Structural properties of polymeric DNA from molecular dynamicssimulations

摘要

Most of the reported DNA structural studies are based on oligonucleotide structures, which haveartifacts due to unstable terminal base pairs (bps). We have carried out molecular dynamicssimulation of DNA oligonucleotides in such a manner that gives rise to properties of polymericDNA of infinite length. Molecular dynamics simulation studies of six homo- and heteropolymericDNA sequences are reported here to understand structural features of all ten unique dinucleotidesequences. We observe that each of these dinucleotide sequences has unique features in agreementwith Calladine's rule [C. R. Calladine, J. Mol. Biol. 161, 343 (1982)]. We noticed significantstructural alternation between B1 and BII forms for d(CA).d(TG) dinucleotide, where one of thestrands showed frequent transitions between usual and unusual εand ζ torsion angles associatedwith bp stacking geometry. In terms of the calculated bending rigidity and persistence length,pyrimidine-purine bp steps, namely, d(TA).d(TA), d(CA).d(TG), and d(CG).d(CG) are the mostflexible dinucleotide bp steps. We estimated the major groove widths from our simulations. We didnot observe much variation in major and minor groove widths depending on the base sequence.However, the distribution of water molecules in the minor groove shows sensitivity to the DNAsequence.