Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling

Sequence-dependent Nucleosome Structural and Dynamic Polymorphism. Potential Involvement of Histone H2B N-Terminal Tail Proximal Domain

“…where Tw o is the most probable twist 26 under the present relaxation conditions: 37 8C in relaxation buffers, with N being the minicircle size (in bp) and h o ¼ 10.54 and 10.49 bp/turn for 5S and pBR series (see Table 1). For a nucleosome in state i, one has the equation:…”

Topoisomerase II, not topoisomerase I, is the proficient relaxase of nucleosomal DNA

“…DNA supercoiling density (s) was calculated with s ¼ DLk/Lk 0 (Wang et al, 1982). Linking number difference (DLk) was determined with DLk ¼ LkÀLk 0 , in which Lk 0 ¼ N/h 0 , where N is the DNA circle size (in bp) and h 0 (10.5 bp/turn) the most probable helical repeat of DNA in the relaxation conditions used (Horowitz and Wang, 1984).…”

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.…”

“…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.…”