Free energy of supercoiling

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. 

Experiments have shown that the obtained distribution is always normal (Depew and Wang, 1975 [11] Pulleyblank et al., 1975 [57] Horowitz and Wang, 1984 [33]). The variance, (r ), of this normal distribution was measured for different DNAs. These experiments have played a very important role in studying the physical properties of ccDNA. They made it possible to determine the free energy of supercoiling, which is directly connected to the variance ... 

The free energy of supercoiling is proportional to the square of the linking number difference in the DNA ... 

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. 

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... 

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. 

Type I topoisomerases catalyze the relaxation of supercoiled DNA, a thermodynamically favorable process. Type II topoisomerases utilize free energy from ATP hydrolysis to add negative supercoils to DNA. The two types of enzymes have several common features, including the use of key tyrosine residues to form covalent links to the polynucleotide backbone that is transiently broken. 

DNA), an increase (relaxation) of 1 unit in linking number decreases its free energy by 9 kcal/mol. Similarly, the binding of a protein that unwinds DNA would be associated with a favorable free energy, as would transitions to alternate structures in DNA, such as cruciforms or Z-DNA, which relieve superhelical stress. The topological state of DNA is thus important to its biological functions, as also indicated by the profound influence of DNA supercoiling on such processes as replication, transcription, and recombination. 

With the backbone of one strand cleaved, the DNA can now rotate around the remaining strand, driven by the release of the energy stored because of the supercoiling. The rotation of the DNA unwinds supercoils. The enzyme controls the rotation so that the unwinding is not rapid. The free hydroxyl group of the DNA attacks the phosphotyrosine residue to reseal the backbone and release tyrosine. The DNA is then free to dissociate from the enzyme. Thus, reversible cleavage of one strand of the DNA allows controlled rotation to partly relax supercoiled DNA. 

Relaxed DNA. The DNA hehx in soluhon will adopt a preferred helical repeat that is function of the base composihon. In linear DNA, in which the ends of the molecule are free to rotate, the DNA will adopt this preferred helical repeat of 10.5 bp per turn in solution. The helical repeat also exists in nicked DNA in which the nick provides a swivel whereby one strand can rotate about the other. The preferred helical repeat of a linear DNA molecule represents the lowest energy form of the molecule. When this state of helical twist exists in a covalently closed molecule, the molecule is relaxed and contains no supercoils. In the relaxed DNA, the linking number equal the twist number (L = T) and W = 0. The linking number of relaxed DNA, Lq is defined as ... 

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