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dc.contributor.authorXiao, Shiyanen
dc.contributor.authorSharpe, Danielen
dc.contributor.authorChakraborty, Debayanen
dc.contributor.authorWales, Daviden
dc.date.accessioned2019-12-12T00:32:48Z
dc.date.available2019-12-12T00:32:48Z
dc.date.issued2019-11en
dc.identifier.issn1948-7185
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/299797
dc.description.abstractStrand hybridization is not only a fundamental molecular mechanism underlying the biological functions of nucleic acids but is also a key step in the design of efficient nanodevices. Despite recent efforts, the microscopic rules governing the hybridization mechanisms remain largely unknown. In this study, we exploit the energy landscape framework to assess how sequence-specificity modulates the hybridization mechanisms in DNA. We find that GG-tracts hybridize much more rapidly compared to GC-tracts, via either zippering or slithering pathways. For the hybridization of GG-tracts, both zippering and slithering mechanisms appear to be kinetically relevant. In contrast, for the GC-tracts, the zippering mechanism is dominant. Our work reveals that even for the relatively small systems considered, the energy landscapes feature multiple metastable states and kinetic traps, which is at odds with the conventional "all-or-nothing" model of DNA hybridization formulated on the basis of thermodynamic arguments alone. Interestingly, entropic effects are found to play an important role in determining the thermal stability of competing conformational ensembles and in determining the preferred hybridization pathways.
dc.description.sponsorshipepsrc
dc.format.mediumPrint-Electronicen
dc.languageengen
dc.rightsAll rights reserved
dc.subjectGuanineen
dc.subjectOligonucleotidesen
dc.subjectNucleic Acid Hybridizationen
dc.subjectNucleic Acid Conformationen
dc.subjectThermodynamicsen
dc.titleEnergy Landscapes and Hybridization Pathways for DNA Hexamer Duplexes.en
dc.typeArticle
prism.endingPage6779
prism.issueIdentifier21en
prism.publicationDate2019en
prism.publicationNameThe journal of physical chemistry lettersen
prism.startingPage6771
prism.volume10en
dc.identifier.doi10.17863/CAM.46867
dcterms.dateAccepted2019-10-14en
rioxxterms.versionofrecord10.1021/acs.jpclett.9b02356en
rioxxterms.versionAM
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserveden
rioxxterms.licenseref.startdate2019-11en
dc.contributor.orcidXiao, Shiyan [0000-0003-1159-1224]
dc.contributor.orcidSharpe, Daniel [0000-0003-2079-2677]
dc.contributor.orcidChakraborty, Debayan [0000-0003-4339-5818]
dc.contributor.orcidWales, David [0000-0002-3555-6645]
dc.identifier.eissn1948-7185
rioxxterms.typeJournal Article/Reviewen
pubs.funder-project-idEPSRC (EP/N035003/1)
cam.orpheus.successThu Jan 30 10:33:56 GMT 2020 - Embargo updated*
rioxxterms.freetoread.startdate2020-11-30


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