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Acid Bases (acid + base)
Kinds of Acid Bases Selected AbstractsAn Electrochemical DNA Biosensor for the Detection of the Apa I Polymorphism in the Vitamin D Receptor Gene Using Meldola's Blue as a Hybridization IndicatorELECTROANALYSIS, Issue 5 2010Nilay Aladag Abstract Electrochemical detection of nucleic acid base mismatches related to Apa I single nucleotide polymorphism (SNP) in the vitamin D receptor gene was performed successfully using 7-dimethyl-amino-1,2-benzophenoxazinium salt (Meldola's blue, MDB) with 10.9,pmol/100,,L of detection limit. MDB reduction signals obtained from probe, mismatch(probe-SNP containing target) and hybrid(probe-target) modified pencil graphite electrode(PGE) increased respectively. The sensor was able to clearly distinguish perfect match from mismatch DNA in a 30,min. detection time. Several factors affecting on the hybridization and indicator response are studied to maximize sensitivity and selectivity. The advantages of the biosensor are discussed in comparison with previous electrochemical assays for DNA hybridization. [source] Coarse-grained model of nucleic acid basesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2010Maciej Maciejczyk Abstract Atomistic simulations of nucleic acids are prohibitively expensive and, consequently, reduced models of these compounds are of great interest in the field. In this work, we propose a physics-based coarse-grained model of nucleic-acid bases in which each base is represented by several (3,5) interaction centers. van der Waals interactions are modeled by Lennard-Jones spheres with a 12,6 potential energy function. The charge distribution is modeled by a set of electric dipole moments located at the centers of the Lennard-Jones spheres. The method for computing the Lennard-Jones parameters, electric dipole moments (their magnitude and orientation) and positions of the interaction centers is described. Several models with different numbers of interaction centers were tested. The model with three-center cytosine, four-center guanine, four-center thymine, and five-center adenine satisfactorily reproduces the canonical Watson,Crick hydrogen bonding and stacking interaction energies of the all-atom AMBER model. The computation time with the coarse-grained model is reduced seven times compared with that of the all-atom model. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] TDDFT investigation on nucleic acid bases: Comparison with experiments and standard approachJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2004M.K. Shukla Abstract A comprehensive theoretical study of electronic transitions of canonical nucleic acid bases, namely guanine, adenine, cytosine, uracil, and thymine, was performed. Ground state geometries were optimized at the MP2/6-311G(d,p) level. The nature of respective potential energy surfaces was determined using the harmonic vibrational frequency analysis. The MP2 optimized geometries were used to compute electronic vertical singlet transition energies at the time-dependent density functional theory (TDDFT) level using the B3LYP functional. The 6-311++G(d,p), 6-311(2+,2+)G(d,p), 6-311(3+,3+)G(df,pd), and 6-311(5+,5+)G(df,pd) basis sets were used for the transition energy calculations. Computed transition energies were found in good agreement with the corresponding experimental data. However, in higher transitions, the Rydberg contaminations were also obtained. The existence of ,,* type Rydberg transition was found near the lowest singlet ,,* state of all bases, which may be responsible for the ultrafast deactivation process in nucleic acid bases. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 768,778, 2004 [source] A post-SCF quantum chemistry study on local minima of 8-oxo-guanine stacked with all four nucleic acid bases in B-DNA conformationsJOURNAL OF HETEROCYCLIC CHEMISTRY, Issue 4 2007Piotr Cysewski The post SCF MP2/6-31G*(d=0.25) method was applied to obtain potential energy surface of 8-oxoguanine stacked with all four canonical DNA bases. The spatial neighbourhood was scanned of stacked complexes found in the native B-DNA. The presented results suggest that the hydroxyl radical modification of guanine at C8 position has significant impact on structural, energetic, orbital and electrostatic properties of stacked complexes with canonical DNA bases. The pair stabilization energy, including electron correlation terms, suggests that the 5,-A/GA-3, pair is the most stable among all of the studied complexes. The 8-oxo-guanine has been found as a source of significant changes in electroaccepting properties compared to stacked pairs formed by canonical guanine since both electron affinities and localization of HOMO orbital were altered. However, electro-donation abilities are not modified after replacement of guanine with 8-oxo-guanine irrespectively on the context of B-DNA bases. [source] Validation of a real-time PCR for the quantitative estimation of a G143A mutation in the cytochrome bc1 gene of Pyrenophora teresPEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 3 2007Arash Kianianmomeni Abstract A single nucleotide polymorphism (SNP) in the cytochrome b gene confers resistance to strobilurin fungicides for several fungal pathogens. Therefore, on the basis of a change at amino acid position 143 from glycine to alanine, a real-time PCR assay was established for the quantitative detection of the analogous SNP in the cytochrome b sequence of Pyrenophora teres Drechsler, which causes barley net blotch. Allelic discrimination was achieved by using allele specific primers with artificially mismatched nucleic acid bases and minor groove binding probes. Validation parameters for the lower limits of the working range, namely limits of detection (LOD) and limits of quantification (LOQ), were statistically determined by the variance of calibration data, as well as by the variance of the 100% non-strobilurin-resistant allele DNA sample (blank values). It was found that the detection was limited by the variance of blank values (five in 801 458 copies; 0.0006%), whereas the quantification was limited by the variance of calibration data (37 in 801 458 copies; 0.0046%). The real-time PCR assay was finally used to monitor strobilurin-resistant cytochrome b alleles in barley net blotch field samples, which were already classified in in vivo biotests to be fully sensitive to strobilurins. All signals for strobilurin-resistant cytochrome b alleles were below the LOD, and therefore the results are in total agreement with the phenotypes revealed by biotests. Copyright © 2006 Society of Chemical Industry [source] Mechanism of DNA Damage Photosensitized by Trisbipyrazyl Ruthenium Complex.PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 5 2000Unusual Role of Cu/Zn Superoxide Dismutase ABSTRACT Trisbipyrazyl ruthenium(II) (Ru[bpz]32+) was examined as DNA photosensitizer. Damage resulting from the photolysis of synthetic oligonucleotides has been monitored by polyacrylamide gel electrophoresis. Photoadduct formation is found on both single- and double-stranded oligonucleotides. On oligonucleotide duplex, oxidative damage occurs selectively at the 5,G of the 5,GG3, site and to a lesser extent at the 5,G of a GA sequence. These findings suggest the involvement of electron transfer and show that this mechanism is the main DNA damaging process involved in Ru(bpz)32+ photosensitization. In addition, photoadducts and oxidative damage are both highly affected by an increase of salt concentration in the reaction medium, stressing the importance of direct interactions between nucleic acid bases and the excited ruthenium complex for efficient electron transfer. On single-stranded oligonucleotides, all the guanines are oxidized to the same extent. In this case, oxidative damage, which is not affected by an increase of salt in the solution, has been attributed, in part, to singlet oxygen. More importantly, Cu/Zn superoxide dismutase (SOD) strongly enhances the yield of all damage, correlated to an increase of both electron transfer and singlet oxygen production. This original activity of SOD is the first example of bioactivation of a polyazaaromatic ruthenium complex. [source] Energy-resolved in-source collisionally induced dissociation for the evaluation of the relative stability of noncovalent complexes in the gas phaseRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 23 2005Nataliya Lyapchenko Energy-resolved in-source collisionally induced dissociation (CID) studies on the complexation of alkali metal cations by some crown ethers, nucleic acid bases, and amino acids have been performed. It has been shown that the cone voltage corresponding to the maximum ion abundance (Vc,Imax) of the breakdown curve is characteristic of a given ion and not influenced by the cone desolvation process or the composition of the solution. Very good agreement of the Vc,Imax value with the bond strength of the ion has been observed. Determination of the Vc,Imax values for different ionic species is a useful, simple, and inexpensive way to obtain their relative stabilities in in-source CID conditions. Copyright © 2005 John Wiley & Sons, Ltd. [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] A Novel Methodological Approach for the Analysis of Host,Ligand Interactions,CHEMPHYSCHEM, Issue 2 2007Daniela Strat Dr. Abstract Traditional analysis of drug-binding data relies upon the Scatchard formalism. These methods rely upon the fitting of a linear equation providing intercept and gradient data that relate to physical properties, such as the binding constant, cooperativity coefficients and number of binding sites. However, the existence of different binding modes with different binding constants makes the implementation of these models difficult. This article describes a novel approach to the binding model of host,ligand interactions by using a derived analytical function describing the observed signal. The benefit of this method is that physically significant parameters, that is, binding constants and number of binding sites, are automatically derived by the use of a minimisation routine. This methodology was utilised to analyse the interactions between a novel antitumour agent and DNA. An optical spectroscopy study confirms that the pentacyclic acridine derivative (DH208) binds to nucleic acids. Two binding modes can be identified: a stronger one that involves intercalation and a weaker one that involves oriented outer-sphere binding. In both cases the plane of the bound acridine ring is parallel to the nucleic acid bases, orthogonal to the phosphate backbone. Ultraviolet (UV) and circular dichroism (CD) data were fitted using the proposed model. The binding constants and the number of binding sites derived from the model remained consistent across the different techniques used. The different wavelengths at which the measurements were made maintained the coherence of the results. [source] Synthesis of the First Chiral Bidendate Bis(trifluoromethyl)phosphane Ligand through Stabilization of the Bis(trifluoromethyl)phosphanide Anion in the Presence of AcetoneCHEMISTRY - A EUROPEAN JOURNAL, Issue 35 2006Berthold Hoge Priv.-Doz. Abstract Lewis acid/Lewis base adduct formation of the P(CF3)2, ion and acetone leads to a reduced negative hyperconjugation and, therefore, limits the CF bond activation. The resulting increased thermal stability of the P(CF3)2, ion in the presence of acetone allows selective substitutions and enables the synthesis of the first example of a chiral, bidentate bis(trifluoromethyl)phosphane ligand: a DIOP derivative, [(2,2-dimethyl-1,3-dioxolane-4,5-diyl)bis(methylene)]bis(diphenylphosphane), in which the phenyl groups at the phosphorus atoms are replaced by strong electron-withdrawing trifluoromethyl groups. The resulting high electron-acceptor strength of the synthesized bidentate (CF3)2P ligand is demonstrated by a structural and vibrational study of the corresponding tetracarbonyl,molybdenum complex. The stabilization of the P(CF3)2, ion in the presence of acetone is based on the formation of a dynamic Lewis acid/Lewis base couple, (CF3)2PC(CH3)2O,. Although there is no spectroscopic evidence for the formation of the formulated alcoholate ion, the intermediate formation of (CF3)2PC(CH3)2O, could be proved through the reaction with (CF3)2PP(CF3)2, which yields the novel phosphane,phosphinite ligand (CF3)2PC(CH3)2OP(CF3)2. This ligand readily forms square-planar Pt(II) complexes upon treatment with solid PtCl2. [source] | ||||||||||