2026-04-17T12:53:31Zhttps://recercat.cat/oai/request

oai:recercat.cat:2445/1024692025-12-04T21:11:34Zcom_2072_1057col_2072_478781col_2072_478908col_2072_478917

00925njm 22002777a 4500 dc Dans, Pablo D. author Danilāne, Linda author Ivani, Ivan author Dršata, Tomáš author Lankaš, Filip author Hospital Gasch, Adam author Walther, Jürgen author Illa Pujagut, Ricard author Battistini, Federica author Gelpí Buchaca, Josep Lluís author Lavery, Richard author Orozco López, Modesto author 2016-10-07T15:26:39Z 2016-10-07T15:26:39Z 2016-04-15 2016-10-07T15:26:44Z 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. Duplicació de l'ADN Biologia computacional DNA replication Computational biology Long-timescale dynamics of the Drew-Dickerson dodecamer