Contributions to Stability of H-Bonding and Stacking between Nucleic Acid Bases

It is well-known that nucleic acid bases engage in complementary G-C and A-T H-bonded pairs. Each such coplanar pair is positioned above another such pair as separate rungs in a double-helical ladder. DFT calculations probe the separate contributions of the H-bonding within each rung and the stacking interactions between the rungs. Various tetramers are constructed by placing two complementary pairs above one another, free of geometrical constraints imposed by the sugar–phosphate backbone. The H-bonding within each coplanar pair is found to be much more important than the stacking which induces only very minor perturbations of the geometries or energetics within each coplanar H-bonded pair. There is very little cooperativity between the two sorts of interactions.