Role of base‐backbone and base‐base interactions in alternating DNA conformations

Sequence‐specific conformational differences between dinucleotide steps are characterised using published crystal coordinates with special attention to steric hindrance of the methyl group of a T base to the neighbouring base, and, more importantly, to the sugar‐phosphate backbone. The TT step is inflexible and B‐like, as it has two methyl groups which interlock with each other and with the sugar‐phosphate backbones. AT slides, or overtwists, so that the methyl groups move away from the 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, purine‐pyrimidine steps, respectively, but to less extent, depending on the number of non‐A: T basepairs in the steps.