muABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F14%3A00077975" target="_blank" >RIV/00216224:14740/14:00077975 - isvavai.cz</a>

Alternative codes found

RIV/68081707:_____/14:00442075 RIV/61388963:_____/14:00442075

Result on the web

<a href="http://nar.oxfordjournals.org/content/early/2014/09/26/nar.gku855.full" target="_blank" >http://nar.oxfordjournals.org/content/early/2014/09/26/nar.gku855.full</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/nar/gku855" target="_blank" >10.1093/nar/gku855</a>

Result language

angličtina

Original language name

muABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

Original language description

We present the results of microsecond molecular dynamics simulations carried out by the ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct tetranucleotide base sequences. We demonstrate that the resulting trajectories haveextensively sampled the conformational space accessible to B-DNA at room temperature. We confirm that base sequence effects depend strongly not only on the specific base pair step, but also on the specific base pairs that flank each step. Beyond sequenceeffects on average helical parameters and conformational fluctuations, we also identify tetranucleotide sequences that oscillate between several distinct conformational substates. By analyzing the conformation of the phosphodiester backbones, it is possible to understand for which sequences these substates will arise, and what impact they will have on specific helical parameters.

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

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2014

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

42

Issue of the periodical within the volume

19

Country of publishing house

GB - UNITED KINGDOM

Number of pages

12

Pages from-to

12272-12283

UT code for WoS article

000347689500044

EID of the result in the Scopus database

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