Isosteric and Nonisosteric Base Pairs in RNA Motifs: Molecular Dynamics and Bioinformatics Study of the Sarcin-Ricin Internal Loop
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F13%3A00070873" target="_blank" >RIV/00216224:14740/13:00070873 - isvavai.cz</a>
Result on the web
<a href="http://dx.doi.org/10.1021/jp408530w" target="_blank" >http://dx.doi.org/10.1021/jp408530w</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/jp408530w" target="_blank" >10.1021/jp408530w</a>
Alternative languages
Result language
angličtina
Original language name
Isosteric and Nonisosteric Base Pairs in RNA Motifs: Molecular Dynamics and Bioinformatics Study of the Sarcin-Ricin Internal Loop
Original language description
The sarcin-ricin RNA motif (SR motif) is one of the most prominent recurrent RNA building blocks that occurs in many different RNA contexts and folds autonomously, that is, in a context-independent manner. In this study, we combined bioinformatics analysis with explicit-solvent molecular dynamics (MD) simulations to better understand the relation between the RNA sequence and the evolutionary patterns of the SR motif. A SHAPE probing experiment was also performed to confirm the fidelity of the MD simulations. We identified 57 instances of the SR motif in a nonredundant subset of the RNA X-ray structure database and analyzed their base pairing, base-phosphate, and backbone-backbone interactions. We extracted sequences aligned to these instances from large rRNA alignments to determine the frequency of occurrence for different sequence variants.
Czech name
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Czech description
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Classification
Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CF - Physical chemistry and theoretical chemistry
OECD FORD branch
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Result continuities
Project
<a href="/en/project/ED1.1.00%2F02.0068" target="_blank" >ED1.1.00/02.0068: Central european institute of technology</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2013
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Journal of Physical Chemistry B
ISSN
1520-6106
e-ISSN
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Volume of the periodical
117
Issue of the periodical within the volume
46
Country of publishing house
US - UNITED STATES
Number of pages
18
Pages from-to
14302-14319
UT code for WoS article
000327557700013
EID of the result in the Scopus database
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