Torsional flexibility of DNA as revealed by conformational analysis

Abstract

The thermal fluctuations of a regular double helix belonging to the family were studied by means of atom-atomic potentials method. The winding angle fluctuation was found to be 2.4° for poly(dA):poly(dT) and 3.0° for poly(dG):poly(dC). The reasonable agreement of these estimations with those obtained experimentally reveals the essential role of the small-amplitude torsional vibrations of atoms in the mechanism of the double helix flexibility. The calculated equilibrium winding angle, essentially depends on the degree of neutralization of phosphate groups, being about 35.5° for the full neutralization. The deoxyribose pucker is closely related to the angle: while proceeds from 30° to 45° the pseudorotation phase angle, P, increases from 126° to 164°. Fluctuations of the angles TL and TW, which specify inclination of the bases to the helix axis, were evaluated to be 5°-10°. Possible correlation between conformational changes in the adjacent nucleotides is discussed. © 1982 IRL Press Limited.