Energetics of coupled twist and writhe changes in closed circular pSM1 DNA

Journal of Molecular Biology
W R BauerCraig J Benham

Abstract

The extent of local denaturation in closed circular pSM1 DNA depends upon the linking difference, delta Lk, and the temperature, t. We have determined the denaturation profiles, using gel electrophoresis, over the ranges -37 < or = delta Lk < or = +16 and 25 degrees C < or = t < or = 65 degrees C. We have applied statistical mechanical methods to these data to evaluate the free energies of superhelix formation, of the twisting of single strands around each other, and of the initration of local denaturation. Because the complete nucleotide sequence is needed for this analysis, the complete pSM1 DNA sequence was determined and is reported here. The values of the free energy parameters found in this work agree closely with those previously obtained from experiments with pBR322 DNA, suggesting that there is little dependence of these values on the particular DNA sequence. We find the temperature dependence of these free energies by the appropriate statistical mechanical analysis of the temperature-dependent denaturation profiles produced by supercoiling. Calculations of the transition probability profiles indicate that the course of local denaturation in pSM1 DNA involves a complex competition among several sites of comparable susc...Continue Reading

Citations

Jun 1, 1997·Journal of Biomolecular Structure & Dynamics·R Negri, E Di Mauro
Dec 8, 2004·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Craig J Benham, Chengpeng Bi

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