Torsional motion and elasticity of the deoxyribonucleic acid double helix and its nucleosomal complexes

Abstract

Torsional thermal oscillations of the DNA double helix within the electron paramagnetic resonance (EPR) time scale (10(-10)-10(-3) s) as indicated by a rigid, intercalating probe are much smaller in the spacer segment between nucleosomes in chromatin than in long, free DNA molecules. Still smaller DNA oscillation is indicated in intact nuclei and yet smaller if the nuclei have been treated with glutaraldehyde. The values of EPR measurements are not affected by the loading density of probe. If the probe were capable of substantial oscillations or movement different from that of the helix, those oscillations would be expected to dominate the spectra when movement of the helix is restrained. We conclude that the correlation time for torsional movement of free DNA inferred from EPR spectra is characteristic of the double helix and that there is no significant independent motion of the probe. The correlation time for the DNA double helix in molecules longer than approximately 500 base pairs is close to 30 ns, corresponding to an elastic constant of 1.5 X 10(-19) ergs cm for deformation by twisting. The motions observed in chromatin are consistent with a model in which spheres of 50-60-A radius are connected by simple elastic rods with the length of spacer DNA and the same elastic constant. The spin-labeled ethidium probe has been characterized in detail by nuclear magnetic resonance, infrared, fluorescence, and visible light spectroscopy. The binding equilibria are consistent with the hypothesis that strongly immobilized probe molecules are preferentially bound to spacer DNA.

DNA–topoisomer analysis on the basis of the helical wormlike chain

“…16 The source of this difference is not clear. However, the effective elastic constants may actually change with the large deformation caused by cyclization, since the DNA helix is not a perfect elastic body.…”

Predicted Effects of Local Conformational Coupling and External Restraints on the Torsional Properties of Single DNA Molecules

“…The present calculations show how end-to-end constraints placed on a DNA molecule, in combination with the natural conformational features of the double helix, can account for discrepancies in the torsional moduli determined with state-of-the-art, single-molecule experiments [6] compared to values extracted from various solution measurements [1,20,21,23,34,43] and/or incorporated into theories to account for the force-extension properties of single molecules [4,35,41,45]. Although the torsional moduli determined here for naturally straight, mixed-sequence DNA molecules with no constraints on the separation of chain ends are substantially lower than values extracted from solution studies (C ≈ 2.0 × 10 -19 vs. 2.0 -4.8 × 10 -19 erg-cm), the computed elastic constants increase substantially if base pairs are inclined with respect to the double helical axis and the deformations of selected conformational variables follow known interdependent patterns.…”

“…The changes are greater if two or three conformational correlations are considered, e.g., ∼ 7% when both Roll-Twist and Twist-Slide coupling are included. The frequencies of the overstretched duplex, however, are quite large compared to those of restraint-free DNA, particularly when all three common conformational correlations (f 23 , f 35 , f 36 )-Roll-Twist, Twist-Slide, and Twist-Rise-are considered. The computed increase in C for the DNA with such features is roughly 1.5 times that of the unrestrained generic molecule free of conformational coupling.…”

“…The variation of k mimics the effect of imposed external force on the torsional modulus. Here the equilibrium values of the base-pair step parameters are set to the generic crystallographic values, and three coupling interactions (f 23 , f 35 , f 36 )-Roll-Twist, Twist-Slide, and Twist-Rise-are considered in the internal energy function. The torsional modulus, which is about 1.9 × 10 -19 erg-cm when there is no restraint on the ends of the homopolymer, increases with increase in k/k 0 .…”

“…Although the bending properties of single DNA molecules are consistent with those reported in solution studies [2,3,11,19,40], values of the torsional modulus, i.e., the global twisting constant C, derived from single-molecule studies of DNA under tension [6] have only added fuel to the long-standing debate over the magnitude of C. The torsional modulus of a DNA monitored by so-called rotor-bead tracking measurements [6] (4.1±0.3 × 10 -19 erg-cm) substantially exceeds the values deduced from many solution experiments [1,20,21,23,34,43]. The DNA in the single-molecule experiment is held at both ends, extended to its full contour length, and over-or undertwisted.…”