Ab initio molecular orbital study on the pairing and stacking interactions between nucleic acid bases in relation to the biological activities

Abstract

Ab initio molecular orbital calculations were performed on the pairing and stacking interaction energies between bases in nucleic acids. Using these values we could explain the biologically important phenomena well. Thus the fact that O 6-methylguanine (which is formed in small amounts) is more promutagenic than N 7-methylguanine (which is formed in larger amounts) could be explained by the difference in pairing interaction energies for these alkylguanines. To clarify the detailed mechanism of mutation induced by a base analogue (2-aminopurine) the interaction energy for the 2-aminopurine-cytosine pair was calculated by taking into account the tautomeric conversion of base and the base analogue. It was concluded that the base pair formed as an intermediate between the normal form of 2-aminopurine and the imino tautomer of cytosine has an important role in inducing the mutation by 2-aminopurine. The stacking interaction energy was found to be a principal factor in determining the conformation of nucleic acids, and it predicted the preference for the A-form or B-form of the deoxyoligonucleotides well. The stacking interaction energy was resolved into its components, and it was shown that electrostatic energy was base sequence-dependent, whereas the overall stability of the stacked polymers was largely dependent on the dispersion energy.