Many-body effect for interactions between nucleobases of A-DNA and B-DNA

Abstract

The many-body interaction energies between nucleobases of DNA were calculated by means of ab initio MO method. We performed ab initio MO calculations for 2 and 3 base-pair steps in the conformations of A-DNA and B-DNA. To construct the stacking conformation for a base-pair in DNA, the geometry optimization was performed for each base-pair (A-T and G-C). Each many-body term in the interaction between nucleobases was obtained in the conformation of the stacked base-pairs. All the calculations were done with the theoretical level of MP2/6-31G(d). Additionally, the calculations in 2 base-pair steps were done with the theoretical level of RI-MP2/aug-cc-pVDZ. As for the interaction between bases, we found that the two-body term is dominant and each many-body term value depends on the base sequence. The calculated interaction energies, i.e. the hydrogen bonding between the bases and the stacking interaction between the base-pairs, were used to estimate the stability of DNA oligomers (ΔE) with various base sequences. Good correlation was found between the estimated ΔE values and the experimental ΔG values. This indicates that the internal energy of DNA oligomer can be estimated from summing-up of the constituent hydrogen bonding and the stacking interaction energies according to the base sequence.