Salt dependent mesoscopic model for RNA at multiple strand concentrations

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dc.creatorIzabela Ferreira da Silva
dc.creatorTauanne Dias Amarante
dc.creatorGerald Weber
dc.date.accessioned2023-10-30T17:32:23Z
dc.date.accessioned2025-09-09T00:11:52Z
dc.date.available2023-10-30T17:32:23Z
dc.date.issued2021
dc.description.sponsorshipCNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico
dc.description.sponsorshipFAPEMIG - Fundação de Amparo à Pesquisa do Estado de Minas Gerais
dc.description.sponsorshipCAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
dc.identifier.doihttps://doi.org/10.1016/j.bpc.2021.106551
dc.identifier.issn0301-4622
dc.identifier.urihttps://hdl.handle.net/1843/60252
dc.languageeng
dc.publisherUniversidade Federal de Minas Gerais
dc.relation.ispartofBiophysical Chemistry
dc.rightsAcesso Restrito
dc.subjectBiofísica
dc.subjectÁcido ribonucleico
dc.subject.otherPeyrard-Bishop
dc.subject.otherMesoscopic model
dc.subject.otherRNA
dc.subject.otherStrand concentration
dc.titleSalt dependent mesoscopic model for RNA at multiple strand concentrations
dc.typeArtigo de periódico
local.citation.epage11
local.citation.spage1
local.citation.volume271
local.description.resumoMesoscopic models can be used for the description of the thermodynamic properties of RNA duplexes. With the use of experimental melting temperatures, its parametrization can provide important insights into its hydrogen bonds and stacking interactions as has been done for high sodium concentrations. However, the RNA parametrization for lower salt concentrations is still missing due to the limited amount of published melting temperature data. While the Peyrard-Bishop (PB) parametrization was found to be largely independent of strand concentrations, it requires that all temperatures are provided at the same strand concentrations. Here we adapted the PB model to handle multiple strand concentrations and in this way we were able to make use of an experimental set of temperatures to model the hydrogen bond and stacking interactions at low and intermediate sodium concentrations. For the parametrizations we make a distinction between terminal and internal base pairs, and the resulting potentials were qualitatively similar as we obtained previously for DNA. The main difference from DNA parameters, was the Morse potentials at low sodium concentrations for terminal r(AU) which is stronger than d(AT), suggesting higher hydrogen bond strength.
local.identifier.orcidhttps://orcid.org/0000-0002-1999-9753
local.identifier.orcidhttps://orcid.org/0000-0002-2935-1571
local.publisher.countryBrasil
local.publisher.departmentICX - DEPARTAMENTO DE FÍSICA
local.publisher.initialsUFMG
local.url.externahttps://www.sciencedirect.com/science/article/pii/S0301462221000119

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