Long-timescale dynamics of the Drew–Dickerson dodecamer

We 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 t...

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Detalles Bibliográficos
Autores: Dans, Pablo D., Danilāne, Linda, Ivani, Ivan, Dršata, Tomáš, Lankaš, Filip, Hospital, Adam, Walther, Jürgen, Illa-Pujagut, Ricard, Battistini, Federica, Gelpí, Josep Lluís, Lavery, Richard, Orozco, Modesto
Tipo de recurso: artículo
Fecha de publicación:2016
País:España
Institución:Universitat Politècnica de Catalunya (UPC)
Repositorio:UPCommons. Portal del coneixement obert de la UPC
Idioma:inglés
OAI Identifier:oai:upcommons.upc.edu:2117/86576
Acceso en línea:https://hdl.handle.net/2117/86576
https://dx.doi.org/10.1093/nar/gkw264
Access Level:acceso abierto
Palabra clave:DNA--Analysis
Molecular dynamics
DNA dynamics
Drew–Dickerson dodecamer
Simulations
ADN
Dinàmica molecular
Àrees temàtiques de la UPC::Enginyeria electrònica
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spelling Long-timescale dynamics of the Drew–Dickerson dodecamerDans, Pablo D.Danilāne, LindaIvani, IvanDršata, TomášLankaš, FilipHospital, AdamWalther, JürgenIlla-Pujagut, RicardBattistini, FedericaGelpí, Josep LluísLavery, RichardOrozco, ModestoDNA--AnalysisMolecular dynamicsDNA dynamicsDrew–Dickerson dodecamerSimulationsADNDinàmica molecularÀrees temàtiques de la UPC::Enginyeria electrònicaWe 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.MINECO 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).Peer ReviewedAward-winning20162016-04-1520162016-05-04journal articlehttp://purl.org/coar/resource_type/c_6501AMhttp://purl.org/coar/version/c_ab4af688f83e57aainfo:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/2117/86576https://dx.doi.org/10.1093/nar/gkw26427084952reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)InglésengMinisterio de Economía y Competitividad http://doi.org/10.13039/501100003329 BIO2012-32868 ESTUDIO DE FORMAS INUSUALES O TENSIONADAS DE LOS ACIDOS NUCLEICOS DE POTENCIAL INTERES BIOMEDICO O BIOTECNOLOGICOMinisterio de Economía y Competitividad http://doi.org/10.13039/501100003329 BFU2014-61670-EXP ESTUDIO DEL PAPEL DEL RNA EN LA CROMATINAEuropean Commission http://doi.org/10.13039/100010661 Horizon 2020 Framework Programme 676556 Multi-Scale Complex GenomicsEuropean Commission http://doi.org/10.13039/100010661 Horizon 2020 Framework Programme 675728 Centre of Excellence for Biomolecular ResearchEuropean Commission http://dx.doi.org/10.13039/100011102 Seventh Framework Programme 291433 Advanced multiscale simulation of DNAopen accesshttp://purl.org/coar/access_right/c_abf2Attribution-NonCommercial-NoDerivs 4.0 Spainhttp://creativecommons.org/licenses/by-nc-nd/4.0/es/info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/865762026-05-27T15:37:01Z
dc.title.none.fl_str_mv Long-timescale dynamics of the Drew–Dickerson dodecamer
title Long-timescale dynamics of the Drew–Dickerson dodecamer
spellingShingle Long-timescale dynamics of the Drew–Dickerson dodecamer
Dans, Pablo D.
DNA--Analysis
Molecular dynamics
DNA dynamics
Drew–Dickerson dodecamer
Simulations
ADN
Dinàmica molecular
Àrees temàtiques de la UPC::Enginyeria electrònica
title_short Long-timescale dynamics of the Drew–Dickerson dodecamer
title_full Long-timescale dynamics of the Drew–Dickerson dodecamer
title_fullStr Long-timescale dynamics of the Drew–Dickerson dodecamer
title_full_unstemmed Long-timescale dynamics of the Drew–Dickerson dodecamer
title_sort Long-timescale dynamics of the Drew–Dickerson dodecamer
dc.creator.none.fl_str_mv Dans, Pablo D.
Danilāne, Linda
Ivani, Ivan
Dršata, Tomáš
Lankaš, Filip
Hospital, Adam
Walther, Jürgen
Illa-Pujagut, Ricard
Battistini, Federica
Gelpí, Josep Lluís
Lavery, Richard
Orozco, Modesto
author Dans, Pablo D.
author_facet Dans, Pablo D.
Danilāne, Linda
Ivani, Ivan
Dršata, Tomáš
Lankaš, Filip
Hospital, Adam
Walther, Jürgen
Illa-Pujagut, Ricard
Battistini, Federica
Gelpí, Josep Lluís
Lavery, Richard
Orozco, Modesto
author_role author
author2 Danilāne, Linda
Ivani, Ivan
Dršata, Tomáš
Lankaš, Filip
Hospital, Adam
Walther, Jürgen
Illa-Pujagut, Ricard
Battistini, Federica
Gelpí, Josep Lluís
Lavery, Richard
Orozco, Modesto
author2_role author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv DNA--Analysis
Molecular dynamics
DNA dynamics
Drew–Dickerson dodecamer
Simulations
ADN
Dinàmica molecular
Àrees temàtiques de la UPC::Enginyeria electrònica
topic DNA--Analysis
Molecular dynamics
DNA dynamics
Drew–Dickerson dodecamer
Simulations
ADN
Dinàmica molecular
Àrees temàtiques de la UPC::Enginyeria electrònica
description We 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.
publishDate 2016
dc.date.none.fl_str_mv 2016
2016-04-15
2016
2016-05-04
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
AM
http://purl.org/coar/version/c_ab4af688f83e57aa
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/2117/86576
https://dx.doi.org/10.1093/nar/gkw264
27084952
url https://hdl.handle.net/2117/86576
https://dx.doi.org/10.1093/nar/gkw264
identifier_str_mv 27084952
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv Ministerio de Economía y Competitividad http://doi.org/10.13039/501100003329 BIO2012-32868 ESTUDIO DE FORMAS INUSUALES O TENSIONADAS DE LOS ACIDOS NUCLEICOS DE POTENCIAL INTERES BIOMEDICO O BIOTECNOLOGICO
Ministerio de Economía y Competitividad http://doi.org/10.13039/501100003329 BFU2014-61670-EXP ESTUDIO DEL PAPEL DEL RNA EN LA CROMATINA
European Commission http://doi.org/10.13039/100010661 Horizon 2020 Framework Programme 676556 Multi-Scale Complex Genomics
European Commission http://doi.org/10.13039/100010661 Horizon 2020 Framework Programme 675728 Centre of Excellence for Biomolecular Research
European Commission http://dx.doi.org/10.13039/100011102 Seventh Framework Programme 291433 Advanced multiscale simulation of DNA
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial-NoDerivs 4.0 Spain
http://creativecommons.org/licenses/by-nc-nd/4.0/es/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial-NoDerivs 4.0 Spain
http://creativecommons.org/licenses/by-nc-nd/4.0/es/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:UPCommons. Portal del coneixement obert de la UPC
instname:Universitat Politècnica de Catalunya (UPC)
instname_str Universitat Politècnica de Catalunya (UPC)
reponame_str UPCommons. Portal del coneixement obert de la UPC
collection UPCommons. Portal del coneixement obert de la UPC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,300724

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