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Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes

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    SYSNO ASEP0571531
    Document TypeJ - Journal Article
    R&D Document TypeJournal Article
    Subsidiary JČlánek ve WOS
    TitleSensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes
    Author(s) Kührová, P. (CZ)
    Mlýnský, Vojtech (BFU-R) ORCID
    Otyepka, M. (CZ)
    Šponer, Jiří (BFU-R) RID, ORCID
    Banáš, P. (CZ)
    Number of authors5
    Source TitleJournal of Chemical Information and Modeling. - : American Chemical Society - ISSN 1549-9596
    Roč. 63, č. 7 (2023), s. 2133-2146
    Number of pages14 s.
    Publication formPrint - P
    Languageeng - English
    CountryUS - United States
    KeywordsAMBER FORCE-FIELD ; NUCLEIC-ACIDS ; CATION-BINDING
    Subject RIVCB - Analytical Chemistry, Separation
    OECD categoryAnalytical chemistry
    R&D ProjectsGA23-05639S GA ČR - Czech Science Foundation (CSF)
    Method of publishingOpen access
    Institutional supportBFU-R - RVO:68081707
    UT WOS000962869500001
    EID SCOPUS85151316708
    DOI10.1021/acs.jcim.2c01438
    AnnotationRNA molecules play a key role in countless biochemical processes. RNA interactions, which are of highly diverse nature, are determined by the fact that RNA is a highly negatively charged polyelectrolyte, which leads to intimate interactions with an ion atmosphere. Although RNA molecules are formally single-stranded, canonical (Watson-Crick) duplexes are key components of folded RNAs. A double-stranded (ds) RNA is also important for the design of RNA-based nanostructures and assemblies. Despite the fact that the description of canonical dsRNA is considered the least problematic part of RNA modeling, the imperfect shape and flexibility of dsRNA can lead to imbalances in the simulations of larger RNAs and RNA-containing assemblies. We present a comprehensive set of molecular dynamics (MD) simulations of four canonical A-RNA duplexes. Our focus was directed toward the characterization of the influence of varying ion concentrations and of the size of the solvation box. We compared several water models and four RNA force fields. The simulations showed that the A-RNA shape was most sensitive to the RNA force field, with some force fields leading to a reduced inclination of the A-RNA duplexes. The ions and water models played a minor role. The effect of the box size was negligible, and even boxes with a small fraction of the bulk solvent outside the RNA hydration sphere were sufficient for the simulation of the dsRNA.
    WorkplaceInstitute of Biophysics
    ContactJana Poláková, polakova@ibp.cz, Tel.: 541 517 244
    Year of Publishing2024
    Electronic addresshttps://pubs.acs.org/doi/10.1021/acs.jcim.2c01438
Number of the records: 1  

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