Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA

Result code in 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>
Alternative codes found
RIV/68081707:_____/14:00431584 RIV/61388963:_____/14:00431584
Result on the web
<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>

Result language
angličtina
Original language name
Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA
Original language description
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
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
BO - Biophysics
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

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