Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F12%3A33142844" target="_blank" >RIV/61989592:15310/12:33142844 - isvavai.cz</a>
Alternative codes found
RIV/68081707:_____/12:00384749 RIV/00216224:14740/12:00057883
Result on the web
<a href="http://dx.doi.org/10.1021/jp3014817" target="_blank" >http://dx.doi.org/10.1021/jp3014817</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/jp3014817" target="_blank" >10.1021/jp3014817</a>

Result language
angličtina
Original language name
Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration
Original language description
We have carried out an extended reference set of explicit solvent molecular dynamics simulations (63 simulations with 8.4 mu s of simulation data) of canonical A-RNA duplexes. Most of the simulations were done using the latest variant of the Cornell et al. AMBER RNA force field bsc0 chi(OL3), while several other RNA force fields have been tested. The calculations show that the A-RNA helix compactness, described mainly by geometrical parameters inclination, base pair roll, and helical rise, is sequencedependent. In the calculated set of structures, the inclination aries from 10 degrees to 24 degrees. On the basis of simulations with modified bases (inosine and 2,6-diaminopurine), we suggest that the sequencedependence of purely canonical A-RNA double helix is caused by the steric shape of the base pairs, i.e., the van der Waals interactions. The electrostatic part of stacking does not appear to affect the A-RNA shape. Especially visible is the role of the minor groove amino group of pur
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
2012
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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