Salerno's model of DNA reanalysed: could solitons have biological significance?

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dc.creatorBashford, J. D.
dc.date2006-02-15
dc.date.accessioned2026-07-07T12:00:27Z
dc.date.available2026-07-07T12:00:27Z
dc.descriptionWe 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.
dc.descriptionLatex file 20 pages, 5 figures. Manuscript of paper to appear in J. Biol. Phys., accepted 02/09/05
dc.identifierhttps://arxiv.org/abs/q-bio/0602019
dc.identifierhttp://arxiv.org/abs/q-bio/0602019
dc.identifierJ.Biol.Phys.32:27-47,2006
dc.identifierdoi:10.1007/s10867-006-2719-1
dc.identifier.urihttp://salesiana.dossiersoluciones.com/handle/123456789/206848
dc.subjectBiomolecules
dc.subjectBiological Physics
dc.titleSalerno's model of DNA reanalysed: could solitons have biological significance?
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