Biopolymers and cell. 1996; 12 (5): 5 - 12

On a quantum-chemical nature of a stereochemical nonrigidity of canonical nucleotide bases

D. M. Hovorun, Ya. R. Mishchuk, I. V. Kondratyuk

An interconversion of canonical nucleotide bases adenine, guanine and cytosine, exactly an inversion about a plane, and anisotropic inner rotation around exocyclic C-N bonds, and structural perturbations and the bases' profanation as well, have AMI and MNDO/H methods with an optimization of full structural parameters and agradient norm <0.01.An mutually coordinated relaxational behaviour of essential struc¬tural parameters which describe valence bond configurations ofamino group N atoms and neighbouring double C—N bonds were analysed. It was found that pit-conjugation of an electron lone pair of an amino group nitrogen atom with a ring a-electron system is a main factor to determine structural-dynamical properties of exocyclic amino groups of canonical nucleotide bases, and moreover, of the bases themselves. Besides appreciable effects of other intramolecular interactions, namely intramolecular H-bonds (first of all ofNH...N type), steric factors, and an electrostatic repulsion of electron lone pairs of neighbouring (endo- and exocyclic) nitrogen atoms as well, were estimated. They determine both nonequivalence of amino group NH bonds (as well as amino group ground-state orientation about a ring plane) and an anisotropy ofamino group inner rotation.