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dc.contributor.authorDans, Pablo D.
dc.contributor.authorDanilāne, Linda
dc.contributor.authorIvani, Ivan
dc.contributor.authorDršata, Tomáš
dc.contributor.authorLankaš, Filip
dc.contributor.authorHospital, Adam
dc.contributor.authorWalther, Jürgen
dc.contributor.authorIlla-Pujagut, Ricard
dc.contributor.authorBattistini, Federica
dc.contributor.authorGelpí, Josep Ll.
dc.contributor.authorLavery, Richard
dc.contributor.authorOrozco, Modesto
dc.contributor.otherBarcelona Supercomputing Center
dc.date.accessioned2016-05-04T14:04:48Z
dc.date.available2016-05-04T14:04:48Z
dc.date.issued2016-04-15
dc.identifier.citationDans, Pablo D. [et al.]. Long-timescale dynamics of the Drew–Dickerson dodecamer. "Nucleic Acids Research", 15 Abril 2016.
dc.identifier.issn0305-1048
dc.identifier.urihttp://hdl.handle.net/2117/86576
dc.description.abstractWe present a systematic study of the long-timescale dynamics of the Drew–Dickerson dodecamer (DDD: d(CGCGAATTGCGC)2) a prototypical B-DNA duplex. Using our newly parameterized PARMBSC1 force field, we describe the conformational landscape of DDD in a variety of ionic environments from minimal salt to 2 M Na+Cl− or K+Cl−. The sensitivity of the simulations to the use of different solvent and ion models is analyzed in detail using multi-microsecond simulations. Finally, an extended (10 μs) simulation is used to characterize slow and infrequent conformational changes in DDD, leading to the identification of previously uncharacterized conformational states of this duplex which can explain biologically relevant conformational transitions. With a total of more than 43 μs of unrestrained molecular dynamics simulation, this study is the most extensive investigation of the dynamics of the most prototypical DNA duplex.
dc.description.sponsorshipMINECO Severo Ochoa Award of Excellence (Government of Spain) (to IRB Barcelona); Spanish Ministry of Science [BIO2012-32868, BFU2014-61670-EXP to M.O.]; Catalan SGR (to M.O.); Instituto Nacional de Bioinformática (to M.O.); European Research Council (ERC SimDNA) (to M.O.); H2020 program (MuG and BioExcel projects) (to M.O.); Czech Republic Grant Agency [14-21893S to T.D., F.L.]; ANR grant CHROME [ANR-12-BSV5-0017-01 to R.L.]. Funding for open access charge: European Research Council (ERC SimDNA).
dc.format.extent15 p.
dc.language.isoeng
dc.rightsAttribution-NonCommercial-NoDerivs 4.0 Spain
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/es/
dc.subjectÀrees temàtiques de la UPC::Enginyeria electrònica
dc.subject.lcshDNA--Analysis
dc.subject.lcshMolecular dynamics
dc.subject.otherDNA dynamics
dc.subject.otherDrew–Dickerson dodecamer
dc.subject.otherSimulations
dc.titleLong-timescale dynamics of the Drew–Dickerson dodecamer
dc.typeArticle
dc.subject.lemacADN
dc.subject.lemacDinàmica molecular
dc.identifier.doi10.1093/nar/gkw264
dc.description.peerreviewedPeer Reviewed
dc.description.awardwinningAward-winning
dc.relation.publisherversionhttp://nar.oxfordjournals.org/content/early/2016/04/15/nar.gkw264.long
dc.rights.accessOpen Access
dc.description.versionPostprint (author's final draft)
dc.relation.projectidinfo:eu-repo/grantAgreement/MINECO/SEV-2011-00067
dc.relation.projectidinfo:eu-repo/grantAgreement/MINECO/1PE/BIO2012-32868
dc.relation.projectidinfo:eu-repo/grantAgreement/MINECO/1PE/BFU2014-61670-EXP
dc.relation.projectidinfo:eu-repo/grantAgreement/EC/H2020/676556/EU/Multi-Scale Complex Genomics/MuG
dc.relation.projectidinfo:eu-repo/grantAgreement/EC/H2020/675728/EU/Centre of Excellence for Biomolecular Research/BioExcel
dc.relation.projectidinfo:eu-repo/grantAgreement/EC/FP7/291433/EU/Advanced multiscale simulation of DNA/SIMDNA
upcommons.citation.publishedtrue
upcommons.citation.publicationNameNucleic Acids Research
dc.identifier.pmid27084952


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