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Nucleic Acids Research, 1982, Vol. 10, No. 5 1811-1830
© 1982

MOLECULAR BIOLOGY

Torsional flexibility of DNA as revealed by conformational analysis

Victor B. Zhurkin, Yury P. Lysov, Vladimir L. Florentiev and Valery I. Ivanov

Institute of Molecular Biology, Academy of Sciences of the USSR Moscow 117984, Vavilov str. 32, USSR

Received September 23, 1981. Revised February 2, 1982. Accepted February 2, 1982.

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.


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