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Title: Long-timescale dynamics of the Drew-Dickerson dodecamer
Author: Dans, Pablo D.
Danilāne, Linda
Ivani, Ivan
Dršata, Tomáš
Lankaš, Filip
Hospital Gasch, Adam
Walther, Jürgen
Illa Pujagut, Ricard
Battistini, Federica
Gelpí Buchaca, Josep Lluís
Lavery, Richard
Orozco López, Modesto
Keywords: Duplicació de l'ADN
Biologia computacional
DNA replication
Computational biology
Issue Date: 15-Apr-2016
Publisher: Oxford University Press
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.
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It is part of: Nucleic Acids Research, 2016, vol. 44, num. 9, p. 4052-4066
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ISSN: 0305-1048
Appears in Collections:Articles publicats en revistes (Institut de Recerca Biomèdica (IRB Barcelona))
Articles publicats en revistes (Bioquímica i Biomedicina Molecular)

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