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dc.contributor.authorChakraborty, Debayanen
dc.contributor.authorWales, Daviden
dc.date.accessioned2018-06-04T09:33:48Z
dc.date.available2018-06-04T09:33:48Z
dc.date.issued2018-01en
dc.identifier.issn1948-7185
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/276494
dc.description.abstractThe recent discovery that Hoogsteen (HG) base pairs are widespread in DNA across diverse sequences and positional contexts could have important implications for understanding DNA replication and DNA-protein recognition. While evidence is emerging that the Hoogsteen conformation could be a thermodynamically accessible conformation of the DNA duplex and provide a means to expand its functionality, relatively little is known about the molecular mechanism underlying the Watson-Crick (WC) to HG transition. In this Perspective, we describe pathways and kinetics for this transition at an atomic level of detail, using the energy landscape perspective. We show that competition between the duplex conformations results in a double funnel landscape, which explains some recent experimental observations. The interconversion pathways feature a number of intermediates, with a variable number of WC and HG base pairs. The relatively slow kinetics, with possible deviations from two-state behavior, suggest that this conformational switch is likely to be a challenging target for both simulation and experiment.
dc.description.sponsorshipepsrc
dc.format.mediumPrint-Electronicen
dc.languageengen
dc.subjectDNAen
dc.subjectBase Sequenceen
dc.subjectBase Pairingen
dc.subjectThermodynamicsen
dc.subjectModels, Molecularen
dc.titleEnergy Landscape and Pathways for Transitions between Watson-Crick and Hoogsteen Base Pairing in DNA.en
dc.typeArticle
prism.endingPage241
prism.issueIdentifier1en
prism.publicationDate2018en
prism.publicationNameThe journal of physical chemistry lettersen
prism.startingPage229
prism.volume9en
dc.identifier.doi10.17863/CAM.23792
dcterms.dateAccepted2017-12-14en
rioxxterms.versionofrecord10.1021/acs.jpclett.7b01933en
rioxxterms.versionAM*
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserveden
rioxxterms.licenseref.startdate2018-01en
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)


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