Long-timescale dynamics of the Drew–Dickerson dodecamer
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Cita com:
hdl:2117/86576
Tipus de documentArticle
Data publicació2016-04-15
Condicions d'accésAccés obert
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Reconeixement-NoComercial-SenseObraDerivada 4.0 Espanya
ProjecteESTUDIO DE FORMAS INUSUALES O TENSIONADAS DE LOS ACIDOS NUCLEICOS DE POTENCIAL INTERES BIOMEDICO O BIOTECNOLOGICO (MINECO-BIO2012-32868)
ESTUDIO DEL PAPEL DEL RNA EN LA CROMATINA (MINECO-BFU2014-61670-EXP)
MuG - Multi-Scale Complex Genomics (EC-H2020-676556)
BioExcel - Centre of Excellence for Biomolecular Research (EC-H2020-675728)
SIMDNA - Advanced multiscale simulation of DNA (EC-FP7-291433)
ESTUDIO DEL PAPEL DEL RNA EN LA CROMATINA (MINECO-BFU2014-61670-EXP)
MuG - Multi-Scale Complex Genomics (EC-H2020-676556)
BioExcel - Centre of Excellence for Biomolecular Research (EC-H2020-675728)
SIMDNA - Advanced multiscale simulation of DNA (EC-FP7-291433)
Abstract
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.
CitacióDans, Pablo D. [et al.]. Long-timescale dynamics of the Drew–Dickerson dodecamer. "Nucleic Acids Research", 15 Abril 2016.
GuardóDocument premiat
ISSN0305-1048
Versió de l'editorhttp://nar.oxfordjournals.org/content/early/2016/04/15/nar.gkw264.long
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