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Single Strand (single + strand)
Terms modified by Single Strand Selected AbstractsTuning and Enhancing Photoluminescence of Light-Emitting Polymer Nanotubes through Electron-Beam IrradiationADVANCED FUNCTIONAL MATERIALS, Issue 4 2009Young Ki Hong A new method for the tuning and enhancing photoluminescence (PL) characteristics of light emitting poly (3-methylthiopnehe) (P3MT) nanotubes through E-beam irradiation under atmospheric environments is reported. An E-beam generated from a linear electron accelerator (1 MeV, 1.6,×,1013,8.0,×,1016 electrons cm,2) is irradiated onto P3MT nanotubes including an Al2O3 template. From laser confocal microscope (LCM) PL experiments, significant enhancements in the PL intensity,up to about 90 times of an isolated single strand of the E-beam irradiated P3MT nanotubes,are observed. The luminescent color of the P3MT nanotubes changes from green to red color depending on the variation of E-beam dosage. These results might originate from the de-doping effect and the conformational modification through E-beam irradiations. Conformational changes of the E-beam irradiated P3MT nanotubes are confirmed by LCM single Raman and ultraviolet-visible (UV/Vis) absorption spectra. From UV/Vis absorption spectra, it is observed that the ,,,* transition peak and the doping induced bipolaron peaks of the P3MT nanotubes dramatically vary with E-beam irradiating conditions. [source] Validity of methyl mercury hair analysis: mercury monitoring in human scalp/nude mouse modelJOURNAL OF APPLIED TOXICOLOGY, Issue 4 2008Grazyna Zareba Abstract Objective. The grafting of human scalp hair was used as a new application of this method to explore methyl mercury incorporation into human hair and to validate this model for mercury monitoring in hair. Methods. Human scalp grafts were transplanted to athymic BALB/c nude mice. The animals were exposed to methyl mercury either as a single dose i.p. or continuously for 4 months, using ALZET osmotic pumps. The mercury concentration in hair was determined using x-ray fluorescence (XRF) spectrometry by segmental (2 mm) analysis of a single strand, and tissue concentrations were measured by cold vapor atomic absorption analysis. Results. Human scalp hair grown in nude mice showed long-term persistence of human features including the expression of histocompatibility antigens (KAB 3, W 6/32, SF 1-1.1.1) and normal hair morphometry. The disposition of methyl mercury in nude mice followed a one-compartment model with a whole body elimination half-life of 6.7 days (elimination constant, k = 0.1/day). Autoradiographic studies revealed that methyl mercury was rapidly incorporated into areas of the hair follicle undergoing active keratinization. Methyl mercury concentrations in human hair transplanted onto nude mice were two orders of magnitude higher than in blood and attained a mean hair: blood ratio of 217 : 1, similar to ratios reported only in human studies. Conclusions. This study demonstrated that human hair grown on nude mice can record the level of exposure to methyl mercury and can serve as a valuable research tool to study mercury incorporation into human hair. Copyright © 2007 John Wiley & Sons, Ltd. [source] Meteoroid ejection velocities deduced from a study of the April Lyrid meteor showerMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 1 2002T.R. Arter The use of meteor shower observations to determine the probable ejection velocity of the stream meteoroids from the parent body depends on the identification of some characteristic of the shower that is very sensitive to the ejection velocity. The April Lyrid meteor shower occasionally produces spectacular displays with rates exceeding 600 meteors per hour, as opposed to the usual rate of no more than meteors per hour. These outbursts occur with an apparent 12-yr periodicity. Arter & Williams have postulated that this is caused by an interplay between the ejection velocity (which determines the initial orbit) and gravitational perturbations from Jupiter. This produces a structure for the stream as a whole that can be described as a hollow tube with a cross-section on to the ecliptic in the form of an elliptical ring. Individual meteoroids follow a single strand along the surface of this tube and arrive at the ecliptic at slightly different times, there being a periodicity of 12 yr in the arrival times. Generation of this pattern is very sensitive to ejection velocity, and this paper investigates the range of ejection velocities over which this behaviour exists and thus, by inference, deduces the ejection velocity of the meteoroids. [source] A novel, rapid, inexpensive, and highly sensitive experiment for demonstration of DNA damage in human leukocytes by single cell gel electrophoresisBIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, Issue 1 2003B. R. Manjunatha Abstract The single cell gel electrophoresis technique (comet assay) has been adopted to demonstrate the DNA damage in human leukocytes of individuals who are habitual smokers. This technique allows the detection of single strand and double strand DNA breaks, which are indicative of the risk of cancer. The method followed is rapid, inexpensive, and a highly sensitive technique for the evaluation of DNA damage and risk assessment in smokers. This experiment should help students understand the effect of cigarette smoking. [source] Circular dichroism spectroscopy reveals invariant conformation of guanine runs in DNABIOPOLYMERS, Issue 4-5 2002Jaroslav Kypr Abstract We demonstrate that the characteristic circular dichroism (CD) features of the parallel-stranded DNA tetraplex of d(G4), especially the strong band at 260 nm, are characteristic for the B and A forms of the antiparallel duplex of d(C4G4). Hence, this band evidently originates from intrastrand guanine,guanine stacking, which is therefore very similar in the duplex and tetraplex DNA. In addition, the same type of the CD spectrum is provided by the ordered single strand of d(GA)10. This observation suggests that the ordered single strand of d(GA)10 is stabilized by a core of guanines stacked like in the parallel tetraplex. This view is used to start the modeling of the molecular structure of the ordered d(GA)10 single strand. Our studies suggest that guanine itself is strong enough to stabilize various secondary structures of DNA, which is a property relevant to thinking about the origin and evolution of molecular replicators. © 2002 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 67: 275,277, 2002 [source] White-Light-Emitting DNA (WED)CHEMISTRY - A EUROPEAN JOURNAL, Issue 37 2009Reji Varghese Dr. White knight: A DNA-based energy donor,acceptor couple exhibits red fluorescence in the single strand that changes to white light upon duplex formation in a completely reversible manner (see picture). [source] Circular dichroism spectroscopy of conformers of (guanine + adenine) repeat strands of DNACHIRALITY, Issue 7 2003Iva Kejnovská Abstract (Guanine+adenine) strands of DNA are known to associate into guanine tetraplexes, homodimerize into parallel or antiparallel duplexes, and fold into a cooperatively melting single strand resembling the protein alpha helix. Using CD spectroscopy and other methods, we studied how this conformational polymorphism depended on the primary structure of DNA. The study showed that d(GGGA)5 and d(GGA)7 associated into homoduplexes at low salt or in the presence of LiCl but were prone to guanine tetraplex formation, especially in the presence of KCl. In addition, they yielded essentially the same CD spectrum in the presence of ethanol as observed with the ordered single strand of d(GA)10. Strands of d(GA)10, d(GGAA)5, d(GAA)7, and d(GAAA)5 associated into homoduplexes in both LiCl and KCl solutions, but not into guanine tetraplexes. d(GAAA)5 and d(GAA)7 further failed to form the single-stranded conformer in aqueous ethanol. Adenine protonation, however, stabilized the single-stranded conformer even in these adenine-rich fragments. The ordered single strands, homoduplexes as well as the guanine tetraplexes, all provided strikingly similar CD spectra, indicating that all of the conformers shared similar base stacking geometries. The increasing adenine content only decreased the conformer thermostability. Chirality 15:584,592, 2003. © 2003 Wiley-Liss, Inc. [source] Evaluation of relative DNA binding affinities of anthrapyrazoles by electrospray ionization mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 5 2007Suncerae I. Smith Abstract Binding interactions of a new series of anthrapyrazoles (APs) with DNA were evaluated by electrospray ionization mass spectrometry (ESI-MS). Relative binding affinities were estimated from the ESI-MS data based on the fraction of bound DNA for DNA/anthrapyrazole mixtures, and they show a correlation to the shift in melting point of the DNA measured from a previous study. Minimal sequence specificity was observed for the series of anthrapyrazoles. Upon collisionally activated dissociation of the duplex/anthrapyrazole complexes, typically ejection of the ligand was the dominant pathway for most of the complexes. However, for complexes containing AP2 or mitoxantrone, strand separation with the ligand remaining on one of the single strands was observed, indicative of a different binding mode or stronger binding. Copyright © 2007 John Wiley & Sons, Ltd. [source] How to visualize the spider mite silk?MICROSCOPY RESEARCH AND TECHNIQUE, Issue 9 2009G. Clotuche Abstract Tetranychus urticae (Acari: Tetranychidae) is a phytophagous mite that forms colonies of several thousand individuals. Like spiders, every individual produces abundant silk strands and is able to construct a common web for the entire colony. Despite the importance of this silk for the biology of this worldwide species, only one previous study suggested how to visualize it. To analyze the web structuration, we developed a simple technique to dye T. urticae'silk on both inert and living substrates. Fluorescent brightener 28 (FB) (Sigma F3543) diluted in different solvents at different concentrations regarding the substrate was used to observe single strands of silk. On glass lenses, a 0.5% dimethyl sulfoxide solution was used and on bean leaves, a 0.1% aqueous solution. A difference of silk deposit was observed depending the substrate: rectilinear threads on glass lenses and more sinuous ones on bean leaves. This visualizing technique will help to carry out future studies about the web architecture and silk used by T. urticae. It might also be useful for the study of other silk-spinning arthropods. Microsc. Res. Tech. 2009. © 2009 Wiley-Liss, Inc. [source] The X philes: structure-specific endonucleases that resolve Holliday junctionsMOLECULAR MICROBIOLOGY, Issue 4 2001Gary J. Sharples Genetic recombination is a critical cellular process that promotes evolutionary diversity, facilitates DNA repair and underpins genome duplication. It entails the reciprocal exchange of single strands between homologous DNA duplexes to form a four-way branched intermediate commonly referred to as the Holliday junction. DNA molecules interlinked in this way have to be separated in order to allow normal chromosome transmission at cell division. This resolution reaction is mediated by structure-specific endonucleases that catalyse dual-strand incision across the point of strand cross-over. Holliday junctions can also arise at stalled replication forks by reversing the direction of fork progression and annealing of nascent strands. Resolution of junctions in this instance generates a DNA break and thus serves to initiate rather than terminate recombination. Junction resolvases are generally small, homodimeric endonucleases with a high specificity for branched DNA. They use a metal-binding pocket to co-ordinate an activated water molecule for phosphodiester bond hydrolysis. In addition, most junction endonucleases modulate the structure of the junction upon binding, and some display a preference for cleavage at specific nucleotide target sequences. Holliday junction resolvases with distinct properties have been characterized from bacteriophages (T4 endo VII, T7 endo I, RusA and Rap), Bacteria (RuvC), Archaea (Hjc and Hje), yeast (CCE1) and poxviruses (A22R). Recent studies have brought about a reappraisal of the origins of junction-specific endonucleases with the discovery that RuvC, CCE1 and A22R share a common catalytic core. [source] Identification of medically important Aspergillus species by single strand conformational polymorphism (SSCP) of the PCR-amplified intergenic spacer region Identifizierung humanmedizinisch relevanter Aspergillus-Arten durch Analyse der Einzelstrang-Konformations-Polymorphismen der amplifizierten Intergenic-Spacer-RegionMYCOSES, Issue 11-12 2000P.-M. Rath Aspergillus; Identifizierung; ITS-Region; PCR; SSCP Summary., The amplified 5.8S RNA coding DNA with the neighbouring internal transcribed spacers ITS I and ITS II (ITS I,5.8S rDNA , ITS II) of 27 culture collection strains of Aspergillus fumigatus, Aspergillus flavus, Aspergillus nidulans, Aspergillus niger, and Aspergillus terreus were investigated by single strand conformational polymorphism (SSCP) analysis. All strains showed a polymerase gel electrophoresis (PCR) product of 0.6 kb. Separation of DNA single strands of the PCR product in an acrylamide-bisacrylamide gel containing formamide SSCP resulted in individual patterns for each of the species. A minor variability within the species A. fumigatus and A. flavus did not affect the correct species identification. The results were confirmed when investigating 55 wild strains from patients and the environment. It is concluded that the analysis of the amplified ITS I,5.8S rDNA , ITS II region by SSCP allows the differentiation of the medically most relevant aspergilli. As the method does not require morphologically fully developed fungal colonies, it yields species diagnosis faster than the conventional macroscopic and microscopic identification. Zusammenfassung., Die amplifizierte 5,8S RNA kodierende DNA mit den benachbarten Internal Transcribed Spacern ITS I und ITS II (ITS I,5,8S rDNA , ITS II) von 27 Referenzstämmen der Spezies Aspergillus fumigatus, A. flavus, A. nidulans, A. niger und A. terreus wurde durch Analyse der Einzelstrang-Konformations-Polymorphismen (SSCP) untersucht. Alle Stämme zeigten ein PCR-Produkt mit einer Größe von 0,6 kb. Die SSCP-Muster nach Auftrennung der DNA-Einzelstränge dieses Produktes in einem Acrylamid-Bisacrylamid Gel mit Formamid waren für jede der untersuchten Spezies charakteristisch. Eine geringfügige Variabilität der Muster bei den Spezies A. fumigatus und A. flavus schränkte die Interpretation nicht ein. Die Ergebnisse wurden bei der Analyse von 55 Isolaten von Patienten und aus der Umwelt bestätigt. Die SSCP-Analyse der amplifizierten ITS I,5,8S rDNA , ITS II Region erlaubt somit eine Differenzierung der humanmedizinisch wichtigsten Aspergillus -Spezies vor der Ausbildung charakteristischer makro- und mikromorphologischer Strukturen. [source] Assessment of adenyl residue reactivity within model nucleic acids by surface enhanced Raman spectroscopyBIOPOLYMERS, Issue 1 2006Lydie Grajcar Abstract We rank the reactivity of the adenyl residues (A) of model DNA and RNA molecules with electropositive subnano size [Ag] sites as a function of nucleic acid primary sequences and secondary structures and in the presence of biological amounts of Cl, and Na+ or Mg2+ ions. In these conditions A is markedly more reactive than any other nucleic acid bases. A reactivity is higher in ribo (r) than in deoxyribo (d) species [pA > pdA and (pA)n , (pdA)n]. Base pairing decreases A reactivity in corresponding duplexes but much less in r than in d. In linear single and paired dCAG or dGAC loci, base stacking inhibits A reactivity even if A is bulged or mispaired (A.A). dA tracts are highly reactive only when dilution prevents self-association and duplex structures. In d hairpins the solvent-exposed A residues are reactive in CAG and GAC triloops and even more in ATC loops. Among the eight rG1N2R3A4 loops, those bearing a single A (A4) are the least reactive. The solvent-exposed A2 is reactive, but synergistic structural transitions make the initially stacked A residues of any rGNAA loop much more reactive. Mg2+ cross-bridging single strands via phosphates may screen A reactivity. In contrast d duplexes cross-bridging enables "A flipping" much more in rA.U pairs than in dA.T. Mg2+ promotes A reactivity in unpaired strands. For hairpins Mg2+ binding stabilizes the stems, but according to A position in the loops, A reactivity may be abolished, reduced, or enhanced. It is emphasized that not only accessibility but also local flexibility, concerted docking, and cation and anion binding control A reactivity. © 2006 Wiley Periodicals, Inc. Biopolymers 82: 6,28, 2006 This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] DNA and RNA-Controlled Switching of Protein Kinase ActivityCHEMBIOCHEM, Issue 4 2009Lars Röglin Dr. Abstract Constrained: The readily programmable nucleic acid mediated recognition is used to constrain a phosphopeptide that was flanked by PNA segments. RNA-based switching allows control over the activity of target enzymes such as the protein kinase Src. It might thus be feasible to transduce changes of the concentration of selected RNA molecules to changes of the activity of signal transduction proteins. Protein switches use the binding energy gained upon recognition of ligands to modulate the conformation and binding properties of protein segments. We explored whether the programmable nucleic acid mediated recognition might be used to design or mimic constraints that limit the conformational freedom of peptide segments. The aim was to design nucleic acid,peptide conjugates in which the peptide portion of the conjugate would change the affinity for a protein target upon hybridization. This approach was used to control the affinity of a PNA,phosphopeptide conjugate for the signal transduction protein Src kinase, which binds the cognate phosphopeptides in a linear conformation. Peptide,nucleic acid arms were attached to known peptide binders. The chimeric molecules were studied in three modes: 1) as single strands, 2) constrained by intermolecular hybridization (duplex formation) and 3) constrained by intramolecular hybridization (hairpin formation). Of note, duplexes that were designed to accommodate bulged peptide structures (for example, in hairpins or bulges) had lower binding affinities than duplexes in which the peptide was allowed to adopt a more relaxed conformation. Greater than 90-fold differences in binding affinities were observed. It was, thus, feasible to make use of DNA hybridization to reversibly switch from no to almost complete inhibition of Src-SH2,peptide binding, and vice versa. A series of DNA and PNA-based hybridization experiments revealed the importance of charges and conformational effects. Nucleic acid mediated switching was extended to the use of RNA; this enabled a regulation of the enzymatic activity of the Src kinase. The proof-of-principle results demonstrate for the first time that PNA,peptide chimeras can transduce changes of the concentration of a given RNA molecule to changes of the activity of a signal transduction enzyme. [source] Comprehensive Analysis of DNA Strand Breaks at the Guanosine Site Induced by Low-Energy Electron AttachmentCHEMPHYSCHEM, Issue 1 2010Jiande Gu Prof. Dr. Abstract To elucidate the role of guanosine in DNA strand breaks caused by low-energy electrons (LEEs), theoretical investigations of the LEE attachment-induced CO ,-bonds and N-glycosidic bond breaking of 2,-deoxyguanosine-3,,5,-diphosphate (3,,5,-dGMP) were performed using the B3LYP/DZP++ approach. The results reveal possible reaction pathways in the gas phase and in aqueous solutions. In the gas phase LEEs could attach to the phosphate group adjacent to the guanosine to form a radical anion. However, the small vertical detachment energy (VDE) of the radical anion of guanosine 3,,5,-diphosphate in the gas phase excludes either CO bond cleavage or N-glycosidic bond breaking. In the presence of the polarizable surroundings, the solvent effects dramatically increase the electron affinities of the 3,,5,-dGDP and the VDE of 3,,5,-dGDP,. Furthermore, the solvent,solute interactions greatly reduce the activation barriers of the CO bond cleavage to 1.06,3.56 kcal,mol,1. These low-energy barriers ensure that either C5,O5, or C3,O3, bond rupture takes place at the guanosine site in DNA single strands. On the other hand, the comparatively high energy barrier of the N-glycosidic bond rupture implies that this reaction pathway is inferior to CO bond cleavage. Qualitative agreement was found between the theoretical sequence of the bond breaking reaction pathways in the PCM model and the ratio for the corresponding bond breaks observed in the experiment of LEE-induced damage in oligonucleotide tetramer CGTA. This concord suggests that the influence of the surroundings in the thin solid film on the LEE-induced DNA damage resembles that of the solvent. 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