2026-04-13T01:03:49Zhttps://recercat.cat/oai/requestoai:recercat.cat:2445/1024692025-12-04T21:11:34Zcom_2072_1057col_2072_478781col_2072_478908col_2072_478917
RECERCAT
author
Dans, Pablo D.
author
Danilāne, Linda
author
Ivani, Ivan
author
Dršata, Tomáš
author
Lankaš, Filip
author
Hospital Gasch, Adam
author
Walther, Jürgen
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Illa Pujagut, Ricard
author
Battistini, Federica
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Gelpí Buchaca, Josep Lluís
author
Lavery, Richard
author
Orozco López, Modesto
2016-10-07T15:26:39Z2016-10-07T15:26:39Z2016-04-152016-10-07T15:26:44Z
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.
cc-by-nc (c) Dans, Pablo D. et al., 2016 http://creativecommons.org/licenses/by-nc/3.0/es info:eu-repo/semantics/openAccess
Duplicació de l'ADN
Biologia computacional
DNA replication
Computational biology
Long-timescale dynamics of the Drew-Dickerson dodecamer
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion