Influence of electrostatic interactions on the sugar-phosphate backbone conformation in DNA.

Abstract

The influence of sugar ring flexibility in DNA on the mechanism of the B <===> A conformational transition is studied. The dipole moment of the deoxyribose as a function of its puckered states is calculated by the quantum-mechanical method using the MINDO/3 approximation. The interaction of the sugar dipole with the neighbor molecular groups in polynucleotide chains is estimated. The sugar dipole interaction with phosphate groups and counterions is shown to be strong and capable to deform the pseudorotation potential of deoxyribose. The effective pseudorotation potential of sugar ring in the B and A helices is obtained. The results are used to explain the behavior of Raman bands in the region of sugar-phosphate vibrations. The mechanism of the effect of electrostatic forces on the sugar-phosphate backbone conformation, which is essential for the B <===> A and other structure transitions, is offered.