The stacking geometries of normal DNA bases (adenine, thymine, guanine and cytosine) and methylated bases (O⁶-methylguanine, O⁴-methylthymine and C⁵-methylcytosine) have been optimized at the MP2/cc-pVDZ level. Counterpoise correction (CP) scheme of Boys-Bernardi has been used to take into account of basis set superposition error (BSSE), and aug-cc-pVXZ (X＝D, T) basis sets were used to extrapolate the complete basis set limit in order to obtain more accurate binding energies. Moreover, the interactions between stacking base-pairs were also analyzed by atoms in molecules (AIM) method. Our calculation results show that the methylation of DNA bases can lead to obvious changes of parallel twist angles between the stacking pyridine-pyridine and pyridine-purine base-pairs, and the increases of interaction energies between the stacking base-pairs can also be attributed to the methylation of DNA bases. Furthermore, AIM analysis reveals that the methylation of bases can enhance the (-( interactions between the stacking base-pairs, and the formation of a variety of hydrogen-bonds, H₂CH…X (X＝O, N, (, CH₃, NH₂), was also confirmed by AIM analysis.

Key words: DNA, methylation, base-pairs, stacking, interaction energies