Many-body effect for stacking interaction and hydrogen bonding between nucleobases

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 conformation of B-DNA. To construct the stacking conformation for a base-pair in B-DNA, the geometry optimization was performed for each base-pair (A-T and G-C). All the stacked base-pairs were assumed to be parallel, with Rise 3.5 Å between them and Twist 36 degrees. 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). 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, 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.