dorsal/arxiv
View SchemaMonte Carlo implementation of supercoiled double-stranded DNA
| Authors | Zhang Yang, Zhou Haijun, Ouyang Zhongcan |
|---|---|
| Categories | |
| ArXiv ID | physics/9911074 |
| URL | https://arxiv.org/abs/physics/9911074 |
| DOI | 10.1016/S0006-3495(00)76745-2 |
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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"abstract": "Metropolis Monte Carlo simulation is used to investigate the elasticity of\ntorsionally stressed double-stranded DNA, in which twist and supercoiling are\nincorporated as a natural result of base-stacking interaction and backbone\nbending constrained by hydrogen bonds formed between DNA complementary\nnucleotide bases. Three evident regimes are found in extension versus torsion\nand/or force versus extension plots: a low-force regime in which over- and\nunderwound molecules behave similarly under stretching; an intermediate-force\nregime in which chirality appears for negatively and positively supercoiled DNA\nand extension of underwound molecule is insensitive to the supercoiling degree\nof the polymer; and a large-force regime in which plectonemic DNA is fully\nconverted to extended DNA and supercoiled DNA behaves quite like a torsionless\nmolecule. The striking coincidence between theoretic calculations and recent\nexperimental measurement of torsionally stretched DNA [Strick et al., Science\n{\\bf 271}, 1835 (1996), Biophys. J. {\\bf 74}, 2016 (1998)] strongly suggests\nthat the interplay between base-stacking interaction and permanent\nhydrogen-bond constraint takes an important role in understanding the novel\nproperties of elasticity of supercoiled DNA polymer.",
"arxiv_id": "physics/9911074",
"authors": [
"Zhang Yang",
"Zhou Haijun",
"Ouyang Zhongcan"
],
"categories": [
"physics.bio-ph",
"cond-mat.soft",
"physics.chem-ph",
"physics.comp-ph",
"q-bio"
],
"doi": "10.1016/S0006-3495(00)76745-2",
"title": "Monte Carlo implementation of supercoiled double-stranded DNA",
"url": "https://arxiv.org/abs/physics/9911074"
},
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