Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F14%3A33152190" target="_blank" >RIV/61989592:15310/14:33152190 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/68081707:_____/14:00431584 RIV/61388963:_____/14:00431584

Výsledek na webu

<a href="http://pubs.acs.org/doi/pdf/10.1021/ct500120v" target="_blank" >http://pubs.acs.org/doi/pdf/10.1021/ct500120v</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/ct500120v" target="_blank" >10.1021/ct500120v</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA

Popis výsledku v původním jazyce

Terminal base pairs of DNA and RNA molecules in solution are known to undergo frequent transient opening events (fraying). Accurate modeling of this process is important because of its involvement in nucleic acid end recognition and enzymatic catalysis.In this article, we describe fraying in molecular dynamics simulations with the ff99bsc0, ff99bsc0 chi(OL3), and ff99bsc0 chi(OL4) force fields, both for DNA and RNA molecules. Comparison with the experiment showed that while some features of fraying areconsistent with the available data, others indicate potential problems with the force field description. In particular, multiple noncanonical structures are formed at the ends of the DNA and RNA duplexes. Among them are tWC/sugar edge pair, C-H edge/Watson-Crick pair, and stacked geometries, in which the terminal bases are stacked above each other. These structures usually appear within the first tens to hundreds of nanoseconds and substantially limit the usefulness of the remaining par

Název v anglickém jazyce

Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA

Popis výsledku anglicky

Terminal base pairs of DNA and RNA molecules in solution are known to undergo frequent transient opening events (fraying). Accurate modeling of this process is important because of its involvement in nucleic acid end recognition and enzymatic catalysis.In this article, we describe fraying in molecular dynamics simulations with the ff99bsc0, ff99bsc0 chi(OL3), and ff99bsc0 chi(OL4) force fields, both for DNA and RNA molecules. Comparison with the experiment showed that while some features of fraying areconsistent with the available data, others indicate potential problems with the force field description. In particular, multiple noncanonical structures are formed at the ends of the DNA and RNA duplexes. Among them are tWC/sugar edge pair, C-H edge/Watson-Crick pair, and stacked geometries, in which the terminal bases are stacked above each other. These structures usually appear within the first tens to hundreds of nanoseconds and substantially limit the usefulness of the remaining par

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

BO - Biofyzika

OECD FORD obor

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Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

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

Rok uplatnění

2014

Kód důvěrnosti údajů

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

Název periodika

Journal of Chemical Theory and Computation

ISSN

1549-9618

e-ISSN

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Svazek periodika

10

Číslo periodika v rámci svazku

8

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

13

Strana od-do

3177-3189

Kód UT WoS článku

000340351200030

EID výsledku v databázi Scopus

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