A PM6 quantum chemical study of the H-bonded and stacked associates of the adenine and thymine DNA bases: The nature of base stacking

The planar H-bonded adenine-thymine (A center dot T) base pair and four stacked hetero associates (A/T) of these bases in a cluster containing 200 water molecules were studied by the new semi-empirical PM6 method. The formation of the planar A center dot T base pair in the water cluster was found to be energetically unfavourable, primarily due to the destabilising contribution of the base-water interactions. Under complete geometry optimisation, the planar A center dot T base pair converted into a nonplanar propeller-twisted and buckled associate. In contrast, the formation of all stacked dimers studied was found to be favourable, with formation energies ranging from -11 to -20 kcal/mol. The preference for the formation of these stacks results from the favourable change in the water structure and distortion of the paired and isolated bases during the base association reaction.