The MP2 quantum chemistry study on the local minima of guanine stacked with all four nucleic acid bases in conformations corresponding to mean B-DNA

Ab initio calculations at the MP2/6-31G*(d=0.25) level were used to perform an energy scan of guanine stacked with all four canonical DNA bases. The structures that were studied correspond to potential energy surface points B-DNA. Seven stacking complexes were analyzed in details: 5′-G/G-3′, 5′-G/A-3′, 5′-A/G-3′, 5′-G/T-3′, 5′-T/G-3′, 5′-G/C-3′ and 5′-C/G-3′. In all cases, local minima on potential energy surface were found with respect of rise and twist angle. Geometrical parameters of mean crystallographic B-DNA conformation are very close to the ones located on potential energy surface. Thus, the mean B-DNA geometry is characterized overall by a minimum of stacking interactions with respect to guanine.