Structural properties of polymeric DNA from molecular dynamics simulations

Abstract

Most of the reported DNA structural studies are based on oligonucleotide structures, which have artifacts due to unstable terminal base pairs (bps). We have carried out molecular dynamics simulation of DNA oligonucleotides in such a manner that gives rise to properties of polymeric DNA of infinite length. Molecular dynamics simulation studies of six homo- and heteropolymeric DNA sequences are reported here to understand structural features of all ten unique dinucleotide sequences. We observe that each of these dinucleotide sequences has unique features in agreement with Calladine's rule [C. R. Calladine, J. Mol. Biol. 161, 343 (1982)]. We noticed significant structural alternation between B(I) and B(II) forms for d(CA).d(TG) dinucleotide, where one of the strands showed frequent transitions between usual and unusual epsilon and zeta torsion angles associated with 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 most flexible dinucleotide bp steps. We estimated the major groove widths from our simulations. We did not 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 DNA sequence.