Home About us Contact
|
Home About us Contact | ||
|
|
||
Nucleotide Bases (nucleotide + base)
Selected AbstractsSynthesis of 3,,3,-Linked Pyrimidine Oligonucleotides Containing an Acridine Moiety for Alternate Strand Triple Helix FormationEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 11 2004Jussara Amato Abstract Oligonucleotides with a 3,,3, inversion of polarity, containing an acridine moiety attached to the nucleotide base flanking the 3,,3, phosphodiester bond, have been synthesised, characterised and used to form alternate-strand triple helix complexes. These have been investigated by UV melting studies and CD experiments. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] Molecular surface electrostatic potentials in relation to noncovalent interactions in biological systemsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2001Peter Politzer Abstract Noncovalent interactions are predominantly electrostatic in nature. It follows that an effective tool for their investigation and elucidation is the electrostatic potential on the molecular surface. We have shown that a variety of condensed phase macroscopic properties can be expressed quantitatively in terms of certain site-specific and global statistical quantities that characterize the overall pattern of the surface potential. We are now extending this approach to interactions in biological systems. Several applications will be discussed, including initial qualitative studies of dioxins, a series of anticonvulsants and some tetracyclines, the nucleotide bases, and a recent quantitative treatment of the anti-HIV activities of three groups of reverse transcriptase inhibitors. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001 [source] Computational characterization of nucleotide bases: Molecular surface electrostatic potentials and local ionization energies, and local polarization energiesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3-4 2001Jane S. Murray Abstract Electrostatic potentials and local ionization energies have been computed at the HF/6-31G* level on the molecular surfaces of the five nucleotide bases. The potentials are analyzed in terms of their most positive and negative values as well as several statistically defined quantities that reflect their patterns over the entire surface. Considerable charge separation and variability are found for all five molecules. The results are consistent with the base pairing that is known to occur. The observed reactive behavior toward electrophiles can be interpreted in terms of the complementary roles of the surface potential and the local electron lability. Local polarization energies, corresponding to a test charge being placed at specific points above the molecules, are also calculated (HF/6-31+G*), and their relationship to the local ionization energies is examined. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 83: 245,254, 2001 [source] An improved nucleic acid parameter set for the GROMOS force fieldJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2005Thereza A. Soares Abstract Over the past decades, the GROMOS force field for biomolecular simulation has primarily been developed for performing molecular dynamics (MD) simulations of polypeptides and, to a lesser extent, sugars. When applied to DNA, the 43A1 and 45A3 parameter sets of the years 1996 and 2001 produced rather flexible double-helical structures, in which the Watson,Crick hydrogen-bonding content was more limited than expected. To improve on the currently available parameter sets, the nucleotide backbone torsional-angle parameters and the charge distribution of the nucleotide bases are reconsidered based on quantum-chemical data. The new 45A4 parameter set resulting from this refinement appears to perform well in terms of reproducing solution NMR data and canonical hydrogen bonding. The deviation between simulated and experimental observables is now of the same order of magnitude as the uncertainty in the experimental values themselves. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 725,737, 2005 [source] Carbon-13 chemical shift anisotropy in DNA bases from field dependence of solution NMR relaxation rates,MAGNETIC RESONANCE IN CHEMISTRY, Issue 3 2006Jinfa Ying Abstract Knowledge of 13C chemical shift anisotropy (CSA) in nucleotide bases is important for the interpretation of solution-state NMR relaxation data in terms of local dynamic properties of DNA and RNA. Accurate knowledge of the CSA becomes particularly important at high magnetic fields, prerequisite for adequate spectral resolution in larger oligonucleotides. Measurement of 13C relaxation rates of protonated carbons in the bases of the so-called Dickerson dodecamer, d(CGCGAATTCGCG)2, at 500 and 800 MHz 1H frequency, together with the previously characterized structure and diffusion tensor yields CSA values for C5 in C, C6 in C and T, C8 in A and G, and C2 in A that are closest to values previously reported on the basis of solid-state FIREMAT NMR measurements, and mostly larger than values obtained by in vacuo DFT calculations. Owing to the noncollinearity of dipolar and CSA interactions, interpretation of the NMR relaxation rates is particularly sensitive to anisotropy of rotational diffusion, and use of isotropic diffusion models can result in considerable errors. Copyright © 2006 John Wiley & Sons, Ltd. [source] Plant genome sequencing: applications for crop improvementPLANT BIOTECHNOLOGY JOURNAL, Issue 1 2010David Edwards Summary DNA sequencing technology is undergoing a revolution with the commercialization of second generation technologies capable of sequencing thousands of millions of nucleotide bases in each run. The data explosion resulting from this technology is likely to continue to increase with the further development of second generation sequencing and the introduction of third generation single-molecule sequencing methods over the coming years. The question is no longer whether we can sequence crop genomes which are often large and complex, but how soon can we sequence them? Even cereal genomes such as wheat and barley which were once considered intractable are coming under the spotlight of the new sequencing technologies and an array of new projects and approaches are being established. The increasing availability of DNA sequence information enables the discovery of genes and molecular markers associated with diverse agronomic traits creating new opportunities for crop improvement. However, the challenge remains to convert this mass of data into knowledge that can be applied in crop breeding programs. [source] Discovering genetic polymorphisms in next-generation sequencing dataPLANT BIOTECHNOLOGY JOURNAL, Issue 4 2009Michael Imelfort Summary The ongoing revolution in DNA sequencing technology now enables the reading of thousands of millions of nucleotide bases in a single instrument run. However, this data quantity is often compromised by poor confidence in the read quality. The identification of genetic polymorphisms from this data is therefore problematic and, combined with the vast quantity of data, poses a major bioinformatics challenge. However, once these difficulties have been addressed, next-generation sequencing will offer a means to identify and characterize the wealth of genetic polymorphisms underlying the vast phenotypic variation in biological systems. We describe the recent advances in next-generation sequencing technology, together with preliminary approaches that can be applied for single nucleotide polymorphism discovery in plant species. [source] Testing hypotheses of speciation in the Plethodon jordani species complex with allozymes and mitochondrial DNA sequencesBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2006DAVID W. WEISROCK Salamander populations of the Plethodon jordani species complex form a challenging system for applying the general lineage concept of species to diagnose population-level lineages. The present study reports and analyses mitochondrial-DNA haplotypes (,1200 nucleotide bases from the genes encoding ND2, tRNATrp, and tRNAAla from 438 salamanders) from 100 populations representing six species of the P. jordani complex (Plethodon amplus, Plethodon cheoah, Plethodon jordani, Plethodon meridianus, Plethodon metcalfi, and Plethodon montanus) with comparative analyses of previously published allozymic data to reconstruct the evolutionary history of this group and to diagnose species lineages. Analyses of mitochondrial haplotypic data include nested-cladistic analysis of phylogeography, analysis of molecular variance, hierarchical analysis of nucleotide-diversity measures, and likelihood-based estimates of recent temporal changes in population size. New analyses of allozymic data include multidimensional scaling and principal component analyses, and both data sets are analysed and compared for congruent genetic structure using Mantel correlation tests. These analyses in combination identify the six named species as distinct evolutionary lineages despite sporadic genetic exchanges among them and some discordance between mitochondrial DNA and allozymic markers. Sexual isolation is not complete for any pair of these six species, but they replace each other geographically and appear to block the geographical spreading of their neighbours. The P. jordani complex is a strong study system for investigating the genetic and ecological processes responsible for vicariant speciation. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 89, 25,51. [source] | |||||||||||||