dorsal/arxiv
View SchemaDNA: From rigid base-pairs to semiflexible polymers
| Authors | Nils B. Becker, Ralf Everaers |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0611044 |
| URL | https://arxiv.org/abs/q-bio/0611044 |
| DOI | 10.1103/PhysRevE.76.021923 |
Abstract
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have been obtained from all-atom MD simulation and from high-resolution structural data. On the scale of a hundred nm, DNA is successfully described by a continuous worm-like chain model with homogeneous elastic properties characterized by a set of four elastic constants, which have been directly measured in single-molecule experiments. We present here a theory that links these experiments on different scales, by systematically coarse-graining the rigid base-pair model for random sequence DNA to an effective worm-like chain description. The average helical geometry of the molecule is exactly taken into account in our approach. We find that the available microscopic parameters sets predict qualitatively similar mesoscopic parameters. The thermal bending and twisting persistence lengths computed from MD data are 42 and 48 nm, respectively. The static persistence lengths are generally much higher, in agreement with cyclization experiments. All microscopic parameter sets predict negative twist-stretch coupling. The variability and anisotropy of bending stiffness in short random chains lead to non-Gaussian bend angle distributions, but become unimportant after two helical turns.
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"abstract": "The sequence-dependent elasticity of double-helical DNA on a nm length scale\ncan be captured by the rigid base-pair model, whose strains are the relative\nposition and orientation of adjacent base-pairs. Corresponding elastic\npotentials have been obtained from all-atom MD simulation and from\nhigh-resolution structural data. On the scale of a hundred nm, DNA is\nsuccessfully described by a continuous worm-like chain model with homogeneous\nelastic properties characterized by a set of four elastic constants, which have\nbeen directly measured in single-molecule experiments. We present here a theory\nthat links these experiments on different scales, by systematically\ncoarse-graining the rigid base-pair model for random sequence DNA to an\neffective worm-like chain description. The average helical geometry of the\nmolecule is exactly taken into account in our approach. We find that the\navailable microscopic parameters sets predict qualitatively similar mesoscopic\nparameters. The thermal bending and twisting persistence lengths computed from\nMD data are 42 and 48 nm, respectively. The static persistence lengths are\ngenerally much higher, in agreement with cyclization experiments. All\nmicroscopic parameter sets predict negative twist-stretch coupling. The\nvariability and anisotropy of bending stiffness in short random chains lead to\nnon-Gaussian bend angle distributions, but become unimportant after two helical\nturns.",
"arxiv_id": "q-bio/0611044",
"authors": [
"Nils B. Becker",
"Ralf Everaers"
],
"categories": [
"q-bio.BM"
],
"doi": "10.1103/PhysRevE.76.021923",
"title": "DNA: From rigid base-pairs to semiflexible polymers",
"url": "https://arxiv.org/abs/q-bio/0611044"
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