[Semiempirical calculation of the relation of the interaction energy between complementary pairs of nitrogenous bases to nucleic acid conformational parameters]

Abstract

The calculations of interaction energy between complementary base pairs of nucleic acids in the function of 5 variables determining parameters of double helix (Arnott's parameters) have been carried out by the method of atom-atom potential functions. Four of these parameters are essential in the case of mutual positions of bases corresponding to conformational A-family, and only two parameters (the distance between pairs along helical axis and the angle of rotation around this axis)--in the case of B-family. Positions of the interaction energy minima over each of the essential variables are close to experimentally determined parameters. The interaction energy minima are more pronounced for A-family conformations. The positions of minima in this case are determined by dispersion and short range repulsion energy.