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Monte Carlo implementation of supercoiled double-stranded DNA

Zhang Yang·Zhou Haijun·Ouyang Zhongcan
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Abstract

Metropolis Monte Carlo simulation is used to investigate the elasticity of torsionally stressed double-stranded DNA, in which twist and supercoiling are incorporated as a natural result of base-stacking interaction and backbone bending constrained by hydrogen bonds formed between DNA complementary nucleotide bases. Three evident regimes are found in extension versus torsion and/or force versus extension plots: a low-force regime in which over- and underwound molecules behave similarly under stretching; an intermediate-force regime in which chirality appears for negatively and positively supercoiled DNA and extension of underwound molecule is insensitive to the supercoiling degree of the polymer; and a large-force regime in which plectonemic DNA is fully converted to extended DNA and supercoiled DNA behaves quite like a torsionless molecule. The striking coincidence between theoretic calculations and recent experimental measurement of torsionally stretched DNA [Strick et al., Science {\bf 271}, 1835 (1996), Biophys. J. {\bf 74}, 2016 (1998)] strongly suggests that the interplay between base-stacking interaction and permanent hydrogen-bond constraint takes an important role in understanding the novel properties of elasticity of supercoiled DNA polymer.

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Zhang Yang, Zhou Haijun, Ouyang Zhongcan. 1999-11-29. Monte Carlo implementation of supercoiled double-stranded DNA. https://doi.org/10.1016/s0006-3495(00)76745-2

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