Configurational specificity of stacking interactions in DNA base pairs: A computational analysis

A theoretical study of stacking patterns of various hydrogen‐bonded base pair complexes has been undertaken. Modified Rayleigh‐Schrodinger perturbation theory for intermediate range interactions, has been employed to evaluate the stacking interactions using multicentered‐multipole expansion method. Net atomic charge and corresponding dipole components located at each of the atomic centers have been computed by CNDO/2 method. An analysis of the intermolecular forces involved in the stable formation of the various base pair complexes, has been presented and the results have been discussed in the light of experimental as well as other theoretical observations. The possibility of relative preference of the left‐handed configuration for alternating sequences has been quantitatively explored.