Supercoiling energy

Camerini-Otero, R. D., and Felsenfeld, G., 1977, Supercoiling energy and nucleosome formation The role of the arginine-rich histone kernel. Nucleic Acids Res. 4 1159. 

G. Ramachandran and T. Schlick. Beyond optimization Simulating the dynamics of supercoiled DNA by a macroscopic model. In P. M. Pardalos, D. Shal-loway, and G. Xue, editors. Global Minimization of Nonconvex Energy Functions Molecular Conformation and Protein Folding, volume 23 of DIM ACS Series in Discrete Mathematics and Theoretical Computer Science, pages 215-231, Providence, Rhode Island, 1996. American Mathematical Society. 

Figure 4.18. Torsion constant a of supercoiled pJMS2 DNA versus ethidium/base pair, denoted by EB/BP. The lilted symbols are torsion constants obtained after correcting for the effects of energy transfer. The open symbols are the apparent torsion constants obtained from FPA data without taking excitation transfer into account. Even after correcting for excitation transfer, the torsion constant of this supercoiled DNA decreases appreciably with increasing intercalated ethidium, in contrast to linear DNAs.

These observations, together with those on supercoiled DNAs relaxed by intercalating dyes and by topoisomerase I, indicate that complete conversion from the prevalent secondary structures in supercoiled DNAs to the normal B-helix must be severely hindered kinetically. It is also clear that the free energies per base pair of the secondary structure states a and b must be nearly identical in order for these states to be interconverted by such a small environmental perturbation. 

P.-G. Wu, L. Song, J. B. Clendenning, B. S. Fujimoto, A. S. Benight, and J. M. Schurr, Interaction of chloroquine with linear and supercoiled DNAs. Effect on the torsional dynamics, rigidity, and twist energy parameter, Biochemistry 27, 8128-8144 (1988). 

Loop most probable conformations and elastic supercoiling free energies The theory. Obtaining Ks jNx from Fig. 5 plots would require a fitting with six parameters (assuming K jN is identical in the three states) instead of five, which is... 

Rybenkov, V.V., Vologodskii, A.V., and Cozzarelli, N.R. (1997) The effect of ionic conditions on DNA helical repeat, effective diameter and free energy of supercoiling. Nucleic Acids Res. 25, 1412-1418. 

Gebe, J.A., Allison, S.A., Clendenning, J.B., and Schurr, J.M. (1995) Monte-Carlo simulations of supercoiling free-energies for unknotted and trefoil knotted DNAs. Biophys. J. 68, 619-633. Beard, D.A. and Schlick, T. (2001) Computational modeling predicts the structure and dynamics of chromatin fiber. Structure 9, 105-114. 

Figure 18 Measured quantum yields, per incident electron, (a) for the induction of DSBs, (b) SSBs, and (c) loss of the supercoiled DNA form, in DNA solids by low-energy electron irradiation as a function of incident electron energy the curves are guides to the eye. (From Ref. 262.)...

Type I and type II topoisomerases relax negatively supercoiled DNA in steps of one and steps of two, respectively. Type II topoisomerases can also add additional negative supercoils (as indicated by the double arrow). The latter reaction requires energy input, which is encoded by ATP cleavage. 

---