Mars samples for nucleobases and nucleosides, affinity and reversed-phase liquid chromatography would be utilized. This technology coupled with scanning UV detection for identification, presents a powerful tool for nucleobase and nucleoside analysis. Mass spectrometric analysis of these compounds would confirm their presence in samples returned form Mars.

  17. Nucleobase but not Sugar Fidelity is Maintained in the Sabin I RNA-Dependent RNA Polymerase

    PubMed Central

    Liu, Xinran; Musser, Derek M.; Lee, Cheri A.; Yang, Xiaorong; Arnold, Jamie J.; Cameron, Craig E.; Boehr, David D.

    2015-01-01

    The Sabin I poliovirus live, attenuated vaccine strain encodes for four amino acid changes (i.e., D53N, Y73H, K250E, and T362I) in the RNA-dependent RNA polymerase (RdRp). We have previously shown that the T362I substitution leads to a lower fidelity RdRp, and viruses encoding this variant are attenuated in a mouse model of poliovirus. Given these results, it was surprising that the nucleotide incorporation rate and nucleobase fidelity of the Sabin I RdRp is similar to that of wild-type enzyme, although the Sabin I RdRp is less selective against nucleotides with modified sugar groups. We suggest that the other Sabin amino acid changes (i.e., D53N, Y73H, K250E) help to re-establish nucleotide incorporation rates and nucleotide discrimination near wild-type levels, which may be a requirement for the propagation of the virus and its efficacy as a vaccine strain. These results also suggest that the nucleobase fidelity of the Sabin I RdRp likely does not contribute to viral attenuation. PMID:26516899

  18. Interaction of nucleobases with silicon doped and defective silicon doped graphene and optical properties.

    PubMed

    Mudedla, Sathish Kumar; Balamurugan, Kanagasabai; Kamaraj, Manoharan; Subramanian, Venkatesan

    2016-01-01

    The interaction of nucleobases (NBs) with the surface of silicon doped graphene (SiGr) and defective silicon doped graphene (dSiGr) has been studied using electronic structure methods. A systematic comparison of the calculated interaction energies (adsorption strength) of NBs with the surface of SiGr and dSiGr with those of pristine graphene (Gr) has also been made. The doping of graphene with silicon increases the adsorption strength of NBs. The introduction of defects in SiGr further enhances the strength of interaction with NBs. The appreciable stability of complexes (SiGr-NBs and dSiGr-NBs) arises due to the partial electrostatic and covalent (Si···O(N)) interaction in addition to π-π stacking. The interaction energy increases with the size of graphene models. The strong interaction between dSiGr-NBs and concomitant charge transfer causes significant changes in the electronic structure of dSiGr in contrast to Gr and SiGr. Further, the calculated optical properties of all the model systems using time dependent density functional theory (TD-DFT) reveal that absorption spectra of SiGr and dSiGr undergo appreciable changes after adsorption of NBs. Thus, the significant variations in the HOMO-LUMO gap and absorption spectra of dSiGr after interaction with the NBs can be exploited for possible applications in the sensing of DNA nucleobases. PMID:26607270

  19. Understanding Prebiotic Chemistry Through the Analysis of Extraterrestrial Amino Acids and Nucleobases in Meteorites

    NASA Technical Reports Server (NTRS)

    Burton, Aaron S.; Stern, Jennifer C.; Elsila, Jamie E.; Glavin, Daniel P.; Dworkin, Jason P.

    2012-01-01

    The discoveries of amino acids of extraterrestrial origin in many meteorites over the last 50 years have revolutionized the Astrobiology field. A variety of non-terrestrial amino acids similar to those found in life on Earth have been detected in meteorites. A few amino acids have even been found with chiral excesses, suggesting that meteorites could have contributed to the origin of homochirality in life on Earth. In addition to amino acids, which have been productively studied for years, sugar-like molecules, activated phosphates, and nucleobases have also been determined to be indigenous to numerous meteorites. Because these molecules are essential for life as we know it, and meteorites have been delivering them to the Earth since accretion, it is plausible that the origines) of life on Earth were aided by extrataterrestrially-synthesized molecules. Understanding the origins of life on Earth guides our search for life elsewhere, helping to answer the question of whether biology is unique to Earth. This tutorial focuses on meteoritic amino acids and nucleobases, exploring modern analytical methods and possible formation mechanisms. We will also discuss the unique window that meteorites provide into the chemistry that preceded life on Earth, a chemical record we do not have access to on Earth due to geologic recycling of rocks and the pervasiveness of biology across the planet. Finally. we will address the future of meteorite research, including asteroid sample return missions.

  20. Ultraviolet Irradiation of Pyrimidine in Interstellar Ice Analogs: Formation and Photo-Stability of Nucleobases

    NASA Technical Reports Server (NTRS)

    Nuevo, Michel; Milam, Stefanie N.; Sandford, Scott A.; Elsila, Jamie E.; Dworkin, Jason P.

    2010-01-01

    Astrochemistry laboratory experiments recently showed that molecules of prebiotic interest can potentially form in space, as supported by the detection of amino acids in organic residues formed by the UV photolysis of ices simulating interstellar and cometary environments (H2O, CO, CO2, CH3OH, NH3, etc.). Although the presence of amino acids in the interstellar medium (ISM) is still under debate, experiments and the detection of amino acids in meteorites both support a scenario in which prebiotic molecules could be of extraterrestrial origin, before they are delivered to planets by comets, asteroids, and interplanetary dust particles. Nucleobases, the informational subunits of DNA and RNA, have also been detected in meteorites, although they have not yet been observed in the ISM. Thus, these molecules constitute another family of prebiotic compounds that can possibly form via abiotical processes in astrophysical environments. Nucleobases are nitrogen-bearing cyclic aromatic species with various functional groups attached, which are divided into two classes: pyrimidines (uracil, cytosine, and thymine) and purines (adenine and guanine). In this work, we study how UV irradiation affects pyrimidine mixed in interstellar ice analogs (H2O, NH3, CH3OH). In particular, we show that the UV irradiation of H2O:pyrimidine mixtures leads to the production of oxidized compounds including uracil, and show that both uracil and cytosine are formed upon irradiation of H2O:NH3:pyrimidine mixtures. We also study the photostability of pyrimidine and its photoproducts formed during these experiments.

  1. Catalytic Role of Manganese Oxides in Prebiotic Nucleobases Synthesis from Formamide

    NASA Astrophysics Data System (ADS)

    Bhushan, Brij; Nayak, Arunima; Kamaluddin

    2016-06-01

    Origin of life processes might have begun with the formation of important biomonomers, such as amino acids and nucleotides, from simple molecules present in the prebiotic environment and their subsequent condensation to biopolymers. While studying the prebiotic synthesis of naturally occurring purine and pyrimidine derivatives from formamide, the manganese oxides demonstrated not only good binding for formamide but demonstrated novel catalytic activity. A novel one pot manganese oxide catalyzed synthesis of pyrimidine nucleobases like thymine is reported along with the formation of other nucleobases like purine, 9-(hydroxyacetyl) purine, cytosine, 4(3 H)-pyrimidinone and adenine in acceptable amounts. The work reported is significant in the sense that the synthesis of thymine has exhibited difficulties especially under one pot conditions and also such has been reported only under the catalytic activity of TiO2. The lower oxides of manganese were reported to show higher potential as catalysts and their existence were favored by the reducing atmospheric conditions prevalent on early Earth; thereby confirming the hypothesis that mineral having metals in reduced form might have been more active during the course of chemical evolution. Our results further confirm the role of formamide as a probable precursor for the formation of purine and pyrimidine bases during the course of chemical evolution and origin of life.

  2. Meteoritic Input of Amino Acids and Nucleobases: Methodology and Implications for the Origins of Life

    NASA Technical Reports Server (NTRS)

    Burton, Aaron S.; Stern, Jennifer C.; Elsila, Jamie E.; Glavin, Daniel P.; Dworkin, Jason P.

    2012-01-01

    The discoveries of amino acids of extraterrestrial origin in many meteorites over the last 40 years have revolutionized the Astrobiology field. A variety of non-terrestrial amino acids similar to those found in life on Earth have been detected in meteorites. A few amino acids have even been found with chiral excesses, suggesting that meteorites could have contributed to the origin of homochirality in life on Earth. In addition to amino acids, which have been productively studied for years, sugar-like molecules, activated phosphates, and nucleobases have also been determined to be indigenous to numerous meteorites. Because these molecules are essential for life as we know it, and meteorites have been delivering them to the Earth since accretion, it is plausible that the origin(s) of life on Earth were aided by extraterrestrially-synthesized molecules. Understanding the origins of life on Earth guides our search for life elsewhere, helping to answer the question of whether biology is unique to Earth. This tutorial review focuses on meteoritic amino acids and nucleobases, exploring modern analytical methods and possible formation mechanisms. We will also discuss the unique window that meteorites provide into the chemistry that preceded life on Earth, a chemical record we do not have access to on Earth due to geologic recycling of rocks and the pervasiveness of biology across the planet. Finally, we will address the future of meteorite research, including asteroid sample return mIssIons.

  3. Physisorption of nucleobases on graphene: a comparative van der Waals study

    NASA Astrophysics Data System (ADS)

    Le, Duy; Kara, Abdelkader; Schröder, Elsebeth; Hyldgaard, Per; Rahman, Talat S.

    2012-10-01

    The physisorption of the nucleobases adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) on graphene is studied using several variants of the density functional theory (DFT): the generalized gradient approximation with the inclusion of van der Waals interaction (vdW) based on the TS approach (Tkatchenko and Scheffer 2009 Phys. Rev. Lett. 102 073005) and our simplified version of this approach (here called sTS), the van der Waals density functional vdW-DF (Dion et al 2004 Phys. Rev. Lett. 92 246401) and vdW-DF2 (Lee et al 2010 Phys. Rev. B 82 081101), and DFT-D2 (Grimme 2006 J. Comput. Chem. 27 1787) and DFT-D3 (Grimme et al 2010 J. Chem. Phys. 132 154104) methods. The binding energies of nucleobases on graphene are found to be in the following order: G > A > T > C > U within TS, sTS, vdW-DF, and DFT-D2, and in the following order: G > A > T ˜ C > U within DFT-D3 and vdW-DF2. The binding separations are found to be different within different methods and in the following order: DFT-D2 < TS < DFT-D3 ˜ vdW-DF2 < vdW-DF. We also comment on the efficiency of combining the DFT-D approach and vdW-DF to study systems with van der Waals interactions.

  4. First-principles photoemission spectroscopy in DNA and RNA nucleobases from Koopmans-compliant functionals

    NASA Astrophysics Data System (ADS)

    Nguyen, Ngoc Linh; Borghi, Giovanni; Ferretti, Andrea; Marzari, Nicola

    The determination of spectral properties of the DNA and RNA nucleobases from first principles can provide theoretical interpretation for experimental data, but requires complex electronic-structure formulations that fall outside the domain of applicability of common approaches such as density-functional theory. In this work, we show that Koopmans-compliant functionals, constructed to enforce piecewise linearity in energy functionals with respect to fractional occupation-i.e., with respect to charged excitations-can predict not only frontier ionization potentials and electron affinities of the nucleobases with accuracy comparable or superior with that of many-body perturbation theory and high-accuracy quantum chemistry methods, but also the molecular photoemission spectra are shown to be in excellent agreement with experimental ultraviolet photoemsision spectroscopy data. The results highlight the role of Koopmans-compliant functionals as accurate and inexpensive quasiparticle approximations to the spectral potential, which transform DFT into a novel dynamical formalism where electronic properties, and not only total energies, can be correctly accounted for.

  5. Ultraviolet Irradiation of Pyrimidine in Interstellar Ice Analogs: Formation and Stability of Nucleobases

    NASA Astrophysics Data System (ADS)

    Milam, Stefanie; Nuevo, Michel; Sandford, Scott; Elsila, Jamie; Dworkin, Jason

    The detection of amino acids in organic residues formed by the UV photolysis of 10 K ices representative of interstellar and cometary environments (H2 O, CO, CO2 , CH3 OH, NH3 , etc.) show that molecules of prebiotic interest could potentially form in space. The detection of amino acids in meteorites supports a scenario where the organic molecules required for life are of extraterrestrial origin. Nucleobases, the informational units of RNA and DNA, have also been detected in meteorites and constitute another family of prebiotic compounds that can possibly form in interstellar environments. These molecules are functionalized heterocyclic aromatic species. There are two classes of nucleobases: pyrimidines (e.g. thymine, uracil, and cytosine) and purines (e.g. adenine and guanine). The functionalization of PAHs from UV photolysis in mixed molecular ices has been proven effective in the laboratory. This work aims at studying how UV irradiation affects pyrimidine in interstellar ice analogs. In particular, we show how H2 O/ pyrimidine mixtures lead to the production of oxidized compounds and study their photostability.

  6. Nucleobase but not Sugar Fidelity is Maintained in the Sabin I RNA-Dependent RNA Polymerase.

    PubMed

    Liu, Xinran; Musser, Derek M; Lee, Cheri A; Yang, Xiaorong; Arnold, Jamie J; Cameron, Craig E; Boehr, David D

    2015-10-01

    The Sabin I poliovirus live, attenuated vaccine strain encodes for four amino acid changes (i.e., D53N, Y73H, K250E, and T362I) in the RNA-dependent RNA polymerase (RdRp). We have previously shown that the T362I substitution leads to a lower fidelity RdRp, and viruses encoding this variant are attenuated in a mouse model of poliovirus. Given these results, it was surprising that the nucleotide incorporation rate and nucleobase fidelity of the Sabin I RdRp is similar to that of wild-type enzyme, although the Sabin I RdRp is less selective against nucleotides with modified sugar groups. We suggest that the other Sabin amino acid changes (i.e., D53N, Y73H, K250E) help to re-establish nucleotide incorporation rates and nucleotide discrimination near wild-type levels, which may be a requirement for the propagation of the virus and its efficacy as a vaccine strain. These results also suggest that the nucleobase fidelity of the Sabin I RdRp likely does not contribute to viral attenuation. PMID:26516899

  7. Functional Studies of DNA-Protein Interactions Using FRET Techniques.

    PubMed

    Blouin, Simon; Craggs, Timothy D; Lafontaine, Daniel A; Penedo, J Carlos

    2015-01-01

    Protein-DNA interactions underpin life and play key roles in all cellular processes and functions including DNA transcription, packaging, replication, and repair. Identifying and examining the nature of these interactions is therefore a crucial prerequisite to understand the molecular basis of how these fundamental processes take place. The application of fluorescence techniques and in particular fluorescence resonance energy transfer (FRET) to provide structural and kinetic information has experienced a stunning growth during the past decade. This has been mostly promoted by new advances in the preparation of dye-labeled nucleic acids and proteins and in optical sensitivity, where its implementation at the level of individual molecules has opened a new biophysical frontier. Nowadays, the application of FRET-based techniques to the analysis of protein-DNA interactions spans from the classical steady-state and time-resolved methods averaging over large ensembles to the analysis of distances, conformational changes, and enzymatic reactions in individual protein-DNA complexes. This chapter introduces the practical aspects of applying these methods for the study of protein-DNA interactions. PMID:26404147

  8. Engineering Dark Chromoprotein Reporters for Photoacoustic Microscopy and FRET Imaging

    PubMed Central

    Li, Yan; Forbrich, Alex; Wu, Jiahui; Shao, Peng; Campbell, Robert E.; Zemp, Roger

    2016-01-01

    A subset of the family of fluorescent proteins are the non-fluorescent chromoproteins which are promising probe molecules for use in photoacoustic imaging and as acceptor chromophores in Förster resonance energy transfer (FRET)-based biosensors. Typical approaches for fluorescent protein optimization by screening of large libraries of variants cannot be effectively applied to chromoproteins due to their characteristic lack of fluorescence. To address this challenge, we have developed a directed evolution method to iteratively screen large libraries of protein variants on the basis of their photoacoustic signal levels. By applying this procedure to the promising Ultramarine and cjBlue chromoprotein templates, we were able to identify improved variants with a 02–04 fold increase in photoacoustic signal-to-noise ratio after only a few evolutionary steps. These improved variants enable more accurate spectral de-mixing and localization of protein-producing bacteria in vivo and serve as effective FRET acceptors for both fluorescence- and photoacoustic-based detection of protease activity. PMID:26926390

  9. Paths to Förster's resonance energy transfer (FRET) theory

    NASA Astrophysics Data System (ADS)

    Masters, B. R.

    2014-02-01

    Theodor Förster (1910-1974) developed a phenomenological theory of nonradiative resonance energy transfer which proved to be transformative in the fields of chemistry, biochemistry, and biology. This paper explores the experimental and the theoretical antecedents of Förster's theory of resonance energy transfer (FRET). Early studies of sensitized fluorescence, fluorescence depolarization, and photosynthesis demonstrated the phenomena of long-range energy transfer. At the same time physicists developed theoretical models which contained common physical mechanisms and parameters: oscillating dipoles as models for the atoms or molecules, dipole-dipole coupling for the interaction, and a distance R0 that is optimal for resonance energy transfer. Early theories predicted R0 that was too large as compared to experiments. Finally, in 1946 Förster developed a classical theory and in 1948 he developed a quantum mechanical theory; both theories predicted an inverse sixth power dependence of the rate of energy transfer and a R0 that agreed with experiments. This paper attempts to determine why Förster succeeded when the other theoreticians failed to develop the correct theory. The putative roles of interdisciplinary education and collaborative research are discussed. Furthermore, I explore the role of science journals and their specific audiences in the popularization of FRET to a broad interdisciplinary community.

  10. Studying DNA Looping by Single-Molecule FRET

    PubMed Central

    Le, Tung T.; Kim, Harold D.

    2014-01-01

    Bending of double-stranded DNA (dsDNA) is associated with many important biological processes such as DNA-protein recognition and DNA packaging into nucleosomes. Thermodynamics of dsDNA bending has been studied by a method called cyclization which relies on DNA ligase to covalently join short sticky ends of a dsDNA. However, ligation efficiency can be affected by many factors that are not related to dsDNA looping such as the DNA structure surrounding the joined sticky ends, and ligase can also affect the apparent looping rate through mechanisms such as nonspecific binding. Here, we show how to measure dsDNA looping kinetics without ligase by detecting transient DNA loop formation by FRET (Fluorescence Resonance Energy Transfer). dsDNA molecules are constructed using a simple PCR-based protocol with a FRET pair and a biotin linker. The looping probability density known as the J factor is extracted from the looping rate and the annealing rate between two disconnected sticky ends. By testing two dsDNAs with different intrinsic curvatures, we show that the J factor is sensitive to the intrinsic shape of the dsDNA. PMID:24998459

  11. Ligament Rupture Pressure of Fretted SG Tubes of PWRs

    SciTech Connect

    Seong Sik Hwang; Man Kyo Jung; Hong Pyo Kim; Joung Soo Kim

    2006-07-01

    A fretting/wear degradation at the tube support in the U-bend region of a steam generator (SG) of a pressurized water reactor (PWR) has been reported. Simulated fretted flaws were machined on SG tubes of 195 mm in length. A pressure test was carried out with the tubes at room temperature by using a high pressure test facility which consisted of a water pressurizing pump, a test specimen section and a control unit. Water leak rates just after a ligament rupture or a burst were measured. Tubes degraded by up to 70% of the tube wall (TW) showed a high safety margin in terms of the burst pressure during normal operating conditions. Tubes degraded by up to 50% of the TW did not show a burst. Burst pressure depended on the defect depths rather than on the wrap angles. The tube with a wrap angle of 0 deg. showed a fish mouth fracture, whereas the tube with a 45 deg. wrap angle showed a three way fracture. (authors)

  12. Engineering Dark Chromoprotein Reporters for Photoacoustic Microscopy and FRET Imaging.

    PubMed

    Li, Yan; Forbrich, Alex; Wu, Jiahui; Shao, Peng; Campbell, Robert E; Zemp, Roger

    2016-01-01

    A subset of the family of fluorescent proteins are the non-fluorescent chromoproteins which are promising probe molecules for use in photoacoustic imaging and as acceptor chromophores in Förster resonance energy transfer (FRET)-based biosensors. Typical approaches for fluorescent protein optimization by screening of large libraries of variants cannot be effectively applied to chromoproteins due to their characteristic lack of fluorescence. To address this challenge, we have developed a directed evolution method to iteratively screen large libraries of protein variants on the basis of their photoacoustic signal levels. By applying this procedure to the promising Ultramarine and cjBlue chromoprotein templates, we were able to identify improved variants with a 02-04 fold increase in photoacoustic signal-to-noise ratio after only a few evolutionary steps. These improved variants enable more accurate spectral de-mixing and localization of protein-producing bacteria in vivo and serve as effective FRET acceptors for both fluorescence- and photoacoustic-based detection of protease activity. PMID:26926390

  13. Engineering Dark Chromoprotein Reporters for Photoacoustic Microscopy and FRET Imaging

    NASA Astrophysics Data System (ADS)

    Li, Yan; Forbrich, Alex; Wu, Jiahui; Shao, Peng; Campbell, Robert E.; Zemp, Roger

    2016-03-01

    A subset of the family of fluorescent proteins are the non-fluorescent chromoproteins which are promising probe molecules for use in photoacoustic imaging and as acceptor chromophores in Förster resonance energy transfer (FRET)-based biosensors. Typical approaches for fluorescent protein optimization by screening of large libraries of variants cannot be effectively applied to chromoproteins due to their characteristic lack of fluorescence. To address this challenge, we have developed a directed evolution method to iteratively screen large libraries of protein variants on the basis of their photoacoustic signal levels. By applying this procedure to the promising Ultramarine and cjBlue chromoprotein templates, we were able to identify improved variants with a 02-04 fold increase in photoacoustic signal-to-noise ratio after only a few evolutionary steps. These improved variants enable more accurate spectral de-mixing and localization of protein-producing bacteria in vivo and serve as effective FRET acceptors for both fluorescence- and photoacoustic-based detection of protease activity.

  14. Analogue-to-Digital and Digital-to-Analogue Conversion.

    ERIC Educational Resources Information Center

    Gregory, Martin

    1997-01-01

    Discusses circuits for three-bit and four-bit analogue digital converters and digital analogue converters. These circuits feature slow operating speeds that enable the circuitry to be used to demonstrate the mode of operation using oscilloscopes and signal generators. (DDR)

  15. MIL-L-87177 and CLT:X-10 Lubricants Improve Electrical Connector Fretting Corrosion Behavior

    SciTech Connect

    AUKLAND,NEIL R.; HANLON,JAMES T.

    1999-10-12

    We have conducted a fretting research project using MIL-L-87177 and CLT: X-10 lubricants on Nano-miniature connectors. When they were fretted without lubricant, individual connectors first exceeded our 0.5 ohm failure criteria from 2,341 to 45,238 fretting cycles. With additional fretting, their contact resistance increased to more than 100,000 ohms. Unmodified MIL-L-87177 lubricant delayed the onset of first failure to between 430,000 and over 20,000,000 fretting cycles. MIL-L-87177 modified by addition of Teflon powder delayed first failure to beyond 5 million fretting cycles. Best results were obtained when Teflon was used and also when both the straight and modified lubricants were poured into and then out of the connector. CLT: X-10 lubricant delayed the onset of first failure to beyond 55 million cycles in one test where a failure was actually observed and to beyond 20 million cycles in another that was terminated without failure. CLT: X-10 recovered an unlubricated connector driven deeply into failure, with six failed pins recovering immediately and four more recovering during an additional 420 thousand fretting cycles. MIL-L-87177 was not able to recover a connector under similar conditions.

  16. Comparison of NIR FRET pairs for quantitative transferrin-based assay

    NASA Astrophysics Data System (ADS)

    Sinsuebphon, Nattawut; Bevington, Travis; Zhao, Lingling; Ken, Abe; Barroso, Margarida; Intes, Xavier

    2014-02-01

    Transferrin (Tfn) is commonly used as a drug delivery carrier for cancer treatment. Tfn cellular internalization can be observed by Förster resonance energy transfer (FRET), which occurs when two fluorophores - donor and acceptor - are a few nanometers apart. Donor fluorescence lifetime can be used to sense and quantify FRET occurrence. In FRET state, the donor is quenched leading to a significant reduction in its lifetime. In this study, donor and acceptor near-infrared (NIR) fluorophore-labeled Tfn were used to quantify cellular internalization in breast cancer cell line (T47D). Based on donor lifetime, quantum yield and spectral data, seven NIR FRET pairs were chosen for this comparison. Performance of the different NIR FRET pairs was evaluated in vitro in multiwell plate settings and by analyzing the relationship between quenched donor fraction and acceptor:donor ratio. Additionally, we performed brightness comparison between each pairs. Several parameters, such as brightness, lifetime, R0 and FRET donor population values are used to identify the most suitable NIR FRET pair for in vivo studies in preclinical settings.

  17. Photochromic fluorescence resonance energy transfer (pcFRET): formalism, implementation, and perspectives

    NASA Astrophysics Data System (ADS)

    Jares-Erijman, Elizabeth A.; Giordano, Luciana; Spagnuolo, Carla; Kawior, Jennifer; Vermeij, Rudolph J.; Jovin, Thomas M.

    2004-06-01

    Photochromic FRET (pcFRET), a member of the family of acceptor depletion FRET techniques (adFRET), embodies a general conceptual and experimental scheme based on a coupled system of a fluorescent donor and a photchromic acceptor. The procedure involves the reversible and cyclic spectroscopic depletion of the acceptor, and was initially conceived for the determination of FRET efficiency on a continuos, pixel-by-pixel basis in the microscopy of living cells. However, the modulation of donor fluorescence in pcFRET has implications for a wide range of applications. We present the formalism for quantitative interpretations of photostationary and kinetic data, from which the relevant kinetic rate constants and quantum uields for the cyclization and cycloreversion reactions of the photochromic acceptor can be derived. The scheme was applied to a model system consisting of a fluorescent donor (Lucifer Yellow) covalently bound to a diheteroarylethene acceptor. In a Perspectives section, we discuss photochromic probes, instrumentation issues, and the potential of pcFRET for analyizing chemical equilibria and kinetics, in the latter case with a new technique we have denoted Photochromic Relaxation Kinetics (pcRelKin).

  18. N-way FRET microscopy of multiple protein-protein interactions in live cells.

    PubMed

    Hoppe, Adam D; Scott, Brandon L; Welliver, Timothy P; Straight, Samuel W; Swanson, Joel A

    2013-01-01

    Fluorescence Resonance Energy Transfer (FRET) microscopy has emerged as a powerful tool to visualize nanoscale protein-protein interactions while capturing their microscale organization and millisecond dynamics. Recently, FRET microscopy was extended to imaging of multiple donor-acceptor pairs, thereby enabling visualization of multiple biochemical events within a single living cell. These methods require numerous equations that must be defined on a case-by-case basis. Here, we present a universal multispectral microscopy method (N-Way FRET) to enable quantitative imaging for any number of interacting and non-interacting FRET pairs. This approach redefines linear unmixing to incorporate the excitation and emission couplings created by FRET, which cannot be accounted for in conventional linear unmixing. Experiments on a three-fluorophore system using blue, yellow and red fluorescent proteins validate the method in living cells. In addition, we propose a simple linear algebra scheme for error propagation from input data to estimate the uncertainty in the computed FRET images. We demonstrate the strength of this approach by monitoring the oligomerization of three FP-tagged HIV Gag proteins whose tight association in the viral capsid is readily observed. Replacement of one FP-Gag molecule with a lipid raft-targeted FP allowed direct observation of Gag oligomerization with no association between FP-Gag and raft-targeted FP. The N-Way FRET method provides a new toolbox for capturing multiple molecular processes with high spatial and temporal resolution in living cells. PMID:23762252

  19. A Study on Fretting Behavior in Room Temperature for Inconel Alloy 690

    NASA Astrophysics Data System (ADS)

    Kwon, Jae Do; Chai, Young Suck; Bae, Yong Tak; Choi, Sung Jong

    The initial crack under fretting condition occurs at lower stress amplitude and lower cycles of cyclic loading than that under plain fatigue condition. The fretting damage, for example, can be observed in fossil and nuclear power plant, aircraft, automobile and petroleum chemical plants etc. INCONEL alloy 690 is a high-chromium nickel alloy having excellent resistance to many corrosive aqueous media and high-temperature atmospheres. This alloy is used extensively in the industries of nuclear power, chemicals, heat-treatment and electronics. In this paper, the effect of fretting damage on fatigue behavior for INCONEL alloy 690 was studied. Also, various kinds of tests on mechanical properties such as hardness, tension and plain fatigue tests are performed. Fretting fatigue tests were carried out with flat-flat contact configuration using a bridge type contact pad and plate type specimen. Through these experiments, it is found that the fretting fatigue strength decreased about 43% compared to the plain fatigue strength. In fretting fatigue, the wear debris is observed on the contact surface, and the oblique micro-cracks are initiated at an earlier stage. These results can be used as the basic data in a structural integrity evaluation of heat and corrosion resistant alloy considering fretting damages.

  20. Partially reduced graphene oxide based FRET on fiber-optic interferometer for biochemical detection.

    PubMed

    Yao, B C; Wu, Y; Yu, C B; He, J R; Rao, Y J; Gong, Y; Fu, F; Chen, Y F; Li, Y R

    2016-01-01

    Fluorescent resonance energy transfer (FRET) with naturally exceptional selectivity is a powerful technique and widely used in chemical and biomedical analysis. However, it is still challenging for conventional FRET to perform as a high sensitivity compact sensor. Here we propose a novel 'FRET on Fiber' concept, in which a partially reduced graphene oxide (prGO) film is deposited on a fiber-optic modal interferometer, acting as both the fluorescent quencher for the FRET and the sensitive cladding for optical phase measurement due to refractive index changes in biochemical detection. The target analytes induced fluorescence recovery with good selectivity and optical phase shift with high sensitivity are measured simultaneously. The functionalized prGO film coated on the fiber-optic interferometer shows high sensitivities for the detections of metal ion, dopamine and single-stranded DNA (ssDNA), with detection limits of 1.2 nM, 1.3 μM and 1 pM, respectively. Such a prGO based 'FRET on fiber' configuration, bridging the FRET and the fiber-optic sensing technology, may serve as a platform for the realization of series of integrated 'FRET on Fiber' sensors for on-line environmental, chemical, and biomedical detection, with excellent compactness, high sensitivity, good selectivity and fast response. PMID:27010752

  1. Simultaneous Live Cell Imaging Using Dual FRET Sensors with a Single Excitation Light

    PubMed Central

    Niino, Yusuke; Hotta, Kohji; Oka, Kotaro

    2009-01-01

    Fluorescence resonance energy transfer (FRET) between fluorescent proteins is a powerful tool for visualization of signal transduction in living cells, and recently, some strategies for imaging of dual FRET pairs in a single cell have been reported. However, these necessitate alteration of excitation light between two different wavelengths to avoid the spectral overlap, resulting in sequential detection with a lag time. Thus, to follow fast signal dynamics or signal changes in highly motile cells, a single-excitation dual-FRET method should be required. Here we reported this by using four-color imaging with a single excitation light and subsequent linear unmixing to distinguish fluorescent proteins. We constructed new FRET sensors with Sapphire/RFP to combine with CFP/YFP, and accomplished simultaneous imaging of cAMP and cGMP in single cells. We confirmed that signal amplitude of our dual FRET measurement is comparable to of conventional single FRET measurement. Finally, we demonstrated to monitor both intracellular Ca2+ and cAMP in highly motile cardiac myocytes. To cancel out artifacts caused by the movement of the cell, this method expands the applicability of the combined use of dual FRET sensors for cell samples with high motility. PMID:19551140

  2. Partially reduced graphene oxide based FRET on fiber-optic interferometer for biochemical detection

    PubMed Central

    Yao, B. C.; Wu, Y.; Yu, C. B.; He, J. R.; Rao, Y. J.; Gong, Y.; Fu, F.; Chen, Y. F.; Li, Y. R.

    2016-01-01

    Fluorescent resonance energy transfer (FRET) with naturally exceptional selectivity is a powerful technique and widely used in chemical and biomedical analysis. However, it is still challenging for conventional FRET to perform as a high sensitivity compact sensor. Here we propose a novel ‘FRET on Fiber’ concept, in which a partially reduced graphene oxide (prGO) film is deposited on a fiber-optic modal interferometer, acting as both the fluorescent quencher for the FRET and the sensitive cladding for optical phase measurement due to refractive index changes in biochemical detection. The target analytes induced fluorescence recovery with good selectivity and optical phase shift with high sensitivity are measured simultaneously. The functionalized prGO film coated on the fiber-optic interferometer shows high sensitivities for the detections of metal ion, dopamine and single-stranded DNA (ssDNA), with detection limits of 1.2 nM, 1.3 μM and 1 pM, respectively. Such a prGO based ‘FRET on fiber’ configuration, bridging the FRET and the fiber-optic sensing technology, may serve as a platform for the realization of series of integrated ‘FRET on Fiber’ sensors for on-line environmental, chemical, and biomedical detection, with excellent compactness, high sensitivity, good selectivity and fast response PMID:27010752

  3. Time-resolved FRET fluorescence spectroscopy of visible fluorescent protein pairs.

    PubMed

    Visser, A J W G; Laptenok, S P; Visser, N V; van Hoek, A; Birch, D J S; Brochon, J-C; Borst, J W

    2010-01-01

    Förster resonance energy transfer (FRET) is a powerful method for obtaining information about small-scale lengths between biomacromolecules. Visible fluorescent proteins (VFPs) are widely used as spectrally different FRET pairs, where one VFP acts as a donor and another VFP as an acceptor. The VFPs are usually fused to the proteins of interest, and this fusion product is genetically encoded in cells. FRET between VFPs can be determined by analysis of either the fluorescence decay properties of the donor molecule or the rise time of acceptor fluorescence. Time-resolved fluorescence spectroscopy is the technique of choice to perform these measurements. FRET can be measured not only in solution, but also in living cells by the technique of fluorescence lifetime imaging microscopy (FLIM), where fluorescence lifetimes are determined with the spatial resolution of an optical microscope. Here we focus attention on time-resolved fluorescence spectroscopy of purified, selected VFPs (both single VFPs and FRET pairs of VFPs) in cuvette-type experiments. For quantitative interpretation of FRET-FLIM experiments in cellular systems, details of the molecular fluorescence are needed that can be obtained from experiments with isolated VFPs. For analysis of the time-resolved fluorescence experiments of VFPs, we have utilised the maximum entropy method procedure to obtain a distribution of fluorescence lifetimes. Distributed lifetime patterns turn out to have diagnostic value, for instance, in observing populations of VFP pairs that are FRET-inactive. PMID:19693494

  4. N-Way FRET Microscopy of Multiple Protein-Protein Interactions in Live Cells

    PubMed Central

    Hoppe, Adam D.; Scott, Brandon L.; Welliver, Timothy P.; Straight, Samuel W.; Swanson, Joel A.

    2013-01-01

    Fluorescence Resonance Energy Transfer (FRET) microscopy has emerged as a powerful tool to visualize nanoscale protein-protein interactions while capturing their microscale organization and millisecond dynamics. Recently, FRET microscopy was extended to imaging of multiple donor-acceptor pairs, thereby enabling visualization of multiple biochemical events within a single living cell. These methods require numerous equations that must be defined on a case-by-case basis. Here, we present a universal multispectral microscopy method (N-Way FRET) to enable quantitative imaging for any number of interacting and non-interacting FRET pairs. This approach redefines linear unmixing to incorporate the excitation and emission couplings created by FRET, which cannot be accounted for in conventional linear unmixing. Experiments on a three-fluorophore system using blue, yellow and red fluorescent proteins validate the method in living cells. In addition, we propose a simple linear algebra scheme for error propagation from input data to estimate the uncertainty in the computed FRET images. We demonstrate the strength of this approach by monitoring the oligomerization of three FP-tagged HIV Gag proteins whose tight association in the viral capsid is readily observed. Replacement of one FP-Gag molecule with a lipid raft-targeted FP allowed direct observation of Gag oligomerization with no association between FP-Gag and raft-targeted FP. The N-Way FRET method provides a new toolbox for capturing multiple molecular processes with high spatial and temporal resolution in living cells. PMID:23762252

  5. Partially reduced graphene oxide based FRET on fiber-optic interferometer for biochemical detection

    NASA Astrophysics Data System (ADS)

    Yao, B. C.; Wu, Y.; Yu, C. B.; He, J. R.; Rao, Y. J.; Gong, Y.; Fu, F.; Chen, Y. F.; Li, Y. R.

    2016-03-01

    Fluorescent resonance energy transfer (FRET) with naturally exceptional selectivity is a powerful technique and widely used in chemical and biomedical analysis. However, it is still challenging for conventional FRET to perform as a high sensitivity compact sensor. Here we propose a novel ‘FRET on Fiber’ concept, in which a partially reduced graphene oxide (prGO) film is deposited on a fiber-optic modal interferometer, acting as both the fluorescent quencher for the FRET and the sensitive cladding for optical phase measurement due to refractive index changes in biochemical detection. The target analytes induced fluorescence recovery with good selectivity and optical phase shift with high sensitivity are measured simultaneously. The functionalized prGO film coated on the fiber-optic interferometer shows high sensitivities for the detections of metal ion, dopamine and single-stranded DNA (ssDNA), with detection limits of 1.2 nM, 1.3 μM and 1 pM, respectively. Such a prGO based ‘FRET on fiber’ configuration, bridging the FRET and the fiber-optic sensing technology, may serve as a platform for the realization of series of integrated ‘FRET on Fiber’ sensors for on-line environmental, chemical, and biomedical detection, with excellent compactness, high sensitivity, good selectivity and fast response

  6. UV laser photoactivation of hexachloroplatinate bound to individual nucleobases in vacuo as molecular level probes of a model photopharmaceutical.

    PubMed

    Matthews, Edward; Sen, Ananya; Yoshikawa, Naruo; Bergström, Ed; Dessent, Caroline E H

    2016-06-01

    Isolated molecular clusters of adenine, cytosine, thymine and uracil bound to hexachloroplatinate, PtCl6(2-), have been studied using laser electronic photodissociation spectroscopy to investigate photoactivation of a platinum complex in the vicinity of a nucleobase. These metal complex-nucleobase clusters represent model systems for identifying the fundamental photochemical processes occurring in photodynamic platinum drug therapies that target DNA. This is the first study to explore the specific role of a strongly photoactive platinum compound in the aggregate complex. Each of the clusters studied displays a broadly similar absorption spectra, with a strong λmax ∼ 4.6 eV absorption band and a subsequent increase in the absorption intensity towards higher spectral-energy. The absorption bands are traced to ligand-to-metal-charge-transfer excitations on the PtCl6(2-) moiety within the cluster, and result in Cl(-)·nucleobase and PtCl5(-) as primary photofragments. These results demonstrate how selective photoexcitation can drive distinctive photodecay channels for a model photo-pharmaceutical. In addition, cluster absorption due to excitation of nucleobase-centred chromophores is observed in the region around 5 eV. For the uracil cluster, photofragments consistent with ultrafast decay of the excited state and vibrational predissociation on the ground-state surface are observed. However, this decay channel becomes successively weaker on going from thymine to cytosine to adenine, due to differential coupling of the excited states to the electron detachment continuum. These effects demonstrate the distinctive photophysical characteristics of the different nucleobases, and are discussed in the context of the recently recorded photoelectron spectra of theses clusters. PMID:27198464

  7. Phosphonate analogues of aminoacyl adenylates.

    PubMed Central

    Southgate, C C; Dixon, H B

    1978-01-01

    Phosphonomethyl analogues of glycyl phosphate and valyl phosphate, i.e. NH2-CHR-CO-CH2-PO(OH)2, were synthesized and esterified with adenosine to give analogues of aminoacyl adenylates. The interaction of these adenylate analogues with valyl-tRNA synthetase from Escherichia coli was studied by fluorescence titration. The analogue of valyl phosphate has an affinity for the enzyme comparable with that of valine, but that of valyl adenylate is bound much less tightly than either valyl adenylate or corresponding derivative of valinol. The affinity of the analogue of glycyl adenylate was too low to be measured. We conclude that this enzyme interacts specifically with both the side chain and the anhydride linkage of the adenylate intermediate. PMID:743207

  8. MagFRET: The First Genetically Encoded Fluorescent Mg2+ Sensor

    PubMed Central

    Oortwijn, Jorn; Aper, Stijn J. A.; Merkx, Maarten

    2013-01-01

    Magnesium has important structural, catalytic and signaling roles in cells, yet few tools exist to image this metal ion in real time and at subcellular resolution. Here we report the first genetically encoded sensor for Mg2+, MagFRET-1. This sensor is based on the high-affinity Mg2+ binding domain of human centrin 3 (HsCen3), which undergoes a transition from a molten-globular apo form to a compactly-folded Mg2+-bound state. Fusion of Cerulean and Citrine fluorescent domains to the ends of HsCen3, yielded MagFRET-1, which combines a physiologically relevant Mg2+ affinity (Kd = 148 µM) with a 50% increase in emission ratio upon Mg2+ binding due to a change in FRET efficiency between Cerulean and Citrine. Mutations in the metal binding sites yielded MagFRET variants whose Mg2+ affinities were attenuated 2- to 100-fold relative to MagFRET-1, thus covering a broad range of Mg2+ concentrations. In situ experiments in HEK293 cells showed that MagFRET-1 can be targeted to the cytosol and the nucleus. Clear responses to changes in extracellular Mg2+ concentration were observed for MagFRET-1-expressing HEK293 cells when they were permeabilized with digitonin, whereas similar changes were not observed for intact cells. Although MagFRET-1 is also sensitive to Ca2+, this affinity is sufficiently attenuated (Kd of 10 µM) to make the sensor insensitive to known Ca2+ stimuli in HEK293 cells. While the potential and limitations of the MagFRET sensors for intracellular Mg2+ imaging need to be further established, we expect that these genetically encoded and ratiometric fluorescent Mg2+ sensors could prove very useful in understanding intracellular Mg2+ homeostasis and signaling. PMID:24312622

  9. Defining the Limits of Single-Molecule FRET Resolution in TIRF Microscopy

    PubMed Central

    Holden, Seamus J.; Uphoff, Stephan; Hohlbein, Johannes; Yadin, David; Le Reste, Ludovic; Britton, Oliver J.; Kapanidis, Achillefs N.

    2010-01-01

    Single-molecule FRET (smFRET) has long been used as a molecular ruler for the study of biology on the nanoscale (∼2–10 nm); smFRET in total-internal reflection fluorescence (TIRF) Förster resonance energy transfer (TIRF-FRET) microscopy allows multiple biomolecules to be simultaneously studied with high temporal and spatial resolution. To operate at the limits of resolution of the technique, it is essential to investigate and rigorously quantify the major sources of noise and error; we used theoretical predictions, simulations, advanced image analysis, and detailed characterization of DNA standards to quantify the limits of TIRF-FRET resolution. We present a theoretical description of the major sources of noise, which was in excellent agreement with results for short-timescale smFRET measurements (<200 ms) on individual molecules (as opposed to measurements on an ensemble of single molecules). For longer timescales (>200 ms) on individual molecules, and for FRET distributions obtained from an ensemble of single molecules, we observed significant broadening beyond theoretical predictions; we investigated the causes of this broadening. For measurements on individual molecules, analysis of the experimental noise allows us to predict a maximum resolution of a FRET change of 0.08 with 20-ms temporal resolution, sufficient to directly resolve distance differences equivalent to one DNA basepair separation (0.34 nm). For measurements on ensembles of single molecules, we demonstrate resolution of distance differences of one basepair with 1000-ms temporal resolution, and differences of two basepairs with 80-ms temporal resolution. Our work paves the way for ultra-high-resolution TIRF-FRET studies on many biomolecules, including DNA processing machinery (DNA and RNA polymerases, helicases, etc.), the mechanisms of which are often characterized by distance changes on the scale of one DNA basepair. PMID:21044609

  10. Correlating Calmodulin Landscapes with Chemical Catalysis in Neuronal Nitric Oxide Synthase using Time-Resolved FRET and a 5-Deazaflavin Thermodynamic Trap

    PubMed Central

    2016-01-01

    A major challenge in enzymology is the need to correlate the dynamic properties of enzymes with, and understand the impact on, their catalytic cycles. This is especially the case with large, multicenter enzymes such as the nitric oxide synthases (NOSs), where the importance of dynamics has been inferred from a variety of structural, single-molecule, and ensemble spectroscopic approaches but where motions have not been correlated experimentally with mechanistic steps in the reaction cycle. Here we take such an approach. Using time-resolved spectroscopy employing absorbance and Förster resonance energy transfer (FRET) and exploiting the properties of a flavin analogue (5-deazaflavin mononucleotide (5-dFMN)) and isotopically labeled nicotinamide coenzymes, we correlate the timing of CaM structural changes when bound to neuronal nitric oxide synthase (nNOS) with the nNOS catalytic cycle. We show that remodeling of CaM occurs early in the electron transfer sequence (FAD reduction), not at later points in the reaction cycle (e.g., FMN reduction). Conformational changes are tightly correlated with FAD reduction kinetics and reflect a transient “opening” and then “closure” of the bound CaM molecule. We infer that displacement of the C-terminal tail on binding NADPH and subsequent FAD reduction are the likely triggers of conformational change. By combining the use of cofactor/coenzyme analogues and time-resolved FRET/absorbance spectrophotometry, we show how the reaction cycles of complex enzymes can be simplified, enabling a detailed study of the relationship between protein dynamics and reaction cycle chemistry—an approach that can also be used with other complex multicenter enzymes. PMID:27563493

  11. Time-resolved FRET and PCT in cationic conjugated polymer/dye-labeled DNA complex

    NASA Astrophysics Data System (ADS)

    Kim, Inhong; Kim, Jihoon; Kim, Bumjin; Kang, Mijeong; Woo, Han Young; Kyhm, Kwangseuk

    2011-12-01

    The energy transfer mechanism between cationic conjugated polyelectrolytes and a single stranded DNA labeled with fluorescein was investigated in terms of Förster resonance energy transfer (FRET) and photo-induced charge transfer (PCT) by time-resolved fluorescence. Both FRET and PCT rate efficiencies were obtained by phenomenological coupled rate equations, which are in excellent agreement with experiments. We found the total energy transfer in the complex is maximized as a consequence of FRET and PCT at an optimum distance 32.7Å.

  12. Electrical behavior of periodically microstructured Sn/CuSn4 contact models under fretting conditions

    SciTech Connect

    Daniel, Claus; M�cklich, Frank

    2004-01-01

    Fretting corrosion caused by vibration of electrical contacts is one of the main causes of failure of the electrical systems used in the automotive industry. The number of electrical contacts in automotive applications increases steadily. An improvement of electrical connectors can be achieved by microstructuring of the coating by interfering laser beams. The evolution of the electrical contact resistance and the friction coefficient in fretting tests are studied and the slip-stick regimes are analyzed. The changes in the electrical behavior after interference irradiation are explained on the base of cross section studies of vibrated contact models after different numbers of fretting cycles. The study is completed by SEM and EDX investigations.

  13. Laser-induced shockwave paired with FRET: a method to study cell signaling.

    PubMed

    Gomez-Godinez, Veronica; Preece, Daryl; Shi, Linda; Khatibzadeh, Nima; Rosales, Derrick; Pan, Yijia; Lei, Lie; Wang, Yingxiao; Berns, Michael W

    2015-03-01

    Cells within the body are subject to various forces; however, the details concerning the way in which cells respond to mechanical stimuli are not well understood. We demonstrate that laser-induced shockwaves (LIS) combined with biosensors based on fluorescence resonance energy transfer (FRET) is a promising new approach to study biological processes in single live cells. As "proof-of-concept," using a FRET biosensor, we show that in response to LIS, cells release intracellular calcium. With the parameters used, cells retain their morphology and remain viable. LIS combined with FRET permits observation of the cells immediate response to a sudden shear force. PMID:25639252

  14. Detection and Quantification of Intracellular Signaling Using FRET-Based Biosensors and High Content Imaging.

    PubMed

    Halls, Michelle L; Poole, Daniel P; Ellisdon, Andrew M; Nowell, Cameron J; Canals, Meritxell

    2015-01-01

    Förster resonance energy transfer (FRET) biosensors represent invaluable tools to detect the spatiotemporal context of second messenger production and intracellular signaling that cannot be attained using traditional methods. Here, we describe a detailed protocol for the use of high content imaging in combination with FRET biosensors to assess second messenger production and intracellular signaling in a time-effective manner. We use four different FRET biosensors to measure cAMP levels, kinase (ERK and PKC), and GTPase activity. Importantly, we provide the protocols to express and measure these sensors in a variety of model cell lines and primary dorsal root ganglia neurons. PMID:26260599

  15. Fretting corrosion of CoCrMo and Ti6Al4V interfaces.

    PubMed

    Swaminathan, Viswanathan; Gilbert, Jeremy L

    2012-08-01

    Mechanically assisted corrosion (fretting corrosion, tribocorrosion etc.,) of metallic biomaterials is a primary concern for numerous implant applications, particularly in the performance of highly-loaded medical devices. While the basic underlying concepts of fretting corrosion or tribocorrosion and fretting crevice corrosion are well known, there remains a need to develop an integrated systematic method for the analysis of fretting corrosion involving metal-on-metal contacts. Such a method can provide detailed and quantitative information on the processes present and explore variations in surfaces, alloys, voltages, loadings, motion and solution conditions. This study reports on development of a fretting corrosion test system and presents elements of an in-depth theoretical fretting corrosion model that incorporates both the mechanical and the electrochemical aspects of fretting corrosion. To demonstrate the capabilities of the new system and validate the proposed model, experiments were performed to understand the effect of applied normal load on fretting corrosion performance of Ti6Al4V/Ti6Al4V, CoCrMo/Ti6Al4V, and CoCrMo/CoCrMo material couples under potentiostatic conditions with a fixed starting surface roughness. The results of this study show that fretting corrosion is affected by material couples, normal load and the motion conditions at the interface. In particular, fretting currents and coefficient of friction (COF) vary with load and are higher for Ti6Al4V/Ti6Al4V couple reaching 3 mA/cm(2) and 0.63 at about 73 MPa nominal contact stress, respectively. Ti6Al4V coupled with CoCrMo displayed lower currents (0.6 mA/cm(2)) and COF (0.3), and the fretting corrosion behavior was comparable to CoCrMo/CoCrMo couple (1.2 mA/cm(2) and 0.3, respectively). Information on the mechanical energy dissipated at the interface, the sticking behavior, and the load dependence of the inter-asperity distance calculated using the model elucidated the influence of

  16. Asymmetric Synthesis and Binding Study of New Long-Chain HPA-12 Analogues as Potent Ligands of the Ceramide Transfer Protein CERT.

    PubMed

    Ďuriš, Andrej; Daïch, Adam; Santos, Cécile; Fleury, Laurence; Ausseil, Frédéric; Rodriguez, Frédéric; Ballereau, Stéphanie; Génisson, Yves; Berkeš, Dušan

    2016-05-01

    A series of 12 analogues of the Cer transfer protein (CERT) antagonist HPA-12 with long aliphatic chains were prepared as their (1R,3S)-syn and (1R,3R)-anti stereoisomers from pivotal chiral oxoamino acids. The enantioselective access to these intermediates as well as their ensuing transformation relied on a practical crystallization-induced asymmetric transformation (CIAT) process. Sonogashira coupling followed by triple bond reduction and thiophene ring hydrodesulfurization (HDS) into the corresponding alkane moieties was then implemented to complete the synthetic routes delivering the targeted HPA-12 analogues in concise 4- to 6-step reaction sequences. Ten compounds were evaluated regarding their ability to bind to the CERT START domain by using the recently developed time-resolved FRET-based homogeneous (HTR-FRET) binding assay. The introduction of a lipophilic appendage on the phenyl moiety led to an overall 10- to 1000-fold enhancement of the protein binding, with the highest effect being observed for a n-hexyl residue in the meta position. The importance of the phenyl ring for the activity was indicated by the reduced potency of the 3-deoxyphytoceramide aliphatic analogues. The 1,3-syn stereoisomers were systematically more potent than their 1,3-anti analogues. In silico studies were used to rationalized these trends, leading to a model of protein recognition coherent with the stronger binding of (1R,3S)-syn HPAs. PMID:27031925

  17. NASA/ESMD Analogue Mission Plans

    NASA Technical Reports Server (NTRS)

    Hoffman, Stephen J.

    2007-01-01

    A viewgraph presentation exploring Earth and its analogues is shown. The topics include: 1) ESMD Goals for the Use of Earth Analogues; 2) Stakeholders Summary; 3) Issues with Current Analogue Situation; 4) Current state of Analogues; 5) External Implementation Plan (Second Step); 6) Recent Progress in Utilizing Analogues; 7) Website Layout Example-Home Page; 8) Website Layout Example-Analogue Site; 9) Website Layout Example-Analogue Mission; 10) Objectives of ARDIG Analog Initiatives; 11) Future Plans; 12) Example: Cold-Trap Sample Return; 13) Example: Site Characterization Matrix; 14) Integrated Analogue Studies-Prerequisites for Human Exploration; and 15) Rating Scale Definitions.

  18. Ultrasensitive Measurements of Microbial Rhodopsin Photocycles Using Photochromic FRET

    PubMed Central

    Bayraktar, Halil; Fields, Alexander P.; Kralj, Joel M.; Spudich, John L.; Rothschild, Kenneth J.; Cohen, Adam E.

    2011-01-01

    Microbial rhodopsins are an important class of light-activated transmembrane proteins whose function is typically studied on bulk samples. Here we apply photochromic fluorescence resonance energy transfer (pcFRET) to investigate the dynamics of these proteins with sensitivity approaching the single-molecule limit. The brightness of a covalently linked organic fluorophore is modulated by changes in the absorption spectrum of the endogenous retinal chromophore that occur as the molecule undergoes a light-activated photocycle. We studied the photocycles of blue-absorbing proteorhodopsin (BPR) and sensory rhodopsin II (SRII). Clusters of 2–3 molecules of SRII clearly showed a light-induced photocycle. Single molecules of SRII showed a photocycle upon signal averaging over several illumination cycles. PMID:22010969

  19. Synthesis Structure and Imaging of Oligodeoxyribonucleotides with Tellurium-nucleobase Derivatization

    SciTech Connect

    J Sheng; A Hassan; W Zhang; J Zhou; B Xu; A Soares; Z Huang

    2011-12-31

    We report here the first synthesis of 5-phenyl-telluride-thymidine derivatives and the Te-phosphoramidite. We also report here the synthesis, structure and STM current-imaging studies of DNA oligonucleotides containing the nucleobases (thymine) derivatized with 5-phenyl-telluride functionality (5-Te). Our results show that the 5-Te-DNA is stable, and that the Te-DNA duplex has the thermo-stability similar to the corresponding native duplex. The crystal structure indicates that the 5-Te-DNA duplex structure is virtually identical to the native one, and that the Te-modified T and native A interact similarly to the native T and A pair. Furthermore, while the corresponding native showed weak signals, the DNA duplex modified with electron-rich tellurium functionality showed strong topographic and current peaks by STM imaging, suggesting a potential strategy to directly image DNA without structural perturbation.

  20. Synthesis, structure and imaging of oligodeoxyribonucleotides with tellurium-nucleobase derivatization

    SciTech Connect

    Sheng, J.; Soares, A.; Hassan, A. E. A.; Zhang, W.; Zhou, J.; Xu, B.; Huang, Z.

    2011-05-01

    We report here the first synthesis of 5-phenyl-telluride-thymidine derivatives and the Te-phosphoramidite. We also report here the synthesis, structure and STM current-imaging studies of DNA oligonucleotides containing the nucleobases (thymine) derivatized with 5-phenyl-telluride functionality (5-Te). Our results show that the 5-Te-DNA is stable, and that the Te-DNA duplex has the thermo-stability similar to the corresponding native duplex. The crystal structure indicates that the 5-Te-DNA duplex structure is virtually identical to the native one, and that the Te-modified T and native A interact similarly to the native T and A pair. Furthermore, while the corresponding native showed weak signals, the DNA duplex modified with electron-rich tellurium functionality showed strong topographic and current peaks by STM imaging, suggesting a potential strategy to directly image DNA without structural perturbation.

  1. Intersystem Crossing Pathways in the Noncanonical Nucleobase 2-Thiouracil: A Time-Dependent Picture

    PubMed Central

    2016-01-01

    The deactivation mechanism after ultraviolet irradiation of 2-thiouracil has been investigated using nonadiabatic dynamics simulations at the MS-CASPT2 level of theory. It is found that after excitation the S2 quickly relaxes to S1, and from there intersystem crossing takes place to both T2 and T1 with a time constant of 400 fs and a triplet yield above 80%, in very good agreement with recent femtosecond experiments in solution. Both indirect S1 → T2 → T1 and direct S1 → T1 pathways contribute to intersystem crossing, with the former being predominant. The results contribute to the understanding of how some noncanonical nucleobases respond to harmful ultraviolet light, which could be relevant for prospective photochemotherapeutic applications. PMID:27167106

  2. Intersystem Crossing Pathways in the Noncanonical Nucleobase 2-Thiouracil: A Time-Dependent Picture.

    PubMed

    Mai, Sebastian; Marquetand, Philipp; González, Leticia

    2016-06-01

    The deactivation mechanism after ultraviolet irradiation of 2-thiouracil has been investigated using nonadiabatic dynamics simulations at the MS-CASPT2 level of theory. It is found that after excitation the S2 quickly relaxes to S1, and from there intersystem crossing takes place to both T2 and T1 with a time constant of 400 fs and a triplet yield above 80%, in very good agreement with recent femtosecond experiments in solution. Both indirect S1 → T2 → T1 and direct S1 → T1 pathways contribute to intersystem crossing, with the former being predominant. The results contribute to the understanding of how some noncanonical nucleobases respond to harmful ultraviolet light, which could be relevant for prospective photochemotherapeutic applications. PMID:27167106

  3. DNA-nucleobases: gate dielectric/passivation layer for flexible GFET-based sensor applications

    NASA Astrophysics Data System (ADS)

    Williams, Adrienne D.; Ouchen, Fahima; Kim, Steve S.; Elhamri, Said; Naik, Rajesh R.; Grote, James

    2015-09-01

    The main goal of this research was to maintain the bulk charge carrier mobility of graphene, after deposition of the gate dielectric layer used for making transistor devices. The approach was introducing a thin film of deoxyribonucleic acid (DNA) nucleobase purine guanine, deposited by physical vapor deposition (PVD), onto layers of graphene that were transferred onto various flexible substrates. Several test platforms were fabricated with guanine as a standalone gate dielectric, as the control, and guanine as a passivation layer between the graphene and PMMA. It was found that the bulk charge carrier mobility of graphene was best maintained and most stable using guanine as a passivation layer between the graphene and PMMA. Other transport properties, such as charge carrier concentration, conductivity type and electrical resistivity were investigated as well. This is an important first step to realizing high performance graphene-based transistors that have potential use in bio and environmental sensors, computer-processing and electronics.

  4. New size-expanded RNA nucleobase analogs: A detailed theoretical study

    NASA Astrophysics Data System (ADS)

    Zhang, Laibin; Zhang, Zhenwei; Ren, Tingqi; Tian, Jianxiang; Wang, Mei

    2015-04-01

    Fluorescent nucleobase analogs have attracted much attention in recent years due to their potential applications in nucleic acids research. In this work, four new size-expanded RNA base analogs were computationally designed and their structural, electronic, and optical properties are investigated by means of DFT calculations. The results indicate that these analogs can form stable Watson-Crick base pairs with natural counterparts and they have smaller ionization potentials and HOMO-LUMO gaps than natural ones. Particularly, the electronic absorption spectra and fluorescent emission spectra are calculated. The calculated excitation maxima are greatly red-shifted compared with their parental and natural bases, allowing them to be selectively excited. In gas phase, the fluorescence from them would be expected to occur around 526, 489, 510, and 462 nm, respectively. The influences of water solution and base pairing on the relevant absorption spectra of these base analogs are also examined.

  5. Catalytic role of Manganese oxides in prebiotic Nucleobases synthesis from Formamide

    NASA Astrophysics Data System (ADS)

    Bhushan, Brij

    2012-07-01

    The evolution of living cell from chemicals is more complicated reaction which could be studied in multistep. A study of prebiotic synthesis of naturally occurring purine and pyrimidine derivatives from formamide under catalytic condition with different oxides of manganese reveals a significant role. Manganese oxides are highly efficient in the conversion of formamide into different nucleobases. Neat formamide is converted to the purine, 9-(hydroxyacetyl) purine, cytosine, 4(3H)-pyrimidinone, thymine and adenine in good yield. Metal oxides have provided their surfaces and catalyzed the reactions from simple molecules to more complex bio-organic molecules. Our results show that probably prebiotic reactions might have occured on the sea floor where the existence of manganese oxide is second to iron transition metal minerals.

  6. Interaction of Nucleobases with Semiconducting Nanotubes and Nanocages: Does the Solvent Matter?

    NASA Astrophysics Data System (ADS)

    Wang, Zhoufei; Slough, William; He, Haiying; Pandey, Ravindra; Karna, Shashi

    2013-03-01

    The tremendous advancement in nanotechnology has brought great promise in the area of bio-applications. Nanoscale materials and structures have attracted a lot of interest for their potential applications in biosensing, biorecognition, luminescent probes for DNA, biomedical labeling, drug delivery etc. Gaining fundamental understanding of the interaction of bio-systems with nanomaterials is critical in putting all these applications into full play. Despite the fact that most of these interactions appear in aqueous environment, the solvent effect has often been neglected in previous computational studies. In this talk, we will report our comparison study of nucleobases interacting with BN nanotubes and chalcogenide nanocages with/without considering the aqueous solution, based on first-principles calculations. The results reveal a significant effect from the water solution, which may largely reduce the interaction energy due to the polarization of the dielectric solvent medium.

  7. Content variations of triterpenic acid, nucleoside, nucleobase, and sugar in jujube (Ziziphus jujuba) fruit during ripening.

    PubMed

    Guo, Sheng; Duan, Jin-Ao; Qian, Dawei; Tang, Yuping; Wu, Dawei; Su, Shulan; Wang, Hanqing; Zhao, Yunan

    2015-01-15

    Jujube (Ziziphus jujuba) fruit is widely consumed as food and traditional Chinese medicine in Asian countries due to its potential effects for human health. To facilitate selection of the maturity stage providing optimum health benefits, jujube fruits were analysed at six stages of growth (S1-6) for triterpenic acids, nucleosides, nucleobases, and sugars by UHPLC-MS/MS or HPLC-ELSD methods. The content levels of most triterpenic acids and sugars increased with ripening, and reached the highest at S5 and S6, respectively. The accumulation of the cyclic nucleotides (cAMP and cGMP) was mainly in the later stage of ripening (S5-6). Therefore, if taking triterpenic acids as the major quality indicator, S5 should be the ideal time to harvest jujube fruit, and the full ripen stage (S6) maybe the best choice when taking sugars and cyclic nucleotides as the most important components. PMID:25149013

  8. Photo-switchable quantum dots based on reversible FRET

    NASA Astrophysics Data System (ADS)

    Fan, Qirui; Nabar, Gauri; Miller, Carl; Castro, Carlos; Winter, Jessica

    2014-02-01

    Super-resolution fluorescence microscopy is anticipated to be a powerful tool in observing biological structures and processes smaller than the diffraction limit of light microscopy (~200nm). Yet, many super-resolution techniques (STORM/PALM, STED) employ photo-switchable fluorescent probes (i.e., dyes and fluorescent proteins) that are limited in brightness and stability, reducing potential image resolution. Here, we describe photo-switchable quantum dots (QDs) with enhanced brightness and stability, and excellent optical properties, including narrow emission spectra and broad excitation spectra, compared to fluorescent dyes. These QDs are composed of one green QD, one gold nanoparticle (AuNP), and complimentary single stranded DNA (ssDNA) modified with photo-sensitive azobenzene groups bound to each of the particles. Because of the azobenzene photosensitive property, the ssDNA strands hybridize when excited with visible light, yielding a QD-AuNP conjugate in which QD fluorescence is quenched through Förster resonance energy transfer (FRET); and dehybridize under visible light, yielding separate QDs and AuNPs that are free to diffuse from each other. Because FRET is strongly distance dependent (i.e., α 1/r6, in this case, a few nanometers), QD fluorescence is restored. Moreover, the photo-switchable QD-AuNP conjugate scheme has the potential to be integrated with a DNA nano-machine platform, adding the potential for photo-manipulated functionality. As a preliminary proof of concept, we tethered different nanocomponents, including QD micelle assemblies and AuNPs, to DNA origami structures (hinge and platform shapes) using ssDNA hybridization.

  9. Mars Global Surveyor observations of Martian fretted terrain

    USGS Publications Warehouse

    Carr, M.H.

    2001-01-01

    The Martian fretted terrain between latitudes 30?? and 50?? N and between 315?? and 360?? W has been reexamined in light of new Mars Orbiter Camera (MOC) and Mars Orbiter Laser Altimeter (MOLA) data from Mars Global Surveyor. Much of the terrain in the 30??-50?? latitude belt in both hemispheres has a characteristic stippled or pitted texture at MOC (1.5 m) scale. The texture appears to result from partial removal of a formerly smooth, thin deposit as a result of sublimation and deflation. A complex history of deposition and exhumation is indicated by remnants of a former, thicker cover of layered deposits. In some hollows and on some slopes, particularly those facing the pole, are smooth textured deposits outlined by an outward facing escarpment. Throughout the study area are numerous escarpments with debris flows at their base. The escarpments typically have slopes in the 20??-30?? range. At the base of the escarpment is commonly a deposit with striae oriented at right angles to the escarpment. Outside this deposit is the main debris apron with a surface that typically slopes 2??-3?? and complex surface textures suggestive of compression, sublimation, and deflation. The presence of undeformed impact craters indicates that the debris flows are no longer forming. Fretted valleys contain lineated fill and are poorly graded. They likely form from fluvial valleys that were initially like those elsewhere on the planet but were subsequently widened and filled by the same mass-wasting processes that formed the debris aprons. Slope reversals indicate that downvalley flow of the lineated fill is minor. The ubiquitous presence of breaks in slope formed by mass wasting and the complex surface textures that result from mass wasting, deflation, and sublimation decreases the recognizability of the shorelines formerly proposed for this area.

  10. Electron Detachment as a Probe of Intrinsic Nucleobase Dynamics in Dianion-Nucleobase Clusters: Photoelectron Spectroscopy of the Platinum II Cyanide Dianion Bound to Uracil, Thymine, Cytosine and Adenine

    SciTech Connect

    Sen, Ananya; Hou, Gao-Lei; Wang, Xue B.; Dessent, Caroline

    2015-08-05

    We report the first low-temperature photodetachment photoelectron spectra of isolated gas-phase complexes of the platinum II cyanide dianion bound to nucleobases. These systems are model systems for understanding platinum-complex photodynamic therapies, and knowledge of the intrinsic photodetachment properties is crucial for understanding their broader photophysical properties. Well-resolved, distinct peaks are observed in the spectra consistent with the complexes where the Pt(CN)42- moiety is largely intact. The adiabatic electron detachment energies for the dianion-nucleobase complexes are measured to be between 2.39-2.46 eV. The magnitudes of the repulsive Coulomb barriers of the complexes are estimated to be between 1.9 and 2.1 eV, values that are lower than for the bare Pt(CN)42- dianion as a result of charge solvation by the nucleobases. In addition to the resolved spectral features, broad featureless bands indicative of delayed electron detachment are observed in the 193 nm photodetachment spectra of the four nucleobase-dianion complexes, and also in the 266 nm spectra of the Pt(CN)42-∙thymine and Pt(CN)42-∙adenine complexes. The selective excitation of these features in the 266 nm spectra is attributed to one-photon excitation of [Pt(CN)42-∙T]* and [Pt(CN)42-∙A]* long-lived excited states that can effectively couple to the electron detachment continuum, producing strong electron detachment signals. We attribute the resonant electron detachment bands observed here for Pt(CN)42-∙T and Pt(CN)42-∙A but not for Pt(CN)42-∙U and Pt(CN)42-∙C to fundamental differences in the individual nucleobase photophysics following 266 nm excitation. This indicates that the Pt(CN)42- dianion in the Pt(CN)42-∙M clusters can be viewed as a “dynamic tag” which has the propensity to emit electrons when the attached nucleobase disaplys a long-lived excited state.

  11. Zn(II)-Coordinated Quantum Dot-FRET Nanosensors for the Detection of Protein Kinase Activity

    PubMed Central

    Lim, Butaek; Park, Ji-In; Lee, Kyung Jin; Lee, Jin-Won; Kim, Tae-Wuk; Kim, Young-Pil

    2015-01-01

    We report a simple detection of protein kinase activity using Zn(II)-mediated fluorescent resonance energy transfer (FRET) between quantum dots (QDs) and dye-tethered peptides. With neither complex chemical ligands nor surface modification of QDs, Zn(II) was the only metal ion that enabled the phosphorylated peptides to be strongly attached on the carboxyl groups of the QD surface via metal coordination, thus leading to a significant FRET efficiency. As a result, protein kinase activity in intermixed solution was efficiently detected by QD-FRET via Zn(II) coordination, especially when the peptide substrate was combined with affinity-based purification. We also found that mono- and di-phosphorylation in the peptide substrate could be discriminated by the Zn(II)-mediated QD-FRET. Our approach is expected to find applications for studying physiological function and signal transduction with respect to protein kinase activity. PMID:26213934

  12. AAV Vectors for FRET-Based Analysis of Protein-Protein Interactions in Photoreceptor Outer Segments

    PubMed Central

    Becirovic, Elvir; Böhm, Sybille; Nguyen, Ong N. P.; Riedmayr, Lisa M.; Hammelmann, Verena; Schön, Christian; Butz, Elisabeth S.; Wahl-Schott, Christian; Biel, Martin; Michalakis, Stylianos

    2016-01-01

    Fluorescence resonance energy transfer (FRET) is a powerful method for the detection and quantification of stationary and dynamic protein-protein interactions. Technical limitations have hampered systematic in vivo FRET experiments to study protein-protein interactions in their native environment. Here, we describe a rapid and robust protocol that combines adeno-associated virus (AAV) vector-mediated in vivo delivery of genetically encoded FRET partners with ex vivo FRET measurements. The method was established on acutely isolated outer segments of murine rod and cone photoreceptors and relies on the high co-transduction efficiency of retinal photoreceptors by co-delivered AAV vectors. The procedure can be used for the systematic analysis of protein-protein interactions of wild type or mutant outer segment proteins in their native environment. Conclusively, our protocol can help to characterize the physiological and pathophysiological relevance of photoreceptor specific proteins and, in principle, should also be transferable to other cell types. PMID:27516733

  13. AAV Vectors for FRET-Based Analysis of Protein-Protein Interactions in Photoreceptor Outer Segments.

    PubMed

    Becirovic, Elvir; Böhm, Sybille; Nguyen, Ong N P; Riedmayr, Lisa M; Hammelmann, Verena; Schön, Christian; Butz, Elisabeth S; Wahl-Schott, Christian; Biel, Martin; Michalakis, Stylianos

    2016-01-01

    Fluorescence resonance energy transfer (FRET) is a powerful method for the detection and quantification of stationary and dynamic protein-protein interactions. Technical limitations have hampered systematic in vivo FRET experiments to study protein-protein interactions in their native environment. Here, we describe a rapid and robust protocol that combines adeno-associated virus (AAV) vector-mediated in vivo delivery of genetically encoded FRET partners with ex vivo FRET measurements. The method was established on acutely isolated outer segments of murine rod and cone photoreceptors and relies on the high co-transduction efficiency of retinal photoreceptors by co-delivered AAV vectors. The procedure can be used for the systematic analysis of protein-protein interactions of wild type or mutant outer segment proteins in their native environment. Conclusively, our protocol can help to characterize the physiological and pathophysiological relevance of photoreceptor specific proteins and, in principle, should also be transferable to other cell types. PMID:27516733

  14. Fretting wear in titanium, Monel-400, and cobalt 25-percent-molybdenum using scanning electron microscopy

    NASA Technical Reports Server (NTRS)

    Bill, R. C.

    1972-01-01

    Damage scar volume measurements taken from like metal fretting pairs combined with scanning electron microscopy observations showed that three sequentially operating mechanisms result in the fretting of titanium, Monel-400, and cobalt - 25-percent molybdenum. Initially, adhesion and plastic deformation of the surface played an important role. This was followed after a few hundred cycles by a fatigue mechanism which produced spall-like pits in the damage scar. Finally, a combination of oxidation and abrasion by debris particles became most significant. Damage scar measurements made on several elemental metals after 600,000 fretting cycles suggested that the ratio of oxide hardness to metal hardness was a measure of the susceptibility of a metal to progressive damage by fretting.

  15. A Two-Step Method for smFRET Data Analysis.

    PubMed

    Chen, Jixin; Pyle, Joseph R; Sy Piecco, Kurt Waldo; Kolomeisky, Anatoly B; Landes, Christy F

    2016-07-28

    We demonstrate a two-step data analysis method to increase the accuracy of single-molecule Förster Resonance Energy Transfer (smFRET) experiments. Most current smFRET studies are at a time resolution on the millisecond level. When the system also contains molecular dynamics on the millisecond level, simulations show that large errors are present (e.g., > 40%) because false state assignment becomes significant during data analysis. We introduce and confirm an additional step after normal smFRET data analysis that is able to reduce the error (e.g., < 10%). The idea is to use Monte Carlo simulation to search ideal smFRET trajectories and compare them to the experimental data. Using a mathematical model, we are able to find the matches between these two sets, and back guess the hidden rate constants in the experimental results. PMID:27379815

  16. Fretting Fatigue of Single Crystal/Polycrystalline Nickel Subjected to Blade/Disk Contact Loading

    NASA Astrophysics Data System (ADS)

    Matlik, J. F.; Murthy, H.; Farris, T. N.

    2002-01-01

    Fretting fatigue describes the formation and growth of cracks at the edge-of-contact of nominally clamped components subjected to cyclic loading. Components that are known to be subject to fretting fatigue include riveted lap joints and blade/disk contacts in launch vehicle turbomachinery. Recent efforts have shown that conventional mechanics tools, both fatigue and fracture based, can be used to model fretting fatigue experiments leading to successful life predictions. In particular, experiments involving contact load configurations similar to those that occur in the blade/disk connection of gas turbine engines have been performed extensively. Predictions of fretting fatigue life have been compared favorably to experimental observations [1]. Recent efforts are aimed at performing experiments at higher temperatures as shown in the photograph below along with a sample fracture surface. The talk will describe the status of these experiments as will as model developments relevant to the single crystal material properties.

  17. Quantitative study of fretting fatigue damage in shot peened titanium-aluminum-vanadium

    NASA Astrophysics Data System (ADS)

    Martinez, Sonia A.

    Fretting fatigue damage has been known to be the origin of premature failure in some of the aerospace engine components. The blade/disk assemblies, for example have been particularly susceptible to fretting induced failure. Several nondestructive evaluation techniques are being used to detect the cracks due to fretting fatigue damage. Although partial success has been achieved in detection of cracks, research is lacking in the area of detection of precursors to the development of cracks due fretting fatigue damage. The goal of the research presented in this thesis is to develop a methodology based on x-ray diffraction residual stress measurements for quantitative nondestructive characterization of accumulated fretting fatigue damage. To achieve the goal a systematic experimental study of the characteristics of the residual stress due to surface treatments of shot peening (SP), Laser Shock Peening (LSP) and Low Plasticity Burnishing (LPB), used in the aerospace industry was conducted. The residual stress in LSP and LPB was found to be complex involving shear stress and spatial non-uniformity. On the other hand in shot peening it was found to be least complex. More over it is the most cost effective and hence often used surface treatment in the industry. In order to gain an understanding of the effect of shot peening parameters on the fretting fatigue life, experiments were conducted on samples with four different peening intensities (0, 4, 7 and 10 A) and two surface coverage (100% and 400%). It was observed that the fretting fatigue life increases with the increasing peening intensity, and increase in surface coverage beyond 100% has virtually no effect. Scanning Electron Microscopic (SEM) observation of fractured surface was utilized to identify crack initiation. On all of the fretting fatigued specimens relaxation of residual stress was observed and it increased with increasing number of cycles. A complete relaxation was observed before failure. To obtain an

  18. Effect of Understress on Fretting Fatigue Crack Initiation of Press-Fitted Axle

    NASA Astrophysics Data System (ADS)

    Kubota, Masanobu; Niho, Sotaro; Sakae, Chu; Kondo, Yoshiyuki

    Axles are one of the most important components in railway vehicles with regard to safety, since a fail-safe design is not available. The problems of fretting fatigue crack initiation in a press-fitted axle have not been completely solved even though up-to-date fatigue design methods are employed. The objective of the present study is to clarify the effect of understress on fretting fatigue crack initiation behavior in the press-fitted axle. Most of the stress amplitude given to the axle in service is smaller than the fretting fatigue limit based on the stress to initiate cracks under a constant load σwf1. Rotating bending fatigue tests were performed using a 40mm-diameter press-fitted axle assembly. Two-step variable stresses consisting of σwf1 and half or one-third of σwf1 were used in the experiment. Crack initiation life was defined as the number of cycles when a fretting fatigue crack, which is longer than 30µm, was found using a metallurgical microscope. Fretting fatigue cracks were initiated even when the variable stress did not contain the stress above the fretting fatigue crack initiation limit. The crack initiation life varied from 4.0×107 to 1.2×108 depending on the stress frequency ratio nL/nH. The sum of the number of cycles of higher stress at crack initiation NH was much smaller than the number of cycles to initiate cracks estimated from the modified Miner's rule. The value of the modified Miner's damage ranged from 0.013 to 0.185. To clarify the effect of variable amplitude on the fretting fatigue crack initiation, a comprehensive investigation related to relative slip, tangential force and fretting wear is necessary.

  19. Ultrafast FRET in a room temperature ionic liquid microemulsion: a femtosecond excitation wavelength dependence study.

    PubMed

    Adhikari, Aniruddha; Das, Dibyendu Kumar; Sasmal, Dibyendu Kumar; Bhattacharyya, Kankan

    2009-04-23

    Fluorescence resonance energy transfer (FRET) from coumarin 480 (C480) to rhodamine 6G (R6G) is studied in a room temperature ionic liquid (RTIL) microemulsion by picosecond and femtosecond emission spectroscopy. The microemulsion is comprised of the RTIL 1-pentyl-3-methylimidazolium tetraflouroborate, [pmim][BF4], in TX-100/ benzene. We have studied the microemulsion with and without water. The time constants of FRET were obtained from the risetime of the acceptor (R6G) emission. In the RTIL microemulsion, FRET occurs on multiple time scales: 1, 250, and 3900 ps. In water containing RTIL microemulsion, the rise components are 1.5, 250, and 3900 ps. The 1 and 1.5 ps components are assigned to FRET at a close contact of donor and acceptor (RDA approximately 12 A). This occurs within the highly polar (RTIL/water) pool of the microemulsion. With increase in the excitation wavelength (lambdaex) from 375 to 435 nm, the relative contribution of the ultrafast component of FRET (1 ps) increases from 4% to 100% in the RTIL microemulsion and 12% to 100% in the water containing RTIL microemulsion. It is suggested that at lambdaex = 435 nm, mainly the highly polar RTIL pool is probed where FRET is very fast due to the close proximity of the donor and the acceptor. The very long 3900 ps (RDA approximately 45 A) component may arise from FRET from a donor in the outer periphery of the microemulsion to an acceptor in the polar RTIL pool. The 250 ps component (RDA approximately 29 A) is assigned to FRET from a donor inside the surfactant chains. PMID:19127996

  20. Versatile FRET-Based Mesoporous Silica Nanoparticles for Real-Time Monitoring of Drug Release

    PubMed Central

    Lai, Jinping; Shah, Birju P.; Garfunkel, Eric; Lee, Ki-Bum

    2013-01-01

    We describe the development of a versatile fluorescence resonance energy transfer (FRET)-based real-time monitoring system, consisting of (a) coumarin-labeled-cysteine tethered mesoporous silica nanoparticles (MSNs) as the drug carrier, (b) a fluorescein isothiocyanate-β-cyclodextrin (FITC-β-CD) as redox-responsive molecular valve blocking the pores, and (c) a FRET donor-acceptor pair of coumarin and FITC integrated within the pore-unlocking event, thereby allowing for monitoring the release of drugs from the pores in real-time. Under non-reducing conditions, when the disulfide bond is intact, the close proximity between coumarin and FITC on the surface of MSNs results in FRET from coumarin to FITC. However, in the presence of the redox stimuli like glutathione (GSH), the disulfide bond is cleaved which leads to the removal of molecular valve (FITC-β-CD), thus triggering drug release and eliminating FRET. By engineering such a FRET-active donor-acceptor structure within the redox-responsive molecular valve, we can monitor the release of the drugs entrapped within the pores of the MSN nanocarrier, following the change in the FRET signal. We have demonstrated that, any exogenous or endogenous change in the GSH concentration will result in a change in the extent of drug release as well as a concurrent change in the FRET signal, allowing us to extend the applications of our FRET-based MSNs for monitoring the release of any type of drug molecule in real-time. PMID:23445171

  1. Synthesis and Properties of a Novel FRET-Based Ratiometric Fluorescent Sensor for Cu(2.).

    PubMed

    Li, Shao; Zhang, Di; Wang, Min; Ma, Saige; Liu, Jihong; Zhao, Yufen; Ye, Yong

    2016-05-01

    A novel FRET-based probe LS3 was designed and synthesized. As expected, it exhibited high selectivity and sensitivity for detecting Cu(2+) over other commonly coexistent metal ions. The detection limit was measured to be 0.0423 μM for Cu(2+), which can meet the selective requirements for practical application. In addition, the newly synthesized compound 3a/b have potential value of further synthesizing more analogous FRET-based probes. PMID:26781110

  2. A Sensitized Emission Based Calibration of FRET Efficiency for Probing the Architecture of Macromolecular Machines.

    PubMed

    Joglekar, Ajit; Chen, Renjie; Lawrimore, Joshua

    2013-01-01

    Macromolecular machines participate in almost every cell biological function. These machines can take the form of well-defined protein structures such as the kinetochore, or more loosely organized protein assemblies like the endocytic coat. The protein architecture of these machines-the arrangement of multiple copies of protein subunits at the nanoscale, is necessary for understanding their cell biological function and biophysical mechanism. Defining this architecture in vivo presents a major challenge. High density of protein molecules within macromolecular machines severely limits the effectiveness of super-resolution microscopy. However, this density is ideal for Forster Resonance Energy Transfer (FRET), which can determine the proximity between neighboring molecules. Here, we present a simple FRET quantitation scheme that calibrates a standard epifluorescence microscope for measuring donor-acceptor separations. This calibration can be used to deduce FRET efficiency fluorescence intensity measurements. This method will allow accurate determination of FRET efficiency over a wide range of values and FRET pair number. It will also allow dynamic FRET measurements with high spatiotemporal resolution under cell biological conditions. Although the poor maturation efficiency of genetically encoded fluorescent proteins presents a challenge, we show that its effects can be alleviated. To demonstrate this methodology, we probe the in vivo architecture of the γ-Tubulin Ring. Our technique can be applied to study the architecture and dynamics of a wide range of macromolecular machines. PMID:24319499

  3. Flow Cytometry Enables Multiplexed Measurements of Genetically Encoded Intramolecular FRET Sensors Suitable for Screening.

    PubMed

    Doucette, Jaimee; Zhao, Ziyan; Geyer, Rory J; Barra, Melanie M; Balunas, Marcy J; Zweifach, Adam

    2016-07-01

    Genetically encoded sensors based on intramolecular FRET between CFP and YFP are used extensively in cell biology research. Flow cytometry has been shown to offer a means to measure CFP-YFP FRET; we suspected it would provide a unique way to conduct multiplexed measurements from cells expressing different FRET sensors, which is difficult to do with microscopy, and that this could be used for screening. We confirmed that flow cytometry accurately measures FRET signals using cells transiently transfected with an ERK activity reporter, comparing responses measured with imaging and cytometry. We created polyclonal long-term transfectant lines, each expressing a different intramolecular FRET sensor, and devised a way to bar-code four distinct populations of cells. We demonstrated the feasibility of multiplexed measurements and determined that robust multiplexed measurements can be conducted in plate format. To validate the suitability of the method for screening, we measured responses from a plate of bacterial extracts that in unrelated experiments we had determined contained the protein kinase C (PKC)-activating compound teleocidin A-1. The multiplexed assay correctly identifying the teleocidin A-1-containing well. We propose that multiplexed cytometric FRET measurements will be useful for analyzing cellular function and for screening compound collections. PMID:26908592

  4. SNP Detection in mRNA in Living Cells Using Allele Specific FRET Probes

    PubMed Central

    Dahan, Liya; Huang, Lingyan; Kedmi, Ranit; Behlke, Mark A.; Peer, Dan

    2013-01-01

    Live mRNA detection allows real time monitoring of specific transcripts and genetic alterations. The main challenge of live genetic detection is overcoming the high background generated by unbound probes and reaching high level of specificity with minimal off target effects. The use of Fluorescence Resonance Energy Transfer (FRET) probes allows differentiation between bound and unbound probes thus decreasing background. Probe specificity can be optimized by adjusting the length and through use of chemical modifications that alter binding affinity. Herein, we report the use of two oligonucleotide FRET probe system to detect a single nucleotide polymorphism (SNP) in murine Hras mRNA, which is associated with malignant transformations. The FRET oligonucleotides were modified with phosphorothioate (PS) bonds, 2′OMe RNA and LNA residues to enhance nuclease stability and improve SNP discrimination. Our results show that a point mutation in Hras can be detected in endogenous RNA of living cells. As determined by an Acceptor Photobleaching method, FRET levels were higher in cells transfected with perfect match FRET probes whereas a single mismatch showed decreased FRET signal. This approach promotes in vivo molecular imaging methods and could further be applied in cancer diagnosis and theranostic strategies. PMID:24039756

  5. Recent developments in Förster resonance energy transfer (FRET) diagnostics using quantum dots.

    PubMed

    Geißler, Daniel; Hildebrandt, Niko

    2016-07-01

    The exceptional photophysical properties and the nanometric dimensions of colloidal semiconductor quantum dots (QD) have strongly attracted the bioanalytical community over the last approximately 20 y. In particular, the integration of QDs in the analysis of biological components and interactions, and the related diagnostics using Förster resonance energy transfer (FRET), have allowed researchers to significantly improve and diversify fluorescence-based biosensing. In this TRENDS article, we review some recent developments in QD-FRET biosensing that have implemented this technology in electronic consumer products, multiplexed analysis, and detection without light excitation for diagnostic applications. In selected examples of smartphone-based imaging, single- and multistep FRET, steady-state and time-resolved spectroscopy, and bio/chemiluminescence detection of QDs used as both FRET donors and acceptors, we highlight the advantages of QD-based FRET biosensing for multiplexed and sensitive diagnostics. Graphical Abstract Quantum dots (QDs) can be applied as donors and/or acceptors for Förster resonance energy transfer- (FRET-) based biosensing for multiplexed and sensitive diagnostics in various assay formats. PMID:26970745

  6. A simple, rapid and sensitive FRET assay for botulinum neurotoxin serotype B detection.

    PubMed

    Guo, Jiubiao; Xu, Ci; Li, Xuechen; Chen, Sheng

    2014-01-01

    Botulinum neurotoxins (BoNTs), the most potent naturally-occurring neurotoxins known to humans, comprise seven distinct serotypes (BoNT/A-G), each of which exhibits unique substrate specificity. Many methods have been developed for BoNT detection, in particular for BoNT/A, with various complexity and sensitivity, while substrate based FRET assay is considered as the most widely used approach due to its simplicity and sensitivity. In this study, we designed a vesicle-associated membrane protein 2 (VAMP2) based FRET assay based on the understanding of the VAMP2 and light chain/B (LC/B) interactions in our previous studies. The current design constituted the shortest peptide, VAMP2 (63-85), with FRET dyes (EDAN and Dabcyl) labelled at position 76 and 85, respectively, which showed minimal effect on VAMP2 substrate catalysis by LC/B and therefore enhanced the sensitivity of the assay. The FRET peptide, designated as FVP-B, was specific to LC/B, with a detection sensitivity as low as ∼20 pM in 2 h. Importantly, FVP-B showed the potential to be scaled up and used in high throughput screening of LC/B inhibitor. The currently developed FRET assay is one of the most economic and rapid FRET assays for LC/B detection. PMID:25437190

  7. Design, synthesis, in silico and in vitro screening of 1,2,4-thiadiazole analogues as non-peptide inhibitors of beta-secretase.

    PubMed

    Gurjar, Archana S; Andrisano, Vincenza; Simone, Angela D; Velingkar, Vinay S

    2014-12-01

    Beta-secretase is the key enzyme involved in Alzheimer's disease thus; inhibition of the enzyme can lead to a potential anti-Alzheimer drug. In the search of an effective lead candidate, we have designed non-peptide inhibitor molecules based on amino aromatic heterocyclic motifs specifically, substituted 1,2,4-thiadiazole analogues. In silico modelling was employed to study interaction of the designed ligands in the enzyme active site using molecular docking approach as well as for Absorption, Distribution, Metabolism and Excretion studies. The synthesized analogues were pharmacologically screened using in vitro FRET technique. Overall results indicate that one of the analogues, compound 8 is the most promising one against beta secretase. PMID:25303313

  8. “Molecular trinity” for soft nanomaterials: Integrating nucleobases, amino acids, and glycosides to construct multifunctional hydrogelators

    PubMed Central

    Li, Xinming; Kuang, Yi

    2013-01-01

    This highlight introduces the development of hydrogelators consisting of nucleobases, amino acids, and glycosides (i.e., molecular trinity), or nucleobases and amino acids (i.e., nucleopeptides). These novel small molecule hydrogelators self-assemble in water to form stable supramolecular nanofibers/hydrogels and exhibit useful biological properties (e.g., biocompatibility, biostability, and the ability to bind and transport DNA into live cells). The approach discussed here not only provides a new strategy to develop soft biomaterials as a form of nanomedicines, but also contributes to the understanding of molecular self-assembly in water by modulating the non-covalent interactions derived from the three basic building blocks used in living organisms. PMID:24368929

  9. 2',4'-BNA bearing a 2-pyridine nucleobase for CG base pair recognition in the parallel motif triplex DNA.

    PubMed

    Hari, Yoshiyuki; Matsugu, Sachiko; Inohara, Hiroyasu; Hatanaka, Yuri; Akabane, Masaaki; Imanishi, Takeshi; Obika, Satoshi

    2010-09-21

    We succeeded in the synthesis of triplex-forming oligonucleotides (TFOs) that contain a deoxyribonucleotide (Py) bearing a 2-pyridine nucleobase or the 2',4'-BNA congener (Py(B)). By UV melting experiments, it was found that 2-pyridine was a very promising nucleobase for the sequence-selective recognition of a CG base pair within double-stranded DNA (dsDNA) in a parallel motif triplex. Moreover, Py(B) in TFOs showed stronger affinity to a CG base pair than Py with further increase in the selectivity. Using TFO including multiple Py(B) units, triplex formation with dsDNA containing three CG base pairs was observed. PMID:20648389

  10. Formation of Nucleobases from Formamide in the Presence of Iron Oxides: Implication in Chemical Evolution and Origin of Life

    NASA Astrophysics Data System (ADS)

    Shanker, Uma; Bhushan, Brij; Bhattacharjee, G.; Kamaluddin

    2011-04-01

    Simple compounds like HCN, which have one C and one N, are proposed as the probable precursors for biomonomers. Formamide, a hydrolysis product of HCN, is known as the precursor of various biologically important compounds, for example, nucleobases (purines and pyrimidines). In this paper, we report our results on the synthesis of nucleobases, adenine, cytosine, purine, 9-(hydroxyacetyl) purine, and 4(3H)-pyrimidinone from formamide, using iron oxide (hematite) and oxide hydroxides (goethite and akaganeite) as a catalyst. Goethite and hematite produced purine in higher yield. The products formed were characterized by high-performance liquid chromatography and electrospray ionization mass spectrometry techniques. Results of our study reveal that iron oxides might have worked as efficient prebiotic catalysts.

  11. A Search for Amino Acids and Nucleobases in the Martian Meteorite Roberts Massif 04262 Using Liquid Chromatography-Mass Spectrometry

    NASA Technical Reports Server (NTRS)

    Callahan, Michael P.; Burton, Aaron S.; Elsila, Jamie E.; Baker, Eleni M.; Smith, Karen E.; Glavin, Daniel P.; Dworkin, Jason P.

    2013-01-01

    The investigation into whether Mars contains signatures of past or present life is of great interest to science and society. Amino acids and nucleobases are compounds that are essential for all known life on Earth and are excellent target molecules in the search for potential Martian biomarkers or prebiotic chemistry. Martian meteorites represent the only samples from Mars that can be studied directly in the laboratory on Earth. Here, we analyzed the amino acid and nucleobase content of the shergottite Roberts Massif (RBT) 04262 using liquid chromatography-mass spectrometry. We did not detect any nucleobases above our detection limit in formic acid extracts; however, we did measure a suite of protein and nonprotein amino acids in hot-water extracts with high relative abundances of beta-alanine and gamma-amino-eta-butyric acid. The presence of only low (to absent) levels of several proteinogenic amino acids and a lack of nucleobases suggest that this meteorite fragment is fairly uncontaminated with respect to these common biological compounds. The distribution of straight-chained amine-terminal eta-omega-amino acids in RBT 04262 resembled those previously measured in thermally altered carbonaceous meteorites. A carbon isotope ratio of -24(0/00) +/- 6(0/00) for beta-alanine in RBT 04262 is in the range of reduced organic carbon previously measured in Martian meteorites (Steele et al. 2012). The presence of eta-omega-amino acids may be due to a high temperature Fischer-Tropschtype synthesis during igneous processing on Mars or impact ejection of the meteorites from Mars, but more experimental data are needed to support these hypotheses.

  12. A search for amino acids and nucleobases in the Martian meteorite Roberts Massif 04262 using liquid chromatography-mass spectrometry

    NASA Astrophysics Data System (ADS)

    Callahan, Michael P.; Burton, Aaron S.; Elsila, Jamie E.; Baker, Eleni M.; Smith, Karen E.; Glavin, Daniel P.; Dworkin, Jason P.

    2013-05-01

    The investigation into whether Mars contains signatures of past or present life is of great interest to science and society. Amino acids and nucleobases are compounds that are essential for all known life on Earth and are excellent target molecules in the search for potential Martian biomarkers or prebiotic chemistry. Martian meteorites represent the only samples from Mars that can be studied directly in the laboratory on Earth. Here, we analyzed the amino acid and nucleobase content of the shergottite Roberts Massif (RBT) 04262 using liquid chromatography-mass spectrometry. We did not detect any nucleobases above our detection limit in formic acid extracts; however, we did measure a suite of protein and nonprotein amino acids in hot-water extracts with high relative abundances of β-alanine and γ-amino-n-butyric acid. The presence of only low (to absent) levels of several proteinogenic amino acids and a lack of nucleobases suggest that this meteorite fragment is fairly uncontaminated with respect to these common biological compounds. The distribution of straight-chained amine-terminal n-ω-amino acids in RBT 04262 resembled those previously measured in thermally altered carbonaceous meteorites (Burton et al. 2012; Chan et al. 2012). A carbon isotope ratio of -24‰ ± 6‰ for β-alanine in RBT 04262 is in the range of reduced organic carbon previously measured in Martian meteorites (Steele et al. 2012). The presence of n-ω-amino acids may be due to a high temperature Fischer-Tropsch-type synthesis during igneous processing on Mars or impact ejection of the meteorites from Mars, but more experimental data are needed to support these hypotheses.

  13. Three-Dimensional Reconstruction of Three-Way FRET Microscopy Improves Imaging of Multiple Protein-Protein Interactions

    PubMed Central

    Scott, Brandon L.; Hoppe, Adam D.

    2016-01-01

    Fluorescence resonance energy transfer (FRET) microscopy is a powerful tool for imaging the interactions between fluorescently tagged proteins in two-dimensions. For FRET microscopy to reach its full potential, it must be able to image more than one pair of interacting molecules and image degradation from out-of-focus light must be reduced. Here we extend our previous work on the application of maximum likelihood methods to the 3-dimensional reconstruction of 3-way FRET interactions within cells. We validated the new method (3D-3Way FRET) by simulation and fluorescent protein test constructs expressed in cells. In addition, we improved the computational methods to create a 2-log reduction in computation time over our previous method (3DFSR). We applied 3D-3Way FRET to image the 3D subcellular distributions of HIV Gag assembly. Gag fused to three different FPs (CFP, YFP, and RFP), assembled into viral-like particles and created punctate FRET signals that become visible on the cell surface when 3D-3Way FRET was applied to the data. Control experiments in which YFP-Gag, RFP-Gag and free CFP were expressed, demonstrated localized FRET between YFP and RFP at sites of viral assembly that were not associated with CFP. 3D-3Way FRET provides the first approach for quantifying multiple FRET interactions while improving the 3D resolution of FRET microscopy data without introducing bias into the reconstructed estimates. This method should allow improvement of widefield, confocal and superresolution FRET microscopy data. PMID:27023704

  14. The effects of fretting on fatigue characteristics of a mechanically fastened aircraft joint

    NASA Astrophysics Data System (ADS)

    Shah, Akbar Hussain

    A research study to investigate the effects of fretting on fatigue characteristics of an aircraft joint was carried out. The selected joint for this study simulates the rotor head of an aircraft capable of taking off vertically. The primary function of this hub-spindle joint is to retain the main rotor blade against the centrifugal forces, both in-plane and out-of-plane bending moments and torsion caused due to the lift, drag and other aerodynamic forces imposed on the rotor blades while the aircraft is in forward flight. The primary objectives of this study were twofold; (a) Verify that the average lives of mechanically fastened joints with combined effects of fretting and fatigue will be lower compared to the average lives due to plain fatigue. (b) Discover whether fretting causes cracks to nucleate and fatigue causes those cracks to propagate. In order to verify the validity of the first hypothesis, seven test joints were tested to failure. Several S/N curves were generated against Mil-Handbook 5H data for comparable plain fatigue response of the same material. Out of the seven specimens that were tested, five were machined from Aluminum 7075-T6, and the other two were machined from Aluminum 7050-T7451. An average fretting fatigue life reduction factor Kff, of 21 was found for all these seven joints. In order to validate the second hypothesis, a detailed investigation under a scanning electron microscope of the fretted/failed surfaces was conducted. Severe fretting damage was observed in all test specimens. It was found that fretting-induced damage provided the crack nucleation sites in all test specimens that failed. These nucleation sites were in the form of fretting scars, pits and gouges providing several regions of stress concentration. Under the influence of high tensile stress fields, these sites allowed several small embryonic cracks to form, coalesce and link up to form primary and multiple cracks, which subsequently propagated under the applied cyclic

  15. Determination of DNA adducts by combining acid-catalyzed hydrolysis and chromatographic analysis of the carcinogen-modified nucleobases.

    PubMed

    Leung, Elvis M K; Deng, Kailin; Wong, Tin-Yan; Chan, Wan

    2016-01-01

    The commonly used method of analyzing carcinogen-induced DNA adducts involves the hydrolysis of carcinogen-modified DNA samples by using a mixture of enzymes, followed by (32)P-postlabeling or liquid chromatography (LC)-based analyses of carcinogen-modified mononucleotides/nucleosides. In the present study, we report the development and application of a new approach to DNA adduct analysis by combining the H(+)/heat-catalyzed release of carcinogen-modified nucleobases and the use of LC-based methods to analyze DNA adducts. Results showed that heating the carcinogen-modified DNA samples at 70 °C for an extended period of 4 to 6 h in the presence of 0.05% HCl can efficiently induce DNA depurination, releasing the intact carcinogen-modified nucleobases for LC analyses. After optimizing the hydrolysis conditions, DNA samples with C8- and N (2) -modified 2'-deoxyguanosine, as well as N (6) -modified 2'-deoxyadenosine, were synthesized by reacting DNA with 1-nitropyrene, acetaldehyde, and aristolochic acids, respectively. These samples were then hydrolyzed, and the released nucleobase adducts were analyzed using LC-based analytical methods. Analysis results demonstrated a dose-dependent release of target DNA adducts from carcinogen-modified DNA samples, indicating that the developed H(+)/heat-catalyzed hydrolysis method was quantitative. Comparative studies with enzymatic digestion method on carcinogen-modified DNA samples revealed that the two hydrolysis methods did not yield systematically different results. PMID:26581621

  16. FUN26 (function unknown now 26) protein from saccharomyces cerevisiae is a broad selectivity, high affinity, nucleoside and nucleobase transporter.

    PubMed

    Boswell-Casteel, Rebba C; Johnson, Jennifer M; Duggan, Kelli D; Roe-Žurž, Zygy; Schmitz, Hannah; Burleson, Carter; Hays, Franklin A

    2014-08-29

    Equilibrative nucleoside transporters (ENTs) are polytopic integral membrane proteins that transport nucleosides and, to a lesser extent, nucleobases across cell membranes. ENTs modulate efficacy for a range of human therapeutics and function in a diffusion-controlled bidirectional manner. A detailed understanding of ENT function at the molecular level has remained elusive. FUN26 (function unknown now 26) is a putative ENT homolog from S. cerevisiae that is expressed in vacuole membranes. In the present system, proteoliposome studies of purified FUN26 demonstrate robust nucleoside and nucleobase uptake into the luminal volume for a broad range of substrates. This transport activity is sensitive to nucleoside modifications in the C(2')- and C(5')-positions on the ribose sugar and is not stimulated by a membrane pH differential. [(3)H]Adenine nucleobase transport efficiency is increased ∼4-fold relative to nucleosides tested with no observed [(3)H]adenosine or [(3)H]UTP transport. FUN26 mutational studies identified residues that disrupt (G463A or G216A) or modulate (F249I or L390A) transporter function. These results demonstrate that FUN26 has a unique substrate transport profile relative to known ENT family members and that a purified ENT can be reconstituted in proteoliposomes for functional characterization in a defined system. PMID:25035431

  17. FUN26 (Function Unknown Now 26) Protein from Saccharomyces cerevisiae Is a Broad Selectivity, High Affinity, Nucleoside and Nucleobase Transporter*

    PubMed Central

    Boswell-Casteel, Rebba C.; Johnson, Jennifer M.; Duggan, Kelli D.; Roe-Žurž, Zygy; Schmitz, Hannah; Burleson, Carter; Hays, Franklin A.

    2014-01-01

    Equilibrative nucleoside transporters (ENTs) are polytopic integral membrane proteins that transport nucleosides and, to a lesser extent, nucleobases across cell membranes. ENTs modulate efficacy for a range of human therapeutics and function in a diffusion-controlled bidirectional manner. A detailed understanding of ENT function at the molecular level has remained elusive. FUN26 (function unknown now 26) is a putative ENT homolog from S. cerevisiae that is expressed in vacuole membranes. In the present system, proteoliposome studies of purified FUN26 demonstrate robust nucleoside and nucleobase uptake into the luminal volume for a broad range of substrates. This transport activity is sensitive to nucleoside modifications in the C(2′)- and C(5′)-positions on the ribose sugar and is not stimulated by a membrane pH differential. [3H]Adenine nucleobase transport efficiency is increased ∼4-fold relative to nucleosides tested with no observed [3H]adenosine or [3H]UTP transport. FUN26 mutational studies identified residues that disrupt (G463A or G216A) or modulate (F249I or L390A) transporter function. These results demonstrate that FUN26 has a unique substrate transport profile relative to known ENT family members and that a purified ENT can be reconstituted in proteoliposomes for functional characterization in a defined system. PMID:25035431

  18. Formamide-based synthesis of nucleobases by metal(II) octacyanomolybdate(IV): implication in prebiotic chemistry.

    PubMed

    Kumar, Anand; Sharma, Rachana; Kamaluddin

    2014-09-01

    We propose that double metal cyanides that formed in primeval seas might have played a vital role in chemical evolution and the origin of life. An array of metal octacyanomolybdates (MOCMos) has been synthesized, and their role as catalyst in the formation of nucleobases from formamide has been studied. Formamide, a hydrolysis product of HCN, was taken as starting material for the formation of nucleobases. Recent studies support the presence of formamide on some celestial bodies. Metal octacyanomolybdates, MOCMos (M = Mn, Fe, Co, Ni, Cu, Zn, Cd), are found to be highly efficient catalysts in the conversion of formamide into different nucleobases. Neat formamide is converted to purine, 4(3H)-pyrimidinone, cytosine, adenine, 9-(hydroxyacetyl)-purine, and thymine in good yield when using MOCMos. The products formed were characterized by high-performance liquid chromatography and electrospray ionization mass spectrometry techniques. The results of our study show that insoluble double metal cyanides might have acted as efficient catalysts in the synthesis of various biologically important compounds (e.g., purines, pyrimidines) under primeval seas on Earth or elsewhere in our solar system. PMID:25192494

  19. Inhibition of Mycoplasma pneumoniae growth by FDA-approved anticancer and antiviral nucleoside and nucleobase analogs

    PubMed Central

    2013-01-01

    Background Mycoplasma pneumoniae (Mpn) is a human pathogen that causes acute and chronic respiratory diseases and has been linked to many extrapulmonary diseases. Due to the lack of cell wall, Mpn is resistant to antibiotics targeting cell wall synthesis such as penicillin. During the last 10 years macrolide-resistant Mpn strains have been frequently reported in Asian countries and have been spreading to Europe and the United States. Therefore, new antibiotics are needed. In this study, 30 FDA-approved anticancer or antiviral drugs were screened for inhibitory effects on Mpn growth and selected analogs were further characterized by inhibition of target enzymes and metabolism of radiolabeled substrates. Results Sixteen drugs showed varying inhibitory effects and seven showed strong inhibition of Mpn growth. The anticancer drug 6-thioguanine had a MIC (minimum inhibitory concentration required to cause 90% of growth inhibition) value of 0.20 μg ml-1, whereas trifluorothymidine, gemcitabine and dipyridamole had MIC values of approximately 2 μg ml-1. In wild type Mpn culture the presence of 6-thioguanine and dipyridamole strongly inhibited the uptake and metabolism of hypoxanthine and guanine while gemcitabine inhibited the uptake and metabolism of all nucleobases and thymidine. Trifluorothymidine and 5-fluorodeoxyuridine, however, stimulated the uptake and incorporation of radiolabeled thymidine and this stimulation was due to induction of thymidine kinase activity. Furthermore, Mpn hypoxanthine guanine phosphoribosyl transferase (HPRT) was cloned, expressed, and characterized. The 6-thioguanine, but not other purine analogs, strongly inhibited HPRT, which may in part explain the observed growth inhibition. Trifluorothymidine and 5-fluorodeoxyuridine were shown to be good substrates and inhibitors for thymidine kinase from human and Mycoplasma sources. Conclusion We have shown that several anticancer and antiviral nucleoside and nucleobase analogs are potent

  20. Optochemical Control of Deoxyoligonucleotide Function Via a Nucleobase-Caging Approach

    PubMed Central

    Liu, Qingyang

    2013-01-01

    Conspectus Synthetic oligonucleotides have been extensively applied to control a wide range of biological processes such as gene expression, gene repair, DNA replication, and protein activity. Based on well-established sequence design rules that typically rely on Watson-Crick base pairing interactions researchers can readily program the function of these oligonucleotides. Therefore oligonucleotides provide a flexible platform for targeting a wide range of biological molecules, including DNA, RNA, and proteins. In addition, oligonucleotides are commonly used research tools in cell biology and developmental biology. However, a lack of conditional control methods has hampered the precise spatial and temporal regulation of oligonucleotide activity, which limits the application of these reagents to investigate complex biological questions. Nature controls biological function with a high level of spatial and temporal resolution and in order to elucidate the molecular mechanism of biological processes, researchers need tools that allow for the perturbation of these processes with Nature's precision. Light represents an excellent external regulatory element as irradiation can be easily controlled spatially and temporally. Thus, researchers have developed several different methods to conditionally control oligonucleotide activity with light. One of the most versatile strategies is optochemical regulation through the installation and removal of photo-labile caging groups on oligonucleotides. To produce switches that can control nucleic acid function with light, chemists introduce caging groups into the oligomer backbone or on specific nucleobases to block oligonucleotide function until the caging groups are removed by light exposure. In this Account, we focus on the application of caged nucleobases to the photo-regulation of DNA function. Using this approach we have both optochemically activated and deactivated gene expression at the transcriptional and translational level

  1. Vertical Ionization Potentials of Nucleobases in a Fully Solvated DNA Environment

    SciTech Connect

    Cauet, Emilie L.; Valiev, Marat; Weare, John H.

    2010-05-06

    Calculations of the direct ionization potentials (DIP) of DNA nucleobases in the fully solvated DNA helix are reported. The results show an unexpected large shift of roughly 3.2-3.3 eV compared to the corresponding gas-phase IP values. The DIP shift is nearly the same for all the four DNA bases and appears to vary slowly with the stacking and H-bonding interactions of the nucleobases. We demonstrate that the large shift in the DIP of bases is due to the electric potential around the DNA resulting from the long range solvent structure created by the negative phosphate groups and positive counterions of the DNA helical structure. Thermal fluctuations in the fluid can result in DIP changes of roughly 1ev on a picosecond time scale. The model used in this work is based on a QM/MM approach in which the base (or clusters of bases) are chosen as the QM system and calculated using a high-level quantum chemistry method. The remaining DNA fragment and the species in solution are included in an exact molecular mechanics (MM) model. The expected high accuracy of the QM/MM model is defended in terms of the essentially Columbic nature of the interactions of the solvent (the MM region) with isolated base in the quantum region. For the test anion, Cl-, the QM/MM approach yields the 3.4 eV (gas-phase) to 9.3 eV (aqueous solution) shift of the ionization energy in agreement with experimental values (3.6 and 9.6 eV). The localization of the electronic excitation inside the QM region is supported by current experimental and theoretical evidence indicating that the HOMO of the nucleotide is localized on the base rather than the sugar or the phosphate backbone. Our calculations performed in the native DNA environment support this localization. The QM/MM model presented in this work provides an important simplification to the difficult problem of incorporating a detailed structural model of the physiological conditions into investigations of the electronic processes in DNA.

  2. Environment influences on the aromatic character of nucleobases and amino acids

    PubMed Central

    Szefler, Beata

    2010-01-01

    Geometric (HOMA) and magnetic (NICS) indices of aromaticity were estimated for aromatic rings of amino acids and nucleobases. Cartesian coordinates were taken directly either from PDB files deposited in public databases at the finest resolution available (≤1.5 Å), or from structures resulting from full gradient geometry optimization in a hybrid QM/MM approach. Significant environmental effects imposing alterations of HOMA values were noted for all aromatic rings analysed. Furthermore, even extra fine resolution (≤1.0 Å) is not sufficient for direct estimation of HOMA values based on Cartesian coordinates provided by PDB files. The values of mean bond errors seem to be much higher than the 0.05 Å often reported for PDB files. The use of quantum chemistry geometry optimization is strongly advised; even a simple QM/MM model comprising only the aromatic substructure within the QM region and the rest of biomolecule treated classically within the MM framework proved to be a promising means of describing aromaticity inside native environments. According to the results presented, three consequences of the interaction with the environment can be observed that induce changes in structural and magnetic indices of aromaticity. First, broad ranges of HOMA or NICS values are usually obtained for different conformations of nearest neighborhood. Next, these values and their means can differ significantly from those characterising isolated monomers. The most significant increase in aromaticities is expected for the six-membered rings of guanine, thymine and cytosine. The same trend was also noticed for all amino acids inside proteins but this effect was much smaller, reaching the highest value for the five-membered ring of tryptophan. Explicit water solutions impose similar changes on HOMA and NICS distributions. Thus, environment effects of protein, DNA and even explicit water molecules are non-negligible sources of aromaticity changes appearing in the rings of

  3. Nucleosome immobilization strategies for single-pair FRET microscopy.

    PubMed

    Koopmans, Wiepke J A; Schmidt, Thomas; van Noort, John

    2008-10-01

    All genomic transactions in eukaryotes take place in the context of the nucleosome, the basic unit of chromatin, which is responsible for DNA compaction. Overcoming the steric hindrance that nucleosomes present for DNA-processing enzymes requires significant conformational changes. The dynamics of these have been hard to resolve. Single-pair Fluorescence Resonance Energy Transfer (spFRET) microscopy is a powerful technique for observing conformational dynamics of the nucleosome. Nucleosome immobilization allows the extension of observation times to a limit set only by photobleaching, and thus opens the possibility of studying processes occurring on timescales ranging from milliseconds to minutes. It is crucial however, that immobilization itself does not introduce artifacts in the dynamics. Here we report on various nucleosome immobilization strategies, such as single-point attachment to polyethylene glycol (PEG) or surfaces coated with bovine serum albumin (BSA), and confinement in porous agarose or polyacrylamide gels. We compare the immobilization specificity and structural integrity of immobilized nucleosomes. A crosslinked star polyethylene glycol coating performs best with respect to tethering specificity and nucleosome integrity, and enables us to reproduce for the first time bulk nucleosome unwrapping kinetics in single nucleosomes without immobilization artifacts. PMID:18792054

  4. FRET-Assisted Determination of CLN3 Membrane Topology

    PubMed Central

    Ramos-Moreno, Juliana; Ruonala, Mika O.

    2014-01-01

    Juvenile neuronal ceroid lipofuscinosis (JNCL) is caused by mutations in the CLN3 gene, which encodes for a putative lysosomal transmembrane protein with thus far undescribed structure and function. Here we investigate the membrane topology of human CLN3 protein with a combination of advanced molecular cloning, spectroscopy, and in silico computation. Using the transposomics cloning method we first created a library of human CLN3 cDNA clones either with a randomly inserted eGFP, a myc-tag, or both. The functionality of the clones was evaluated by assessing their ability to revert a previously reported lysosomal phenotype in immortalized cerebellar granular cells derived from Cln3Δex7/8 mice (CbCln3Δex7/8). The double-tagged clones were expressed in HeLa cells, and FRET was measured between the donor eGFP and an acceptor DyLight547 coupled to a monoclonal α-myc antibody to assess their relative membrane orientation. The data were used together with previously reported experimental data to compile a constrained membrane topology model for hCLN3 using TOPCONS consensus membrane prediction algorithm. Our model with six transmembrane domains and cytosolic N- and C-termini largely agrees with those previously suggested but differs in terms of the transmembrane domain positions as well as in the size of the luminal loops. This finding improves understanding the function of the native hCLN3 protein. PMID:25051496

  5. Fretting and Corrosion in Modular Shoulder Arthroplasty: A Retrieval Analysis

    PubMed Central

    Panzram, Benjamin

    2016-01-01

    Tribocorrosion in taper junctions of retrieved anatomic shoulder arthroplasty implants was evaluated. A comparison of the tribocorrosion between cobalt-chromium and titanium alloy stems was conducted and the observations were correlated with the individual's clinical data. Adverse effects caused by metal debris and subsequent elevated serum metal ion levels are frequently reported in total hip arthroplasty. In total shoulder arthroplasty, to date only a small number of retrieval analyses are available and even fewer address the issue of tribocorrosion at the taper junctions. A total of 36 retrieved hemiarthroplasties and total shoulder arthroplasties were assessed using the modified Goldberg score. The prevalence of fretting and corrosion was confirmed in this cohort. Titanium stems seem to be more susceptible to damage caused by tribocorrosion than cobalt-chromium stems. Furthermore, stemless designs offered less tribocorrosion at the taper junction than stemmed designs. A weak correlation between time to revision and increased levels of tribocorrosion was seen. Whether or not tribocorrosion can lead to adverse clinical reactions and causes failure of shoulder arthroplasties remains to be examined. PMID:27433471

  6. Quantitative Analysis of Tau-Microtubule Interaction Using FRET

    PubMed Central

    Di Maïo, Isabelle L.; Barbier, Pascale; Allegro, Diane; Brault, Cédric; Peyrot, Vincent

    2014-01-01

    The interaction between the microtubule associated protein, tau and the microtubules is investigated. A fluorescence resonance energy transfer (FRET) assay was used to determine the distance separating tau to the microtubule wall, as well as the binding parameters of the interaction. By using microtubules stabilized with Flutax-2 as donor and tau labeled with rhodamine as acceptor, a donor-to-acceptor distance of 54 ± 1 Å was found. A molecular model is proposed in which Flutax-2 is directly accessible to tau-rhodamine molecules for energy transfer. By titration, we calculated the stoichiometric dissociation constant to be equal to 1.0 ± 0.5 µM. The influence of the C-terminal tails of αβ-tubulin on the tau-microtubule interaction is presented once a procedure to form homogeneous solution of cleaved tubulin has been determined. The results indicate that the C-terminal tails of α- and β-tubulin by electrostatic effects and of recruitment seem to be involved in the binding mechanism of tau. PMID:25196605

  7. FRETsg: Biomolecular structure model building from multiple FRET experiments

    NASA Astrophysics Data System (ADS)

    Schröder, G. F.; Grubmüller, H.

    2004-04-01

    Fluorescence energy transfer (FRET) experiments of site-specifically labelled proteins allow one to determine distances between residues at the single molecule level, which provide information on the three-dimensional structural dynamics of the biomolecule. To systematically extract this information from the experimental data, we describe a program that generates an ensemble of configurations of residues in space that agree with the experimental distances between these positions. Furthermore, a fluctuation analysis allows to determine the structural accuracy from the experimental error. Program summaryTitle of program: FRETsg Catalogue identifier: ADTU Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTU Computer: SGI Octane, Pentium II/III, Athlon MP, DEC Alpha Operating system: Unix, Linux, Windows98/NT/XP Programming language used: ANSI C No. of bits in a word: 32 or 64 No. of processors used: 1 No. of bytes in distributed program, including test data, etc.: 11407 No. of lines in distributed program, including test data, etc.: 1647 Distribution format: gzipped tar file Nature of the physical problem: Given an arbitrary number of distance distributions between an arbitrary number of points in three-dimensional space, find all configurations (set of coordinates) that obey the given distances. Method of solution: Each distance is described by a harmonic potential. Starting from random initial configurations, their total energy is minimized by steepest descent. Fluctuations of positions are chosen to generate distance distribution widths that best fit the given values.

  8. Hybridization accompanying FRET event in labeled natural nucleoside-unnatural nucleoside containing chimeric DNA duplexes.

    PubMed

    Bag, Subhendu Sekhar; Das, Suman K; Pradhan, Manoj Kumar; Jana, Subhashis

    2016-09-01

    Förster resonance energy transfer (FRET) is a highly efficient strategy in illuminating the structures, structural changes and dynamics of DNA, proteins and other biomolecules and thus is being widely utilized in studying such phenomena, in designing molecular/biomolecular probes for monitoring the hybridization event of two single stranded DNA to form duplex, in gene detection and in many other sensory applications in chemistry, biology and material sciences. Moreover, FRET can give information about the positional status of chromophores within the associated biomolecules with much more accuracy than other methods can yield. Toward this end, we want to report here the ability of fluorescent unnatural nucleoside, triazolylphenanthrene ((TPhen)BDo) to show FRET interaction upon hybridization with fluorescently labeled natural nucleosides, (Per)U or (OxoPy)U or (Per)U, forming two stable chimeric DNA duplexes. The pairing selectivity and the thermal duplex stability of the chimeric duplexes are higher than any of the duplexes with natural nucleoside formed. The hybridization results in a Förster resonance energy transfer (FRET) from donor triazolylphenanthrene of (TPhen)BDo to acceptor oxopyrene of (OxoPy)U and/or to perylene chromophore of (Per)U, respectively, in two chimeric DNA duplexes. Therefore, we have established the FRET process in two chimeric DNA duplexes wherein a fluorescently labeled natural nucleoside ((OxoPy)U or (Per)U) paired against an unnatural nucleoside ((TPhen)BDo) without sacrificing the duplex stability and B-DNA conformation. The hybridization accompanying FRET event in these classes of interacting fluorophores is new. Moreover, there is no report of such designed system of chimeric DNA duplex. Our observed phenomenon and the design can potentially be exploited in designing more of such efficient FRET pairs for useful application in the detection and analysis of biomolecular interactions and in material science application. PMID:27498231

  9. Three-Dimensional FRET Reconstruction Microscopy for Analysis of Dynamic Molecular Interactions in Live Cells

    PubMed Central

    Hoppe, Adam D.; Shorte, Spencer L.; Swanson, Joel A.; Heintzmann, Rainer

    2008-01-01

    Analysis of cellular pathways requires concentration measurements of dynamically interacting molecules within the three-dimensional (3D) space of single living cells. Förster resonance energy transfer (FRET) microscopy from widefield, from confocal, and potentially from superresolution microscopes can access this information; however, these measurements are distorted by the inherent 3D blurring of optical imaging, spectral overlap of fluorophores, and detection noise. We propose a mathematical model of these processes and demonstrate, through simulation, how these distortions limit the dynamic range and sensitivity of conventional FRET microscopy. Using this model, we devise and validate a new approach (called 3D-FRET stoichiometry reconstruction, 3DFSR) for reconstructing 3D distributions of bound and free fluorescent molecules. Previous attempts to reconstruct 3D-FRET data relied on sequential spectral unmixing and deconvolution, a process that corrupts the detection statistics. We demonstrate that 3DFSR is superior to these approaches since it simultaneously models spectral mixing, optical blurring, and detection noise. To achieve the full potential of this technique, we developed an instrument capable of acquiring 3D-FRET data rapidly and sensitively from single living cells. Compared with conventional FRET microscopy, our 3D-FRET reconstruction technique and new instrumentation provides orders of magnitude gains in both sensitivity and accuracy wherein sustained high-resolution four-dimensional (x,y,z,t) imaging of molecular interactions inside living cells was achieved. These results verify previous observations that Cdc42 signaling is localized to the advancing margins of forming phagosomes in macrophages. PMID:18339754

  10. FRET microscopy for real-time monitoring of signaling events in live cells using unimolecular biosensors.

    PubMed

    Sprenger, Julia U; Perera, Ruwan K; Götz, Konrad R; Nikolaev, Viacheslav O

    2012-01-01

    Förster resonance energy transfer (FRET) microscopy continues to gain increasing interest as a technique for real-time monitoring of biochemical and signaling events in live cells and tissues. Compared to classical biochemical methods, this novel technology is characterized by high temporal and spatial resolution. FRET experiments use various genetically-encoded biosensors which can be expressed and imaged over time in situ or in vivo. Typical biosensors can either report protein-protein interactions by measuring FRET between a fluorophore-tagged pair of proteins or conformational changes in a single protein which harbors donor and acceptor fluorophores interconnected with a binding moiety for a molecule of interest. Bimolecular biosensors for protein-protein interactions include, for example, constructs designed to monitor G-protein activation in cells, while the unimolecular sensors measuring conformational changes are widely used to image second messengers such as calcium, cAMP, inositol phosphates and cGMP. Here we describe how to build a customized epifluorescence FRET imaging system from single commercially available components and how to control the whole setup using the Micro-Manager freeware. This simple but powerful instrument is designed for routine or more sophisticated FRET measurements in live cells. Acquired images are processed using self-written plug-ins to visualize changes in FRET ratio in real-time during any experiments before being stored in a graphics format compatible with the build-in ImageJ freeware used for subsequent data analysis. This low-cost system is characterized by high flexibility and can be successfully used to monitor various biochemical events and signaling molecules by a plethora of available FRET biosensors in live cells and tissues. As an example, we demonstrate how to use this imaging system to perform real-time monitoring of cAMP in live 293A cells upon stimulation with a β-adrenergic receptor agonist and blocker. PMID

  11. Steam generator fretting-wear damage: A summary of recent findings

    SciTech Connect

    Guerout, F.M.; Fisher, N.J.

    1999-08-01

    Flow-induced vibration of steam generator (SG) tubes may sometimes result in fretting-wear damage at the tube-to-support locations. Fretting-wear damage predictions are largely based on experimental data obtained at representative test conditions. Fretting-wear of SG materials has been studied at the Chalk River Laboratories for two decades. Tests are conducted in fretting-wear test machines that simulate SG environmental conditions and tube-to-support dynamic interactions. A new high-temperature force and displacement measuring system was developed to monitor tube-to-support interaction (i.e., work-rate) at operating conditions. This improvement in experimental fretting-wear technology was used to perform a comprehensive study of the effect of various environment and design parameters on SG tube wear damage. This paper summarizes the results of tests performed over the past 4 yr to study the effect of temperature, water chemistry, support geometry, and tube material on fretting-wear. The results show a significant effect of temperature on tube wear damage. Therefore, fretting-wear tests must be performed at operating temperatures in order to be relevant. No significant effect of the type of water treatment on tube wear damage was observed. For predominantly impacting motion, the wear of SG tubes in contact with 410 stainless steel is similar regardless of whether Alloy 690 or Alloy 800 is used as tubing material or whether lattice bars or broached hole supports are used. Based on results presented in this paper, an average wear coefficient value is recommended that is used for the prediction of SG tube wear depth versus time.

  12. Phosphonomethyl analogues of hexose phosphates.

    PubMed

    Webster, D; Jondorf, W R; Dixon, H B

    1976-05-01

    The analogue of fructose 1,6-bisphosphate in which the phosphate group, -O-PO3H2, on C-6 is replaced by the phosphonomethyl group, -CH2-PO3H2, was made enzymically from the corresponding analogue of 3-phosphoglycerate. It was a substrate for aldolase, which was used to form it, but not for fructose 1,6-bisphosphatase. It was hydrolysed chemically to yield the corresponding analogue of fructose 6-phosphate [i.e. 6-deoxy-6-(phosphonomethyl)-D-fructose, or, more strictly, 6,7-dideoxy-7-phosphono-D-arabino-2-heptulose]. This proved to be a substrate for the sequential actions of glucose 6-phosphate isomerase, glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase. Thus seven out of the nine enzymes of the glycolytic and pentose phosphate pathways so far tested catalyse the reactions of the phosphonomethyl isosteres of their substrates. PMID:7247

  13. Pyrolysis of simple amino acids and nucleobases: survivability limits and implications for extraterrestrial delivery

    NASA Astrophysics Data System (ADS)

    Basiuk, V. A.; Douda, J.

    1999-04-01

    The idea of extraterrestrial delivery of organic matter to the early Earth is strongly supported by the detection of a large variety of organic compounds in the interstellar medium, comets, and carbonaceous chondrites. Whether organic compounds essential for the emergence and evolution of life, particularly amino acids and nucleic acid bases found in the meteorites, can be efficiently delivered by other space bodies is unclear and depends primarily on capability of the biomolecules to survive high temperatures during atmospheric deceleration and impacts to the terrestrial surface. In the present study we estimated survivability of simple amino acids (glycine, Lalanine, α-aminoisobutyric acid, L-valine and L-leucine), purines (adenine and guanine) and pyrimidines (uracil and cytosine) under rapid heating to temperatures of 400-1000°C under N2 or CO2 atmosphere. We have found that most of the compounds studied cannot survive the temperatures substantially higher than 700°C however at 500600°C, the recovery can be at a percent level (or even 10%-level for adenine, uracil, alanine, and valine). The final fate of amino acids and nucleobases during the atmospheric deceleration and surface impacts is discussed depending on such factors as size of the space body, nature and altitude of the heating, chemical composition of the space body and of the atmosphere.

  14. An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies

    PubMed Central

    Chawla, Mohit; Oliva, Romina; Bujnicki, Janusz M.; Cavallo, Luigi

    2015-01-01

    Posttranscriptional modifications greatly enhance the chemical information of RNA molecules, contributing to explain the diversity of their structures and functions. A significant fraction of RNA experimental structures available to date present modified nucleobases, with half of them being involved in H-bonding interactions with other bases, i.e. ‘modified base pairs’. Herein we present a systematic investigation of modified base pairs, in the context of experimental RNA structures. To this end, we first compiled an atlas of experimentally observed modified base pairs, for which we recorded occurrences and structural context. Then, for each base pair, we selected a representative for subsequent quantum mechanics calculations, to find out its optimal geometry and interaction energy. Our structural analyses show that most of the modified base pairs are non Watson–Crick like and are involved in RNA tertiary structure motifs. In addition, quantum mechanics calculations quantify and provide a rationale for the impact of the different modifications on the geometry and stability of the base pairs they participate in. PMID:26117545

  15. Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases.

    PubMed

    Improta, Roberto; Santoro, Fabrizio; Blancafort, Lluís

    2016-03-23

    The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research. PMID:26928320

  16. High-resolution photoelectron spectra of the pyrimidine-type nucleobases

    SciTech Connect

    Fulfer, K. D.; Hardy, D.; Poliakoff, E. D.; Aguilar, A. A.

    2015-06-14

    High-resolution photoelectron spectra of the gas phase pyrimidine-type nucleobases, thymine, uracil, and cytosine, were collected using synchrotron radiation over the photon energy range 17 ≤ hν ≤ 150 eV. These data provide the highest resolution photoelectron spectra of thymine, uracil, and cytosine published to date. By comparing integrated regions of the energy dependent photoelectron spectra of thymine, the ionization potentials of the first four ionic states of thymine were estimated to be 8.8, 9.8, 10.3, and 10.8 eV. The thymine data also show evidence for low energy shape resonances in three of the outermost valence electronic states. Comparing the uracil spectrum with the thymine spectrum, the four outermost valence electronic states of uracil likely begin at binding energies 9.3, 9.9, 10.5, and 11.0 eV. High-resolution spectra indicate only one tautomeric form of cytosine contributes significantly to the spectrum with the four outermost valence electronic states beginning at binding energies 8.9, 9.9, 10.4, and 10.85 eV.

  17. Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA

    PubMed Central

    Malik, Shuja S.; Coey, Christopher T.; Varney, Kristen M.; Pozharski, Edwin; Drohat, Alexander C.

    2015-01-01

    Thymine DNA Glycosylase (TDG) performs essential functions in maintaining genetic integrity and epigenetic regulation. Initiating base excision repair, TDG removes thymine from mutagenic G·T mispairs caused by 5-methylcytosine (mC) deamination and other lesions including uracil (U) and 5-hydroxymethyluracil (hmU). In DNA demethylation, TDG excises 5-formylcytosine (fC) and 5-carboxylcytosine (caC), which are generated from mC by Tet (ten–eleven translocation) enzymes. Using improved crystallization conditions, we solved high-resolution (up to 1.45 Å) structures of TDG enzyme–product complexes generated from substrates including G·U, G·T, G·hmU, G·fC and G·caC. The structures reveal many new features, including key water-mediated enzyme–substrate interactions. Together with nuclear magnetic resonance experiments, the structures demonstrate that TDG releases the excised base from its tight product complex with abasic DNA, contrary to previous reports. Moreover, DNA-free TDG exhibits no significant binding to free nucleobases (U, T, hmU), indicating a Kd >> 10 mM. The structures reveal a solvent-filled channel to the active site, which might facilitate dissociation of the excised base and enable caC excision, which involves solvent-mediated acid catalysis. Dissociation of the excised base allows TDG to bind the beta rather than the alpha anomer of the abasic sugar, which might stabilize the enzyme–product complex. PMID:26358812

  18. High-energy chemistry of formamide: A unified mechanism of nucleobase formation

    PubMed Central

    Ferus, Martin; Nesvorný, David; Šponer, Jiří; Kubelík, Petr; Michalčíková, Regina; Shestivská, Violetta; Šponer, Judit E.; Civiš, Svatopluk

    2015-01-01

    The coincidence of the Late Heavy Bombardment (LHB) period and the emergence of terrestrial life about 4 billion years ago suggest that extraterrestrial impacts could contribute to the synthesis of the building blocks of the first life-giving molecules. We simulated the high-energy synthesis of nucleobases from formamide during the impact of an extraterrestrial body. A high-power laser has been used to induce the dielectric breakdown of the plasma produced by the impact. The results demonstrate that the initial dissociation of the formamide molecule could produce a large amount of highly reactive CN and NH radicals, which could further react with formamide to produce adenine, guanine, cytosine, and uracil. Based on GC-MS, high-resolution FTIR spectroscopic results, as well as theoretical calculations, we present a comprehensive mechanistic model, which accounts for all steps taking place in the studied impact chemistry. Our findings thus demonstrate that extraterrestrial impacts, which were one order of magnitude more abundant during the LHB period than before and after, could not only destroy the existing ancient life forms, but could also contribute to the creation of biogenic molecules. PMID:25489115

  19. Low-energy positron scattering from DNA nucleobases: the effects from permanent dipoles

    NASA Astrophysics Data System (ADS)

    Franz, Jan; Gianturco, Francesco Antonio

    2014-10-01

    Ab initio quantum calculations for low-energy positron scattering from gas-phase isolated molecular nucleobases which are part of the DNA structure are presented and discussed over the range of 1 eV to 25 eV. The calculations report the integral cross sections (ICSs) and the momentum-transfer cross sections (MTCSs) for Adenine, Guanine, Thymine and Cytosine. The calculations show very clearly the important role of the dominant long-range interaction between the positron projectile and the permanent dipole-moments of the target molecules in deciding the relative sizes of the ICSs and MTCSs for the present series of molecules. Such results confirm the largely repulsive interaction between positron and DNA bases, which is nevertheless producing very large cross sections and marked deflection functions from the latter molecules. Contribution to the Topical Issue "Nano-scale Insights into Ion-beam Cancer Therapy", edited by Andrey V. Solov'yov, Nigel Mason, Paulo Limão-Vieira and Malgorzata Smialek-Telega.

  20. High-energy chemistry of formamide: a unified mechanism of nucleobase formation.

    PubMed

    Ferus, Martin; Nesvorný, David; Šponer, Jiří; Kubelík, Petr; Michalčíková, Regina; Shestivská, Violetta; Šponer, Judit E; Civiš, Svatopluk

    2015-01-20

    The coincidence of the Late Heavy Bombardment (LHB) period and the emergence of terrestrial life about 4 billion years ago suggest that extraterrestrial impacts could contribute to the synthesis of the building blocks of the first life-giving molecules. We simulated the high-energy synthesis of nucleobases from formamide during the impact of an extraterrestrial body. A high-power laser has been used to induce the dielectric breakdown of the plasma produced by the impact. The results demonstrate that the initial dissociation of the formamide molecule could produce a large amount of highly reactive CN and NH radicals, which could further react with formamide to produce adenine, guanine, cytosine, and uracil. Based on GC-MS, high-resolution FTIR spectroscopic results, as well as theoretical calculations, we present a comprehensive mechanistic model, which accounts for all steps taking place in the studied impact chemistry. Our findings thus demonstrate that extraterrestrial impacts, which were one order of magnitude more abundant during the LHB period than before and after, could not only destroy the existing ancient life forms, but could also contribute to the creation of biogenic molecules. PMID:25489115

  1. Ranking of Molecular Biomarker Interaction with Targeted DNA Nucleobases via Full Atomistic Molecular Dynamics.

    PubMed

    Zhang, Wenjun; Wang, Ming L; Cranford, Steven W

    2016-01-01

    DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study and rank the strength of interaction between four single DNA nucleotides (Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)) on single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with acetone, ethanol, H2S and HCl. By sampling forward and reverse interaction paths, we compute the free-energy profiles of eight systems for the four targeted molecules. We find that dsDNA react differently than ssDNA to the targeted molecules, requiring more energy to move the molecule close to DNA as indicated by the potential of mean force (PMF). Comparing the PMF values of different systems, we obtain a relative ranking of DNA base for the detection of each molecule. Via the same procedure, we could generate a library of DNA sequences for the detection of a wide range of chemicals. A DNA sensor array built with selected sequences differentiating many disease biomarkers can be used in disease diagnosis and monitoring. PMID:26750747

  2. Ranking of Molecular Biomarker Interaction with Targeted DNA Nucleobases via Full Atomistic Molecular Dynamics

    PubMed Central

    Zhang, Wenjun; Wang, Ming L.; Cranford, Steven W.

    2016-01-01

    DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study and rank the strength of interaction between four single DNA nucleotides (Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)) on single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with acetone, ethanol, H2S and HCl. By sampling forward and reverse interaction paths, we compute the free-energy profiles of eight systems for the four targeted molecules. We find that dsDNA react differently than ssDNA to the targeted molecules, requiring more energy to move the molecule close to DNA as indicated by the potential of mean force (PMF). Comparing the PMF values of different systems, we obtain a relative ranking of DNA base for the detection of each molecule. Via the same procedure, we could generate a library of DNA sequences for the detection of a wide range of chemicals. A DNA sensor array built with selected sequences differentiating many disease biomarkers can be used in disease diagnosis and monitoring. PMID:26750747

  3. Peptidyl α-Ketoamides with Nucleobases, Methylpiperazine, and Dimethylaminoalkyl Substituents as Calpain Inhibitors

    PubMed Central

    Ovat, Asli; Li, Zhao Zhao; Hampton, Christina Y.; Asress, Seneshaw A.; Fernández, Facundo M.; Glass, Jonathan D.; Powers, James C.

    2010-01-01

    A series of peptidyl α-ketoamides with the general structure Cbz-L-Leu-D,L-AA-CONH-R were synthesized and evaluated as inhibitors for the cysteine proteases calpain I, calpain II and cathepsin B. Nucleobases, methylpiperazine and dimethylaminoalkyl groups were incorporated into the primed region of the inhibitors to generate compounds that potentially cross the blood-brain barrier. Two of these compounds (Cbz-Leu-D,L-Abu-CONH-(CH2)3-adenin-9-yl and Cbz-Leu-D,L-Abu-CONH-(CH2)3-(4-methylpiperazin-1-yl) have been shown to have useful concentrations in the brain in animals. The best inhibitor for calpain I was Cbz-Leu-D,L-Abu-CONH-(CH2)3-2-methoxyadenin-9-yl (Ki = 23 nM) and the best inhibitor for calpain II was Cbz-Leu-D,L-Phe-CONH-(CH2)3-adenin-9-yl (Ki = 68 nM). Based on the crystal structure obtained with heterocyclic peptidyl α-ketoamides, we have improved inhibitor potency by introducing a small hydrophobic group on the adenine ring. These inhibitors have good potential to be used in the treatment of neurodegenerative diseases. PMID:20690647

  4. Symmetrical and unsymmetrical α,ω-nucleobase amide-conjugated systems

    PubMed Central

    Boncel, Sławomir; Mączka, Maciej; Koziol, Krzysztof K K; Motyka, Radosław

    2010-01-01

    Summary We present the synthesis and selected physicochemical properties of several novel symmetrical and unsymmetrical α,ω-nucleobase mono- and bis-amide conjugated systems containing aliphatic, aromatic or saccharidic linkages. The final stage of the synthesis involves condensation of a subunit bearing carboxylic group with an amine subunit. 4-(4,6-Dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMT-MM) was found to be a particularly effective condensing agent. The subunits containing carboxylic groups were obtained by acidic hydrolysis of N-1 Michael adducts of uracils or N-9 Michael adducts of 6-chloropurine with methyl acrylate. The amines used were aliphatic/aromatic diamines, adenine, 5-substituted 1-(ω-aminoalkyl)uracils and 5′-amino-2′,5′-dideoxythymidine. The title compounds may find application as antiprotozoal agents. Moreover, preliminary microscopy TEM studies of supramolecular behaviour showed that target molecules with bolaamphiphilic structures were capable of forming highly ordered assemblies, mainly nanofibres. PMID:20502605

  5. Preliminary studies on unusual polymorphs of thymine: Structural comparison with other nucleobases

    NASA Astrophysics Data System (ADS)

    Chennuru, Ramanaiah; Muthudoss, Prakash; Ramakrishnan, Srividya; Mohammad, Amjad Basha; Ravi Chandra Babu, R.; Mahapatra, Sudarshan; Nayak, Susanta K.

    2016-09-01

    Two polymorphs Form-R2 and Form-R4 of anhydrous thymine, one of the four nucleobases in the nucleic acid of DNA were obtained via sublimation crystallization and desolvation technique respectively. Form-R2 crystallizes in monoclinic C 2/c with a = 25.107(7) Å, b = 6.846(2) Å, c = 6.715(2) Å, β = 90.529(6)⁰ and V = 1154.1(5) Å3. The supramolecular assembly in Form-R2 is a sheet of hydrogen bonded network similar to that found in the crystal structures of other reported anhydrous form of thymine (Form-R1). Interestingly the thermal behavior is similar for these two forms with a minor difference in powder X-ray diffraction pattern. Further thymine Form-R2 closely matches with one of the predicted form of thymine using Polymorph module of Accelrys. Form-R4 is obtained by the dehydration of the mono hydrated form (Form-R3) and characterized by powder X-ray diffraction, FTIR spectroscopic techniques and thermal analysis.

  6. An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies.

    PubMed

    Chawla, Mohit; Oliva, Romina; Bujnicki, Janusz M; Cavallo, Luigi

    2015-08-18

    Posttranscriptional modifications greatly enhance the chemical information of RNA molecules, contributing to explain the diversity of their structures and functions. A significant fraction of RNA experimental structures available to date present modified nucleobases, with half of them being involved in H-bonding interactions with other bases, i.e. 'modified base pairs'. Herein we present a systematic investigation of modified base pairs, in the context of experimental RNA structures. To this end, we first compiled an atlas of experimentally observed modified base pairs, for which we recorded occurrences and structural context. Then, for each base pair, we selected a representative for subsequent quantum mechanics calculations, to find out its optimal geometry and interaction energy. Our structural analyses show that most of the modified base pairs are non Watson-Crick like and are involved in RNA tertiary structure motifs. In addition, quantum mechanics calculations quantify and provide a rationale for the impact of the different modifications on the geometry and stability of the base pairs they participate in. PMID:26117545

  7. Binding energies of nucleobase complexes: Relevance to homology recognition of DNA

    NASA Astrophysics Data System (ADS)

    León, Sergio Cruz; Prentiss, Mara; Fyta, Maria

    2016-06-01

    The binding energies of complexes of DNA nucleobase pairs are evaluated using quantum mechanical calculations at the level of dispersion corrected density functional theory. We begin with Watson-Crick base pairs of singlets, duplets, and triplets and calculate their binding energies. At a second step, mismatches are incorporated into the Watson-Crick complexes in order to evaluate the variation in the binding energy with respect to the canonical Watson-Crick pairs. A linear variation of this binding energy with the degree of mismatching is observed. The binding energies for the duplets and triplets containing mismatches are further compared to the energies of the respective singlets in order to assess the degree of collectivity in these complexes. This study also suggests that mismatches do not considerably affect the energetics of canonical base pairs. Our work is highly relevant to the recognition process in DNA promoted through the RecA protein and suggests a clear distinction between recognition in singlets, and recognition in duplets or triplets. Our work assesses the importance of collectivity in the homology recognition of DNA.

  8. Formation of Nucleobases from the UV Photo-Irradiation of Pyrimidine in Astrophysical Ice Analogs

    NASA Technical Reports Server (NTRS)

    Milam, S. N.; Nuevo, M.; Sandford, S. A.; Elsila, J. E.; Dworkin, J. P.

    2010-01-01

    Astrochemistry laboratory simulations have shown that complex organic molecules including compounds of astrobiological interest can be formed under interstellarl/circumstellar conditions from the vacuum UV irradiation of astrophysical ice analogs containing H2O, CO, CO2, CH3OH, NH13, etc. Of all prebiotic compounds, the formation of amino acids under such experimental conditions has been the most extensively studied. Although the presence of amino acids in the interstellar medium (ISM) has yet to be confirmed, they have been detected in meteorites, indicating that biomolecules and/or their precursors can be formed under extraterrestrial, abiotic conditions. Nucleobases, the building blocks of DNA and RNA, as well as other 1V-heterocycles, have also been detected in meteorites, but like amino acids, they have yet to be observed in the ISM. In this work, we present an experimental study of the formation of pyrimidine-based compounds from the UV photo-irradiation of pyrimidine in ice mixtures containing H2O, NH3, and/or CH3OH at low temperature and pressure.

  9. Ranking of Molecular Biomarker Interaction with Targeted DNA Nucleobases via Full Atomistic Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Zhang, Wenjun; Wang, Ming L.; Cranford, Steven W.

    2016-01-01

    DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study and rank the strength of interaction between four single DNA nucleotides (Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)) on single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with acetone, ethanol, H2S and HCl. By sampling forward and reverse interaction paths, we compute the free-energy profiles of eight systems for the four targeted molecules. We find that dsDNA react differently than ssDNA to the targeted molecules, requiring more energy to move the molecule close to DNA as indicated by the potential of mean force (PMF). Comparing the PMF values of different systems, we obtain a relative ranking of DNA base for the detection of each molecule. Via the same procedure, we could generate a library of DNA sequences for the detection of a wide range of chemicals. A DNA sensor array built with selected sequences differentiating many disease biomarkers can be used in disease diagnosis and monitoring.

  10. Semiconductive and magnetic one-dimensional coordination polymers of Cu(II) with modified nucleobases.

    PubMed

    Amo-Ochoa, Pilar; Castillo, Oscar; Gómez-García, Carlos J; Hassanein, Khaled; Verma, Sandeep; Kumar, Jitendra; Zamora, Félix

    2013-10-01

    Four new copper(II) coordination complexes, obtained by reaction of CuX2 (X = acetate or chloride) with thymine-1-acetic acid and uracil-1-propionic acid as ligands, of formulas [Cu(TAcO)2(H2O)4]·4H2O (1), [Cu(TAcO)2(H2O)2]n (2), [Cu3(TAcO)4(H2O)2(OH)2]n·4H2O (3), and [Cu3(UPrO)2Cl2(OH)2(H2O)2]n (4) (TAcOH = thymine-1-acetic acid, UPrOH = uracil-1-propionic acid) are described. While 1 is a discrete complex, 2-4 are one-dimensional coordination polymers. Complexes 2-4 present dc conductivity values between 10(-6) and 10(-9) S/cm(-1). The magnetic behavior of complex 2 is typical for almost isolated Cu(II) metal centers. Moderate-weak antiferromagnetic interactions have been found in complex 3, whereas a combination of strong and weak antiferromagnetic interactions have been found in complex 4. Quantum computational calculations have been done to estimate the individual "J" magnetic coupling constant for each superexchange pathway in complexes 3 and 4. Compounds 2-4 are the first known examples of semiconductor and magnetic coordination polymers containing nucleobases. PMID:24040754

  11. A general method for quantifying sequence effects on nucleobase oxidation in DNA.

    PubMed

    Margolin, Yelena; Dedon, Peter C

    2010-01-01

    Oxidative damage to DNA has long been associated with aging and disease, with guanine serving as the primary target for oxidation owing to its low ionization potential. Emerging evidence points to a critical role for sequence context as a determinant of the guanine ionization potential and the associated chemical reactivity of the guanine, as well as the spectrum of damage products that arise from oxidation. Recent studies also suggest that the generally accepted model of oxidation hotspots in runs of guanine bases may not hold for biologically relevant oxidants. One of the primary methods used to address these important problems of sequence context utilizes gel electrophoresis to identify the location and quantity of base damage arising in model oligonucleotides. However, this approach has limited study to those agents that produce few strand breaks arising from deoxyribose oxidation, while ionizing radiation, Fenton chemistry and other biologically relevant oxidants produce sizeable proportions of both base and sugar damage. To this end, we have developed a universal method to quantify sequence context effects on nucleobase damage without interference by strand breaks from deoxyribose oxidation. PMID:20013187

  12. Potential and frequency effects on fretting corrosion of Ti6Al4V and CoCrMo surfaces.

    PubMed

    Swaminathan, Viswanathan; Gilbert, Jeremy L

    2013-09-01

    Fretting corrosion has been reported at the metal-metal interfaces of a wide range of medical devices, including total joint replacements, spinal devices, and overlapping cardiovascular stents. Currently, the fretting corrosion phenomenon associated with metal-on-metal contacts is not fully understood. This study investigated the effect of potential and fretting frequency on the fretting corrosion performance of Ti6Al4V/Ti6Al4V, Ti6Al4V/CoCrMo, and CoCrMo/CoCrMo alloy combinations at fixed normal load and displacement conditions using a custom built fretting corrosion test system. The results showed that the fretting current densities increased with increases in potential and were highest for Ti6Al4V/Ti6Al4V couple (1.5 mA/cm(2) at 0 V vs. Ag/AgCl). The coefficient of friction varied with potential and was about two times higher for Ti6Al4V/Ti6Al4V (0.71 V at 0 V vs. Ag/AgCl). In most of the potential range tested, the fretting corrosion behavior of CoCrMo/Ti6Al4V and CoCrMo/CoCrMo was similar and dominated by the CoCrMo surface. Increase in applied fretting frequency linearly increased the fretting current densities in the regions where the passive film is stable. Also, the model-based fretting current densities were in excellent agreement with the experimental results. Overall, Ti6Al4V/Ti6Al4V couple was more susceptible to fretting corrosion compared with other couples. However, the effects of these processes on the biological system were not assessed. PMID:23404905

  13. Evaluating Quantum Dot Performance in Homogeneous FRET Immunoassays for Prostate Specific Antigen.

    PubMed

    Bhuckory, Shashi; Lefebvre, Olivier; Qiu, Xue; Wegner, Karl David; Hildebrandt, Niko

    2016-01-01

    The integration of semiconductor quantum dots (QDs) into homogeneous Förster resonance energy transfer (FRET) immunoassay kits for clinical diagnostics can provide significant advantages concerning multiplexing and sensitivity. Here we present a facile and functional QD-antibody conjugation method using three commercially available QDs with different photoluminescence (PL) maxima (605 nm, 655 nm, and 705 nm). The QD-antibody conjugates were successfully applied for FRET immunoassays against prostate specific antigen (PSA) in 50 µL serum samples using Lumi4-Tb (Tb) antibody conjugates as FRET donors and time-gated PL detection on a KRYPTOR clinical plate reader. Förster distance and Tb donor background PL were directly related to the analytical sensitivity for PSA, which resulted in the lowest limits of detection for Tb-QD705 (2 nM), followed by Tb-QD655 (4 nM), and Tb-QD605 (23 nM). Duplexed PSA detection using the Tb-QD655 and Tb-QD705 FRET-pairs demonstrated the multiplexing ability of our immunoassays. Our results show that FRET based on QD acceptors is suitable for multiplexed and sensitive biomarker detection in clinical diagnostics. PMID:26861327

  14. Gate-width impact on NIR FRET lifetime fitting using gated ICCD

    NASA Astrophysics Data System (ADS)

    Chen, Sez-Jade; Intes, Xavier

    2016-03-01

    Förster Resonance Energy Transfer (FRET) is widely used to sense molecular interactions occurring at the nanoscale. In vitro and ex vivo protocols for visualizing FRET are already well-established, but in vivo studies have proven to be more challenging. One issue that hinders in vivo visualization of FRET is the higher absorption and scattering of visible light within tissues. In this case, light in the near-infrared (NIR) spectral window is required for increased depth sensing. Moreover, due to spectral variation in optical properties as well as heterogeneous spatial distribution, lifetime-based FRET imaging is preferred. Herein, we investigate the effect of temporal acquisition settings on the lifetime-based estimation of the fraction of quenched donor molecules (A1) as well as the quenched donor lifetime (τ1). We performed in silico, in vitro, and in vivo experiments under gate widths of 300ps to 1000ps in 100ps intervals to determine the effect on quantification of A1 and τ1. Even though the NIR fluorescent dyes have shorter lifetimes then visible fluorophores, we were still able to accurately quantify FRET under all tested system gate widths and experimental conditions.

  15. Evaluating Quantum Dot Performance in Homogeneous FRET Immunoassays for Prostate Specific Antigen

    PubMed Central

    Bhuckory, Shashi; Lefebvre, Olivier; Qiu, Xue; Wegner, Karl David; Hildebrandt, Niko

    2016-01-01

    The integration of semiconductor quantum dots (QDs) into homogeneous Förster resonance energy transfer (FRET) immunoassay kits for clinical diagnostics can provide significant advantages concerning multiplexing and sensitivity. Here we present a facile and functional QD-antibody conjugation method using three commercially available QDs with different photoluminescence (PL) maxima (605 nm, 655 nm, and 705 nm). The QD-antibody conjugates were successfully applied for FRET immunoassays against prostate specific antigen (PSA) in 50 µL serum samples using Lumi4-Tb (Tb) antibody conjugates as FRET donors and time-gated PL detection on a KRYPTOR clinical plate reader. Förster distance and Tb donor background PL were directly related to the analytical sensitivity for PSA, which resulted in the lowest limits of detection for Tb-QD705 (2 ng/mL), followed by Tb-QD655 (4 ng/mL), and Tb-QD605 (23 ng/mL). Duplexed PSA detection using the Tb-QD655 and Tb-QD705 FRET-pairs demonstrated the multiplexing ability of our immunoassays. Our results show that FRET based on QD acceptors is suitable for multiplexed and sensitive biomarker detection in clinical diagnostics. PMID:26861327

  16. Construction, imaging and analysis of FRET-based tension sensors in living cells

    PubMed Central

    LaCroix, Andrew S.; Rothenberg, Katheryn E.; Berginski, Matthew E.; Urs, Aarti N.; Hoffman, Brenton D.

    2015-01-01

    Due to an increased appreciation for the importance of mechanical stimuli in many biological contexts, an interest in measuring the forces experienced by specific proteins in living cells has recently emerged. The development and use of Forster resonance energy transfer (FRET)-based molecular tension sensors has enabled these types of studies and led to important insights into the mechanisms those cells utilize to probe and respond to the mechanical nature of their surrounding environment. The process for creating and utilizing FRET-based tension sensors can be divided into three main parts: construction, imaging, and analysis. First we review several methods for the construction of genetically encoded FRET-based tension sensors, including restriction enzyme-based methods as well as the more recently developed overlap extension or Gibson Assembly protocols. Next, we discuss the intricacies associated with imaging tension sensors, including optimizing imaging parameters as well as common techniques for estimating artifacts within standard imaging systems. Then, we detail the analysis of such data and describe how to extract useful information from a FRET experiment. Finally, we provide a discussion on identifying and correcting common artifacts in the imaging of FRET-based tension sensors. PMID:25640429

  17. Assembling programmable FRET-based photonic networks using designer DNA scaffolds

    PubMed Central

    Buckhout-White, Susan; Spillmann, Christopher M; Algar, W. Russ; Khachatrian, Ani; Melinger, Joseph S.; Goldman, Ellen R.; Ancona, Mario G.; Medintz, Igor L.

    2014-01-01

    DNA demonstrates a remarkable capacity for creating designer nanostructures and devices. A growing number of these structures utilize Förster resonance energy transfer (FRET) as part of the device's functionality, readout or characterization, and, as device sophistication increases so do the concomitant FRET requirements. Here we create multi-dye FRET cascades and assess how well DNA can marshal organic dyes into nanoantennae that focus excitonic energy. We evaluate 36 increasingly complex designs including linear, bifurcated, Holliday junction, 8-arm star and dendrimers involving up to five different dyes engaging in four-consecutive FRET steps, while systematically varying fluorophore spacing by Förster distance (R0). Decreasing R0 while augmenting cross-sectional collection area with multiple donors significantly increases terminal exciton delivery efficiency within dendrimers compared with the first linear constructs. Förster modelling confirms that best results are obtained when there are multiple interacting FRET pathways rather than independent channels by which excitons travel from initial donor(s) to final acceptor. PMID:25504073

  18. Random coil negative control reproduces the discrepancy between scattering and FRET measurements of denatured protein dimensions

    PubMed Central

    Watkins, Herschel M.; Simon, Anna J.; Sosnick, Tobin R.; Lipman, Everett A.; Hjelm, Rex P.; Plaxco, Kevin W.

    2015-01-01

    Small-angle scattering studies generally indicate that the dimensions of unfolded single-domain proteins are independent (to within experimental uncertainty of a few percent) of denaturant concentration. In contrast, single-molecule FRET (smFRET) studies invariably suggest that protein unfolded states contract significantly as the denaturant concentration falls from high (∼6 M) to low (∼1 M). Here, we explore this discrepancy by using PEG to perform a hitherto absent negative control. This uncharged, highly hydrophilic polymer has been shown by multiple independent techniques to behave as a random coil in water, suggesting that it is unlikely to expand further on the addition of denaturant. Consistent with this observation, small-angle neutron scattering indicates that the dimensions of PEG are not significantly altered by the presence of either guanidine hydrochloride or urea. smFRET measurements on a PEG construct modified with the most commonly used FRET dye pair, however, produce denaturant-dependent changes in transfer efficiency similar to those seen for a number of unfolded proteins. Given the vastly different chemistries of PEG and unfolded proteins and the significant evidence that dye-free PEG is well-described as a denaturant-independent random coil, this similarity raises questions regarding the interpretation of smFRET data in terms of the hydrogen bond- or hydrophobically driven contraction of the unfolded state at low denaturant. PMID:25964362

  19. Photochemistry of nucleic acid bases and their thio- and aza-analogues in solution.

    PubMed

    Pollum, Marvin; Martínez-Fernández, Lara; Crespo-Hernández, Carlos E

    2015-01-01

    The steady-state and time-resolved photochemistry of the natural nucleic acid bases and their sulfur- and nitrogen-substituted analogues in solution is reviewed. Emphasis is given to the experimental studies performed over the last 3-5 years that showcase topical areas of scientific inquiry and those that require further scrutiny. Significant progress has been made toward mapping the radiative and nonradiative decay pathways of nucleic acid bases. There is a consensus that ultrafast internal conversion to the ground state is the primary relaxation pathway in the nucleic acid bases, whereas the mechanism of this relaxation and the level of participation of the (1)πσ*, (1) nπ*, and (3)ππ* states are still matters of debate. Although impressive research has been performed in recent years, the microscopic mechanism(s) by which the nucleic acid bases dissipate excess vibrational energy to their environment, and the role of the N-glycosidic group in this and in other nonradiative decay pathways, are still poorly understood. The simple replacement of a single atom in a nucleobase with a sulfur or nitrogen atom severely restricts access to the conical intersections responsible for the intrinsic internal conversion pathways to the ground state in the nucleic acid bases. It also enhances access to ultrafast and efficient inter-system crossing pathways that populate the triplet manifold in yields close to unity. Determining the coupled nuclear and electronic pathways responsible for the significantly different photochemistry in these nucleic acid base analogues serves as a convenient platform to examine the current state of knowledge regarding the photodynamic properties of the DNA and RNA bases from both experimental and computational perspectives. Further investigations should also aid in forecasting the prospective use of sulfur- and nitrogen-substituted base analogues in photochemotherapeutic applications. PMID:25238718

  20. De novo pyrimidine nucleotide synthesis mainly occurs outside of plastids, but a previously undiscovered nucleobase importer provides substrates for the essential salvage pathway in Arabidopsis.

    PubMed

    Witz, Sandra; Jung, Benjamin; Fürst, Sarah; Möhlmann, Torsten

    2012-04-01

    Nucleotide de novo synthesis is highly conserved among organisms and represents an essential biochemical pathway. In plants, the two initial enzymatic reactions of de novo pyrimidine synthesis occur in the plastids. By use of green fluorescent protein fusions, clear support is provided for a localization of the remaining reactions in the cytosol and mitochondria. This implies that carbamoyl aspartate, an intermediate of this pathway, must be exported and precursors of pyrimidine salvage (i.e., nucleobases or nucleosides) are imported into plastids. A corresponding uracil transport activity could be measured in intact plastids isolated from cauliflower (Brassica oleracea) buds. PLUTO (for plastidic nucleobase transporter) was identified as a member of the Nucleobase:Cation-Symporter1 protein family from Arabidopsis thaliana, capable of transporting purine and pyrimidine nucleobases. A PLUTO green fluorescent protein fusion was shown to reside in the plastid envelope after expression in Arabidopsis protoplasts. Heterologous expression of PLUTO in an Escherichia coli mutant lacking the bacterial uracil permease uraA allowed a detailed biochemical characterization. PLUTO transports uracil, adenine, and guanine with apparent affinities of 16.4, 0.4, and 6.3 μM, respectively. Transport was markedly inhibited by low concentrations of a proton uncoupler, indicating that PLUTO functions as a proton-substrate symporter. Thus, a protein for the absolutely required import of pyrimidine nucleobases into plastids was identified. PMID:22474184

  1. The influence of contact conditions and micromotions on the fretting behavior of modular titanium alloy taper connections.

    PubMed

    Baxmann, M; Jauch, S Y; Schilling, C; Blömer, W; Grupp, T M; Morlock, M M

    2013-05-01

    Modularity of femoral stems and neck components has become a more frequently used tool for an optimized restoration of the hip joint center and improvement of patient biomechanics. The additional taper interface increases the risk of mechanical failure due to fretting and crevice corrosion. Several failures of titanium alloy neck adapters have been documented in case-reports. An experimental fretting device was developed in this study to systematically investigate the effect of micromotion and contact pressure on fretting damage in contact situations similar to taper interfaces of modular hip prostheses under cyclic loading representative of in vivo load conditions. As a first application, the fretting behavior of Ti-6Al-4V titanium alloy components was investigated. Micromotions were varied between 10μm and 50μm, maximum contact pressures between 400 and 860N/mm(2). All modes of fretting damage were observed: Fretting wear was found for high micromotions in combination with low contact pressures. Fretting fatigue occurred with reduced movement or increased contact pressures. With small micromotions or high normal pressures, low fretting damage was observed. The developed device can be used to evaluate taper design (and especially contact geometry) as well as different materials prior to clinical use. PMID:22940445

  2. Fretting fatigue behaviour of Ni-free high-nitrogen stainless steel in a simulated body fluid

    NASA Astrophysics Data System (ADS)

    Maruyama, Norio; Hiromoto, Sachiko; Akiyama, Eiji; Nakamura, Morihiko

    2013-04-01

    Fretting fatigue behaviour of Ni-free high-nitrogen steel (HNS) with a yield strength of about 800 MPa, which was prepared by nitrogen gas pressurized electroslag remelting, was studied in air and in phosphate-buffered saline (PBS(-)). For comparison, fretting fatigue behaviour of cold-rolled SUS316L steel (SUS316L(CR)) with similar yield strength was examined. The plain fatigue limit of HNS was slightly lower than that of SUS316L(CR) although the former had a higher tensile strength than the latter. The fretting fatigue limit of HNS was higher than that of SUS316L(CR) both in air and in PBS(-). A decrease in fatigue limit of HNS by fretting was significantly smaller than that of SUS316L(CR) in both environments, indicating that HNS has better fretting fatigue resistance than SUS316L(CR). The decrease in fatigue limit by fretting is discussed taking into account the effect of friction stress due to fretting and the additional influences of wear, tribocorrosion and plastic deformation in the fretted area.

  3. Compact, Polyvalent Mannose Quantum Dots as Sensitive, Ratiometric FRET Probes for Multivalent Protein-Ligand Interactions.

    PubMed

    Guo, Yuan; Sakonsinsiri, Chadamas; Nehlmeier, Inga; Fascione, Martin A; Zhang, Haiyan; Wang, Weili; Pöhlmann, Stefan; Turnbull, W Bruce; Zhou, Dejian

    2016-04-01

    A highly efficient cap-exchange approach for preparing compact, dense polyvalent mannose-capped quantum dots (QDs) has been developed. The resulting QDs have been successfully used to probe multivalent interactions of HIV/Ebola receptors DC-SIGN and DC-SIGNR (collectively termed as DC-SIGN/R) using a sensitive, ratiometric Förster resonance energy transfer (FRET) assay. The QD probes specifically bind DC-SIGN, but not its closely related receptor DC-SIGNR, which is further confirmed by its specific blocking of DC-SIGN engagement with the Ebola virus glycoprotein. Tuning the QD surface mannose valency reveals that DC-SIGN binds more efficiently to densely packed mannosides. A FRET-based thermodynamic study reveals that the binding is enthalpy-driven. This work establishes QD FRET as a rapid, sensitive technique for probing structure and thermodynamics of multivalent protein-ligand interactions. PMID:26990806

  4. Fretting of Secondary-Seal-Ring Candidate Materials in Air at Temperatures to 816 C

    NASA Technical Reports Server (NTRS)

    Bill, R. C.

    1972-01-01

    Superalloys containing chromium showed decreasing fretting damage with increasing temperature of 816 C. This trend was related to the ability of the alloys to generate self-protecting oxide films. The damage at 816 C was one-third to one-tenth of that at 23 C. Osmium, chromium, and chromium carbide platings were fretted at 23 and 450 C. Osmium was extremely protective at 23 C but oxidized excessively at 450 C. Chromium and chromium carbide gave about the same protection at 450 C as the oxide films that formed on the superalloys. High graphite and low graphite carbons were fretted at 23 and 327 C. High graphite carbon was superior at 327 C, but low graphite carbon was the best material examined at 23 C.

  5. Fretting fatigue studies of titanium nitride-coated biomedical titanium alloys

    NASA Astrophysics Data System (ADS)

    Vadiraj, Aravind; Kamaraj, M.

    2006-10-01

    Fretting fatigue is an adhesive wear mechanism caused by repetitive tangential micro-oscillation between two contacting materials pressed together under cyclic load. Bioimplants, such as hip joints and bone plates, are prone to undergo fretting fatigue failures during their service within the body. This article presents the fretting fatigue damage characterization of physical vapor deposition (PVD) TiN-coated biomedical titanium alloys (Ti-6Al-4V and Ti-6Al-7Nb) subjected to cyclic loads. The PVD TiN layer delayed the damage because of superior tribological properties compared with uncoated alloys. Delamination and abrasive wear damage of TiN at contact caused failure of the alloy. Friction coefficient curves of the PVD TiN-coated pair showed an irregular pattern caused by the influence of wear particulates and Ringer fluid at the contact.

  6. FRET detection of lymphocyte function–associated antigen-1 conformational extension

    PubMed Central

    Chigaev, Alexandre; Smagley, Yelena; Haynes, Mark K.; Ursu, Oleg; Bologa, Cristian G.; Halip, Liliana; Oprea, Tudor; Waller, Anna; Carter, Mark B.; Zhang, Yinan; Wang, Wei; Buranda, Tione; Sklar, Larry A.

    2015-01-01

    Lymphocyte function–associated antigen 1 (LFA-1, CD11a/CD18, αLβ2-integrin) and its ligands are essential for adhesion between T-cells and antigen-presenting cells, formation of the immunological synapse, and other immune cell interactions. LFA-1 function is regulated through conformational changes that include the modulation of ligand binding affinity and molecular extension. However, the relationship between molecular conformation and function is unclear. Here fluorescence resonance energy transfer (FRET) with new LFA-1–specific fluorescent probes showed that triggering of the pathway used for T-cell activation induced rapid unquenching of the FRET signal consistent with extension of the molecule. Analysis of the FRET quenching at rest revealed an unexpected result that can be interpreted as a previously unknown LFA-1 conformation. PMID:25378583

  7. Multiplexed 3D FRET imaging in deep tissue of live embryos

    PubMed Central

    Zhao, Ming; Wan, Xiaoyang; Li, Yu; Zhou, Weibin; Peng, Leilei

    2015-01-01

    Current deep tissue microscopy techniques are mostly restricted to intensity mapping of fluorophores, which significantly limit their applications in investigating biochemical processes in vivo. We present a deep tissue multiplexed functional imaging method that probes multiple Förster resonant energy transfer (FRET) sensors in live embryos with high spatial resolution. The method simultaneously images fluorescence lifetimes in 3D with multiple excitation lasers. Through quantitative analysis of triple-channel intensity and lifetime images, we demonstrated that Ca2+ and cAMP levels of live embryos expressing dual FRET sensors can be monitored simultaneously at microscopic resolution. The method is compatible with a broad range of FRET sensors currently available for probing various cellular biochemical functions. It opens the door to imaging complex cellular circuitries in whole live organisms. PMID:26387920

  8. A comparison of ALPHAScreen, TR-FRET, and TRF as assay methods for FXR nuclear receptors.

    PubMed

    Glickman, J Fraser; Wu, Xiang; Mercuri, Robert; Illy, Chantal; Bowen, Benjamin R; He, Yang; Sills, Matthew

    2002-02-01

    New developments in detection technologies are providing a variety of biomolecular screening strategies from which to choose. Consequently, we performed a detailed analysis of both separation-based and non-separation-based formats for screening nuclear receptor ligands. In this study, time-resolved fluorescence resonance energy transfer (TR-FRET), ALPHAScreen, and time-resolved fluorescence (TRF) assays were optimized and compared with respect to sensitivity, reproducibility, and miniaturization capability. The results showed that the ALPHAScreen system had the best sensitivity and dynamic range. The TRF assay was more time consuming because of the number of wash steps necessary. The TR-FRET assay had less interwell variation, most likely because of ratiometric measurement. Both the ALPHAScreen and the TR-FRET assays were miniaturized to 8-microl volumes. Of the photomultiplier tube-based readers, the ALPHAScreen reader (ALPHAQuest) presented the advantage of faster reading times through simultaneous reading with four photomultiplier tubes. PMID:11897050

  9. Visualization of Signaling Molecules During Neutrophil Recruitment in Transgenic Mice Expressing FRET Biosensors.

    PubMed

    Mizuno, Rei; Kamioka, Yuji; Sakai, Yoshiharu; Matsuda, Michiyuki

    2016-01-01

    A number of chemical mediators regulate neutrophil recruitment to inflammatory sites either positively or negatively. Although the actions of each chemical mediator on the intracellular signaling networks controlling cell migration have been studied with neutrophils cultured in vitro, how such chemical mediators act cooperatively or counteractively in vivo remains largely unknown. To understand the mechanisms regulating neutrophil recruitment to the inflamed intestine in vivo, we recently generated transgenic mice expressing biosensors based on FRET (Förster resonance energy transfer) and set up two-photon excitation microscopy to observe the gastrointestinal tract in living mice. By measuring FRET in neutrophils, we showed activity changes of protein kinases in the neutrophils recruited to inflamed intestines. In this chapter, we describe the protocol used to visualize the protein kinase activities in neutrophils of the inflamed intestine of transgenic mice expressing the FRET biosensors. PMID:27246030

  10. Single-Molecule FRET Studies of HIV TAR–DNA Hairpin Unfolding Dynamics

    PubMed Central

    2015-01-01

    We directly measure the dynamics of the HIV trans-activation response (TAR)–DNA hairpin with multiple loops using single-molecule Förster resonance energy transfer (smFRET) methods. Multiple FRET states are identified that correspond to intermediate melting states of the hairpin. The stability of each intermediate state is calculated from the smFRET data. The results indicate that hairpin unfolding obeys a “fraying and peeling” mechanism, and evidence for the collapse of the ends of the hairpin during folding is observed. These results suggest a possible biological function for hairpin loops serving as additional fraying centers to increase unfolding rates in otherwise stable systems. The experimental and analytical approaches developed in this article provide useful tools for studying the mechanism of multistate DNA hairpin dynamics and of other general systems with multiple parallel pathways of chemical reactions. PMID:25254491

  11. Detection of heteromerization of more than two proteins by sequential BRET-FRET.

    PubMed

    Carriba, Paulina; Navarro, Gemma; Ciruela, Francisco; Ferré, Sergi; Casadó, Vicent; Agnati, Luigi; Cortés, Antoni; Mallol, Josefa; Fuxe, Kjell; Canela, Enric I; Lluís, Carmen; Franco, Rafael

    2008-08-01

    Identification of higher-order oligomers in the plasma membrane is essential to decode the properties of molecular networks controlling intercellular communication. We combined bioluminescence resonance energy transfer (BRET) and fluorescence resonance energy transfer (FRET) in a technique called sequential BRET-FRET (SRET) that permits identification of heteromers formed by three different proteins. In SRET, the oxidation of a Renilla luciferase (Rluc) substrate by an Rluc fusion protein triggers acceptor excitation of a second fusion protein by BRET and subsequent FRET to a third fusion protein. We describe two variations of SRET that use different Rluc substrates with appropriately paired acceptor fluorescent proteins. Using SRET, we identified complexes of cannabinoid CB(1), dopamine D(2) and adenosine A(2A) receptors in living cells. SRET is an invaluable technique to identify heteromeric complexes of more than two neurotransmitter receptors, which will allow us to better understand how signals are integrated at the molecular level. PMID:18587404

  12. Development of a Molecularly Evolved, Highly Sensitive CaMKII FRET Sensor with Improved Expression Pattern

    PubMed Central

    Shibata, Akihiro C. E.; Maebashi, Hiroshi K.; Nakahata, Yoshihisa; Nabekura, Junichi; Murakoshi, Hideji

    2015-01-01

    Genetically encoded fluorescence resonance energy transfer (FRET) biosensors have been successfully used to visualize protein activity in living cells. The sensitivity and accuracy of FRET measurements directly depend on biosensor folding efficiency, expression pattern, sensitivity, and dynamic range. Here, to improve the folding efficiency of the Ca2+/calmodulin-dependent protein kinase II alpha (CaMKIIα) FRET biosensor, we amplified the association domain of the CaMKIIα gene using error-prone polymerase chain reaction (PCR) and fused it to the N-terminus of mCherry in a bacterial expression vector. We also created an Escherichia coli expression library based on a previously reported fluorescent protein folding reporter method, and found a bright red fluorescent colony that contained the association domain with four mutations (F394L, I419V, A430T, and I434T). In vitro assays using the purified mutant protein confirmed improved folding kinetics of the downstream fluorescent protein, but not of the association domain itself. Furthermore, we introduced these mutations into the previously reported CaMKIIα FRET sensor and monitored its Ca2+/calmodulin-dependent activation in HeLa cells using 2-photon fluorescence lifetime imaging microscopy (2pFLIM), and found that the expression pattern and signal reproducibility of the mutant sensor were greatly improved without affecting the autophosphorylation function and incorporation into oligomeric CaMKIIα. We believe that our improved CaMKIIα FRET sensor would be useful in various types of cells and tissues, providing data with high accuracy and reproducibility. In addition, the method described here may also be applicable for improving the performance of all currently available FRET sensors. PMID:25799407

  13. A FRET based mechanical stress sensor for specific proteins in situ

    PubMed Central

    Meng, Fanjie; Suchyna, Thomas M.; Sachs, Frederick

    2008-01-01

    To measure mechanical stress in real time we designed a fluorescence energy transfer (FRET) cassette, noted stFRET, which could be inserted into structural protein hosts. The probe was made of a green fluorescence protein (GFP) pair, Cerulean and Venus, linked with a stable α-helix. We measured the FRET efficiency of the free cassette protein as function of the length of the linker, the angles of the fluorophores, temperature and urea denaturation and protease treatment. The linking helix was stable to 80C°, unfolded in 8M urea, and was rapidly digested by proteases, but in all cases the fluorophores were unaffected. We modified the α-helix linker by adding and subtracting residues to vary the angles and distance between the donor and acceptor, and assuming the cassette was a rigid body we calculated its geometry. We tested the strain sensitivity of stFRET by linking both ends to a rubber sheet subjected to equibiaxial stretch. FRET decreased proportionally to the substrate strain. The naked cassette expressed well in human embryonic kidney (HEK-293) cells and surprisingly was concentrated in the nucleus. However, when the cassette was located into host proteins such alpha-actinin, non-erythrocyte spectrin and filamin A, the labeled hosts expressed well and distributed normally in cell lines such as 3T3 where they were stressed at the leading edge of migrating cells and relaxed at the trailing edge. When COL-19 was labeled near its middle with stFRET, it expressed well in C. elegans, distributing similarly to hosts labeled with a terminal GFP and the worms behaved normally. PMID:18479457

  14. Experimental verification of the kinetic theory of FRET using optical microspectroscopy and obligate oligomers.

    PubMed

    Patowary, Suparna; Pisterzi, Luca F; Biener, Gabriel; Holz, Jessica D; Oliver, Julie A; Wells, James W; Raicu, Valerică

    2015-04-01

    Förster resonance energy transfer (FRET) is a nonradiative process for the transfer of energy from an optically excited donor molecule (D) to an acceptor molecule (A) in the ground state. The underlying theory predicting the dependence of the FRET efficiency on the sixth power of the distance between D and A has stood the test of time. In contrast, a comprehensive kinetic-based theory developed recently for FRET efficiencies among multiple donors and acceptors in multimeric arrays has waited for further testing. That theory has been tested in the work described in this article using linked fluorescent proteins located in the cytoplasm and at the plasma membrane of living cells. The cytoplasmic constructs were fused combinations of Cerulean as donor (D), Venus as acceptor (A), and a photo-insensitive molecule (Amber) as a nonfluorescent (N) place holder: namely, NDAN, NDNA, and ADNN duplexes, and the fully fluorescent quadruplex ADAA. The membrane-bound constructs were fused combinations of GFP2 as donor (D) and eYFP as acceptor (A): namely, two fluorescent duplexes (i.e., DA and AD) and a fluorescent triplex (ADA). According to the theory, the FRET efficiency of a multiplex such as ADAA or ADA can be predicted from that of analogs containing a single acceptor (e.g., NDAN, NDNA, and ADNN, or DA and AD, respectively). Relatively small but statistically significant differences were observed between the measured and predicted FRET efficiencies of the two multiplexes. While elucidation of the cause of this mismatch could be a worthy endeavor, the discrepancy does not appear to question the theoretical underpinnings of a large family of FRET-based methods for determining the stoichiometry and quaternary structure of complexes of macromolecules in living cells. PMID:25863053

  15. 8-spot smFRET analysis using two 8-pixel SPAD arrays

    PubMed Central

    Ingargiola, Antonino; Panzeri, Francesco; Sarkosh, Niusha; Gulinatti, Angelo; Rech, Ivan; Ghioni, Massimo; Weiss, Shimon; Michalet, Xavier

    2013-01-01

    Single-molecule Förster resonance energy transfer (smFRET) techniques are now widely used to address outstanding problems in biology and biophysics. In order to study freely diffusing molecules, current approaches consist in exciting a low concentration (<100 pM) sample with a single confocal spot using one or more lasers and detecting the induced single-molecule fluorescence in one or more spectrally- and/or polarization-distinct channels using single-pixel Single-Photon Avalanche Diodes (SPADs). A large enough number of single-molecule bursts must be accumulated in order to compute FRET efficiencies with sufficient statistics. As a result, the minimum timescale of observable phenomena is set by the minimum acquisition time needed for accurate measurements, typically a few minutes or more, limiting this approach mostly to equilibrium studies. Increasing smFRET analysis throughput would allow studying dynamics with shorter timescales. We recently demonstrated a new multi-spot excitation approach, employing a novel multi-pixel SPAD array, using a simplified dual-view setup in which a single 8-pixel SPAD array was used to collect FRET data from 4 independent spots. In this work we extend our results to 8 spots and use two 8-SPAD arrays to collect donor and acceptor photons and demonstrate the capabilities of this system by studying a series of doubly labeled dsDNA samples with different donor-acceptor distances ranging from low to high FRET efficiencies. Our results show that it is possible to enhance the throughput of smFRET measurements in solution by almost one order of magnitude, opening the way for studies of single-molecule dynamics with fast timescale once larger SPAD arrays become available. PMID:24386541

  16. FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET

    PubMed Central

    Lerner, Eitan; Chung, SangYoon; Weiss, Shimon; Michalet, Xavier

    2016-01-01

    Single-molecule Förster Resonance Energy Transfer (smFRET) allows probing intermolecular interactions and conformational changes in biomacromolecules, and represents an invaluable tool for studying cellular processes at the molecular scale. smFRET experiments can detect the distance between two fluorescent labels (donor and acceptor) in the 3-10 nm range. In the commonly employed confocal geometry, molecules are free to diffuse in solution. When a molecule traverses the excitation volume, it emits a burst of photons, which can be detected by single-photon avalanche diode (SPAD) detectors. The intensities of donor and acceptor fluorescence can then be related to the distance between the two fluorophores. While recent years have seen a growing number of contributions proposing improvements or new techniques in smFRET data analysis, rarely have those publications been accompanied by software implementation. In particular, despite the widespread application of smFRET, no complete software package for smFRET burst analysis is freely available to date. In this paper, we introduce FRETBursts, an open source software for analysis of freely-diffusing smFRET data. FRETBursts allows executing all the fundamental steps of smFRET bursts analysis using state-of-the-art as well as novel techniques, while providing an open, robust and well-documented implementation. Therefore, FRETBursts represents an ideal platform for comparison and development of new methods in burst analysis. We employ modern software engineering principles in order to minimize bugs and facilitate long-term maintainability. Furthermore, we place a strong focus on reproducibility by relying on Jupyter notebooks for FRETBursts execution. Notebooks are executable documents capturing all the steps of the analysis (including data files, input parameters, and results) and can be easily shared to replicate complete smFRET analyzes. Notebooks allow beginners to execute complex workflows and advanced users to

  17. Investigation of Protein-Protein Interactions and Conformational Changes in Hedgehog Signaling Pathway by FRET.

    PubMed

    Fu, Lin; Lv, Xiangdong; Xiong, Yue; Zhao, Yun

    2015-01-01

    Protein-protein interactions and signal-induced protein conformational changes are fundamental molecular events that are considered as essential in modern life sciences. Among various techniques developed to study such phenomena, fluorescence resonance energy transfer (FRET) is a widely used method with many advantages in detecting these molecular events. Here, we describe the application of FRET in the mechanistic investigation of cell signal transduction, taking the example of the Hh signaling pathway, which plays a critical role in embryonic development and tissue homeostasis. A number of general guidelines as well as some key notes have been summarized as a protocol for reader's reference. PMID:26179039

  18. FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET.

    PubMed

    Ingargiola, Antonino; Lerner, Eitan; Chung, SangYoon; Weiss, Shimon; Michalet, Xavier

    2016-01-01

    Single-molecule Förster Resonance Energy Transfer (smFRET) allows probing intermolecular interactions and conformational changes in biomacromolecules, and represents an invaluable tool for studying cellular processes at the molecular scale. smFRET experiments can detect the distance between two fluorescent labels (donor and acceptor) in the 3-10 nm range. In the commonly employed confocal geometry, molecules are free to diffuse in solution. When a molecule traverses the excitation volume, it emits a burst of photons, which can be detected by single-photon avalanche diode (SPAD) detectors. The intensities of donor and acceptor fluorescence can then be related to the distance between the two fluorophores. While recent years have seen a growing number of contributions proposing improvements or new techniques in smFRET data analysis, rarely have those publications been accompanied by software implementation. In particular, despite the widespread application of smFRET, no complete software package for smFRET burst analysis is freely available to date. In this paper, we introduce FRETBursts, an open source software for analysis of freely-diffusing smFRET data. FRETBursts allows executing all the fundamental steps of smFRET bursts analysis using state-of-the-art as well as novel techniques, while providing an open, robust and well-documented implementation. Therefore, FRETBursts represents an ideal platform for comparison and development of new methods in burst analysis. We employ modern software engineering principles in order to minimize bugs and facilitate long-term maintainability. Furthermore, we place a strong focus on reproducibility by relying on Jupyter notebooks for FRETBursts execution. Notebooks are executable documents capturing all the steps of the analysis (including data files, input parameters, and results) and can be easily shared to replicate complete smFRET analyzes. Notebooks allow beginners to execute complex workflows and advanced users to

  19. Multiscale Modelling of UniMolecular FRET Probes Using Monte Carlo Simulations

    NASA Astrophysics Data System (ADS)

    Sanyal, Shourjya; MacKernan, Donal; Coker, David F.

    2015-09-01

    Föster Resonance Energy Transfer (FRET) based biosensors are widely used in experimental biology to understand spatiotemporal dynamics of protein pairs both in-vivo and in-vitro. In our study we have developed an idealised model consisting of two macroparticles, representing proteins attached to fluorescent chromophores, linked with an idealized flexible linker consisting of N point-like beads joined by harmonic springs. Monte Carlo simulations with these models are used to investigate the influence of flexible linkers on unimolecular FRET based bio-sensors. The results provide qualitative insight into the efficacy of designing flexible peptide linkers.

  20. Time resolved FRET measurement in various heterogeneous media using merocyanine dye as a donor

    NASA Astrophysics Data System (ADS)

    Kedia, Niraja; Bagchi, Sanjib

    2015-06-01

    Ultrafast fluorescence resonance energy transfer (FRET) from a merocyanine dye to a Rhodamine 6G (R6G) molecule in micelles formed by the surfactants SDS and DTAB and also in a catanionic vesicle formed by SDS and DTAB has been studied by picosecond time resolved emission spectroscopy. Here the dye acts as a donor molecule and R6G acts as the acceptor molecule. Multiple timescales of FRET have been detected, namely, an ultrafast component of 100-500 ps and relatively long component (1800-3300 ps). The different time scales are attributed to different donor-acceptor distances.

  1. CASL Virtual Reactor Predictive Simulation: Grid-to-Rod Fretting Wear

    SciTech Connect

    Roger, Lu Y.; Karoutas, Zeses; Sham, Sam

    2011-01-01

    Grid-to-Rod Fretting (GTRF) wear is currently one of the main causes of fuel rod leaking in pressurized water reactors. The Consortium for Advanced Simulation of Light Water Reactors (CASL) has identified GTRF as one of the Challenge Problems that drive the requirement for the development and application of a modeling and simulation computational environment for predictive simulation of light water reactors. This paper presents fretting wear simulation methodology currently employed by Westinghouse, a CASL industrial partner, to address GTRF. The required advancements in the computational and materials science modeling areas to develop a predictive simulation environment by CASL to address GTRF are outlined.

  2. Alternating Laser Excitation for Solution-Based Single-Molecule FRET.

    PubMed

    Kapanidis, Achillefs; Majumdar, Devdoot; Heilemann, Mike; Nir, Eyal; Weiss, Shimon

    2015-11-01

    Single-molecule fluorescence resonance energy transfer (smFRET) has been widely applied to the study of fluorescently labeled biomolecules on surfaces and in solution. Sorting single molecules based on fluorescent dye stoichiometry provides one with further layers of information and also enables "filtering" of unwanted molecules from the analysis. We accomplish this sorting by using alternating laser excitation (ALEX) in combination with smFRET measurements; here we describe the implementation of these methodologies for the study of biomolecules in solution. PMID:26527772

  3. The Necessity of a New Type Test Rig for the Development of an Evaluation Method in Grid Fretting Problems

    SciTech Connect

    Lee, Young-Ho; Kim, Hyung-Kyu

    2007-07-01

    A grid fretting problem is recognized as one of the most important degradation mechanisms even though the examination results of fretting experiments could be applied to the development and design of spacer grid structures. This is because it is difficult to develop a fretting wear model for a grid fretting problem due to the various wear mechanisms involved according to the mechanical and environmental variables, the contact condition with a spring/dimple and the material properties. A number of spring shapes has been developed in KAERI and their performance tests such as fretting wear, flow-induced vibration (FIV) tests, etc. have been carried out from a part unit to a full assembly scale. From the unit part fretting test results, one of the noticeable results is that the contacting force (normal load) was gradually decreased with increasing number of fretting cycles due to a depth increase and this behavior was closely related to the contacting spring shape. When considering the actual contact condition between a fuel rod and a spring/dimple, if a fretting wear progresses due to a FIV under a specific normal load exerted on the fuel rod by an elastic deformation of the spring, the contacting force between the fuel rod and dimple that are located in the opposite side should be decreased. Consequently, an evaluation of developed spacer grids against fretting wear damage should be performed with the results of 1x1 cell unit experiments because a contacting force is one of the most important variables that influences a fretting wear mechanism. The discussion was focused on the development procedure of a new test rig and its performance by using a 1x1 cell unit test rig. (authors)

  4. Structural, Dynamical and Electronic Transport Properties of Modified DNA Duplexes Containing Size-Expanded Nucleobases

    SciTech Connect

    Sumpter, Bobby G; Fuentes-Cabrera, Miguel A

    2011-01-01

    Among the distinct strategies proposed to expand the genetic alphabet, size-expanded nucleobases are promising for the development of modified DNA duplexes with improved biotechnological properties. In particular, duplexes built up by replacing canonical bases with the corresponding benzo-fused counterparts could be valuable as molecular nanowires. In this context, this study reports the results of classical molecular dynamics simulations carried out to examine the structural and dynamical features of size-expanded DNAs, including both hybrid duplexes containing mixed pairs of natural and benzo-fused bases (xDNA) and pure size-expanded (xxDNA) duplexes. Furthermore, the electronic structure of both natural and size-expanded duplexes is examined by means of density functional computations. The results confirm that the structural and flexibility properties of the canonical DNA are globally little affected by the presence of benzo-fused bases. The most relevant differences are found in the enhanced size of the grooves, and the reduction in the twist. However, the analysis also reveals subtle structural effects related to the nature and sequence of benzo-fused bases in the duplex. On the other hand, electronic structure calculations performed for xxDNAs confirm the reduction in the HOMO-LUMO gap predicted from the analysis of the natural bases and their size-expanded counterparts, which suggests that pure size-expanded DNAs can be good conductors. A more complex situation is found for xDNAs, where fluctuations in the electrostatic interaction between base pairs exerts a decisive influence on the modulation of the energy gap.

  5. Remarkable stabilization of antiparallel DNA triplexes by strong stacking effects of consecutively modified nucleobases containing thiocarbonyl groups.

    PubMed

    Yamada, Kenji; Hattori, Yusaku; Inde, Takeshi; Kanamori, Takashi; Ohkubo, Akihiro; Seio, Kohji; Sekine, Mitsuo

    2013-02-01

    The consecutive arrangement of 2'-deoxy-6-thioguanosines (s(6)Gs) and 4-thiothymidines (s(4)Ts) in antiparallel triplex-forming oligonucleotides (TFOs) considerably stabilized the resulting antiparallel triplexes with high base recognition ability by the strong stacking effects of thiocarbonyl groups. This result was remarkable because chemical modifications of the sugar moieties and nucleobases of antiparallel TFOs generally destabilize triplex structures. Moreover, in comparison with unmodified TFOs, it was found that TFOs containing s(6)Gs and s(4)Ts could selectively bind to the complementary DNA duplex but not to mismatched DNA duplexes or single-stranded RNA. PMID:23287737

  6. Natural versus artificial creation of base pairs in DNA: origin of nucleobases from the perspectives of unnatural base pair studies.

    PubMed

    Hirao, Ichiro; Kimoto, Michiko; Yamashige, Rie

    2012-12-18

    Since life began on Earth, the four types of bases (A, G, C, and T(U)) that form two sets of base pairs have remained unchanged as the components of nucleic acids that replicate and transfer genetic information. Throughout evolution, except for the U to T modification, the four base structures have not changed. This constancy within the genetic code raises the question of how these complicated nucleotides were generated from the molecules in a primordial soup on the early Earth. At some prebiotic stage, the complementarity of base pairs might have accelerated the generation and accumulation of nucleotides or oligonucleotides. We have no clues whether one pair of nucleobases initially appeared on the early Earth during this process or a set of two base pairs appeared simultaneously. Recently, researchers have developed new artificial pairs of nucleobases (unnatural base pairs) that function alongside the natural base pairs. Some unnatural base pairs in duplex DNA can be efficiently and faithfully amplified in a polymerase chain reaction (PCR) using thermostable DNA polymerases. The addition of unnatural base pair systems could expand the genetic alphabet of DNA, thus providing a new mechanism for the generation novel biopolymers by the site-specific incorporation of functional components into nucleic acids and proteins. Furthermore, the process of unnatural base pair development might provide clues to the origin of the natural base pairs in a primordial soup on the early Earth. In this Account, we describe the development of three representative types of unnatural base pairs that function as a third pair of nucleobases in PCR and reconsider the origin of the natural nucleic acids. As researchers developing unnatural base pairs, they use repeated "proof of concept" experiments. As researchers design new base pairs, they improve the structures that function in PCR and eliminate those that do not. We expect that this process is similar to the one functioning in the

  7. Nucleobase-mediated, photocatalytic production of amphiphiles to promote the self-assembly of a simple self-replicating protocell.

    NASA Astrophysics Data System (ADS)

    Monnard, Pierre-Alain; Maurer, Sarah, E.; Albertsen, Anders, N.; Boncella, James, M.; Cape, Jonathan, L.

    replaced by a single nucleobase, 8-oxoguanine, which is tethered to one bipyridine ligand of the metal center. We report here the following major steps towards this chemical protocell: 1) the spontaneous formation of chemical structures consisting of decanoic acid, its precursor, and the simplified NA-ruthenium complexes. 2) the metabolism mediation by a nucleobase to effectively promote the photochemical amphiphile synthesis. 3) the demonstration of reaction selectivity dependent on the nature of the information molecule since only one specific nucleobase that has the required redox potential allows the metabolism to function. Finally, 4) the photochemical formation of amphiphiles can occur efficiently within a preformed membrane, i.e., the protocell compartment. The next step is the integration of short nucleic acid oligomers as opposed to a single nucleobase as the information material to study their photocatalytic activity mediation and polymerization.

  8. Muscarinic interactions of bisindolylmaleimide analogues.

    PubMed

    Lazareno, S; Popham, A; Birdsall, N J

    1998-11-01

    We have used radioligand binding studies to determine the affinities of seven bisindolylmaleimide analogues, six of which are selective inhibitors of protein kinase C, at human muscarinic M1-M4 receptors. The compounds were most potent at M1 receptors, and Ro-31-8220 was the most potent analogue, with a Kd of 0.6 microM at M1 receptors. The weakest compounds, bisindolylmaleimide IV and bisindolylmaleimide V, had Kd values of 100 microM. If it is necessary to use protein kinase C inhibitors at concentrations of 10 microM or more in studies involving muscarinic receptors then bisindolylmaleimide IV may be the most appropriate inhibitor to use. PMID:9851596

  9. Substrate analogues for isoprenoid enzymes

    SciTech Connect

    Stremler, K.E.

    1987-01-01

    Diphosphonate analogues of geranyl diphosphate, resistant to degradation by phosphatases, were found to be alternate substrates for the reaction with farnesyl diphosphate synthetase isolated from avian liver. The difluoromethane analogue was shown to be the better alternate substrate, in agreement with solvolysis results which indicate that the electronegativity of the difluoromethylene unit more closely approximates that of the normal bridging oxygen. The usefulness of the C/sub 10/ difluoro analogue, for detecting low levels of isoprenoid enzymes in the presence of high levels of phosphatase activity, was demonstrated with a cell-free preparation from lemon peel. A series of C/sub 5/ through C/sub 15/ homoallylic and allylic diphosphonates, as well as two 5'-nucleotide diphosphonates, was prepared in high overall yield using the activation-displacement sequence. Radiolabeled samples of several of the allylic diphosphonates were prepared with tritium located at C1. A series of geraniols, stereospecifically deuterated at C1, was prepared. The enantiomeric purities and absolute configurations were determined by derivatization as the mandelate esters for analysis by /sup 1/H NMR. The stereochemistry of the activation-displacement sequence was examined using C1-deuterated substrates.

  10. Policy issues in space analogues

    NASA Astrophysics Data System (ADS)

    Auger, Robin N.; Facktor, Debra D.

    Space mission planning is increasingly focusing on destinations beyond Earth orbit. Advancements in technology will inevitably be required to enable long-duration human spaceflight missions, and breakthroughs in the policy arena will also be needed to achieve success in such missions. By exploring how policy issues have been addressed in analogous extreme environments, policymakers can develop a framework for addressing these issues as they apply to long-term human spaceflight. Policy issues that need to be addressed include: crew selection, training, organization, and activities, medical testing, illness, injury, and death; communication; legal accountability and liability; mission safety and risk management; and environmental contamination. This paper outlines the approach of a study underway by The George Washington University and ANSER to examine how these policy issues have been addressed in several analogues and how the experiences of these analogues can help formulate policies for long-duration human spaceflight missions. Analogues being studied include Antarctic bases, submarine voyages, undersea stations, Biosphere 2, and the U.S. Skylab and Russian Mir space stations.

  11. Phosphonate analogue substrates for enolase.

    PubMed

    Anderson, V E; Cleland, W W

    1990-11-20

    Phosphonate analogues in which the bridge between C-2 and phosphorus is a CH2 group are slow substrates for yeast enolase. The pH variation of the kinetic parameters for the methylene analogue of 2-phosphoglycerate suggests that the substrate binds as a dianion and that Mg2+ can bind subsequently only if a metal ligand and the catalytic base are unprotonated. Primary deuterium isotope effects of 4-8 on V/KMg, but ones of only 1.15-1.32 on V for dehydration, show that proton removal to give the carbanion intermediate largely limits V/KMg and that a slow step follows which largely limits V (presumably carbanion breakdown). Since there is a D2O solvent isotope effect on V for the reverse reaction of 5, but not an appreciable one on the forward reaction, it appears that the slow rates with phosphonate analogues result from the fact that the carbanion intermediate is more stable than that formed from the normal substrates, and its reaction in both directions limits V. Increased stability as a result of replacement of oxygen by carbon at C-2 of the carbanion is the expected chemical behavior. PMID:2271661

  12. FRET Studies Between CdTe Capped by Small-Molecule Ligands and Fluorescent Protein

    NASA Astrophysics Data System (ADS)

    Zhang, Yue; Zhou, Dejian; He, Junhui

    2014-12-01

    Water-soluble luminescent semiconductor nanocrystals also known as quantum dots (QDs) that have prominent photostability, wide absorption cross sections and tunable narrow emission, have been shown as promising probes in immunoassays. QDs are often used as donors in fluorescence resonance energy transfer (FRET) based sensors using organic dyes or fluorescent proteins as acceptors. Here, the FRET between a QD donor and fluorescent protein acceptors has been studied. The fluorescent protein (FP)mCherry appended with a hexa-histidine-tag could effectively self-assemble onto CdTe to produce small donor-acceptor distances and hence highly efficient FRET (efficiency > 80%) at relatively low FP:CdTe copy numbers (ca.1). Using the Förster dipole-dipole interaction formula, the Förster radius (R0) and respective donor-acceptor distances for the CdTe-FP FRET systems have been calculated. The binding constants (Kd) of the QD-FP systems have also been evaluated by the emission spectra.

  13. Evaluation of Ti-48Al-2Cr-2Nb Under Fretting Conditions

    NASA Technical Reports Server (NTRS)

    Miyoshi, Kazuhisa; Lerch, Bradley A.; Draper, Susan L.; Raj, Sai V.

    2001-01-01

    The fretting behavior of Ti-48Al-2Cr-2Nb (y-TiAl) in contact with the nickel-base superalloy 718 was examined in air at temperatures from 296 to 823 K (23 to 550 C). The interfacial adhesive bonds between Ti-48Al-2Cr-2Nb and superalloy 718 were generally stronger than the cohesive bonds within Ti-48Al-2Cr-2Nb. The failed Ti-48Al-2Cr-2Nb debris subsequently transferred to the superalloy 718. In reference experiments conducted with Ti-6Al-4V against superalloy 718 under identical fretting conditions, the degree of transfer was greater for Ti-6A1-4V than for Ti-48Al-2Cr-2Nb. Wear of Ti-48Al-2Cr-2Nb generally decreased with increasing fretting frequency. The increasing rate of oxidation at elevated temperatures led to a drop in wear at 473 K. However, fretting wear increased as the temperature was increased from 473 to 823 K. At 723 and 823 K, oxide film disruption generated cracks, loose wear debris, and pits on the Ti-48Al-2Cr-2Nb wear surface. Both increasing slip amplitude and increasing load tended to produce more metallic wear debris, causing severe abrasive wear in the contacting metals.

  14. FRET study of G-quadruplex forming fluorescent oligonucleotide probes at the lipid monolayer interface

    NASA Astrophysics Data System (ADS)

    Swiatkowska, Angelika; Kosman, Joanna; Juskowiak, Bernard

    2016-01-01

    Spectral properties and G-quadruplex folding ability of fluorescent oligonucleotide probes at the cationic dioctadecyldimethylammonium bromide (DODAB) monolayer interface are reported. Two oligonucleotides, a 19-mer bearing thrombin binding aptamer sequence and a 21-mer with human telomeric sequence, were end-labeled with fluorescent groups (FAM and TAMRA) to give FRET probes F19T and F21T, respectively. The probes exhibited abilities to fold into a quadruplex structure and to bind metal cations (Na+ and K+). Fluorescence spectra of G-quadruplex FRET probes at the monolayer interface are reported for the first time. Investigations included film balance measurements (π-A isotherms) and fluorescence spectra recording using a fiber optic accessory interfaced with a spectrofluorimeter. The effect of the presence of DODAB monolayer, metal cations and the surface pressure of monolayer on spectral behavior of FRET probes were examined. Adsorption of probe at the cationic monolayer interface resulted in the FRET signal enhancement even in the absence of metal cations. Variation in the monolayer surface pressure exerted rather modest effect on the spectral properties of probes. The fluorescence energy transfer efficiency of monolayer adsorbed probes increased significantly in the presence of sodium or potassium ion in subphase, which indicated that the probes retained their cation binding properties when adsorbed at the monolayer interface.

  15. Highly Sensitive Homogeneous Immunoassays Based on Construction of Silver Triangular Nanoplates-Quantum Dots FRET System

    PubMed Central

    Zeng, Qinghui; Li, Qin; Ji, Wenyu; Bin, Xue; Song, Jie

    2016-01-01

    With growing concerns about health issues worldwide, elegant sensors with high sensitivity and specificity for virus/antigens (Ag) detection are urgent to be developed. Homogeneous immunoassays (HIA) are an important technique with the advantages of small sample volumes requirement and pretreatment-free process. HIA are becoming more favorable for the medical diagnosis and disease surveillance than heterogeneous immunoassays. An important subset of HIA relies on the effect of fluorescence resonance energy transfer (FRET) via a donor-acceptor (D–A) platform, e.g., quantum dots (QDs) donor based FRET system. Being an excellent plasmonic material, silver triangular nanoplates (STNPs) have unique advantages in displaying surface plasmon resonance in the visible to near infrared spectral region, which make them a better acceptor for pairing with QDs in a FRET-based sensing system. However, the reported STNPs generally exhibited broad size distributions, which would greatly restrict their application as HIA acceptor for high detection sensitivity and specificity purpose. In this work, uniform STNPs and red-emitting QDs are firstly applied to construct FRET nanoplatform in the advanced HIA and further be exploited for analyzing virus Ag. The uniform STNPs/QDs nanoplatform based medical sensor provides a straightforward and highly sensitive method for Ag analysis in homogeneous form. PMID:27198713

  16. Highly Sensitive Homogeneous Immunoassays Based on Construction of Silver Triangular Nanoplates-Quantum Dots FRET System

    NASA Astrophysics Data System (ADS)

    Zeng, Qinghui; Li, Qin; Ji, Wenyu; Bin, Xue; Song, Jie

    2016-05-01

    With growing concerns about health issues worldwide, elegant sensors with high sensitivity and specificity for virus/antigens (Ag) detection are urgent to be developed. Homogeneous immunoassays (HIA) are an important technique with the advantages of small sample volumes requirement and pretreatment-free process. HIA are becoming more favorable for the medical diagnosis and disease surveillance than heterogeneous immunoassays. An important subset of HIA relies on the effect of fluorescence resonance energy transfer (FRET) via a donor-acceptor (D–A) platform, e.g., quantum dots (QDs) donor based FRET system. Being an excellent plasmonic material, silver triangular nanoplates (STNPs) have unique advantages in displaying surface plasmon resonance in the visible to near infrared spectral region, which make them a better acceptor for pairing with QDs in a FRET-based sensing system. However, the reported STNPs generally exhibited broad size distributions, which would greatly restrict their application as HIA acceptor for high detection sensitivity and specificity purpose. In this work, uniform STNPs and red-emitting QDs are firstly applied to construct FRET nanoplatform in the advanced HIA and further be exploited for analyzing virus Ag. The uniform STNPs/QDs nanoplatform based medical sensor provides a straightforward and highly sensitive method for Ag analysis in homogeneous form.

  17. Sequential data assimilation for single-molecule FRET photon-counting data

    SciTech Connect

    Matsunaga, Yasuhiro; Kidera, Akinori; Sugita, Yuji

    2015-06-07

    Data assimilation is a statistical method designed to improve the quality of numerical simulations in combination with real observations. Here, we develop a sequential data assimilation method that incorporates one-dimensional time-series data of smFRET (single-molecule Förster resonance energy transfer) photon-counting into conformational ensembles of biomolecules derived from “replicated” molecular dynamics (MD) simulations. A particle filter using a large number of “replicated” MD simulations with a likelihood function for smFRET photon-counting data is employed to screen the conformational ensembles that match the experimental data. We examine the performance of the method using emulated smFRET data and coarse-grained (CG) MD simulations of a dye-labeled polyproline-20. The method estimates the dynamics of the end-to-end distance from smFRET data as well as revealing that of latent conformational variables. The particle filter is also able to correct model parameter dependence in CG MD simulations. We discuss the applicability of the method to real experimental data for conformational dynamics of biomolecules.

  18. Nano-biophotonic hybrid materials with controlled FRET efficiency engineered from quantum dots and bacteriorhodopsin

    NASA Astrophysics Data System (ADS)

    Bouchonville, Nicolas; Le Cigne, Anthony; Sukhanova, Alyona; Molinari, Michael; Nabiev, Igor

    2013-08-01

    Förster resonance energy transfer (FRET) between CdSe/ZnS core/shell quantum dots (QDs) and the photochromic protein bacteriorhodopsin (bR) in its natural purple membrane (PM) has been modulated by independent tuning of the Förster radius, the overlap integral between the donor emission spectrum and the acceptor absorption spectrum, and the distance between the donor (QD) and acceptor (bR retinal). The results have shown that the observed energy transfer from QDs to bR corresponds to that predicted by a multiple-acceptor geometric model describing the FRET phenomenon for QDs quasi-epitaxied on a crystalline lattice of bR trimers. Linking of QDs and bR via streptavidin-biotin linkers of different lengths improved FRET, with an efficiency as high as 82%, substantially exceeding the values predicted by the classical FRET theory. The data not only demonstrate the possibility of nano-bioengineering of efficient hybrid materials with controlled energy transfer properties, but also emphasize the necessity to develop an advanced theory of nano-bio energy transfer that would explain experimental effects contradicting the existing theoretical models.

  19. Controlled FRET efficiency in nano-bio hybrid materials made from semiconductor quantum dots and bacteriorhodopsin

    NASA Astrophysics Data System (ADS)

    Bouchonville, Nicolas; Le Cigne, Anthony; Sukhanova, Alyona; Saab, Marie-belle; Troyon, Michel; Molinari, Michael; Nabiev, Igor

    2012-10-01

    Förster resonance energy transfer (FRET) between CdSe/ZnS core/shell quantum dots (QDs) and the photochromic protein bacteriorhodopsin (bR) in its natural purple membrane (PM) has been modulated by independent tuning of the Förster radius, overlap integral of the donor emission spectrum and acceptor absorption spectrum, and the distance between the donor (QD) and acceptor (bR retinal). The results have shown that the observed energy transfer from QDs to bR corresponds to that predicted by a multiple-acceptors geometric model describing the FRET phenomenon for QDs quasi-epitaxied on a crystalline lattice of bR trimers. Linking of QDs and bR via streptavidin-biotin linkers of different lengths caused FRET with an efficiency reaching 82%, strongly exceeding the values predicted by the classical FRET theory. The data not only demonstrate the possibility of nano-bioengineering of efficient hybrid materials with controlled energy-transfer properties, but also emphasize the necessity to develop an advanced theory of nano-bio energy transfer that would explain experimental effects contradicting the existing theoretical models.

  20. Highly sensitive detection of DNA methylation levels by using a quantum dot-based FRET method.

    PubMed

    Ma, Yunfei; Zhang, Honglian; Liu, Fangming; Wu, Zhenhua; Lu, Shaohua; Jin, Qinghui; Zhao, Jianlong; Zhong, Xinhua; Mao, Hongju

    2015-11-01

    DNA methylation is the most frequently studied epigenetic modification that is strongly involved in genomic stability and cellular plasticity. Aberrant changes in DNA methylation status are ubiquitous in human cancer and the detection of these changes can be informative for cancer diagnosis. Herein, we reported a facile quantum dot-based (QD-based) fluorescence resonance energy transfer (FRET) technique for the detection of DNA methylation. The method relies on methylation-sensitive restriction enzymes for the differential digestion of genomic DNA based on its methylation status. Digested DNA is then subjected to PCR amplification for the incorporation of Alexa Fluor-647 (A647) fluorophores. DNA methylation levels can be detected qualitatively through gel analysis and quantitatively by the signal amplification from QDs to A647 during FRET. Furthermore, the methylation levels of three tumor suppressor genes, PCDHGB6, HOXA9 and RASSF1A, in 20 lung adenocarcinoma and 20 corresponding adjacent nontumorous tissue (NT) samples were measured to verify the feasibility of the QD-based FRET method and a high sensitivity for cancer detection (up to 90%) was achieved. Our QD-based FRET method is a convenient, continuous and high-throughput method, and is expected to be an alternative for detecting DNA methylation as a biomarker for certain human cancers. PMID:26446775

  1. Complex RNA Folding Kinetics Revealed by Single-Molecule FRET and Hidden Markov Models

    PubMed Central

    2014-01-01

    We have developed a hidden Markov model and optimization procedure for photon-based single-molecule FRET data, which takes into account the trace-dependent background intensities. This analysis technique reveals an unprecedented amount of detail in the folding kinetics of the Diels–Alderase ribozyme. We find a multitude of extended (low-FRET) and compact (high-FRET) states. Five states were consistently and independently identified in two FRET constructs and at three Mg2+ concentrations. Structures generally tend to become more compact upon addition of Mg2+. Some compact structures are observed to significantly depend on Mg2+ concentration, suggesting a tertiary fold stabilized by Mg2+ ions. One compact structure was observed to be Mg2+-independent, consistent with stabilization by tertiary Watson–Crick base pairing found in the folded Diels–Alderase structure. A hierarchy of time scales was discovered, including dynamics of 10 ms or faster, likely due to tertiary structure fluctuations, and slow dynamics on the seconds time scale, presumably associated with significant changes in secondary structure. The folding pathways proceed through a series of intermediate secondary structures. There exist both compact pathways and more complex ones, which display tertiary unfolding, then secondary refolding, and, subsequently, again tertiary refolding. PMID:24568646

  2. Fast Folding Dynamics of an Intermediate State in RNase H Measured by Single-Molecule FRET.

    PubMed

    Stockmar, Florian; Kobitski, Andrei Yu; Nienhaus, Gerd Ulrich

    2016-02-01

    We have studied the folding kinetics of the core intermediate (I) state of RNase H by using a combination of single-molecule FRET (smFRET) and hidden Markov model analysis. To measure fast dynamics in thermal equilibrium as a function of the concentration of the denaturant GdmCl, a special FRET labeled variant, RNase H 60-113, which is sensitive to folding of the protein core, was immobilized on PEGylated surfaces. Conformational transitions between the unfolded (U) state and the I state could be described by a two-state model within our experimental time resolution, with millisecond mean residence times. The I state population was always a minority species in the entire accessible range of denaturant concentrations. By introducing the measured free energy differences between the U and I states as constraints in global fits of the GdmCl dependence of FRET histograms of a differently labeled RNase H variant (RNase H 3-135), we were able to reveal the free energy differences and, thus, population ratios of all three macroscopic state ensembles, U, I and F (folded state) as a function of denaturant concentration. PMID:26747376

  3. Facile creation of FRET systems from a pH-responsive AIE fluorescent vesicle.

    PubMed

    Wang, Xing; Yang, Yanyu; Zuo, Yunfei; Yang, Fei; Shen, Hong; Wu, Decheng

    2016-04-18

    We demonstrate a facile approach to constructing aggregation induced emission (AIE) fluorescent vesicles assembled using a PEG-POSS-(TPE)7 polymer. The narrow wall thickness provides an ideal confined space for creating fluorescence resonance energy transfer (FRET) systems between TPE donors and encapsulated FITC or DOX acceptors. PMID:27001923

  4. Real-time submillisecond single-molecule FRET dynamics of freely diffusing molecules with liposome tethering

    NASA Astrophysics Data System (ADS)

    Kim, Jae-Yeol; Kim, Cheolhee; Lee, Nam Ki

    2015-04-01

    Single-molecule fluorescence resonance energy transfer (smFRET) is one of the powerful techniques for deciphering the dynamics of unsynchronized biomolecules. However, smFRET is limited in its temporal resolution for observing dynamics. Here, we report a novel method for observing real-time dynamics with submillisecond resolution by tethering molecules to freely diffusing 100-nm-sized liposomes. The observation time for a diffusing molecule is extended to 100 ms with a submillisecond resolution, which allows for direct analysis of the transition states from the FRET time trace using hidden Markov modelling. We measure transition rates of up to 1,500 s-1 between two conformers of a Holliday junction. The rapid diffusional migration of Deinococcus radiodurans single-stranded DNA-binding protein (SSB) on single-stranded DNA is resolved by FRET, faster than that of Escherichia coli SSB by an order of magnitude. Our approach is a powerful method for studying the dynamics and movements of biomolecules at submillisecond resolution.

  5. Highly Sensitive Homogeneous Immunoassays Based on Construction of Silver Triangular Nanoplates-Quantum Dots FRET System.

    PubMed

    Zeng, Qinghui; Li, Qin; Ji, Wenyu; Bin, Xue; Song, Jie

    2016-01-01

    With growing concerns about health issues worldwide, elegant sensors with high sensitivity and specificity for virus/antigens (Ag) detection are urgent to be developed. Homogeneous immunoassays (HIA) are an important technique with the advantages of small sample volumes requirement and pretreatment-free process. HIA are becoming more favorable for the medical diagnosis and disease surveillance than heterogeneous immunoassays. An important subset of HIA relies on the effect of fluorescence resonance energy transfer (FRET) via a donor-acceptor (D-A) platform, e.g., quantum dots (QDs) donor based FRET system. Being an excellent plasmonic material, silver triangular nanoplates (STNPs) have unique advantages in displaying surface plasmon resonance in the visible to near infrared spectral region, which make them a better acceptor for pairing with QDs in a FRET-based sensing system. However, the reported STNPs generally exhibited broad size distributions, which would greatly restrict their application as HIA acceptor for high detection sensitivity and specificity purpose. In this work, uniform STNPs and red-emitting QDs are firstly applied to construct FRET nanoplatform in the advanced HIA and further be exploited for analyzing virus Ag. The uniform STNPs/QDs nanoplatform based medical sensor provides a straightforward and highly sensitive method for Ag analysis in homogeneous form. PMID:27198713

  6. Development of the High Temperature Fretting Wear Simulator for Steam Generator

    NASA Astrophysics Data System (ADS)

    Lee, Choon Yeol; Kim, Joong Ho; Bae, Joon Woo; Chai, Young Suck

    In nuclear power plant, fretting wear due to a combination of impact and sliding motions of the U-tubes against the supports and/or foreign objects caused by flow induced vibration, can make a serious problem in steam generator. A test rig, fretting wear simulator, is developed to elucidate fretting wear mechanism qualitatively and quantitatively. The realistic condition of steam generator of high temperature up to 320°C, high pressure up to 15 MPa, and water environment could be achieved by a test rig. The fretting wear simulator consists of main frame, water loop system, and control unit. Actual contact region under a realistic condition of steam generator was isolated using autoclave. Effects of various parameters such as the amounts of impact and sliding motions, applied loads and initial gaps and so forth are considered in this research. After the experiment, wear damage was measured by a three-dimensional profiler and the surface was also studied by SEM microscopically. Initial results were also presented.

  7. Tracing the conformational changes in BSA using FRET with environmentally-sensitive squaraine probes

    NASA Astrophysics Data System (ADS)

    Govor, Iryna V.; Tatarets, Anatoliy L.; Obukhova, Olena M.; Terpetschnig, Ewald A.; Gellerman, Gary; Patsenker, Leonid D.

    2016-06-01

    A new potential method of detecting the conformational changes in hydrophobic proteins such as bovine serum albumin (BSA) is introduced. The method is based on the change in the Förster resonance energy transfer (FRET) efficiency between protein-sensitive fluorescent probes. As compared to conventional FRET based methods, in this new approach the donor and acceptor dyes are not covalently linked to protein molecules. Performance of the new method is demonstrated using the protein-sensitive squaraine probes Square-634 (donor) and Square-685 (acceptor) to detect the urea-induced conformational changes of BSA. The FRET efficiency between these probes can be considered a more sensitive parameter to trace protein unfolding as compared to the changes in fluorescence intensity of each of these probes. Addition of urea followed by BSA unfolding causes a noticeable decrease in the emission intensities of these probes (factor of 5.6 for Square-634 and 3.0 for Square-685), and the FRET efficiency changes by a factor of up to 17. Compared to the conventional method the new approach therefore demonstrates to be a more sensitive way to detect the conformational changes in BSA.

  8. Spectroscopic investigation of alloyed quantum dot-based FRET to cresyl violet dye.

    PubMed

    Kotresh, M G; Adarsh, K S; Shivkumar, M A; Mulimani, B G; Savadatti, M I; Inamdar, S R

    2016-05-01

    Quantum dots (QDs), bright luminescent semiconductor nanoparticles, have found numerous applications ranging from optoelectronics to bioimaging. Here, we present a systematic investigation of fluorescence resonance energy transfer (FRET) from hydrophilic ternary alloyed quantum dots (CdSeS/ZnS) to cresyl violet dye with a view to explore the effect of composition of QD donors on FRET efficiency. Fluorescence emission of QD is controlled by varying the composition of QD without altering the particle size. The results show that quantum yield of the QDs increases with increase in the emission wavelength. The FRET parameters such as spectral overlap J(λ), Förster distance R0 , intermolecular distance (r) , rate of energy transfer kT (r), and transfer efficiency (E) are determined by employing both steady-state and time-resolved fluorescence spectroscopy. Additionally, dynamic quenching is noticed to occur in the present FRET system. Stern-Volmer (KD ) and bimolecular quenching constants (kq ) are determined from the Stern-Volmer plot. It is observed that the transfer efficiency follows a linear dependence on the spectral overlap and the quantum yield of the donor as predicted by the Förster theory upon changing the composition of the QD. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26333828

  9. Paramagnetic Nanoparticles as a Platform for FRET-Based Sarcosine Picomolar Detection

    PubMed Central

    Heger, Zbynek; Cernei, Natalia; Krizkova, Sona; Masarik, Michal; Kopel, Pavel; Hodek, Petr; Zitka, Ondrej; Adam, Vojtech; Kizek, Rene

    2015-01-01

    Herein, we describe an ultrasensitive specific biosensing system for detection of sarcosine as a potential biomarker of prostate carcinoma based on Förster resonance energy transfer (FRET). The FRET biosensor employs anti-sarcosine antibodies immobilized on paramagnetic nanoparticles surface for specific antigen binding. Successful binding of sarcosine leads to assembly of a sandwich construct composed of anti-sarcosine antibodies keeping the Förster distance (Ro) of FRET pair in required proximity. The detection is based on spectral overlap between gold-functionalized green fluorescent protein and antibodies@quantum dots bioconjugate (λex 400 nm). The saturation curve of sarcosine based on FRET efficiency (F604/F510 ratio) was tested within linear dynamic range from 5 to 50 nM with detection limit down to 50 pM. Assembled biosensor was then successfully employed for sarcosine quantification in prostatic cell lines (PC3, 22Rv1, PNT1A), and urinary samples of prostate adenocarcinoma patients. PMID:25746688

  10. Solution-Based Single-Molecule FRET Studies of K(+) Channel Gating in a Lipid Bilayer.

    PubMed

    Sadler, Emma E; Kapanidis, Achillefs N; Tucker, Stephen J

    2016-06-21

    Ion channels are dynamic multimeric proteins that often undergo multiple unsynchronized structural movements as they switch between their open and closed states. Such structural changes are difficult to measure within the context of a native lipid bilayer and have often been monitored via macroscopic changes in Förster resonance energy transfer (FRET) between probes attached to different parts of the protein. However, the resolution of this approach is limited by ensemble averaging of structurally heterogeneous subpopulations. These problems can be overcome by measurement of FRET in single molecules, but this presents many challenges, in particular the ability to control labeling of subunits within a multimeric protein with acceptor and donor fluorophores, as well as the requirement to image large numbers of individual molecules in a membrane environment. To address these challenges, we randomly labeled tetrameric KirBac1.1 potassium channels, reconstituted them into lipid nanodiscs, and performed single-molecule FRET confocal microscopy with alternating-laser excitation as the channels diffused in solution. These solution-based single-molecule FRET measurements of a multimeric ion channel in a lipid bilayer have allowed us to probe the structural changes that occur upon channel activation and inhibition. Our results provide direct evidence of the twist-to-shrink movement of the helix bundle crossing during channel gating and demonstrate how this method might be applied to real-time structural studies of ion channel gating. PMID:27332124

  11. Closing the Gap between Single Molecule and Bulk FRET Analysis of Nucleosomes

    PubMed Central

    Gansen, Alexander; Hieb, Aaron R.; Böhm, Vera; Tóth, Katalin; Langowski, Jörg

    2013-01-01

    Nucleosome structure and stability affect genetic accessibility by altering the local chromatin morphology. Recent FRET experiments on nucleosomes have given valuable insight into the structural transformations they can adopt. Yet, even if performed under seemingly identical conditions, experiments performed in bulk and at the single molecule level have given mixed answers due to the limitations of each technique. To compare such experiments, however, they must be performed under identical conditions. Here we develop an experimental framework that overcomes the conventional limitations of each method: single molecule FRET experiments are carried out at bulk concentrations by adding unlabeled nucleosomes, while bulk FRET experiments are performed in microplates at concentrations near those used for single molecule detection. Additionally, the microplate can probe many conditions simultaneously before expending valuable instrument time for single molecule experiments. We highlight this experimental strategy by exploring the role of selective acetylation of histone H3 on nucleosome structure and stability; in bulk, H3-acetylated nucleosomes were significantly less stable than non-acetylated nucleosomes. Single molecule FRET analysis further revealed that acetylation of histone H3 promoted the formation of an additional conformational state, which is suppressed at higher nucleosome concentrations and which could be an important structural intermediate in nucleosome regulation. PMID:23637734

  12. Detection of receptor heteromers involving dopamine receptors by the sequential BRET-FRET technology.

    PubMed

    Navarro, Gemma; McCormick, Peter J; Mallol, Josefa; Lluís, Carme; Franco, Rafael; Cortés, Antoni; Casadó, Vicent; Canela, Enric I; Ferré, Sergi

    2013-01-01

    Until very recently, dopamine receptors, like other G-protein-coupled receptors, were believed to function as individual units on the cell surface. Now it has been described by several groups including ours that dopamine receptors not only function as homomers but also form heteromers with other receptors at the membrane level. Bioluminescence and fluorescence resonance energy transfer (BRET and FRET) based techniques have been very useful to determine the interaction between two receptors, but to demonstrate the existence of higher-order complexes involving more than two molecules requires more sophisticated techniques. Combining BRET and FRET in the Sequential BRET-FRET (SRET) technique permits heteromers formed by three different proteins to be identified. In SRET experiments, the oxidation of a Renilla Luciferase substrate triggers acceptor excitation by BRET and subsequent energy transfer to a FRET acceptor. Using this methodology here we describe the heteromerization between adenosine A(2A), dopamine D(2), and cannabinoids CB(1) receptors in living cells. PMID:23296780

  13. Sequential data assimilation for single-molecule FRET photon-counting data

    NASA Astrophysics Data System (ADS)

    Matsunaga, Yasuhiro; Kidera, Akinori; Sugita, Yuji

    2015-06-01

    Data assimilation is a statistical method designed to improve the quality of numerical simulations in combination with real observations. Here, we develop a sequential data assimilation method that incorporates one-dimensional time-series data of smFRET (single-molecule Förster resonance energy transfer) photon-counting into conformational ensembles of biomolecules derived from "replicated" molecular dynamics (MD) simulations. A particle filter using a large number of "replicated" MD simulations with a likelihood function for smFRET photon-counting data is employed to screen the conformational ensembles that match the experimental data. We examine the performance of the method using emulated smFRET data and coarse-grained (CG) MD simulations of a dye-labeled polyproline-20. The method estimates the dynamics of the end-to-end distance from smFRET data as well as revealing that of latent conformational variables. The particle filter is also able to correct model parameter dependence in CG MD simulations. We discuss the applicability of the method to real experimental data for conformational dynamics of biomolecules.

  14. Correlative Förster Resonance Electron Transfer-Proximity Ligation Assay (FRET-PLA) Technique for Studying Interactions Involving Membrane Proteins.

    PubMed

    Ivanusic, Daniel; Denner, Joachim; Bannert, Norbert

    2016-01-01

    This unit provides a guide and detailed protocol for studying membrane protein-protein interactions (PPI) using the acceptor-sensitized Förster resonance electron transfer (FRET) method in combination with the proximity ligation assay (PLA). The protocol in this unit is focused on the preparation of FRET-PLA samples and the detection of correlative FRET/PLA signals as well as on the analysis of FRET-PLA data and interpretation of correlative results when using cyan fluorescent protein (CFP) as a FRET donor and yellow fluorescent protein (YFP) as a FRET acceptor. The correlative application of FRET and PLA combines two powerful tools for monitoring PPI, yielding results that are more reliable than with either technique alone. © 2016 by John Wiley & Sons, Inc. PMID:27479505

  15. A practical method for monitoring FRET-based biosensors in living animals using two-photon microscopy.

    PubMed

    Tao, Wen; Rubart, Michael; Ryan, Jennifer; Xiao, Xiao; Qiao, Chunping; Hato, Takashi; Davidson, Michael W; Dunn, Kenneth W; Day, Richard N

    2015-12-01

    The commercial availability of multiphoton microscope systems has nurtured the growth of intravital microscopy as a powerful technique for evaluating cell biology in the relevant context of living animals. In parallel, new fluorescent protein (FP) biosensors have become available that enable studies of the function of a wide range of proteins in living cells. Biosensor probes that exploit Förster resonance energy transfer (FRET) are among the most sensitive indicators of an array of cellular processes. However, differences between one-photon and two-photon excitation (2PE) microscopy are such that measuring FRET by 2PE in the intravital setting remains challenging. Here, we describe an approach that simplifies the use of FRET-based biosensors in intravital 2PE microscopy. Based on a systematic comparison of many different FPs, we identified the monomeric (m) FPs mTurquoise and mVenus as particularly well suited for intravital 2PE FRET studies, enabling the ratiometric measurements from linked FRET probes using a pair of experimental images collected simultaneously. The behavior of the FPs is validated by fluorescence lifetime and sensitized emission measurements of a set of FRET standards. The approach is demonstrated using a modified version of the AKAR protein kinase A biosensor, first in cells in culture, and then in hepatocytes in the liver of living mice. The approach is compatible with the most common 2PE microscope configurations and should be applicable to a variety of different FRET probes. PMID:26333599

  16. A Novel [15N] Glutamine Flux using LC-MS/MS-SRM for Determination of Nucleosides and Nucleobases

    PubMed Central

    Jin, Feng; Bhowmik, Salil Kumar; Putluri, Vasanta; Gu, Franklin; Gohlke, Jie; Von Rundstedt, Friedrich Carl; Dasgupta, Subhamoy; Krishnapuram, Rashmi; O’Malley, Bert W.; Sreekumar, Arun; Putluri, Nagireddy

    2016-01-01

    The growth of cancer cells relies more on increased proliferation and autonomy compared to non-malignant cells. The rate of de novo nucleotide biosynthesis correlates with cell proliferation rates. In part, glutamine is needed to sustain high rates of cellular proliferation as a key nitrogen donor in purine and pyrimidine nucleotide biosynthesis. In addition, glutamine serves as an essential substrate for key enzymes involved in the de novo synthesis of purine and pyrimidine nucleotides. Here, we developed a novel liquid chromatography (LC-MS) to quantify glutamine-derived [15N] nitrogen flux into nucleosides and nucleobases (purines and pyrimidines). For this, DNA from 5637 bladder cancer cell line cultured in 15N labelled glutamine and then enzymatically hydrolyzed by sequential digestion. Subsequently, DNA hydrolysates were separated by LC-MS and Selected Reaction Monitoring (SRM) was employed to identify the nucleobases and nucleosides. Thus, high sensitivity and reproducibility of the method make it a valuable tool to identify the nitrogen flux primarily derived from glutamine and can be further adaptable for high throughput analysis of large set of DNA in a clinical setting. PMID:27158554

  17. Fast Simultaneous Determination of 13 Nucleosides and Nucleobases in Cordyceps sinensis by UHPLC-ESI-MS/MS.

    PubMed

    Zong, Shi-Yu; Han, Han; Wang, Bing; Li, Ning; Dong, Tina Ting-Xia; Zhang, Tong; Tsim, Karl W K

    2015-01-01

    A reliable ultra-high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UHPLC-ESI-MS/MS) method for the fast simultaneous determination of 13 nucleosides and nucleobases in Cordyceps sinensis (C. sinensis) with 2-chloroadenosine as internal standard was developed and validated. Samples were ultrasonically extracted in an ice bath thrice, and the optimum analyte separation was performed on an ACQUITY UPLC(TM) HSS C18 column (100 mm × 2.1 mm, 1.8 μm) with gradient elution. All targeted analytes were separated in 5.5 min. Furthermore, all calibration curves showed good linear regression (r > 0.9970) within the test ranges, and the limits of quantitation and detection of the 13 analytes were less than 150 and 75 ng/mL, respectively. The relative standard deviations (RSDs) of intra- and inter-day precisions were <6.23%. Recoveries of the quantified analytes ranged within 85.3%-117.3%, with RSD < 6.18%. The developed UHPLC-ESI-MS/MS method was successfully applied to determine nucleosides and nucleobases in 11 batches of C. sinensis samples from different regions in China. The range for the total content in the analyzed samples was 1329-2057 µg/g. PMID:26690105

  18. Three new double-headed nucleotides with additional nucleobases connected to C-5 of pyrimidines; synthesis, duplex and triplex studies.

    PubMed

    Kumar, Pawan; Sharma, Pawan K; Hansen, Jonas; Jedinak, Lukas; Reslow-Jacobsen, Charlotte; Hornum, Mick; Nielsen, Poul

    2016-02-15

    In the search for double-coding DNA-systems, three new pyrimidine nucleosides, each coded with an additional nucleobase anchored to the major groove face, are synthesized. Two of these building blocks carry a thymine at the 5-position of 2'-deoxyuridine through a methylene linker and a triazolomethylene linker, respectively. The third building block carries an adenine at the 6-position of pyrrolo-2'-deoxycytidine through a methylene linker. These double-headed nucleosides are introduced into oligonucleotides and their effects on the thermal stabilities of duplexes are studied. All studied double-headed nucleotide monomers reduce the thermal stability of the modified duplexes, which is partially compensated by using consecutive incorporations of the modified monomers or by flanking the new double-headed analogs with members of our former series containing propyne linkers. Also their potential in triplex-forming oligonucleotides is studied for two of the new double-headed nucleotides as well as the series of analogs with propyne linkers. The most stable triplexes are obtained with single incorporations of additional pyrimidine nucleobases connected via the propyne linker. PMID:26778611

  19. Dispersion Interactions between Urea and Nucleobases Contribute to the Destabilization of RNA by Urea in Aqueous Solution

    PubMed Central

    Kasavajhala, Koushik; Bikkina, Swetha; Patil, Indrajit; MacKerell, Alexander D.; Priyakumar, U. Deva

    2015-01-01

    Urea has long been used to investigate protein folding and, more recently, RNA folding. Studies have proposed that urea denatures RNA by participating in stacking interactions and hydrogen bonds with nucleic acid bases. In this study, the ability of urea to form unconventional stacking interactions with RNA bases is investigated using ab initio calculations (RI-MP2 and CCSD(T) methods with the aug-cc-pVDZ basis set). A total of 29 stable nucleobase-urea stacked complexes are identified in which the intermolecular interaction energies (up to −14 kcal/mol) are dominated by dispersion effects. Natural bond orbital (NBO) and atoms in molecules (AIM) calculations further confirm strong interactions between urea and nucleobases. Calculations on model systems with multiple urea and water molecules interacting with a guanine base lead to a hypothesis that urea molecules along with water are able to form cage-like structures capable of trapping nucleic acid bases in extrahelical states by forming both hydrogen bonded and dispersion interactions, thereby contributing to the unfolding of RNA in the presence of urea in aqueous solution. PMID:25668757

  20. Gas-phase Watson-Crick and Hoogsteen isomers of the nucleobase mimic 9-methyladenine x 2-pyridone.

    PubMed

    Frey, Jann A; Leist, Roman; Müller, Andreas; Leutwyler, Samuel

    2006-07-17

    2-Pyridone (pyridin-2-one) is a mimic of the uracil and thymine nucleobases, with only one N--H and C==O group. It provides a single H-bonding site, compared to three for the canonical pyrimidine nucleobases. Employing the supersonically cooled 9-methyladenine2-pyridone (9MAd x 2PY) complex, which is the simplest base pair to mimic adenine-uracil or adenine-thymine, we show that its gas-phase UV spectrum consists of contributions from two isomers. Based on the H-bonding sites of 9-methyladenine, these are the Watson-Crick and Hoogsteen forms. Combining two-color two-photon ionisation (2C-R2PI), UV-UV depletion and laser-induced fluorescence spectroscopies allows separation of the two band systems, revealing characteristic intermolecular in-plane vibrations of the two isomers. The calculated S(0) and S(1) intermolecular frequencies are in good agreement with the experimental ones. Ab initio calculations predict the Watson-Crick isomer to be slightly more stable (D(0)=-16.0 kcal mol(-1)) than the Hoogsteen isomer (D(0)=-15.0 kcal mol(-1)). The calculated free energies Delta(f)G(0) of the Watson-Crick and Hoogsteen isomers agree qualitatively with the experimental isomer concentration ratio of 3:1. PMID:16755637

  1. A long-wavelength quantum dot-concentric FRET configuration: characterization and application in a multiplexed hybridization assay.

    PubMed

    Li, Jia Jun; Algar, W Russ

    2016-06-21

    Quantum dot-based concentric Förster resonance energy transfer (cFRET) is a promising modality for the development of multifunctional fluorescent probes for bioanalysis and bioimaging. To date, the scope of cFRET has been largely limited to a prototypical configuration with a particular combination of quantum dot (QD) and fluorescent dyes linked through peptides. Expansion of the scope of cFRET is critical for its further development. Here, we expand the scope of cFRET in two capacities. First, we design and characterize a new long-wavelength cFRET configuration that combines red- and deep-red fluorescent dyes, Alexa Fluor 633 and Alexa Fluor 680, with an orange-emitting QD. Sequential and competitive energy transfer pathways are characterized through a rate analysis, where the balance of these rates more strongly favours competitive energy transfer in the new long-wavelength configuration versus sequential energy transfer in the previous prototypical configuration. Although the new cFRET configuration is more susceptible to photobleaching, its superior brightness and longer-wavelength excitation and emission provide an order of magnitude higher signal-to-background ratios in biological matrices (e.g., serum, blood) than the previous prototypical configuration. Second, we demonstrate that an oligonucleotide-linked, long-wavelength cFRET configuration has energy transfer similar to an analogous peptide-linked configuration, where the oligonucleotide-linked cFRET configuration can be combined with toehold-mediated strand displacement for the multiplexed detection of unlabeled nucleic acid targets as a single vector. Overall, this work establishes the general applicability of cFRET and introduces new strategies for its bioanalytical application. PMID:27048838

  2. Development of bright fluorescent quadracyclic adenine analogues: TDDFT-calculation supported rational design

    PubMed Central

    Foller Larsen, Anders; Dumat, Blaise; Wranne, Moa S.; Lawson, Christopher P.; Preus, Søren; Bood, Mattias; Gradén, Henrik; Marcus Wilhelmsson, L.; Grøtli, Morten

    2015-01-01

    Fluorescent base analogues (FBAs) comprise a family of increasingly important molecules for the investigation of nucleic acid structure and dynamics. We recently reported the quantum chemical calculation supported development of four microenvironment sensitive analogues of the quadracyclic adenine (qA) scaffold, the qANs, with highly promising absorptive and fluorescence properties that were very well predicted by TDDFT calculations. Herein, we report on the efficient synthesis, experimental and theoretical characterization of nine novel quadracyclic adenine derivatives. The brightest derivative, 2-CNqA, displays a 13-fold increased brightness (εΦF = 4500) compared with the parent compound qA and has the additional benefit of being a virtually microenvironment-insensitive fluorophore, making it a suitable candidate for nucleic acid incorporation and use in quantitative FRET and anisotropy experiments. TDDFT calculations, conducted on the nine novel qAs a posteriori, successfully describe the relative fluorescence quantum yield and brightness of all qA derivatives. This observation suggests that the TDDFT-based rational design strategy may be employed for the development of bright fluorophores built up from a common scaffold to reduce the otherwise costly and time-consuming screening process usually required to obtain useful and bright FBAs. PMID:26227585

  3. Development of bright fluorescent quadracyclic adenine analogues: TDDFT-calculation supported rational design

    NASA Astrophysics Data System (ADS)

    Foller Larsen, Anders; Dumat, Blaise; Wranne, Moa S.; Lawson, Christopher P.; Preus, Søren; Bood, Mattias; Gradén, Henrik; Marcus Wilhelmsson, L.; Grøtli, Morten

    2015-07-01

    Fluorescent base analogues (FBAs) comprise a family of increasingly important molecules for the investigation of nucleic acid structure and dynamics. We recently reported the quantum chemical calculation supported development of four microenvironment sensitive analogues of the quadracyclic adenine (qA) scaffold, the qANs, with highly promising absorptive and fluorescence properties that were very well predicted by TDDFT calculations. Herein, we report on the efficient synthesis, experimental and theoretical characterization of nine novel quadracyclic adenine derivatives. The brightest derivative, 2-CNqA, displays a 13-fold increased brightness (ɛΦF = 4500) compared with the parent compound qA and has the additional benefit of being a virtually microenvironment-insensitive fluorophore, making it a suitable candidate for nucleic acid incorporation and use in quantitative FRET and anisotropy experiments. TDDFT calculations, conducted on the nine novel qAs a posteriori, successfully describe the relative fluorescence quantum yield and brightness of all qA derivatives. This observation suggests that the TDDFT-based rational design strategy may be employed for the development of bright fluorophores built up from a common scaffold to reduce the otherwise costly and time-consuming screening process usually required to obtain useful and bright FBAs.

  4. Preliminary Study on Fatigue Strengths of Fretted Ti-48Al-2Cr-2Nb

    NASA Technical Reports Server (NTRS)

    Miyoshi, Kazuhisa; Lerch, Bradley A.; Draper, Susan L.

    2002-01-01

    The fatigue behavior (stress-life curve) of gamma titanium aluminide (Ti-48Al-2Cr-2Nb, atomic percent) was examined by conducting two tests: first, a fretting wear test with a fatigue specimen in contact with a typical nickel-based superalloy contact pad in air at temperatures of 296 and 823 K and second, a high-cycle fatigue test of the prefretted Ti-48Al-2Cr-2Nb fatigue specimen at 923 K. Reference high-cycle fatigue tests were also conducted with unfretted Ti-48Al-2Cr-2Nb specimens at 923 K. All Ti-48Al-2Cr-2Nb fatigue specimens were machined from cast slabs. The results indicate that the stress-life results for the fretted Ti-48Al-2Cr-2Nb specimens exhibited a behavior similar to those of the unfretted Ti-48Al-2Cr-2Nb specimens. The values of maximum stress and life for the fretted specimens were almost the same as those for the unfretted specimens. The resultant stress-life curve for the unfretted fatigue specimens was very flat. The flat appearance in the stress-life curve of the unfretted specimens is attributed to the presence of a high density of casting pores. The fatigue strengths of both the fretted and unfretted specimens can be significantly affected by the presence of this porosity, which can decrease the fatigue life of Ti-48Al-2Cr-2Nb. The presence of the porosity made discerning the effect of fretting damage on fatigue strength and life of the specimens difficult.

  5. Visualizing dynamic cytoplasmic forces with a compliance-matched FRET sensor

    PubMed Central

    Meng, Fanjie; Sachs, Frederick

    2011-01-01

    Mechanical forces are ubiquitous modulators of cell activity but little is known about the mechanical stresses in the cell. Genetically encoded FRET-based force sensors now allow the measurement of local stress in specific host proteins in vivo in real time. For a minimally invasive probe, we designed one with a mechanical compliance matching that of many common cytoskeleton proteins. sstFRET is a cassette composed of Venus and Cerulean linked by a spectrin repeat. The stress sensitivity of the probe was measured in solution using DNA springs to push the donor and acceptor apart with 5–7 pN and this produced large changes in FRET. To measure cytoskeletal stress in vivo we inserted sstFRET into α-actinin and expressed it in HEK and BAEC cells. Time-lapse imaging showed the presence of stress gradients in time and space, often uncorrelated with obvious changes in cell shape. The gradients could be rapidly relaxed by thrombin-induced cell contraction associated with inhibition of myosin II. The tension in actinin fluctuated rapidly (scale of seconds) illustrating a cytoskeleton in dynamic equilibrium. Stress in the cytoskeleton can be driven by macroscopic stresses applied to the cell. Using sstFRET as a tool to measure internal stress, we tested the prediction that osmotic pressure increases cytoskeletal stress. As predicted, hypotonic swelling increased the tension in actinin, confirming the model derived from AFM. Anisotonic stress also produced a novel transient (~2 minutes) decrease in stress upon exposure to a hypotonic challenge, matched by a transient increase with hypertonic stress. This suggests that, at rest, the stress axis of actinin is not parallel to the stress axis of actin and that swelling can reorient actinin to lie more parallel where it can absorb a larger fraction of the total stress. Protein stress sensors are opening new perspectives in cell biology. PMID:21172803

  6. FRET imaging of diatoms expressing a biosilica-localized ribose sensor.

    PubMed

    Marshall, Kathryn E; Robinson, Errol W; Hengel, Shawna M; Paša-Tolić, Ljiljana; Roesijadi, Guritno

    2012-01-01

    Future materials are envisioned to include bio-assembled, hybrid, three-dimensional nanosystems that incorporate functional proteins. Diatoms are amenable to genetic modification for localization of recombinant proteins in the biosilica cell wall. However, the full range of protein functionalities that can be accommodated by the modified porous biosilica has yet to be described. Our objective was to functionalize diatom biosilica with a reagent-less sensor dependent on ligand-binding and conformational change to drive FRET-based signaling capabilities. A fusion protein designed to confer such properties included a bacterial periplasmic ribose binding protein (R) flanked by CyPet (C) and YPet (Y), cyan and yellow fluorescent proteins that act as a FRET pair. The structure and function of the CRY recombinant chimeric protein was confirmed by expression in E. coli prior to transformation of the diatom Thalassiosira pseudonana. Mass spectrometry of the recombinant CRY showed 97% identity with the deduced amino acid sequence. CRY with and without an N-terminal Sil3 tag for biosilica localization exhibited characteristic ribose-dependent changes in FRET, with similar dissociation constants of 123.3 µM and 142.8 µM, respectively. The addition of the Sil3 tag did not alter the affinity of CRY for the ribose substrate. Subsequent transformation of T. pseudonana with a vector encoding Sil3-CRY resulted in fluorescence localization in the biosilica and changes in FRET in both living cells and isolated frustules in response to ribose. This work demonstrated that the nano-architecture of the genetically modified biosilica cell wall was able to support the functionality of the relatively complex Sil3-CyPet-RBP-YPet fusion protein with its requirement for ligand-binding and conformational change for FRET-signal generation. PMID:22470473

  7. Intracellular cascade FRET for temperature imaging of living cells with polymeric ratiometric fluorescent thermometers.

    PubMed

    Hu, Xianglong; Li, Yang; Liu, Tao; Zhang, Guoying; Liu, Shiyong

    2015-07-22

    Intracellular temperature plays a prominent role in cellular functions and biochemical activities inside living cells, but effective intracellular temperature sensing and imaging is still in its infancy. Herein, thermoresponsive double hydrophilic block copolymers (DHBCs)-based fluorescent thermometers were fabricated to investigate their application in intracellular temperature imaging. Blue-emitting coumarin monomer, CMA, green-emitting 7-nitro-2,1,3-benzoxadiazole (NBD) monomer, NBDAE, and red-emitting rhodamine B monomer, RhBEA, were copolymerized separately with N-isopropylacrylamide (NIPAM) to afford dye-labeled PEG-b-P(NIPAM-co-CMA), PEG-b-P(NIPAM-co-NBDAE), and PEG-b-P(NIPAM-co-RhBEA). Because of the favorable fluorescence resonance energy transfer (FRET) potentials between CMA and NBDAE, NBDAE and RhBEA, as well as the slight tendency between CMA and RhBEA fluorophore pairs, three polymeric thermometers based on traditional one-step FRET were fabricated by facile mixing two of these three fluorescent DHBCs, whereas exhibiting limited advantages. Thus, two-step cascade FRET among three polymeric fluorophores was further interrogated, in which NBD acted as a bridging dye by transferring energy from CMA to RhBEA. Through the delicate optimization of the molar contents of three polymeric components, a ∼8.4-fold ratio change occurred in the temperature range of 20-44 °C, and the detection sensitivity improved significantly, reached as low as ∼0.4 °C, which definitely outperformed other one-step FRET thermometers in the intracellular temperature imaging of living cells. To our knowledge, this work represents the first example of polymeric ratiometric thermometer employing thermoresponsive polymer-based cascade FRET mechanism. PMID:26114380

  8. FRET Imaging of Diatoms Expressing a Biosilica-Localized Ribose Sensor

    SciTech Connect

    Marshall, Kathryn E.; Robinson, E. W.; Hengel, Shawna M.; Pasa-Tolic, Ljiljana; Roesijadi, Guritno

    2012-03-21

    Future materials are envisioned to include bio-assembled, hybrid, three-dimensional nanosystems that incorporate functional proteins. Diatoms are amenable to genetic modification that enables localization of recombinant proteins in the biosilica cell wall. Our objective was to functionalize diatom biosilica with a reagent-less biosensor with FRET-based imaging capabilities for signaling. The design of the fusion protein conferring these properties included a bacterial periplasmic ribose binding protein (R) flanked by CyPet (C) and YPet (Y), cyan and yellow fluorescent proteins that act as a FRET pair. The structure and function of the recombinant chimeric protein was first confirmed in E. coli-expressed proteins, prior to transformation of the diatom Thalassiosira pseudonana. Mass spectrometry of CRY showed 95% identity with the deduced amino acid sequence. CRY with and without an N-terminal Sil3 tag for biosilica targeting exhibited characteristic ribose-dependent changes in FRET, with similar dissociation constants of 123.3 {mu}M and 142.8 {mu}M, respectively. The addition of the silaffin tag for biosilica localization did not influence the affinity of CRY for the ribose substrate. Subsequent transformation of T. pseudonana with a vector encoding Sil3-CRY resulted in fluorescence localization in the biosilica and changes in FRET in both living cells and isolated biosilica in response to ribose. This work demonstrated that the nano-architecture of the genetically modified biosilica cell wall was able to support the functionality of the relatively complex Sil3-CyPet-RBP-YPet fusion protein with its requirement for ligand binding and conformational change for FRET-signal generation.

  9. Temporal Data Set Reduction Based on D-Optimality for Quantitative FLIM-FRET Imaging

    PubMed Central

    Omer, Travis; Intes, Xavier; Hahn, Juergen

    2015-01-01

    Fluorescence lifetime imaging (FLIM) when paired with Förster resonance energy transfer (FLIM-FRET) enables the monitoring of nanoscale interactions in living biological samples. FLIM-FRET model-based estimation methods allow the quantitative retrieval of parameters such as the quenched (interacting) and unquenched (non-interacting) fractional populations of the donor fluorophore and/or the distance of the interactions. The quantitative accuracy of such model-based approaches is dependent on multiple factors such as signal-to-noise ratio and number of temporal points acquired when sampling the fluorescence decays. For high-throughput or in vivo applications of FLIM-FRET, it is desirable to acquire a limited number of temporal points for fast acquisition times. Yet, it is critical to acquire temporal data sets with sufficient information content to allow for accurate FLIM-FRET parameter estimation. Herein, an optimal experimental design approach based upon sensitivity analysis is presented in order to identify the time points that provide the best quantitative estimates of the parameters for a determined number of temporal sampling points. More specifically, the D-optimality criterion is employed to identify, within a sparse temporal data set, the set of time points leading to optimal estimations of the quenched fractional population of the donor fluorophore. Overall, a reduced set of 10 time points (compared to a typical complete set of 90 time points) was identified to have minimal impact on parameter estimation accuracy (≈5%), with in silico and in vivo experiment validations. This reduction of the number of needed time points by almost an order of magnitude allows the use of FLIM-FRET for certain high-throughput applications which would be infeasible if the entire number of time sampling points were used. PMID:26658308

  10. Parallel multispot smFRET analysis using an 8-pixel SPAD array

    PubMed Central

    Ingargiola, A.; Colyer, R. A.; Kim, D.; Panzeri, F.; Lin, R.; Gulinatti, A.; Rech, I.; Ghioni, M.; Weiss, S.; Michalet, X.

    2012-01-01

    Single-molecule Förster resonance energy transfer (smFRET) is a powerful tool for extracting distance information between two fluorophores (a donor and acceptor dye) on a nanometer scale. This method is commonly used to monitor binding interactions or intra- and intermolecular conformations in biomolecules freely diffusing through a focal volume or immobilized on a surface. The diffusing geometry has the advantage to not interfere with the molecules and to give access to fast time scales. However, separating photon bursts from individual molecules requires low sample concentrations. This results in long acquisition time (several minutes to an hour) to obtain sufficient statistics. It also prevents studying dynamic phenomena happening on time scales larger than the burst duration and smaller than the acquisition time. Parallelization of acquisition overcomes this limit by increasing the acquisition rate using the same low concentrations required for individual molecule burst identification. In this work we present a new two-color smFRET approach using multispot excitation and detection. The donor excitation pattern is composed of 4 spots arranged in a linear pattern. The fluorescent emission of donor and acceptor dyes is then collected and refocused on two separate areas of a custom 8-pixel SPAD array. We report smFRET measurements performed on various DNA samples synthesized with various distances between the donor and acceptor fluorophores. We demonstrate that our approach provides identical FRET efficiency values to a conventional single-spot acquisition approach, but with a reduced acquisition time. Our work thus opens the way to high-throughput smFRET analysis on freely diffusing molecules. PMID:24382989

  11. Diagnosis of canine leptospirosis by a highly sensitive FRET-PCR targeting the lig genes.

    PubMed

    Xu, Chuanling; Loftis, Amanda; Ahluwalia, Sudhir K; Gao, Dongya; Verma, Ashutosh; Wang, Chengming; Kaltenboeck, Bernhard

    2014-01-01

    Canine leptospirosis is underdiagnosed due to its wide spectrum of clinical presentations and the lack of a rapid and sensitive test for the accurate diagnosis of acute and chronic infections. In this study, we developed a highly sensitive and specific fluorescence resonance energy transfer (FRET)-PCR to detect common pathogenic leptospires in dogs, including Leptospira interrogans serovars Autumnalis, Canicola, Copenhageni (Icterohaemorrhagiae serogroup) and Pomona, and Leptospira kirschneri serovar Grippotyphosa. This PCR targets the lig genes, exclusively found in the pathogenic Leptospira species but not in saprophytic species (L. biflexa). A robust, high-stringency step-down real-time platform was coupled to the highly specific detection of leptospiral DNA by fluorescently labeled FRET probes. This enabled the detection of a single copy of the lig gene in a PCR containing DNA from up to 50 µL canine blood or 400 µL urine. Sensitivity determination by use of limiting serial dilutions of extracted leptospiral DNA indicated that the lig FRET-PCR we established was almost 100-fold more sensitive than the widely accepted lipL32 SYBR assay and 10-fold more sensitive than a 16S rRNA TaqMan assay. Application of this method to 207 dogs with potential leptospiral infection enabled us to diagnose three cases of canine leptospirosis characterized by low amounts of leptospiral DNA in body fluids. Detection of canine leptospirosis with the lig FRET-PCR was more sensitive with the lig FRET-PCR than with the 16S rRNA TaqMan PCR, which detected only 2 of the 3 cases, and the lipL32 SYBR PCR, which detected none of the 3 dogs with leptospirosis. PMID:24586833

  12. Molecularly imprinted polymer for recognition of 5-fluorouracil by RNA-type nucleobase pairing.

    PubMed

    Huynh, Tan-Phat; Pieta, Piotr; D'Souza, Francis; Kutner, Wlodzimierz

    2013-09-01

    A 6-aminopurine (adenine) derivative of bis(2,2'-bithienyl)methane, vis., 4-[2-(6-amino-9H-purin-9-yl)ethoxy]phenyl-4-[bis(2,2'-bithienyl)methane] or Ade-BTM, was designed and synthesized for recognition of 5-fluorouracil (FU), an antitumor chemotherapy agent, by RNA-type (nucleobase pairing)-driven molecular imprinting. The prepolymerization complex stoichiometry involved one FU molecule and two molecules of the Ade-BTM functional monomer. Molecular structure of this complex was thermodynamically optimized via density functional theory at the B3LYP/3-21G* level. The stability constant of the FU-Ade-BTM complex of 1:2 stoichiometry was K = 2.17(±0.07) × 10(7) M(-2), as determined by titration with quenching of fluorescence of the bis(2,2'-bithienyl)methane moiety of Ade-BTM by the FU titrant, in benzonitrile, at 352 nm excitation. Next, (5-fluorouracil)-templated molecularly imprinted polymer (MIP-FU) films were deposited on indium-tin oxide (ITO) or Au film-coated glass slides, Pt disk electrodes, or 10-MHz quartz crystal resonators by potentiodynamic electropolymerization from solution of FU, Ade-BTM, and tris([2,2'-bithiophen]-5-yl)methane (TTM) cross-linking monomer at FU:Ade-BTM:TTM = 1:2:3 mol ratio. Then UV-visible and Fourier transform infrared (FT-IR) spectra of the MIP-FU films were recorded to confirm the FU template presence in the MIP-FU film and its subsequent release by extraction with methanol from this film. For determination of the stability constant of the complex of the MIP cavity and FU, piezoelectric microgravimetry (PM) under both batch- and flow-injection analysis conditions was used. For sensing application, three different transduction platforms [differential pulse voltammetry (DPV), capacitive impedimetry (CI), and PM] were integrated with the MIP-FU recognition unit. The limit of detection (LOD) was 56 nM, 75 nM, and 0.26 mM, for these chemosensors, respectively, indicating suitability of the former two for FU determination in blood

  13. Connectivity patterns and rotamer states of nucleobases determine acid-base properties of metalated purine quartets.

    PubMed

    Lüth, Marc Sven; Freisinger, Eva; Kampf, Gunnar; Garijo Anorbe, Marta; Griesser, Rolf; Operschall, Bert P; Sigel, Helmut; Lippert, Bernhard

    2015-07-01

    Potentiometric pH titrations and pD dependent (1)H NMR spectroscopy have been applied to study the acidification of the exocyclic amino group of adenine (A) model nucleobases (N9 position blocked by alkyl groups) when carrying trans-a2Pt(II) (with a=NH3 or CH3NH2) entities both at N1 and N7 positions. As demonstrated, in trinuclear complexes containing central A-Pt-A units, it depends on the connectivity pattern of the adenine bases (N7/N7 or N1/N1) and their rotamer states (head-head or head-tail), how large the acidifying effect is. Specifically, a series of trinuclear complexes with (A-N7)-Pt-(N7-A) and (A-N1)-Pt-(N1-A) cross-linking patterns and terminal 9-alkylguanine ligands (9MeGH, 9EtGH) have been analyzed in this respect, and it is shown that, for example, the 9MeA ligands in trans-,trans-,trans-[Pt(NH3)2(N7-9MeA-N1)2{Pt(NH3)2(9EtGH-N7)}2](ClO4)6·6H2O (4a) and trans-,trans-,trans-[Pt(NH3)2(N7-9EtA-N1)2{Pt(CH3NH2)2(9-MeGH-N7)}2](ClO4)6·3H2O (4b) are more acidic, by ca. 1.3 units (first pKa), than the linkage isomer trans-,trans-,trans-[Pt(CH3NH2)2(N1-9MeA-N7)2{Pt(NH3)2(9MeGH-N7)}2](NO3)6·6.25H2O (1b). Overall, acidifications in these types of complexes amount to 7-9 units, bringing the pKa values of such adenine ligands in the best case close to the physiological pH range. Comparison with pKa values of related trinuclear Pt(II) complexes having different co-ligands at the Pt ions, confirms this picture and supports our earlier proposal that the close proximity of the exocyclic amino groups in a head-head arrangement of (A-N7)-Pt-(N7-A), and the stabilization of the resulting N6H(-)⋯H2N6 unit, is key to this difference. PMID:25773716

  14. Probing Nucleic Acid Interactions and Pre-mRNA Splicing by Förster Resonance Energy Transfer (FRET) Microscopy

    PubMed Central

    Šimková, Eva; Staněk, David

    2012-01-01

    Förster resonance energy transfer (FRET) microscopy is a powerful technique routinely used to monitor interactions between biomolecules. Here, we focus on the techniques that are used for investigating the structure and interactions of nucleic acids (NAs). We present a brief overview of the most commonly used FRET microscopy techniques, their advantages and drawbacks. We list experimental approaches recently used for either in vitro or in vivo studies. Next, we summarize how FRET contributed to the understanding of pre-mRNA splicing and spliceosome assembly. PMID:23203103

  15. Electroporation and Microinjection Successfully Deliver Single-Stranded and Duplex DNA into Live Cells as Detected by FRET Measurements

    PubMed Central

    Bamford, Rosemary A.; Zhao, Zheng-yun; Hotchin, Neil A.; Styles, Iain B.; Nash, Gerard B.; Tucker, James H. R.; Bicknell, Roy

    2014-01-01

    Förster resonance energy transfer (FRET) technology relies on the close proximity of two compatible fluorophores for energy transfer. Tagged (Cy3 and Cy5) complementary DNA strands forming a stable duplex and a doubly-tagged single strand were shown to demonstrate FRET outside of a cellular environment. FRET was also observed after transfecting these DNA strands into fixed and live cells using methods such as microinjection and electroporation, but not when using lipid based transfection reagents, unless in the presence of the endosomal acidification inhibitor bafilomycin. Avoiding the endocytosis pathway is essential for efficient delivery of intact DNA probes into cells. PMID:24755680

  16. Theoretical Study of the Photophysics of 8-Vinylguanine, an Isomorphic Fluorescent Analogue of Guanine.

    PubMed

    Kochman, Michał A; Pola, Martina; Miller, R J Dwayne

    2016-08-11

    Paving the way for the application of the algebraic-diagrammatic construction scheme of second-order (ADC(2)) to systems based on the guanine chromophore, we demonstrate the this excited-state electronic structure method provides a realistic description of the photochemistry of 9H-guanine, in close agreement with the benchmark provided by the CASPT2 method. We then proceed to apply the ADC(2) method to the photochemistry of 8-vinylguanine (8vG), a minimally modified analogue of guanine which, unlike the naturally occurring nucleobase, displays intense fluorescence, indicative of a much longer-lived excited electronic state. The emissive electronic state of 8vG is identified as an ππ*-type intramolecular charge transfer (ICT) state, in which a charge of roughly -0.2 e is transferred from the guanine moiety onto the vinyl substituent. The main radiationless deactivation pathway competing with fluorescence is predicted to involve the molecule leaving the minimum on the ICT ππ* state, and reaching a region of the S1 adiabatic state where it resembles the La ππ* state of unmodified 9H-guanine. The topology of the La ππ* region of the S1 state favors subsequent internal conversion at a crossing seam with the ground electronic state. The sensitivity of this process to environment polarity may explain the experimentally observed fluorescence quenching of 8vG upon incorporation in single- and double-stranded DNA. PMID:27427772

  17. Highly sensitive detection of DNA methylation levels by using a quantum dot-based FRET method

    NASA Astrophysics Data System (ADS)

    Ma, Yunfei; Zhang, Honglian; Liu, Fangming; Wu, Zhenhua; Lu, Shaohua; Jin, Qinghui; Zhao, Jianlong; Zhong, Xinhua; Mao, Hongju

    2015-10-01

    DNA methylation is the most frequently studied epigenetic modification that is strongly involved in genomic stability and cellular plasticity. Aberrant changes in DNA methylation status are ubiquitous in human cancer and the detection of these changes can be informative for cancer diagnosis. Herein, we reported a facile quantum dot-based (QD-based) fluorescence resonance energy transfer (FRET) technique for the detection of DNA methylation. The method relies on methylation-sensitive restriction enzymes for the differential digestion of genomic DNA based on its methylation status. Digested DNA is then subjected to PCR amplification for the incorporation of Alexa Fluor-647 (A647) fluorophores. DNA methylation levels can be detected qualitatively through gel analysis and quantitatively by the signal amplification from QDs to A647 during FRET. Furthermore, the methylation levels of three tumor suppressor genes, PCDHGB6, HOXA9 and RASSF1A, in 20 lung adenocarcinoma and 20 corresponding adjacent nontumorous tissue (NT) samples were measured to verify the feasibility of the QD-based FRET method and a high sensitivity for cancer detection (up to 90%) was achieved. Our QD-based FRET method is a convenient, continuous and high-throughput method, and is expected to be an alternative for detecting DNA methylation as a biomarker for certain human cancers.DNA methylation is the most frequently studied epigenetic modification that is strongly involved in genomic stability and cellular plasticity. Aberrant changes in DNA methylation status are ubiquitous in human cancer and the detection of these changes can be informative for cancer diagnosis. Herein, we reported a facile quantum dot-based (QD-based) fluorescence resonance energy transfer (FRET) technique for the detection of DNA methylation. The method relies on methylation-sensitive restriction enzymes for the differential digestion of genomic DNA based on its methylation status. Digested DNA is then subjected to PCR

  18. FUNCTION GENERATOR FOR ANALOGUE COMPUTERS

    DOEpatents

    Skramstad, H.K.; Wright, J.H.; Taback, L.

    1961-12-12

    An improved analogue computer is designed which can be used to determine the final ground position of radioactive fallout particles in an atomic cloud. The computer determines the fallout pattern on the basis of known wind velocity and direction at various altitudes, and intensity of radioactivity in the mushroom cloud as a function of particle size and initial height in the cloud. The output is then displayed on a cathode-ray tube so that the average or total luminance of the tube screen at any point represents the intensity of radioactive fallout at the geographical location represented by that point. (AEC)

  19. Ecstasy analogues found in cacti.

    PubMed

    Bruhn, Jan G; El-Seedi, Hesham R; Stephanson, Nikolai; Beck, Olof; Shulgin, Alexander T

    2008-06-01

    Human interest in psychoactive phenethylamines is known from the use of mescaline-containing cacti and designer drugs such as Ecstasy. From the alkaloid composition of cacti we hypothesized that substances resembling Ecstasy might occur naturally. In this article we show that lophophine, homopiperonylamine and lobivine are new minor constituents of two cactus species, Lophophora williamsii (peyote) and Trichocereus pachanoi (San Pedro). This is the first report of putatively psychoactive phenethylamines besides mescaline in these cacti. A search for further biosynthetic analogues may provide new insights into the structure-activity relationships of mescaline. An intriguing question is whether the new natural compounds can be called "designer drugs." PMID:18720674

  20. The combination of analytical-scale HPLC separation with a TR-FRET assay to investigate JAK2 inhibitory compounds in a Boysenberry drink.

    PubMed

    McGhie, Tony K; Martin, Harry; Lunken, Rona C M

    2012-11-01

    We report the detection of JAK2 inhibitory activity in a Boysenberry (Rubus loganbaccus x R. baileyanus Britt.) drink using a combination of analytical-scale high performance liquid chromatography (HPLC) with a high-sensitivity time-resolved fluorescence coupled with fluorescence resonance energy transfer (TR-FRET) method. Phytochemical components of a Boysenberry drink were separated by reversed phase HPLC , and 84 separate fractions were collected. HPLC fractions corresponding to the ellagitannin and ellagic acid peaks observed in the chromatogram inhibited JAK2 activity. Anthocyanins, while they were the major phytochemical components of the Boysenberry drink, had no JAK2 inhibitory activity even though anthocyanins have previously been shown to be anti-inflammatory. This study demonstrates the usefulness of combining rapid analytical-scale HPLC separation with a highly sensitive fluorescence bioassay for characterising bioactivity in complex plant extracts. Ellagic acid was found to have an IC(50) of 92 nM against JAK2 and complete inhibition of JAK2 activity was observed in HPLC fractions of Boysenberry extract which had been diluted several hundred fold. To the best of our knowledge, this is the first demonstration that ellagitannins and other natural ellagic acid analogues are potent inhibitors of JAK2. Thus a drink containing Boysenberry juice concentrate may have anti-inflammatory properties. PMID:22899007

  1. Millisecond spatiotemporal dynamics of FRET biosensors by the pair correlation function and the phasor approach to FLIM

    PubMed Central

    Hinde, Elizabeth; Digman, Michelle A.; Hahn, Klaus M.; Gratton, Enrico

    2013-01-01

    Here we present a fluctuation-based approach to biosensor Förster resonance energy transfer (FRET) detection that can measure the molecular flow and signaling activity of proteins in live cells. By simultaneous use of the phasor approach to fluorescence lifetime imaging microscopy (FLIM) and cross–pair correlation function (pCF) analysis along a line scanned in milliseconds, we detect the spatial localization of Rho GTPase activity (biosensor FRET signal) as well as the diffusive route adopted by this active population. In particular we find, for Rac1 and RhoA, distinct gradients of activation (FLIM-FRET) and a molecular flow pattern (pCF analysis) that explains the observed polarized GTPase activity. This multiplexed approach to biosensor FRET detection serves as a unique tool for dissection of the mechanism(s) by which key signaling proteins are spatially and temporally coordinated. PMID:23248275

  2. Novel multistep BRET-FRET energy transfer using nanoconjugates of firefly proteins, quantum dots, and red fluorescent proteins

    NASA Astrophysics Data System (ADS)

    Alam, Rabeka; Zylstra, Joshua; Fontaine, Danielle M.; Branchini, Bruce R.; Maye, Mathew M.

    2013-05-01

    Sequential bioluminescence resonance energy transfer (BRET) and fluorescence resonance energy transfer (FRET) from firefly luciferase to red fluorescent proteins using quantum dot or rod acceptor/donor linkers is described. The effect of morphology and tuned optical properties on the efficiency of this unique BRET-FRET system was evaluated.Sequential bioluminescence resonance energy transfer (BRET) and fluorescence resonance energy transfer (FRET) from firefly luciferase to red fluorescent proteins using quantum dot or rod acceptor/donor linkers is described. The effect of morphology and tuned optical properties on the efficiency of this unique BRET-FRET system was evaluated. Electronic supplementary information (ESI) available: Experimental details, Fig. S1 and Table S1-S4. See DOI: 10.1039/c3nr01842c

  3. FLIM FRET Technology for Drug Discovery: Automated Multiwell-Plate High-Content Analysis, Multiplexed Readouts and Application in Situ**

    PubMed Central

    Kumar, Sunil; Alibhai, Dominic; Margineanu, Anca; Laine, Romain; Kennedy, Gordon; McGinty, James; Warren, Sean; Kelly, Douglas; Alexandrov, Yuriy; Munro, Ian; Talbot, Clifford; Stuckey, Daniel W; Kimberly, Christopher; Viellerobe, Bertrand; Lacombe, Francois; Lam, Eric W-F; Taylor, Harriet; Dallman, Margaret J; Stamp, Gordon; Murray, Edward J; Stuhmeier, Frank; Sardini, Alessandro; Katan, Matilda; Elson, Daniel S; Neil, Mark A A; Dunsby, Chris; French, Paul M W

    2011-01-01

    A fluorescence lifetime imaging (FLIM) technology platform intended to read out changes in Förster resonance energy transfer (FRET) efficiency is presented for the study of protein interactions across the drug-discovery pipeline. FLIM provides a robust, inherently ratiometric imaging modality for drug discovery that could allow the same sensor constructs to be translated from automated cell-based assays through small transparent organisms such as zebrafish to mammals. To this end, an automated FLIM multiwell-plate reader is described for high content analysis of fixed and live cells, tomographic FLIM in zebrafish and FLIM FRET of live cells via confocal endomicroscopy. For cell-based assays, an exemplar application reading out protein aggregation using FLIM FRET is presented, and the potential for multiple simultaneous FLIM (FRET) readouts in microscopy is illustrated. PMID:21337485

  4. Homo-FRET Based Biosensors and Their Application to Multiplexed Imaging of Signalling Events in Live Cells

    PubMed Central

    Warren, Sean C.; Margineanu, Anca; Katan, Matilda; Dunsby, Chris; French, Paul M. W.

    2015-01-01

    Multiplexed imaging of Förster Resonance Energy Transfer (FRET)-based biosensors potentially presents a powerful approach to monitoring the spatio-temporal correlation of signalling pathways within a single live cell. Here, we discuss the potential of homo-FRET based biosensors to facilitate multiplexed imaging. We demonstrate that the homo-FRET between pleckstrin homology domains of Akt (Akt-PH) labelled with mCherry may be used to monitor 3′-phosphoinositide accumulation in live cells and show how global analysis of time resolved fluorescence anisotropy measurements can be used to quantify this accumulation. We further present multiplexed imaging readouts of calcium concentration, using fluorescence lifetime measurements of TN-L15-a CFP/YFP based hetero-FRET calcium biosensor-with 3′-phosphoinositide accumulation. PMID:26133241

  5. The Valles natural analogue project

    SciTech Connect

    Stockman, H.; Krumhansl, J.; Ho, C.; McConnell, V.

    1994-12-01

    The contact between an obsidian flow and a steep-walled tuff canyon was examined as an analogue for a highlevel waste repository. The analogue site is located in the Valles Caldera in New Mexico, where a massive obsidian flow filled a paleocanyon in the Battleship Rock tuff. The obsidian flow provided a heat source, analogous to waste panels or an igneous intrusion in a repository, and caused evaporation and migration of water. The tuff and obsidian samples were analyzed for major and trace elements and mineralogy by INAA, XRF, X-ray diffraction; and scanning electron microscopy and electron microprobe. Samples were also analyzed for D/H and {sup 39}Ar/{sup 4O} isotopic composition. Overall,the effects of the heating event seem to have been slight and limited to the tuff nearest the contact. There is some evidence of devitrification and migration of volatiles in the tuff within 10 meters of the contact, but variations in major and trace element chemistry are small and difficult to distinguish from the natural (pre-heating) variability of the rocks.

  6. Revolutionizing the FRET-based light emission in core-shell nanostructures via comprehensive activity of surface plasmons.

    PubMed

    Kochuveedu, Saji Thomas; Son, Taehwang; Lee, Youmin; Lee, Minyung; Kim, Donghyun; Kim, Dong Ha

    2014-01-01

    We demonstrate the surface-plasmon-induced enhancement of Förster resonance energy transfer (FRET)using a model multilayer core-shell nanostructure consisting of an Au core and surrounding FRET pairs, i.e., CdSe quantum dot donors and S101 dye acceptors. The multilayer configuration was demonstrated to exhibit synergistic effects of surface plasmon energy transfer from the metal to the CdSe and plasmon-enhanced FRET from the quantum dots to the dye. With precise control over the distance between the components in the nanostructure, significant improvement in the emission of CdSe was achieved by combined resonance energy transfer and near-field enhancement by the metal, as well as subsequent improvement in the emission of dye induced by the enhanced emission of CdSe. Consequently, the Förster radius was increased to 7.92 nm and the FRET efficiency was improved to 86.57% in the tailored plasmonic FRET nanostructure compared to the conventional FRET system (22.46%) without plasmonic metals. PMID:24751860

  7. Improving brightness and photostability of green and red fluorescent proteins for live cell imaging and FRET reporting.

    PubMed

    Bajar, Bryce T; Wang, Emily S; Lam, Amy J; Kim, Bongjae B; Jacobs, Conor L; Howe, Elizabeth S; Davidson, Michael W; Lin, Michael Z; Chu, Jun

    2016-01-01

    Many genetically encoded biosensors use Förster resonance energy transfer (FRET) to dynamically report biomolecular activities. While pairs of cyan and yellow fluorescent proteins (FPs) are most commonly used as FRET partner fluorophores, respectively, green and red FPs offer distinct advantages for FRET, such as greater spectral separation, less phototoxicity, and lower autofluorescence. We previously developed the green-red FRET pair Clover and mRuby2, which improves responsiveness in intramolecular FRET reporters with different designs. Here we report the engineering of brighter and more photostable variants, mClover3 and mRuby3. mClover3 improves photostability by 60% and mRuby3 by 200% over the previous generation of fluorophores. Notably, mRuby3 is also 35% brighter than mRuby2, making it both the brightest and most photostable monomeric red FP yet characterized. Furthermore, we developed a standardized methodology for assessing FP performance in mammalian cells as stand-alone markers and as FRET partners. We found that mClover3 or mRuby3 expression in mammalian cells provides the highest fluorescence signals of all jellyfish GFP or coral RFP derivatives, respectively. Finally, using mClover3 and mRuby3, we engineered an improved version of the CaMKIIα reporter Camuiα with a larger response amplitude. PMID:26879144

  8. Improving brightness and photostability of green and red fluorescent proteins for live cell imaging and FRET reporting

    PubMed Central

    Bajar, Bryce T.; Wang, Emily S.; Lam, Amy J.; Kim, Bongjae B.; Jacobs, Conor L.; Howe, Elizabeth S.; Davidson, Michael W.; Lin, Michael Z.; Chu, Jun

    2016-01-01

    Many genetically encoded biosensors use Förster resonance energy transfer (FRET) to dynamically report biomolecular activities. While pairs of cyan and yellow fluorescent proteins (FPs) are most commonly used as FRET partner fluorophores, respectively, green and red FPs offer distinct advantages for FRET, such as greater spectral separation, less phototoxicity, and lower autofluorescence. We previously developed the green-red FRET pair Clover and mRuby2, which improves responsiveness in intramolecular FRET reporters with different designs. Here we report the engineering of brighter and more photostable variants, mClover3 and mRuby3. mClover3 improves photostability by 60% and mRuby3 by 200% over the previous generation of fluorophores. Notably, mRuby3 is also 35% brighter than mRuby2, making it both the brightest and most photostable monomeric red FP yet characterized. Furthermore, we developed a standardized methodology for assessing FP performance in mammalian cells as stand-alone markers and as FRET partners. We found that mClover3 or mRuby3 expression in mammalian cells provides the highest fluorescence signals of all jellyfish GFP or coral RFP derivatives, respectively. Finally, using mClover3 and mRuby3, we engineered an improved version of the CaMKIIα reporter Camuiα with a larger response amplitude. PMID:26879144

  9. Evaluation of quantum dot-based concentric FRET configurations with a fluorescent dye and dark quencher for multiplexed bioanalyses

    NASA Astrophysics Data System (ADS)

    Conroy, Erin M.; Algar, W. Russ

    2014-03-01

    Semiconductor quantum dots (QDs) continue to emerge as a highly advantageous platform for bioanalysis. Their unique physical and optical properties are especially well suited for Förster resonance energy transfer (FRET)-based bioprobes. Concentric FRET configurations are a recent development in this area of research and are best described as QD bioconjugates where multiple energy transfer pathways have been assembled around the central QD. Concentric FRET configurations permit multiplexed bioanalysis using one type of QD vector, but require more sophisticated analyses than conventional FRET pairs. In this paper, we describe the design and characterization of a new concentric FRET configuration that assembles both a fluorescent dye, Alexa Fluor 555 or Alexa Fluor 647, and a dark quencher, QSY9, at different ratios around a central CdSeS/ZnS QD. It was found that the magnitudes of the total photoluminescence (PL) intensity and either the A555/QD or A647/QD PL ratio can be related to the number of QSY9 and A555 or A647 per QD. The trends in these parameters with changes in the number of each dye molecule per QD have both similarities and differences between configurations with A555 and A647. In each case, a system of equations can be defined to permit calculation of the number of each dye molecule per QD from PL measurements. Both of these dark quencher-based concentric FRET configurations are therefore good candidates for quantitative, multiplexed bioanalysis.

  10. The Impact of Heterogeneity and Dark Acceptor States on FRET: Implications for Using Fluorescent Protein Donors and Acceptors

    PubMed Central

    Vogel, Steven S.; Nguyen, Tuan A.; van der Meer, B. Wieb; Blank, Paul S.

    2012-01-01

    Förster resonance energy transfer (FRET) microscopy is widely used to study protein interactions in living cells. Typically, spectral variants of the Green Fluorescent Protein (FPs) are incorporated into proteins expressed in cells, and FRET between donor and acceptor FPs is assayed. As appreciable FRET occurs only when donors and acceptors are within 10 nm of each other, the presence of FRET can be indicative of aggregation that may denote association of interacting species. By monitoring the excited-state (fluorescence) decay of the donor in the presence and absence of acceptors, dual-component decay analysis has been used to reveal the fraction of donors that are FRET positive (i.e., in aggregates)._However, control experiments using constructs containing both a donor and an acceptor FP on the same protein repeatedly indicate that a large fraction of these donors are FRET negative, thus rendering the interpretation of dual-component analysis for aggregates between separately donor-containing and acceptor-containing proteins problematic. Using Monte-Carlo simulations and analytical expressions, two possible sources for such anomalous behavior are explored: 1) conformational heterogeneity of the proteins, such that variations in the distance separating donor and acceptor FPs and/or their relative orientations persist on time-scales long in comparison with the excited-state lifetime, and 2) FP dark states. PMID:23152925

  11. Theoretical study of physisorption of nucleobases on boron nitride nanotubes: a new class of hybrid nano-biomaterials.

    PubMed

    Mukhopadhyay, Saikat; Gowtham, S; Scheicher, Ralph H; Pandey, Ravindra; Karna, Shashi P

    2010-04-23

    We investigate the adsorption of the nucleic acid bases-adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U)-on the outer wall of a high curvature semiconducting single-walled boron nitride nanotube (BNNT) by first-principles density functional theory calculations. The calculated binding energy shows the order: G > A approximately C approximately T approximately U, implying that the interaction strength of the high curvature BNNT with the nucleobases, G being an exception, is nearly the same. A higher binding energy for the G-BNNT conjugate appears to result from hybridization of the molecular orbitals of G and the BNNT. A smaller energy gap predicted for the G-BNNT conjugate relative to that of the pristine BNNT may be useful in the application of this class of biofunctional materials to the design of next-generation sensing devices. PMID:20351402

  12. Gas Phase Synthesis of (Iso)Quinoline and Its Role in the Formation of Nucleobases in the Interstellar Medium

    NASA Astrophysics Data System (ADS)

    Parker, Dorian S. N.; Kaiser, Ralf. I.; Kostko, Oleg; Troy, Tyler P.; Ahmed, Musahid; Mebel, Alexander M.; Tielens, Alexander G. G. M.

    2015-04-01

    Nitrogen-substituted polycyclic aromatic hydrocarbons (NPAHs) have been proposed to play a key role in the astrochemical evolution of the interstellar medium, yet the formation mechanisms of even their simplest prototypes—quinoline and isoquinoline—remain elusive. Here, we reveal a novel concept that under high temperature conditions representing circumstellar envelopes of carbon stars, (iso)quinoline can be synthesized via the reaction of pyridyl radicals with two acetylene molecules. The facile gas phase formation of (iso)quinoline in circumstellar envelopes defines a hitherto elusive reaction class synthesizing aromatic structures with embedded nitrogen atoms that are essential building blocks in contemporary biological-structural motifs. Once ejected from circumstellar shells and incorporated into icy interstellar grains in cold molecular clouds, these NPAHs can be functionalized by photo processing forming nucleobase-type structures as sampled in the Murchison meteorite.

  13. Ultrasensitive Direct Quantification of Nucleobase Modifications in DNA by Surface-Enhanced Raman Scattering: The Case of Cytosine.

    PubMed

    Morla-Folch, Judit; Xie, Hai-nan; Gisbert-Quilis, Patricia; Gómez-de Pedro, Sara; Pazos-Perez, Nicolas; Alvarez-Puebla, Ramon A; Guerrini, Luca

    2015-11-01

    Recognition of chemical modifications in canonical nucleobases of nucleic acids is of key importance since such modified variants act as different genetic encoders, introducing variability in the biological information contained in DNA. Herein, we demonstrate the feasibility of direct SERS in combination with chemometrics and microfluidics for the identification and relative quantification of 4 different cytosine modifications in both single- and double-stranded DNA. The minute amount of DNA required per measurement, in the sub-nanogram regime, removes the necessity of pre-amplification or enrichment steps (which are also potential sources of artificial DNA damages). These findings show great potentials for the development of fast, low-cost and high-throughput screening analytical devices capable of detecting known and unknown modifications in nucleic acids (DNA and RNA) opening new windows of activity in several fields such as biology, medicine and forensic sciences. PMID:26447808

  14. Nucleobase-Based Barbiturates: Their Protective Effect against DNA Damage Induced by Bleomycin-Iron, Antioxidant, and Lymphocyte Transformation Assay

    PubMed Central

    Dhorajiya, Bhaveshkumar D.; Dholakiya, Bharatkumar Z.; Ibrahim, Ahmed S.; Badria, Farid A.

    2014-01-01

    A number of nucleobase-based barbiturates have been synthesized by combination of nucleic acid bases and heterocyclic amines and barbituric acid derivatives through green and efficient multicomponent route and one pot reaction. This approach was accomplished efficiently using aqueous medium to give the corresponding products in high yield. The newly synthesized compounds were characterized by spectral analysis (FT-IR, 1H NMR, 13C NMR, HMBC, and UV spectroscopy) and elemental analysis. Representative of all synthesized compounds was tested and evaluated for antioxidant, bleomycin-dependent DNA damage, and Lymphocyte Transformation studies. Compounds TBC > TBA > TBG showed highest lymphocyte transformation assay, TBC > TBA > BG showed inhibitory antioxidant activity using ABTS methods, and TBC > BPA > BAMT > TBA > 1, 3-TBA manifested the best protective effect against DNA damage induced by bleomycin. PMID:24900997

  15. Development of Diubiquitin-Based FRET Probes To Quantify Ubiquitin Linkage Specificity of Deubiquitinating Enzymes.

    PubMed

    Geurink, Paul P; van Tol, Bianca D M; van Dalen, Duco; Brundel, Paul J G; Mevissen, Tycho E T; Pruneda, Jonathan N; Elliott, Paul R; van Tilburg, Gabriëlle B A; Komander, David; Ovaa, Huib

    2016-05-01

    Deubiquitinating enzymes (DUBs) are proteases that fulfill crucial roles in the ubiquitin (Ub) system, by deconjugation of Ub from its targets and disassembly of polyUb chains. The specificity of a DUB towards one of the polyUb chain linkages largely determines the ultimate signaling function. We present a novel set of diubiquitin FRET probes, comprising all seven isopeptide linkages, for the absolute quantification of chain cleavage specificity of DUBs by means of Michaelis-Menten kinetics. Each probe is equipped with a FRET pair consisting of Rhodamine110 and tetramethylrhodamine to allow the fully synthetic preparation of the probes by SPPS and NCL. Our synthetic strategy includes the introduction of N,N'-Boc-protected 5-carboxyrhodamine as a convenient building block in peptide chemistry. We demonstrate the value of our probes by quantifying the linkage specificities of a panel of nine DUBs in a high-throughput manner. PMID:26996281

  16. Selected fretting-wear-resistant coatings for Ti-6 pct Al-4 pct V alloy

    NASA Technical Reports Server (NTRS)

    Bill, R. C.

    1985-01-01

    The ability of several wear-resistant coatings to reduce fretting in the Ti-6Al-4V alloy is investigated. The experimental apparatus and procedures for evaluating fretting in uncoated Ti-6Al-4V alloy and in the alloy with plasma-sprayed coatings, polymer-bonded coating, and surface treatments are described. The wear volume and wear rate for the alloys are measured and compared. It is concluded that Al2O3 with 13 percent TiO2, preoxidation and nitride surface treatments, and MoS2 sputtering result in wear-resistant surfaces; however, the polyimide coating is the most wear resistant coating in both dry and moist air, and it causes the least wear to the uncoated alloy surface.

  17. FRET-assisted laser emission in colloidal suspensions of dye-doped latex nanoparticles

    NASA Astrophysics Data System (ADS)

    Cerdán, Luis; Enciso, Eduardo; Martín, Virginia; Bañuelos, Jorge; López-Arbeloa, Iñigo; Costela, Angel; García-Moreno, Inmaculada

    2012-09-01

    The use of commercial long-wavelength (>650 nm) laser dyes in many biophotonic applications has several important limitations, including low absorption at the standard pump wavelength (532 nm) and poor photostability. Here, we demonstrate that the use of Förster type (FRET) energy transfer can overcome these problems to enable efficient, stable near-infrared lasing in a colloidal suspension of latex nanoparticles containing a mixture of Rhodamine 6G and Nile Blue dyes. Experimental and theoretical analyses of the photophysics suggest that the dominant energy transfer mechanism is Förster type via dipole-dipole coupling, and also reveal an unexpected core/shell morphology in the dye-doped nanoparticles. FRET-assisted incoherent random lasing is also demonstrated in solid samples obtained by evaporation of colloidal suspensions.

  18. Development of Diubiquitin-Based FRET Probes To Quantify Ubiquitin Linkage Specificity of Deubiquitinating Enzymes

    PubMed Central

    Geurink, Paul P.; van Tol, Bianca D.M.; van Dalen, Duco; Brundel, Paul J.G.; Mevissen, Tycho E.T.; Pruneda, Jonathan N.; Elliott, Paul R.; van Tilburg, Gabriëlle B.A.; Komander, David; Ovaa, Huib

    2016-01-01

    Deubiquitinating enzymes (DUBs) are proteases that fulfill crucial roles in the ubiquitin (Ub) system, by deconjugation of Ub from its targets and disassembly of polyUb chains. The specificity of a DUB towards one of the polyUb chain linkages largely determines the ultimate signaling function. We present a novel set of diubiquitin FRET probes, comprising all seven isopeptide linkages, for the absolute quantification of chain cleavage specificity of DUBs by means of Michaelis–Menten kinetics. Each probe is equipped with a FRET pair consisting of Rhodamine110 and tetramethylrhodamine to allow the fully synthetic preparation of the probes by SPPS and NCL. Our synthetic strategy includes the introduction of N,N'-Boc-protected 5-carboxyrhodamine as a convenient building block in peptide chemistry. We demonstrate the value of our probes by quantifying the linkage specificities of a panel of nine DUBs in a high-throughput manner. PMID:26996281

  19. Universal limiting shape of worn profile under multiple-mode fretting conditions: theory and experimental evidence

    PubMed Central

    Dmitriev, Andrey I.; Voll, Lars B.; Psakhie, Sergey G.; Popov, Valentin L.

    2016-01-01

    We consider multiple-mode fretting wear in a frictional contact of elastic bodies subjected to a small-amplitude oscillation, which may include in-plane and out-of-plane translation, torsion and tilting (“periodic rolling”). While the detailed kinetics of wear depends on the particular loading history and wear mechanism, the final worn shape, under some additional conditions, occurs to be universal for all types and loading and wear mechanisms. This universal form is determined solely by the radius of the permanent stick region and the maximum indentation depth during the loading cycle. We provide experimental evidence for the correctness of the theoretically predicted limiting shape. The existence of the universal limiting shape can be used for designing joints which are resistant to fretting wear. PMID:26979092

  20. Cold-Sprayed Cu-MoS2 and Its Fretting Wear Behavior

    NASA Astrophysics Data System (ADS)

    Zhang, Yinyin; Descartes, Sylvie; Vo, Phuong; Chromik, Richard R.

    2016-02-01

    Cu and Cu-MoS2 coatings were fabricated by cold spray, and the fretting wear performance of the two coatings was compared. A mixture (95 wt.% Cu + 5 wt.% MoS2) was used as feedstock for the composite coating. Coatings were sprayed with identical gas flow conditions on the substrates pre-heated to approximately 170 °C. The morphology of coating top surface and polished cross sections was analyzed by scanning electron microscopy (SEM) and light optical microscopy (LOM). The influence of MoS2 on Cu deposition was examined. The local MoS2 concentration within the coating was found to affect the hardness. Fretting tests were carried out at two different normal loads, and the influence of MoS2 on friction and wear was studied. The morphology and elemental compositions of the wear scars and wear debris were observed by SEM and energy dispersive x-ray spectroscopy (EDS), respectively.

  1. The character of fracture of iron based thermal coating during fretting

    NASA Astrophysics Data System (ADS)

    Kovalevskaya, Zh G.; Kovalevskiy, E. A.; Khimich, M. A.

    2016-04-01

    The character of destruction of thermal coatings during fretting has been investigated. An iron based plasma coating has been tested with oscillation amplitude from 30 to 200 microns. The tests were conducted in air. It has been determined that the main factor influencing the rate of the wear of the coating during fretting corrosion is the size of the coating area involved into the wear process. The coating exhibits high wear resistance when the amplitude of the oscillation is commensurate with the size of the sprayed particles. During destruction of the coating the leading role belongs to fatigue-oxidation processes. The wear of the coating acquires a catastrophic character when coating macro defects - pores and interlayer boundaries - are involved into the wear process.

  2. Universal limiting shape of worn profile under multiple-mode fretting conditions: theory and experimental evidence.

    PubMed

    Dmitriev, Andrey I; Voll, Lars B; Psakhie, Sergey G; Popov, Valentin L

    2016-01-01

    We consider multiple-mode fretting wear in a frictional contact of elastic bodies subjected to a small-amplitude oscillation, which may include in-plane and out-of-plane translation, torsion and tilting ("periodic rolling"). While the detailed kinetics of wear depends on the particular loading history and wear mechanism, the final worn shape, under some additional conditions, occurs to be universal for all types and loading and wear mechanisms. This universal form is determined solely by the radius of the permanent stick region and the maximum indentation depth during the loading cycle. We provide experimental evidence for the correctness of the theoretically predicted limiting shape. The existence of the universal limiting shape can be used for designing joints which are resistant to fretting wear. PMID:26979092

  3. Universal limiting shape of worn profile under multiple-mode fretting conditions: theory and experimental evidence

    NASA Astrophysics Data System (ADS)

    Dmitriev, Andrey I.; Voll, Lars B.; Psakhie, Sergey G.; Popov, Valentin L.

    2016-03-01

    We consider multiple-mode fretting wear in a frictional contact of elastic bodies subjected to a small-amplitude oscillation, which may include in-plane and out-of-plane translation, torsion and tilting (“periodic rolling”). While the detailed kinetics of wear depends on the particular loading history and wear mechanism, the final worn shape, under some additional conditions, occurs to be universal for all types and loading and wear mechanisms. This universal form is determined solely by the radius of the permanent stick region and the maximum indentation depth during the loading cycle. We provide experimental evidence for the correctness of the theoretically predicted limiting shape. The existence of the universal limiting shape can be used for designing joints which are resistant to fretting wear.

  4. Investigation of pH and temperature effects on FRET systems for glucose sensing

    NASA Astrophysics Data System (ADS)

    Meledeo, Michael A.; Ibey, Bennett L.; O'Neal, D. P.; Pishko, Michael V.; Cote, Gerard L.

    2002-05-01

    Glucose monitoring is of critical importance in the life of Type I and many Type II diabetics. This research furthers work toward a minimally invasive implantable glucose sensor based on fluorescence detection. Current experimental models use heterogeneous fluorescence resonance energy transfer (FRET) systems for sensing; ideally, the response of one fluorophore bound to a large polysaccharide is enhanced greatly in the presence of glucose while the other fluorophore bound to a glucose sensitive protein is diminished or unaffected. Many fluorophores are affected by environmental factors such as pH and temperature. FRET experiments using two fluorophores, tetramethylrodamine isothiocyanate (TRITC) and fluoroscein isothiocyanate (FITC), are performed evaluating the effects of fluctuations over the range of pH 4-8 and temperature 25-45 degree(s)C for various concentrations of glucose in a flow cell. TRITC is bound to the lectin Concanavalin A (Con A), and FITC is bound to dextran molecules of varying sizes.

  5. Cellular uptake of titanium and vanadium from addition of salts or fretting corrosion in vitro

    SciTech Connect

    Maurer, A.M.; Merritt, K.; Brown, S.A. . Dept. of Biomedical Engineering)

    1994-02-01

    The use of titanium and titanium-6% aluminum-4% vanadium alloy for dental and orthopedic implants has increased in the last decade. The implants are presumed to be compatible because oseointegration, bony apposition, and cell attachment are known. However, the cellular association of titanium and vanadium have remained unknown. This study examined the uptake of salts or fretting corrosion products. Titanium was not observed to be toxic to the cells. Vanadium was toxic at levels greater than 10[mu]g/mL. The percentage of cellular association of titanium was shown to be about 10 times that of vanadium. The percentage of cellular association of either element was greater from fretting corrosion than from the addition of salts. The presence of vanadium did not affect the cellular uptake of titanium. The presence of titanium decreased the cell association of vanadium.

  6. Compact, Polyvalent Mannose Quantum Dots as Sensitive, Ratiometric FRET Probes for Multivalent Protein–Ligand Interactions

    PubMed Central

    Sakonsinsiri, Chadamas; Nehlmeier, Inga; Fascione, Martin A.; Zhang, Haiyan; Wang, Weili; Pöhlmann, Stefan; Turnbull, W. Bruce

    2016-01-01

    Abstract A highly efficient cap‐exchange approach for preparing compact, dense polyvalent mannose‐capped quantum dots (QDs) has been developed. The resulting QDs have been successfully used to probe multivalent interactions of HIV/Ebola receptors DC‐SIGN and DC‐SIGNR (collectively termed as DC‐SIGN/R) using a sensitive, ratiometric Förster resonance energy transfer (FRET) assay. The QD probes specifically bind DC‐SIGN, but not its closely related receptor DC‐SIGNR, which is further confirmed by its specific blocking of DC‐SIGN engagement with the Ebola virus glycoprotein. Tuning the QD surface mannose valency reveals that DC‐SIGN binds more efficiently to densely packed mannosides. A FRET‐based thermodynamic study reveals that the binding is enthalpy‐driven. This work establishes QD FRET as a rapid, sensitive technique for probing structure and thermodynamics of multivalent protein–ligand interactions.

  7. Compact, Polyvalent Mannose Quantum Dots as Sensitive, Ratiometric FRET Probes for Multivalent Protein–Ligand Interactions

    PubMed Central

    Sakonsinsiri, Chadamas; Nehlmeier, Inga; Fascione, Martin A.; Zhang, Haiyan; Wang, Weili; Pöhlmann, Stefan; Turnbull, W. Bruce

    2016-01-01

    Abstract A highly efficient cap‐exchange approach for preparing compact, dense polyvalent mannose‐capped quantum dots (QDs) has been developed. The resulting QDs have been successfully used to probe multivalent interactions of HIV/Ebola receptors DC‐SIGN and DC‐SIGNR (collectively termed as DC‐SIGN/R) using a sensitive, ratiometric Förster resonance energy transfer (FRET) assay. The QD probes specifically bind DC‐SIGN, but not its closely related receptor DC‐SIGNR, which is further confirmed by its specific blocking of DC‐SIGN engagement with the Ebola virus glycoprotein. Tuning the QD surface mannose valency reveals that DC‐SIGN binds more efficiently to densely packed mannosides. A FRET‐based thermodynamic study reveals that the binding is enthalpy‐driven. This work establishes QD FRET as a rapid, sensitive technique for probing structure and thermodynamics of multivalent protein–ligand interactions. PMID:26990806

  8. Monitoring of Apoptosis in 3D Cell Cultures by FRET and Light Sheet Fluorescence Microscopy

    PubMed Central

    Weber, Petra; Schickinger, Sarah; Wagner, Michael; Angres, Brigitte; Bruns, Thomas; Schneckenburger, Herbert

    2015-01-01

    Non-radiative cell membrane associated Förster Resonance Energy Transfer (FRET) from an enhanced cyan fluorescent protein (ECFP) to an enhanced yellow fluorescent protein (EYFP) is used for detection of apoptosis in 3-dimensional cell cultures. FRET is visualized in multi-cellular tumor spheroids by light sheet based fluorescence microscopy in combination with microspectral analysis and fluorescence lifetime imaging (FLIM). Upon application of staurosporine and to some extent after treatment with phorbol-12-myristate-13-acetate (PMA), a specific activator of protein kinase c, the caspase-3 sensitive peptide linker DEVD is cleaved. This results in a reduction of acceptor (EYFP) fluorescence as well as a prolongation of the fluorescence lifetime of the donor (ECFP). Fluorescence spectra and lifetimes may, therefore, be used for monitoring of apoptosis in a realistic 3-dimensional system, while light sheet based microscopy appears appropriate for 3D imaging at low light exposure. PMID:25761242

  9. FRET-based dimeric aptamer probe for selective and sensitive Lup an 1 allergen detection.

    PubMed

    Mairal, T; Nadal, P; Svobodova, M; O'Sullivan, C K

    2014-04-15

    A sensitive method for the rapid and sensitive detection of the anaphylactic food allergen Lup an 1 (β-conglutin) exploiting fluorescence resonance energy transfer (FRET) has been developed. A high affinity dimeric form of a truncated 11-mer aptamer against β-conglutin was used, with each monomeric aptamer being flanked by donor/acceptor moieties. The dimeric form in the absence of target yields fluorescence emission due to the FRET from the excited fluorophore to the proximal second fluorophore. However, upon addition of β-conglutin, the specific interaction induces a change in the bi-aptameric structure resulting in an increase in fluorescence emission. The method is highly specific and sensitive, with a detection limit of 150 pM, providing an effective tool for the direct detection of the toxic β-conglutin subunit in foodstuffs in just 1 min at room temperature. PMID:24280051

  10. Two-photon excited fluorescence lifetime imaging microscopy for FRET study on protein interactions

    NASA Astrophysics Data System (ADS)

    Qu, Junle; Lin, Ziyang; Liu, Lixin; Guo, Xuan; Chen, Danni; Niu, Hanben

    2005-01-01

    Two-photon excited fluorescence lifetime imaging (2P-FLIM) provides a more direct and precise approach to fluorescence resonance energy transfer (FRET), which allows studying the dynamic behavior of protein-protein interactions in living cells. In this paper, we describe the combination of a Leica TCS SP2 laser scanning microscope and a time-correlated single photon counting (TCSPC) lifetime imaging module developed by Becker & Hickl for two-photon excited fluorescence lifetime imaging. This 2P-FLIM system was used for FRET study on the interaction of heat shock protein hsp27 with p38 MAP kinase in the single living cell. Results show that the reduction in donor (CFP) lifetime in the presence of acceptor (YFP) reveals interactions between the two proteins.

  11. Universal scaling behavior of molecular electronic stopping cross section for protons colliding with small molecules and nucleobases

    NASA Astrophysics Data System (ADS)

    Trujillo-López, L. N.; Martínez-Flores, C.; Cabrera-Trujillo, R.

    2013-10-01

    The electronic stopping cross section and mean excitation energy for molecules and 5 nucleobases have been calculated within the first Born approximation in terms of an orbital decomposition to take into account the molecular structure. The harmonic oscillator (HO) description of the stopping cross section together with a Floating Spherical Gaussian Orbital (FSGO) model is implemented to account for the chemical composition of the target. This approach allows us to use bonds, cores, and lone pairs as HO basis to describe the ground state molecular structure. In the HO model, the orbital angular frequency is the only parameter that connects naturally with the mean excitation energy. As a result, we obtain a simple expression for the equivalent mean excitation energy in terms of the orbital radius parameter, as well as an analytical expression of the stopping cross section. For gas phase molecular targets, we provide HO based orbital mean excitation energies to describe any molecule containing C, N, O, H, and P atoms. We present results for protons colliding with H2, N2, O2, H2O, CO2, propylene (C3H6), methane (CH4), ethylene (C2H4) and the nucleobases - guanine (C5H5N5O), cytosine (C4H5N2O2), thymine (C5H6N2O2), adenine (C5H5N5) and uracil (C4H4N2O2). The results for the stopping cross section are compared with available experimental and theoretical data showing good to excellent agreement in the region of validity of the model. The HO approach allows us to obtain a universal stopping cross section formula to describe a universal scaling behavior for the energy loss process. The universal scaled curve is confirmed by the experimental data.

  12. Discriminating unalike single nucleobase mismatches using a molecularly resolved, label-free, interfacial LNA-based assay.

    PubMed

    Lahiri, Hiya; Mishra, Sourav; Mana, Tanushree; Mukhopadhyay, Rupa

    2016-06-20

    A number of reports have been made in recent times on label-free detection of nucleic acid sequences. However, most of these studies deal with ensemble measurements, therefore lacking in molecular level resolution. These assays have usually employed ssDNA sensor probes, and often suffered from problems of irreproducibility and poor sequence-selectivity. Herein, the applicability of surface-anchored single stranded locked nucleic acid (ssLNA) probes has been assessed in the detection of target DNA sequences, as an alternative to the DNA-based assay. Importantly, the effectiveness of the LNA-based assay in identifying different types of single nucleobase mismatches has been tested. Since the duplex melting temperature is an indicator of duplex stability, the ensemble on-surface Tm values of the surface-confined LNA-DNA duplexes have been compared to the duplex unbinding force values obtained from atomic force spectroscopy (AFS) experiments. A common mismatch discrimination pattern elicited by both the ensemble and the molecular level AFS approach could be identified. Apart from quantitative delineation of the different types of mismatches, the label-free AFS analysis confirms different degrees of efficiency of the purine and pyrimidine bases, present on the LNA backbone, in discriminating different nucleobase mismatch types. Importantly, the LNA-based AFS analysis can distinguish between the disease-relevant gene fragments, e.g., multidrug-resistant Mycobacterium tuberculosis (MTB) mutation, and the wild type. Since LNA probes are nuclease-resistant, these findings could potentially pave way to diagnostic applications of the LNA-based AFS assay. PMID:27124266

  13. On modeling biomolecular-surface nonbonded interactions: application to nucleobase adsorption on single-wall carbon nanotube surfaces

    NASA Astrophysics Data System (ADS)

    Akdim, B.; Pachter, R.; Day, P. N.; Kim, S. S.; Naik, R. R.

    2012-04-01

    In this work we explored the selectivity of single nucleobases towards adsorption on chiral single-wall carbon nanotubes (SWCNTs) by density functional theory calculations. Specifically, the adsorption of molecular models of guanine (G), adenine (A), thymine (T), and cytosine (C), as well as of AT and GC Watson-Crick (WC) base pairs on chiral SWCNT C(6, 5), C(9, 1) and C(8, 3) model structures, was analyzed in detail. The importance of correcting the exchange-correlation functional for London dispersion was clearly demonstrated, yet limitations in modeling such interactions by considering the SWCNT as a molecular model may mask subtle effects in a molecular-macroscopic material system. The trend in the calculated adsorption energies of the nucleobases on same diameter C(6, 5) and C(9, 1) SWCNT surfaces, i.e. G > A > T > C, was consistent with related computations and experimental work on graphitic surfaces, however contradicting experimental data on the adsorption of single-strand short homo-oligonucleotides on SWCNTs that demonstrated a trend of G > C > A > T (Albertorio et al 2009 Nanotechnology 20 395101). A possible role of electrostatic interactions in this case was partially captured by applying the effective fragment potential method, emphasizing that the interplay of the various contributions in modeling nonbonded interactions is complicated by theoretical limitations. Finally, because the calculated adsorption energies for Watson-Crick base pairs have shown little effect upon adsorption of the base pair farther from the surface, the results on SWCNT sorting by salmon genomic DNA could be indicative of partial unfolding of the double helix upon adsorption on the SWCNT surface.

  14. CO2 Capture with Enzyme Synthetic Analogue

    SciTech Connect

    Cordatos, Harry

    2010-11-08

    Overview of an ongoing, 2 year research project partially funded by APRA-E to create a novel, synthetic analogue of carbonic anhydrase and incorporate it into a membrane for removal of CO2 from flue gas in coal power plants. Mechanism background, preliminary feasibility study results, molecular modeling of analogue-CO2 interaction, and program timeline are provided.

  15. Accuracy of maximum likelihood estimates of a two-state model in single-molecule FRET

    SciTech Connect

    Gopich, Irina V.

    2015-01-21

    Photon sequences from single-molecule Förster resonance energy transfer (FRET) experiments can be analyzed using a maximum likelihood method. Parameters of the underlying kinetic model (FRET efficiencies of the states and transition rates between conformational states) are obtained by maximizing the appropriate likelihood function. In addition, the errors (uncertainties) of the extracted parameters can be obtained from the curvature of the likelihood function at the maximum. We study the standard deviations of the parameters of a two-state model obtained from photon sequences with recorded colors and arrival times. The standard deviations can be obtained analytically in a special case when the FRET efficiencies of the states are 0 and 1 and in the limiting cases of fast and slow conformational dynamics. These results are compared with the results of numerical simulations. The accuracy and, therefore, the ability to predict model parameters depend on how fast the transition rates are compared to the photon count rate. In the limit of slow transitions, the key parameters that determine the accuracy are the number of transitions between the states and the number of independent photon sequences. In the fast transition limit, the accuracy is determined by the small fraction of photons that are correlated with their neighbors. The relative standard deviation of the relaxation rate has a “chevron” shape as a function of the transition rate in the log-log scale. The location of the minimum of this function dramatically depends on how well the FRET efficiencies of the states are separated.

  16. A novel FRET-based optical fiber biosensor for rapid detection of Salmonella typhimurium.

    PubMed

    Ko, Sungho; Grant, Sheila A

    2006-01-15

    A biosensor that is portable and permits on-site analysis of samples would significantly reduce the large economical burden of food products recalls. A fiber optic portable biosensor utilizing the principle of fluorescence resonance energy transfer (FRET) was developed for fast detection of Salmonella typhimurium (S. typhimurium) in ground pork samples. Labeled antibody-protein G complexes were formed via the incubation of anti-Salmonella antibodies labeled with FRET donor fluorophores (Alexa Fluor 546) and protein G (PG) labeled with FRET acceptor fluorophores (Alexa Fluor 594). Utilizing silanization, the labeled antibodies-PG complexes were then immobilized on decladded, tapered silica fiber cores to form the evanescent wave-sensing region. The biosensors were tested in two different solutions: (1) PBS doped with S. typhimurium and (2) homogenized pork sample with S. typhimurium. The fiber probes tested in a S. typhimurium doped phosphate buffered solution demonstrated the feasibility of the biosensor for detecting S. typhimurium as well as determined the optimal packing density of the labeled antibody-PG complexes on the surface of fibers. The results showed that a packing density of 0.033 mg/ml produced the lowest limit of detection of 10(3)cells/ml with 8.2% change in fluorescence. The fiber probes placed in homogenized pork samples inoculated with S. typhimurium showed a limit of detection of 10(5)CFU/g with a 6.67% in fluorescence within a 5-min response time. These results showed that the FRET-based fiber optic biosensor can become a useful analytical tool for detection of S. typhimurium in real food samples. PMID:16040238

  17. Handheld Fluorescence Resonance Energy Transfer (FRET)-Aptamer Sensor for Bone Markers

    NASA Technical Reports Server (NTRS)

    Bruno, John G.

    2015-01-01

    Astronauts lose significant bone mass during lengthy space flights. NASA wishes to monitor this bone loss in order to develop nutritional and exercise countermeasures. Operational Technologies Corporation (OpTech) has developed a handheld device that quantifies bone loss in a spacecraft environment. The innovation works by adding fluorescent dyes and quenchers to aptamers to enable pushbutton, one-step bind-and-detect FRET assays that can be freeze-dried, rehydrated with body fluids, and used to quantify bone loss.

  18. Detection of glutamate release from neurons by genetically encoded surface-displayed FRET nanosensors

    NASA Astrophysics Data System (ADS)

    Okumoto, Sakiko; Looger, Loren L.; Micheva, Kristina D.; Reimer, Richard J.; Smith, Stephen J.; Frommer, Wolf B.

    2005-06-01

    Glutamate is the predominant excitatory neurotransmitter in the mammalian brain. Once released, its rapid removal from the synaptic cleft is critical for preventing excitotoxicity and spillover to neighboring synapses. Despite consensus on the role of glutamate in normal and disease physiology, technical issues limit our understanding of its metabolism in intact cells. To monitor glutamate levels inside and at the surface of living cells, genetically encoded nanosensors were developed. The fluorescent indicator protein for glutamate (FLIPE) consists of the glutamate/aspartate binding protein ybeJ from Escherichia coli fused to two variants of the green fluorescent protein. Three sensors with lower affinities for glutamate were created by mutation of residues peristeric to the ybeJ binding pocket. In the presence of ligands, FLIPEs show a concentration-dependent decrease in FRET efficiency. When expressed on the surface of rat hippocampal neurons or PC12 cells, the sensors respond to extracellular glutamate with a reversible concentration-dependent decrease in FRET efficiency. Depolarization of neurons leads to a reduction in FRET efficiency corresponding to 300 nM glutamate at the cell surface. No change in FRET was observed when cells expressing sensors in the cytosol were superfused with up to 20 mM glutamate, consistent with a minimal contribution of glutamate uptake to cytosolic glutamate levels. The results demonstrate that FLIPE sensors can be used for real-time monitoring of glutamate metabolism in living cells, in tissues, or in intact organisms, providing tools for studying metabolism or for drug discovery. aspartate | hippocampal neuron | neurotransmitter | secretion | transport

  19. Conformations of the signal recognition particle protein Ffh from Escherichia coli as determined by FRET.

    PubMed

    Buskiewicz, Iwona; Peske, Frank; Wieden, Hans-Joachim; Gryczynski, Ignacy; Rodnina, Marina V; Wintermeyer, Wolfgang

    2005-08-12

    The signal recognition particle (SRP) initiates the co-translational targeting of proteins to the plasma membrane in bacteria by binding to the N-terminal signal sequence emerging from the translating ribosome. SRP in Escherichia coli is composed of one protein, Ffh, and 4.5S RNA. In the present work, we probe the structure of Ffh alone and in the complex with 4.5S RNA by measuring distances between different positions within Ffh and between Ffh and 4.5S RNA by fluorescence resonance energy transfer (FRET). According to the FRET distances, NG and M domains in free Ffh are in close contact, as in the A/A arrangement in the crystal structure of Ffh from Thermus aquaticus, in agreement with the formation of a crosslink between cysteine residues at two critical positions in the G and M domains. Upon Ffh binding to 4.5S RNA or a 61 nucleotide fragment comprising internal loops A-C, the G and M domains move apart to assume a more open conformation, as indicated by changes of FRET distances. The movement is smaller when Ffh binds to a 49 nucleotide fragment of 4.5S RNA comprising only internal loops A and B, i.e. lacking the binding site of the NG domain. The FRET results suggest that in the SRP complex 4.5S RNA is present in a bent, rather than extended, conformation. The domain rearrangement of Ffh that takes place upon formation of the SRP is probably important for subsequent steps of membrane targeting, including interactions with the translating ribosome and the SRP receptor. PMID:16005894

  20. Kinetics of precursor interactions with the bacterial Tat translocase detected by real-time FRET.

    PubMed

    Whitaker, Neal; Bageshwar, Umesh K; Musser, Siegfried M

    2012-03-30

    The Escherichia coli twin-arginine translocation (Tat) system transports fully folded and assembled proteins across the inner membrane into the periplasmic space. Traditionally, in vitro protein translocation studies have been performed using gel-based transport assays. This technique suffers from low time resolution, and often, an inability to distinguish between different steps in a continuously occurring translocation process. To address these limitations, we have developed an in vitro FRET-based assay that reports on an early step in the Tat translocation process in real-time. The natural Tat substrate pre-SufI was labeled with Alexa532 (donor), and the fluorescent protein mCherry (acceptor) was fused to the C terminus of TatB or TatC. The colored Tat proteins were easily visible during purification, enabling identification of a highly active inverted membrane vesicle (IMV) fraction yielding transport rates with NADH almost an order of magnitude faster than previously reported. When pre-SufI was bound to the translocon, FRET was observed for both Tat proteins. FRET was diminished upon addition of nonfluorescent pre-SufI, indicating that the initial binding step is reversible. When the membranes were energized with NADH, the FRET signal was lost after a short delay. These data suggest a model in which a Tat cargo initially associates with the TatBC complex, and an electric field gradient is required for the cargo to proceed to the next stage of transport. This cargo migration away from the TatBC complex requires a significant fraction of the total transport time. PMID:22315217

  1. Niche nanoparticle-based FRET assay for bleomycin detection via DNA scission.

    PubMed

    Pei, Haimeng; Zheng, Yiqun; Kong, Rongmei; Xia, Lian; Qu, Fengli

    2016-11-15

    We describe a highly sensitive nanoparticle-based fluorescence resonance energy transfer (FRET) probe developed without using molecular fluorophores as donors and acceptors. The success of this work relies on the strategy that DNA scission was designed to occur to the probe when target presented, which enabled the fluorescence signal "turn-on" of graphene quantum dots (GQDs) and thus quantitative analysis. In particular, amino-modified SiO2 NPs were initially coated by GQDs to form highly emitting SiO2/GQDs, followed by conjunction with DNA functionalized gold nanoparticles (Au NPs-DNA) to form SiO2/GQDs-DNA-Au NPs composite. Owing to the FRET interactions between the GQDs and Au NPs, the fluorescence of GQDs was effectively quenched by Au NPs. When bleomycin (BLM), a model analyte, was mixed with the probe, the fluorescence signal of GQDs would be restored due to the removal of Au NPs from the SiO2/GQDs surface by DNA scission treatment with BLM in the presence of Fe (II). The current FRET probe shows a good linear relationship between the fluorescence intensity and the concentration of BLM in the range from 0.5nM to 1μM with a detection limit of 0.2nM. The probe also shows satisfactory results for the analysis of clinical serum samples. This method provides versatility to the application of GQDs in FRET biosensing and could be potentially extended to other similar systems by replacing the linker between the GQDs and Au NPs. PMID:27155119

  2. Compact quantum dot-antibody conjugates for FRET immunoassays with subnanomolar detection limits.

    PubMed

    Mattera, Lucia; Bhuckory, Shashi; Wegner, K David; Qiu, Xue; Agnese, Fabio; Lincheneau, Christophe; Senden, Tim; Djurado, David; Charbonnière, Loïc J; Hildebrandt, Niko; Reiss, Peter

    2016-06-01

    A novel two-step approach for quantum dot (QD) functionalization and bioconjugation is presented, which yields ultra-compact, stable, and highly luminescent antibody-QD conjugates suitable for use in FRET immunoassays. Hydrophobic InPZnS/ZnSe/ZnS (emission wavelength: 530 nm), CdSe/ZnS (605 nm), and CdSeTe/ZnS (705 nm) QDs were surface functionalized with zwitterionic penicillamine, enabling aqueous phase transfer under conservation of the photoluminescence properties. Post-functionalization with a heterobifunctional crosslinker, containing a lipoic acid group and a maleimide function, enabled the subsequent coupling to sulfhydryl groups of proteins. This was demonstrated by QD conjugation with fragmented antibodies (F(ab)). The obtained F(ab)-QD conjugates range among the smallest antibody-functionalized nanoprobes ever reported, with a hydrodynamic diameter <13 nm, PL quantum yield up to 66% at 705 nm, and colloidal stability of several months in various buffers. They were applied as FRET acceptors in homogeneous, time-gated immunoassays using Tb-antibodies as FRET donors, both coupled by an immunological sandwich complex between the two antibodies and a PSA (prostate specific antigen) biomarker. The advantages of the compact surface coating for FRET could be demonstrated by an 6.2 and 2.5 fold improvement of the limit of detection (LOD) for PSA compared to commercially available hydrophilic QDs emitting at 605 and 705 nm, respectively. While the commercial QDs contain identical inorganic cores responsible for their fluorescence, they are coated with a comparably thick amphiphilic polymer layer leading to much larger hydrodynamic diameters (>26 nm without biomolecules). The LODs of 0.8 and 3.7 ng mL(-1) obtained in 50 μL serum samples are below the clinical cut-off level of PSA (4 ng mL(-1)) and demonstrate their direct applicability in clinical diagnostics. PMID:27188210

  3. A TR-FRET-based functional assay for screening activators of CARM1.

    PubMed

    Zeng, Hao; Wu, Jiacai; Bedford, Mark T; Sbardella, Gianluca; Hoffmann, F Michael; Bi, Kun; Xu, Wei

    2013-05-10

    Epigenetics is an emerging field that demands selective cell-permeable chemical probes to perturb, especially in vivo, the activity of specific enzymes involved in modulating the epigenetic codes. Coactivator-associated arginine methyltransferase 1 (CARM1) is a coactivator of estrogen receptor α (ERα), the main target in human breast cancer. We previously showed that twofold overexpression of CARM1 in MCF7 breast cancer cells increased the expression of ERα-target genes involved in differentiation and reduced cell proliferation, thus leading to the hypothesis that activating CARM1 by chemical activators might be therapeutically effective in breast cancer. Selective, potent, cell-permeable CARM1 activators will be essential to test this hypothesis. Here we report the development of a cell-based, time-resolved (TR) FRET assay that uses poly(A) binding protein 1 (PABP1) methylation to monitor cellular activity of CARM1. The LanthaScreen TR-FRET assay uses MCF7 cells expressing GFP-PABP1 fusion protein through BacMam gene delivery system, methyl-PABP1 specific antibody, and terbium-labeled secondary antibody. This assay has been validated as reflecting the expression and/or activity of CARM1 and optimized for high throughput screening to identify CARM1 allosteric activators. This TR-FRET platform serves as a generic tool for functional screening of cell-permeable, chemical modulators of CARM1 for elucidation of its in vivo functions. PMID:23585185

  4. Single-Molecule FRET Reveals Hidden Complexity in a Protein Energy Landscape

    PubMed Central

    Tsytlonok, Maksym; Ibrahim, Shehu M.; Rowling, Pamela J.E.; Xu, Wenshu; Ruedas-Rama, Maria J.; Orte, Angel; Klenerman, David; Itzhaki, Laura S.

    2015-01-01

    Summary Here, using single-molecule FRET, we reveal previously hidden conformations of the ankyrin-repeat domain of AnkyrinR, a giant adaptor molecule that anchors integral membrane proteins to the spectrin-actin cytoskeleton through simultaneous binding of multiple partner proteins. We show that the ankyrin repeats switch between high-FRET and low-FRET states, controlled by an unstructured “safety pin” or “staple” from the adjacent domain of AnkyrinR. Opening of the safety pin leads to unravelling of the ankyrin repeat stack, a process that will dramatically affect the relative orientations of AnkyrinR binding partners and, hence, the anchoring of the spectrin-actin cytoskeleton to the membrane. Ankyrin repeats are one of the most ubiquitous molecular recognition platforms in nature, and it is therefore important to understand how their structures are adapted for function. Our results point to a striking mechanism by which the order-disorder transition and, thereby, the activity of repeat proteins can be regulated. PMID:25565106

  5. A FRET-Based Biosensor for Imaging SYK Activities in Living Cells

    PubMed Central

    Xiang, Xue; Sun, Jie; Wu, Jianhua; He, Hai-Tao; Wang, Yingxiao; Zhu, Cheng

    2014-01-01

    Spleen tyrosine kinase (SYK) is crucial to cellular functions mediated by immunoreceptors and integrins. We have developed and characterized a new genetically-encoded Förster resonance energy transfer (FRET)-based biosensor for studying the dynamics of SYK activities in living cells at a subcellular level. It contains an N-terminal ECFP, SH2 domain, a peptide derived from a SYK substrate VAV2, and a C-terminal YPet. Upon the specific phosphorylation by SYK in vitro, the biosensor substrate peptide bound to the intramolecular SH2 domain to reduce the FRET efficiency. Transfection of the biosensor did not affect activation of the endogenous SYK in host cells. Phosphorylation of the biosensor followed the same kinetics as the endogenous VAV2. Using FRET imaging and ratiometric analysis with this SYK biosensor, we visualized and quantified the realtime activation of SYK in K562 cells upon IgG Fc engagement of Fcc receptor IIA and in mouse embryonic fibroblasts upon stimulation by the platelet derived growth factor. These results demonstrate our biosensor as a powerful tool for studying cellular signaling that involves SYK. PMID:25541586

  6. Experimental research on stable fretting wear of stainless steel wires in transformable component

    NASA Astrophysics Data System (ADS)

    Dong, Xiu-ping; Liu, Guo-quan; Zhang, Li; Bai, Hong-bai; Yang, Jian-chun

    2009-07-01

    Cool-drawn 1Cr18Ni9 stainless steel wires of φ 0.1~0.5 mm can be woven and punched to prepare transformable component which has loose, reticulate structures. When it is uploaded with vibrating force, the displacement will cause intense frictions between wires' surfaces which will dissipate abundant energy and thus it can serve as dampers like natural rubbers. Since such new type of material has double characteristics of both rubbers and metals, it is commonly called "Metal Rubber". There is certain amount of contact point/surface on wires in the transformable component and the displacements between wires are at micron levels. Experiments showed that wear course of 'fretting cell' could be plotted as four phases: polish, adherence, forming of the third bed and stabilization. The stabilization phase, in which the friction coefficients are comparatively stable, dominates the whole course. Based on data of Metal Rubber vibration fatigue experiment, φ 0.3 mm cool-drawn 1Cr18Ni9 stainless steel wires' dry fretting experiments at 10 N load are made on SRV high temperature wear tester, friction coefficients are collected and fret traces are studied by laser scanning confocal microscope (LSCM). Results indicate that wire's stabilization wear phase is the circulation process of grindings' forming, concentrating to blocks of φ 20 μm, busting and discharging. Deformation induced martensite transit in wire's cool drawing has significant effects on grinding blocks' bursting performances.

  7. Detection of low abundant mutations in DNA using single-molecule FRET and ligase detection reactions

    NASA Astrophysics Data System (ADS)

    Wabuyele, Musundi B.; Farquar, Hannah; Stryjewski, Wieslaw J.; Hammer, Robert P.; Soper, Steven A.; Cheng, Yu-Wei; Barany, Francis

    2003-06-01

    New strategies for analyzing molecular signatures of disease states in real time using single pair fluorescence resonance energy transfer (spFRET) were developed to rapidly detect point mutations in unamplified genomic DNA (DNA diagnostics). The assay was carried out using allele-specific primers, which flanked the point mutation in the target gene fragment and were ligated using a thremostable ligase enzyme only when the genomic DNA carried this mutation (ligase detection reaction, LDR). We coupled LDR with spFRET to identify a single base mutation in codon 12 of a K-ras oncogene that has high diagnostic value for colorectal cancers. A simple diode laser-based fluorescence system capable of interrogating single fluorescent molecules undergoing FRET was used to detect photon bursts generated from the MB probes formed upon ligation. We demonstrated the ability to rapidly discriminate single base differences in heterogeneous populations having as little as 600 copies of human genomic DNA without PCR amplification. Single base difference in the K-ras gene was discriminated in less than 5 min at a frequency of 1 mutant DNA per 10 normals using only a single LDR thermal cycle of genomic DNA. Real time analyses of point mutations were also performed in PMMA microfluidic device.

  8. FRET-based voltage probes for confocal imaging: membrane potential oscillations throughout pancreatic islets.

    PubMed

    Kuznetsov, Andrey; Bindokas, Vytautas P; Marks, Jeremy D; Philipson, Louis H

    2005-07-01

    Insulin secretion is dependent on coordinated pancreatic islet physiology. In the present study, we found a way to overcome the limitations of cellular electrophysiology to optically determine cell membrane potential (V(m)) throughout an islet by using a fast voltage optical dye pair. Using laser scanning confocal microscopy (LSCM), we observed fluorescence (Förster) resonance energy transfer (FRET) with the fluorescent donor N-(6-chloro-7-hydroxycoumarin-3-carbonyl)-dimyristoylphosphatidyl-ethanolamine and the acceptor bis-(1,3-diethylthiobarbiturate) trimethine oxonol in the plasma membrane of essentially every cell within an islet. The FRET signal was approximately linear from V(m) -70 to +50 mV with a 2.5-fold change in amplitude. We evaluated the responses of islet cells to glucose and tetraethylammonium. Essentially, every responding cell in a mouse islet displayed similar time-dependent changes in V(m). When V(m) was measured simultaneously with intracellular Ca2+, all active cells showed tight coupling of V(m) to islet cell Ca2+ changes. Our findings indicate that FRET-based, voltage-sensitive dyes used in conjunction with LSCM imaging could be extremely useful in studies of excitation-secretion coupling in intact islets of Langerhans. PMID:15758044

  9. FRET based biosensor for detection of active NF-kB

    NASA Astrophysics Data System (ADS)

    Baldini, Francesco; Citti, Lorenzo; Domenici, Claudio; Giannetti, Ambra; Tedeschi, Lorena; Vo-Dinh, Tuan; Wabuyele, Musundi B.

    2005-05-01

    The Nuclear Factor kB is a transcription factor, ubiquitously expressed, involved in the regulation of a large number of genes and in a variety of human disease including inflammation, asthma, atherosclerosis, AIDS, septic shock, arthritis and cancer. The critical need for a simple and direct method to evaluate the quantity of active NF-kB in a biological sample can be addressed using a suitable and reusable biosensor. For this purpose, a novel method, using fluorescence resonance energy transfer (FRET), to detect the active form of NF-kB binding a specific DNA sequence has been developed. A single-stranded DNA (ssDNA) with auto-complementary sequence has been properly designed and synthesized. In order to evaluate FRET due to the DNA/protein binding interaction taking place between double-stranded DNA (dsDNA) immobilized in a capillary wall and NF-kB proteins, a highly sensitive FRET-based biosensor system developed in our laboratory was used. Preliminary results show that our system was capable of detecting the active form of NF-kB protein with a detection efficiency of about 90% and that the system has a good regenerability.

  10. Application of quantum-dots for analysis of nanosystems by either utilizing or preventing FRET

    NASA Astrophysics Data System (ADS)

    Kim, Joong H.; Chaudhary, Sumit; Stephens, Jared P.; Singh, Krishna V.; Ozkan, Mihrimah

    2005-04-01

    We have developed conjugates with quantum-dots (QDs) for the purpose of analysis of nanosystems that are organic or inorganic in nature such as DNA and carbon nanotubes. First, by employing Florescence Resonant Energy Transfer (FRET) principles, a hybrid molecular beacon conjugates are synthesized. For water- solubilization of QDs, we modified the surface of CdSe-ZnS core-shell QD by using mercaptoacetic acid ligand. This modification does not affect the size of QDs from that of unmodified QDs. After linking molecular beacons to the carboxyl groups of the modified QDs using 1-Ethyl-3- (3-dimethylaminopropyl) carbodiimide hydrochloride, hybrid molecular beacons are prepared as a DNA probe. After hybridization with specific target DNA and non-specific target DNA, the hybrid conjugates show high specificity to the target DNA with 5-fold increase in the intensity of fluorescence. By developing atomic model of the conjugates, we calculated with 8 numbers of molecular beacons on a single quantum dots, we could increase the efficiency of FRET up to 90%. In other hands, for application of quantum dots to the carbon nanotubes, FRET is a barrier. Thus, after employing 1 % sodium-dodecyl-sulfonate (SDS), single-walled carbon nanotubes are decorated with QDs at their outer surface. This enables fluorescent microscopy imaging of single-walled carbon nanotubes which is a more common technique than electron microscopy. In summary, QDs can be used for analysis or detection of both organic and inorganic based nanosystems.

  11. Quantum dot-based concentric FRET configuration for the parallel detection of protease activity and concentration.

    PubMed

    Wu, Miao; Petryayeva, Eleonora; Algar, W Russ

    2014-11-18

    Protease expression, activity, and inhibition play crucial roles in a multitude of biological processes; however, these three aspects of their function are difficult for any one bioanalytical probe to measure. To help address this challenge, we report a multifunctional concentric Förster resonance energy transfer (FRET) configuration that combines two modes of biorecognition using aptamers and peptide substrates coassembled to a central semiconductor quantum dot (QD). The aptamer is sensitive to the concentration of protease and the peptide is sensitive to its hydrolytic activity. The role of the QD is to serve as a nanoscale scaffold and initial donor for energy transfer with both Cyanine 3 (Cy3) and Alexa Fluor 647 (A647) fluorescent dyes associated with the aptamer and peptide, respectively. Using thrombin as a model protease, we show that a ratiometric analysis of the emission from the QD, Cy3, and A647 permits discrimination between thrombin and thrombin-like activity, and distinguishes between active, reversibly inhibited, and irreversibly inhibited thrombin. Reliable quantitative results were obtained from a kinetic analysis of the changes in FRET. This concentric FRET format, which capitalizes on both the physical and optical properties of QDs, should be adaptable to other protease targets for which both peptide substrates and binding aptamers are known. It is thus expected to become valuable a tool for the real-time analysis of protease activity and regulation. PMID:25361050

  12. Dance of the SNAREs: assembly and rearrangements detected with FRET at neuronal synapses.

    PubMed

    Degtyar, Vadim; Hafez, Ismail M; Bray, Christopher; Zucker, Robert S

    2013-03-27

    Soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptors (SNAREs) mediate vesicle fusion with the plasma membrane on activation by calcium binding to synaptotagmin. In the present study, we used fluorescence resonance energy transfer (FRET) and fluorescence lifetime imaging microscopy between fluorescently labeled SNARE proteins expressed in cultured rat hippocampal neurons to detect resting SNARE complexes, their conformational rearrangement on exocytosis, their disassembly before endocytosis of vesicular proteins, and SNARE assembly at newly docked vesicles. Assembled SNAREs are not only present in docked vesicles; unexpected residual "orphan SNARE complexes" also reside in para-active zone regions. Real-time changes in FRET between N-terminally labeled SNAP-25 and VAMP reported a reorientation of the SNARE motif upon exocytosis, SNARE disassembly in the active zone periphery, and SNARE reassembly in newly docked vesicles. With VAMP labeled C-terminally, decreased fluorescence in C-terminally labeled syntaxin (extracellular) reported trans-cis-conformational changes in SNAREs on vesicle fusion. After fusion SNAP-25 and syntaxin disperse along with VAMP, as well as the FRET signal itself, indicating diffusion of intact SNAREs after vesicle fusion but before their peripheral disassembly. Our measurements of spatiotemporal dynamics of SNARE conformational changes and movements refine models of SNARE function. Technical advances required to detect tiny changes in fluorescence in small fractions of labeled proteins in presynaptic boutons on a time scale of seconds permit the detection of rapid intermolecular interactions between small proportions of protein partners in cellular subcompartments. PMID:23536066

  13. Quantum dot FRET-based probes in thin films grown in microfluidic channels.

    PubMed

    Crivat, Georgeta; Da Silva, Sandra Maria; Reyes, Darwin R; Locascio, Laurie E; Gaitan, Michael; Rosenzweig, Nitsa; Rosenzweig, Zeev

    2010-02-10

    This paper describes the development of new fluorescence resonance energy transfer (FRET)-based quantum dot probes for proteolytic activity. The CdSe/ZnS quantum dots are incorporated into a thin polymeric film, which is prepared by layer-by-layer deposition of alternately charged polyelectrolytes. The quantum dots, which serve as fluorescent donors, are separated from rhodamine acceptor molecules, which are covalently attached to the film surface by a varying number of polyelectrolyte layers. When excited with visible light, the emission color of the polyelectrolyte multilayer film appears orange due to FRET between the quantum dots and molecular acceptors. The emission color changes to green when the rhodamine molecules are removed from the surface by enzymatic cleavage. The new probe design enables the use of quantum dots in bioassays, in this study for real-time monitoring of trypsin activity, while alleviating concerns about their potential toxicity. Application of these quantum dot FRET-based probes in microfluidic channels enables bioanalysis of volume-limited samples and single-cell studies in an in vivo-like environment. PMID:20073459

  14. One- and two-component analysis of cyan fluorescent protein: FLIM-FRET microscopy

    NASA Astrophysics Data System (ADS)

    Chen, Ye; King, Michelle; Periasamy, Ammasi

    2005-03-01

    Remarkable advances have been made in studying the dynamic events of protein molecules in living cells and tissues using advanced light microscopy imaging techniques and green fluorescent proteins (GFPs). Identification of the interacting protein partners is critical in understanding its function and place in the biochemical pathway, thereby establishing its role in important disease processes. FLIM-FRET microscopy technique, allow the study of proteins in multiple ways including what proteins are expressed, where they are expressed- and where they move over time. It has been observed that the eCFP-eYFP FRET pair may not be that suitable to localize the association of protein molecules since the eCFP has two-components lifetime. The new Cerulean green fluorescent protein appears to have only one-component lifetime. We describe the extensive investigation of eCFP and Cerulean to study the dimerization of the transcription factor CCAAT/enhancer binding protein alpha in GHFT1-5 living cell nucleus using the time-correlated single photon counting (TCSPC) FLIM-FRET microscopy.

  15. Real-time detecting gelatinases activity in living cells by FRET imaging

    NASA Astrophysics Data System (ADS)

    Yang, Jie; Zhang, Zhihong; Liu, Bifeng; Luo, Qingming

    2006-01-01

    Degradation of the extracellular matrix by Matrix metalloproteinases (MMPs) not only enhances tumor invasion, but also affects tumor cell behaviour and leads to cancer progression. To monitor gelatinases (contain MMP2 and MMP9) activity in living cells, we constructed a vector that encoded a gelatinases recognition site (GRS) between citrine (mutation of EYFP Q69M) in N terminal and ECFP in C terminal. Because Gelatinases are secretory proteins and act outside of cell, an expressing vector displayed the fusion protein on cellular surface was used for this FRET gene probe. On expression of YFP-GRS-ECFP in MCF-7 cells that expressed no gelatinases, we were able to observe the efficient transfer of energy from excited ECFP to YFP within the YFP-GRS-ECFP molecule. However, the fusion protein YFP-GRS-ECFP was expressed in MDA-MB 453s cell line with high secretory gelatinases, so YFP-GRS-ECFP was cleaved by gelatinases, no such transfer of energy was detected and fluorescence signal disappeared in YFP channel since YFP protein was cut down. Moreover, Doxycycline, a MMP inhibitor, could make FRET signal increase and fluorescence signal appeared in YFP channel. Thus, the FRET probe YFP-GRS-ECFP can sensitively and reliably monitor gelatinases activation in living cells and can be used for screening MMP inhibitors.

  16. Monitoring Integrated Activity of Individual Neurons Using FRET-Based Voltage-Sensitive Dyes.

    PubMed

    Briggman, Kevin L; Kristan, William B; González, Jesús E; Kleinfeld, David; Tsien, Roger Y

    2015-01-01

    Pairs of membrane-associated molecules exhibiting fluorescence resonance energy transfer (FRET) provide a sensitive technique to measure changes in a cell's membrane potential. One of the FRET pair binds to one surface of the membrane and the other is a mobile ion that dissolves in the lipid bilayer. The voltage-related signal can be measured as a change in the fluorescence of either the donor or acceptor molecules, but measuring their ratio provides the largest and most noise-free signal. This technology has been used in a variety of ways; three are documented in this chapter: (1) high throughput drug screening, (2) monitoring the activity of many neurons simultaneously during a behavior, and (3) finding synaptic targets of a stimulated neuron. In addition, we provide protocols for using the dyes on both cultured neurons and leech ganglia. We also give an updated description of the mathematical basis for measuring the coherence between electrical and optical signals. Future improvements of this technique include faster and more sensitive dyes that bleach more slowly, and the expression of one of the FRET pair genetically. PMID:26238052

  17. Ultrasensitive FRET-based DNA sensor using PNA/DNA hybridization.

    PubMed

    Yang, Lan-Hee; Ahn, Dong June; Koo, Eunhae

    2016-12-01

    In the diagnosis of genetic diseases, rapid and highly sensitive DNA detection is crucial. Therefore, many strategies for detecting target DNA have been developed, including electrical, optical, and mechanical methods. Herein, a highly sensitive FRET based sensor was developed by using PNA (Peptide Nucleic Acid) probe and QD, in which red color QDs are hybridized with capture probes, reporter probes and target DNAs by EDC-NHS coupling. The hybridized probe with target DNA gives off fluorescent signal due to the energy transfer from QD to Cy5 dye in the reporter probe. Compared to the conventional DNA sensor using DNA probes, the DNA sensor using PNA probes shows higher FRET factor and efficiency due to the higher reactivity between PNA and target DNA. In addition, to elicit the effect of the distance between the donor and the acceptor, we have investigated two types of the reporter probes having Cy5 dyes attached at the different positions of the reporter probes. Results show that the shorter the distance between QDs and Cy5s, the stronger the signal intensity. Furthermore, based on the fluorescence microscopy images using microcapillary chips, the FRET signal is enhanced to be up to 276% times stronger than the signal obtained using the cuvette by the fluorescence spectrometer. These results suggest that the PNA probe system conjugated with QDs can be used as ultrasensitive DNA nanosensors. PMID:27612755

  18. Measurement of caspase-2 activation during different anti-tumor drugs induced apoptosis by FRET technique

    NASA Astrophysics Data System (ADS)

    Lin, Juqiang; Zeng, Shaoqun; Luo, Qingming; Rong, Chen; Zhang, Zhihong

    2007-11-01

    Caspase-2 is important for the engagement of the mitochondrial apoptotic pathway, in the presence of DNA-damaging agents, such as cisplatin; however, the mechanism by which caspase-2 executes apoptosis remains obscure. In this study, we carried out the measurements of the dynamics of caspase-2 activation in a single living cell by a FRET (fluorescence resonance energy transfer) probe. A FRET probe was constructed that encoded a CRS (caspase-2 recognition site) fused with a cyan fluorescent protein (CFP) and a red fluorescent protein (DsRed) (CFP-CRS-DsRed). Using this probe, we found that during TRAIL-induced apoptosis, caspase-2 was not activated, and caspase-2 activation occurred in etoposide and cisplatin treated cells. However, during cisplatin-induced apoptosis caspase-2 activation was initiated much earlier than that of etoposide. Cisplatin and etoposide is one of the most broadly used drugs in the Clinical applications of cancer chemotherapy, and TRAIL, which belongs to the TNF family proteins, can selectively induce apoptosis in many transformed cells but not in normal cells. Most of anticancer drugs can induce apoptosis mediated by the activation of caspase pathway. Thus, the perfect synergistic effect group of multi-drug can be selected by using our FRET probe.

  19. Fully analogue photonic reservoir computer.

    PubMed

    Duport, François; Smerieri, Anteo; Akrout, Akram; Haelterman, Marc; Massar, Serge

    2016-01-01

    Introduced a decade ago, reservoir computing is an efficient approach for signal processing. State of the art capabilities have already been demonstrated with both computer simulations and physical implementations. If photonic reservoir computing appears to be promising a solution for ultrafast nontrivial computing, all the implementations presented up to now require digital pre or post processing, which prevents them from exploiting their full potential, in particular in terms of processing speed. We address here the possibility to get rid simultaneously of both digital pre and post processing. The standalone fully analogue reservoir computer resulting from our endeavour is compared to previous experiments and only exhibits rather limited degradation of performances. Our experiment constitutes a proof of concept for standalone physical reservoir computers. PMID:26935166

  20. An analogue study of intrusions.

    PubMed

    Laposa, Judith M; Alden, Lynn E

    2006-07-01

    According to cognitive theorists, intrusive trauma memories have their origin in how information during the event is processed. Two studies investigated functional cognitive strategies during medical crises that might protect against intrusions. In Study 1, interviews with health-care professionals were used to identify cognitive strategies judged to be effective in controlling emotions and dealing with medical crises. Study 2 systematically manipulated the use of those strategies in a trauma analogue film paradigm. Experimental participants reported fewer intrusions, and less fear and avoidance of film-related stimuli during the subsequent week than controls. The manipulation did not affect anxiety during the film or memory disorganization. Implications for cognitive theories of intrusion development are discussed. PMID:16125135