On the origin of sequence dependent structural changes in DNA

Sequence specificity in the backbone conformation of DNA is controlled mostly by the electrostatic part of the base backbone interactions. However, local mobility or orientation of the bases depends on stacking and base backbone interactions. Latter has both non-bonded and electrostatic components. Environmental factors manifest themselves essentially through the electrostatic part of base-backbone interactions. They affect both backbone as well as internal core conformation and play a great role in biological recognition.