dorsal/arxiv
View SchemaSalerno's model of DNA reanalysed: could solitons have biological significance?
| Authors | J. D. Bashford |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0602019 |
| URL | https://arxiv.org/abs/q-bio/0602019 |
| DOI | 10.1007/s10867-006-2719-1 |
| Journal | J.Biol.Phys.32:27-47,2006 |
Abstract
We investigate the sequence-dependent behaviour of localised excitations in a toy, nonlinear model of DNA base-pair opening originally proposed by Salerno. Specifically we ask whether ``breather'' solitons could play a role in the facilitated location of promoters by RNA polymerase. In an effective potential formalism, we find excellent correlation between potential minima and {\em Escherichia coli} promoter recognition sites in the T7 bacteriophage genome. Evidence for a similar relationship between phage promoters and downstream coding regions is found and alternative reasons for links between AT richness and transcriptionally-significant sites are discussed. Consideration of the soliton energy of translocation provides a novel dynamical picture of sliding: steep potential gradients correspond to deterministic motion, while ``flat'' regions, corresponding to homogeneous AT or GC content, are governed by random, thermal motion. Finally we demonstrate an interesting equivalence between planar, breather solitons and the helical motion of a sliding protein ``particle'' about a bent DNA axis.
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"abstract": "We investigate the sequence-dependent behaviour of localised excitations in a\ntoy, nonlinear model of DNA base-pair opening originally proposed by Salerno.\nSpecifically we ask whether ``breather\u0027\u0027 solitons could play a role in the\nfacilitated location of promoters by RNA polymerase. In an effective potential\nformalism, we find excellent correlation between potential minima and {\\em\nEscherichia coli} promoter recognition sites in the T7 bacteriophage genome.\nEvidence for a similar relationship between phage promoters and downstream\ncoding regions is found and alternative reasons for links between AT richness\nand transcriptionally-significant sites are discussed. Consideration of the\nsoliton energy of translocation provides a novel dynamical picture of sliding:\nsteep potential gradients correspond to deterministic motion, while ``flat\u0027\u0027\nregions, corresponding to homogeneous AT or GC content, are governed by random,\nthermal motion. Finally we demonstrate an interesting equivalence between\nplanar, breather solitons and the helical motion of a sliding protein\n``particle\u0027\u0027 about a bent DNA axis.",
"arxiv_id": "q-bio/0602019",
"authors": [
"J. D. Bashford"
],
"categories": [
"q-bio.BM",
"physics.bio-ph"
],
"doi": "10.1007/s10867-006-2719-1",
"journal_ref": "J.Biol.Phys.32:27-47,2006",
"title": "Salerno\u0027s model of DNA reanalysed: could solitons have biological significance?",
"url": "https://arxiv.org/abs/q-bio/0602019"
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