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 per-form 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. (c) 2005 Elsevier B.V. All rights reserved.