Monte Carlo implementation of supercoiled double-stranded DNA.
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 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. 271:1835, 1996; Biophys. J. 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.
Yang
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Institute of Theoretical Physics, Academia Sinica, P.O. Box 2735, Beijing 100080, China. zhangy@itp.ac.cn
Haijun
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Zhong-Can
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D055592:Biophysical Phenomena; D001703:Biophysics; D004278:DNA, Superhelical / Q000737:chemistry*; D004548:Elasticity; D006860:Hydrogen Bonding; D008956:Models, Chemical; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation
D004278:DNA, Superhelical