Abstract

Calculations are reported using the potential field of Momany, Carruthers, McGuire and Scheraga of the intra-pair interaction energy for all 29 base-pairing schemes proposed by Donohue. Optimized relative orientations and separations of the DNA bases are given. The observed base pairing would appear to be determined principally by the base positions and orientations imposed by the fairly rigid sugar-phosphate backbone. The inter-pair interaction energies for the various possible combinations of the DNA bases in the double-helix models for the A and B forms of DNA are reported. In the model for the B form, the inter-pair interaction energy was found to be almost independent of the base-pair combination. The importance of base overlap in determining the extent to which one base pair is rotated with respect to an adjacent pair was also investigated in a preliminary manner.