Publication:
Role of helicity in DNA hairpin folding dynamics

dc.contributor.departmentDepartment of Physics
dc.contributor.departmentGraduate School of Sciences and Engineering
dc.contributor.kuauthorKabakçıoğlu, Alkan
dc.contributor.kuauthorLi, Huaping
dc.contributor.schoolcollegeinstituteCollege of Sciences
dc.contributor.schoolcollegeinstituteGRADUATE SCHOOL OF SCIENCES AND ENGINEERING
dc.date.accessioned2024-11-09T11:43:39Z
dc.date.issued2018
dc.description.abstractWe 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.fulltextYES
dc.description.indexedbyWOS
dc.description.indexedbyScopus
dc.description.indexedbyPubMed
dc.description.issue13
dc.description.openaccessYES
dc.description.publisherscopeInternational
dc.description.sponsoredbyTubitakEuTÜBİTAK
dc.description.sponsorshipScientific and Technological Research Council of Turkey (TÜBİTAK)
dc.description.versionPublisher version
dc.description.volume121
dc.identifier.doi10.1103/PhysRevLett.121.138101
dc.identifier.eissn1079-7114
dc.identifier.embargoNO
dc.identifier.filenameinventorynoIR01450
dc.identifier.issn0031-9007
dc.identifier.quartileQ1
dc.identifier.scopus2-s2.0-85053878271
dc.identifier.urihttps://hdl.handle.net/20.500.14288/352
dc.identifier.wos445603400021
dc.keywordsFluorescence fluctuation spectroscopy
dc.keywordsPhase-transitions
dc.keywordsRna catalysis
dc.keywordsLandscape
dc.keywordsBarriers
dc.keywordsKinetics
dc.keywordsAcids
dc.language.isoeng
dc.publisherAmerican Physical Society (APS)
dc.relation.grantnoMFAG-114F348
dc.relation.ispartofPhysical Review Letters
dc.relation.urihttp://cdm21054.contentdm.oclc.org/cdm/ref/collection/IR/id/8045
dc.subjectPhysics, multidisciplinary
dc.titleRole of helicity in DNA hairpin folding dynamics
dc.typeJournal Article
dspace.entity.typePublication
local.contributor.kuauthorLi, Huaping
local.contributor.kuauthorKabakçıoğlu, Alkan
local.publication.orgunit1College of Sciences
local.publication.orgunit1GRADUATE SCHOOL OF SCIENCES AND ENGINEERING
local.publication.orgunit2Department of Physics
local.publication.orgunit2Graduate School of Sciences and Engineering
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