The effect of methylation on the hydrogen-bonding and stacking interaction of nucleic acid bases

Methylated nucleosides play an important role in DNA/RNA function, and may affect republication by inter- rupting the base-pairing and base-stacking. In order to investigate the effect of methylation on the interaction between nucleic acid bases, this work presents the hydrogen- bonding and stacking interactions between 5-methylcytosine and guanine (G), cytosine (C) and G, 1-methyladenine and thymine (T), as well as adenine and T. Geometry optimiza- tion and potential energy surface scan have been performed for the involved complexes by MP2 calculations. The interaction energies, which were corrected for the basis-set superposition error by the full Boys-Bernardi counterpoise correction scheme, were used to evaluate the interaction intensity of these nucleic acid bases. The atoms in molecules theory and natural bond orbital analysis have been performed to study the hydrogen bonds in these complexes. The result shows that the methyl substitute contributes the stability to these complexes because it enhances either the hydrogen bonding or the staking interaction between nucleic acid bases studied.