INTERACTION ENERGIES IN NON WATSON-CRICK PAIRS: AN AB INITIO STUDY OF G·U AND U·U PAIRS

Abstract

Ab initio calculations at the MP2/6-31G** level have been carried out on the non-Watson-Crick nucleic acids pairs G·U and U·U to obtain the interaction energies and to see whether the derived values are comparable or not with the canonical G-C, A-T and A-U pairs. Optimized geometries of the pairs show that the structural parameters of the isolated bases differ very little on pairing. The guanine -NH2 group does not participate in the hydrogen bonding formation and possesses a pyramidal structure; its intrinsic nonplanarity plays an important role in the out-of-plane intermolecular interactions. Thus, the G·U pair projects three hydrogen bonding acceptor sites, namely, N7(G), O6(G) and O4(U) to the RNA major groove. The interaction energy (DHoint) calculated for the G·U pair (-13.6 kcal/mol) is comparable to that determined for A-T (-13.0 kcal/mol), but considerable smaller than the experimental value reported for G-C (-21.0 kcal/mol). The U·U pair follows the trend that pairing between pyrimidines bases should have lower interacting energies than purine-pyrimidine pairs