Long-timescale dynamics of the Drew-Dickerson dodecamer

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22310%2F16%3A43902851" target="_blank" >RIV/60461373:22310/16:43902851 - isvavai.cz</a>

Alternative codes found

RIV/61388963:_____/16:00462092

Result on the web

<a href="http://dx.doi.org/10.1093/nar/gkw264" target="_blank" >http://dx.doi.org/10.1093/nar/gkw264</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/nar/gkw264" target="_blank" >10.1093/nar/gkw264</a>

Result language

angličtina

Original language name

Long-timescale dynamics of the Drew-Dickerson dodecamer

Original language 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 mu s) 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 mu s of unrestrained molecular dynamics simulation, this study is the most extensive investigation of the dynamics of the most prototypical DNA duplex.

Czech name

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Czech description

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Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

CF - Physical chemistry and theoretical chemistry

OECD FORD branch

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Project

<a href="/en/project/GA14-21893S" target="_blank" >GA14-21893S: Nanomechanics of RNA and DNA structural motifs</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2016

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Nucleic Acids Research

ISSN

0305-1048

e-ISSN

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Volume of the periodical

44

Issue of the periodical within the volume

9

Country of publishing house

GB - UNITED KINGDOM

Number of pages

15

Pages from-to

4052-4066

UT code for WoS article

000377472100018

EID of the result in the Scopus database

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