Replacing salt correction factors with optimized RNA nearest-neighbour enthalpy and entropy parameters

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dc.creatorIzabela Ferreira da Silva
dc.creatorElizabeth A. Jolley
dc.creatorBrent M. Znosko
dc.creatorGerald Weber
dc.date.accessioned2024-02-29T15:23:57Z
dc.date.accessioned2025-09-09T00:14:52Z
dc.date.available2024-02-29T15:23:57Z
dc.date.issued2019
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.chemphys.2019.01.016
dc.identifier.issn1873-4421
dc.identifier.urihttps://hdl.handle.net/1843/64957
dc.languageeng
dc.publisherUniversidade Federal de Minas Gerais
dc.relation.ispartofChemical Physics
dc.rightsAcesso Restrito
dc.subjectÁcido ribonucleico
dc.subject.otherRNA stability
dc.subject.otherNearest-neighbour model
dc.subject.otherMelting temperature calculation
dc.titleReplacing salt correction factors with optimized RNA nearest-neighbour enthalpy and entropy parameters
dc.typeArtigo de periódico
local.citation.epage76
local.citation.spage69
local.citation.volume521
local.description.resumoWe calculate the nearest-neighbour enthalpies and entropies at 5 salt concentrations of 18 RNA sequences, each for at least 9 different species concentrations, totalling 757 melting temperatures, using a melting temperature optimization method. These new parameters do not need to be salt-corrected and are shown to provide overall improved melting temperature predictions. They show a marked quadratic dependence with salt concentrations which are compensated to form linear Gibbs free energies. Two different parameter schemes were tested, with fixed or variable initial parameters. We have found that using variable initial parameters provides better predictive results than using salt correction factors and that the prediction uncertainty is considerably reduced for a validation set of independent sequences. An interpolation scheme is introduced to generate model parameters for arbitrary salt concentrations which performs better against a validation set than predictions using salt corrections.
local.identifier.orcidhttps://orcid.org/0000-0002-6823-6218
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/S0301010418311200?via%3Dihub

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