Publication: Role of helicity in DNA hairpin folding dynamics
dc.contributor.department | Department of Physics | |
dc.contributor.department | Graduate School of Sciences and Engineering | |
dc.contributor.kuauthor | Kabakçıoğlu, Alkan | |
dc.contributor.kuauthor | Li, Huaping | |
dc.contributor.schoolcollegeinstitute | College of Sciences | |
dc.contributor.schoolcollegeinstitute | GRADUATE SCHOOL OF SCIENCES AND ENGINEERING | |
dc.date.accessioned | 2024-11-09T11:43:39Z | |
dc.date.issued | 2018 | |
dc.description.abstract | We study hairpin folding dynamics by means of extensive molecular dynamics simulations, with particular attention paid to the influence of helicity on the folding time. We find that the dynamical exponent a in the anomalous scaling n(t) similar to t(1/alpha) of the hairpin length n with time changes from 1.6 (similar or equal to 1 + nu, where nu is the Flory exponent) to 1.2 (similar or equal to 2 nu) in three dimensions, when duplex helicity is removed. The relation alpha = 2 nu in rotationless hairpin folding is further verified in two dimensions (nu = 0.75) and for a ghost chain (nu = 0.5). Our findings suggest that the folding dynamics in long helical chains is governed by the duplex dynamics, contrasting the earlier understanding based on the stem-flower picture of unpaired segments. We propose a scaling argument for alpha = 1 + nu in helical chains, assuming that duplex relaxation required for orientational positioning of the next pair of bases is the rate-limiting process. | |
dc.description.fulltext | YES | |
dc.description.indexedby | WOS | |
dc.description.indexedby | Scopus | |
dc.description.indexedby | PubMed | |
dc.description.issue | 13 | |
dc.description.openaccess | YES | |
dc.description.publisherscope | International | |
dc.description.sponsoredbyTubitakEu | TÜBİTAK | |
dc.description.sponsorship | Scientific and Technological Research Council of Turkey (TÜBİTAK) | |
dc.description.version | Publisher version | |
dc.description.volume | 121 | |
dc.identifier.doi | 10.1103/PhysRevLett.121.138101 | |
dc.identifier.eissn | 1079-7114 | |
dc.identifier.embargo | NO | |
dc.identifier.filenameinventoryno | IR01450 | |
dc.identifier.issn | 0031-9007 | |
dc.identifier.quartile | Q1 | |
dc.identifier.scopus | 2-s2.0-85053878271 | |
dc.identifier.uri | https://hdl.handle.net/20.500.14288/352 | |
dc.identifier.wos | 445603400021 | |
dc.keywords | Fluorescence fluctuation spectroscopy | |
dc.keywords | Phase-transitions | |
dc.keywords | Rna catalysis | |
dc.keywords | Landscape | |
dc.keywords | Barriers | |
dc.keywords | Kinetics | |
dc.keywords | Acids | |
dc.language.iso | eng | |
dc.publisher | American Physical Society (APS) | |
dc.relation.grantno | MFAG-114F348 | |
dc.relation.ispartof | Physical Review Letters | |
dc.relation.uri | http://cdm21054.contentdm.oclc.org/cdm/ref/collection/IR/id/8045 | |
dc.subject | Physics, multidisciplinary | |
dc.title | Role of helicity in DNA hairpin folding dynamics | |
dc.type | Journal Article | |
dspace.entity.type | Publication | |
local.contributor.kuauthor | Li, Huaping | |
local.contributor.kuauthor | Kabakçıoğlu, Alkan | |
local.publication.orgunit1 | College of Sciences | |
local.publication.orgunit1 | GRADUATE SCHOOL OF SCIENCES AND ENGINEERING | |
local.publication.orgunit2 | Department of Physics | |
local.publication.orgunit2 | Graduate School of Sciences and Engineering | |
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relation.isOrgUnitOfPublication | 3fc31c89-e803-4eb1-af6b-6258bc42c3d8 | |
relation.isOrgUnitOfPublication.latestForDiscovery | c43d21f0-ae67-4f18-a338-bcaedd4b72a4 | |
relation.isParentOrgUnitOfPublication | af0395b0-7219-4165-a909-7016fa30932d | |
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