ROLE OF BASE-BACKBONE AND BASE-BASE INTERACTIONS IN ALTERNATING DNA CONFORMATIONS

Sequence-specific conformational differences between dinucleotide step s are characterised using published crystal coordinates with special a ttention to steric hindrance of the methyl group of a T base to the ne ighbouring base, and, more importantly, to the sugar-phosphate backbon e. The TT step is inflexible and B-like, as it has two methyl groups w hich interlock with each other and with the sugar-phosphate backbones. AT slides, or overtwists, so that the methyl groups move away from th e backbones, both lead the step towards the A-conformation. TA is most flexible as it does not have such restriction. These characteristics are observed with other pyrimidine-pyrimidine, pyrimidine-purine, puri ne-pyrimidine steps, respectively, but to less extent, depending on th e number of non-A:T basepairs in the steps.