An asymmetric mesoscopic model for single bulges in RNA

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dc.creatorErik de Oliveira Martins
dc.creatorGerald Weber
dc.date.accessioned2024-02-29T17:11:08Z
dc.date.accessioned2025-09-09T00:46:45Z
dc.date.available2024-02-29T17:11:08Z
dc.date.issued2017
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/10.1063/1.5006948
dc.identifier.issn1089-7690
dc.identifier.urihttps://hdl.handle.net/1843/64979
dc.languageeng
dc.publisherUniversidade Federal de Minas Gerais
dc.relation.ispartofThe Journal of Chemical Physics
dc.rightsAcesso Restrito
dc.subjectÁcido ribonucleico
dc.subject.otherAsymmetric mesoscopic model
dc.subject.otherPeyrard-Bishop
dc.subject.otherRNA
dc.titleAn asymmetric mesoscopic model for single bulges in RNA
dc.typeArtigo de periódico
local.citation.epage155102-8
local.citation.issue15
local.citation.spage155102-1
local.citation.volume147
local.description.resumoSimple one-dimensional DNA or RNA mesoscopic models are of interest for their computational efficiency while retaining the key elements of the molecular interactions. However, they only deal with perfectly formed DNA or RNA double helices and consider the intra-strand interactions to be the same on both strands. This makes it difficult to describe highly asymmetric structures such as bulges and loops and, for instance, prevents the application of mesoscopic models to determine RNA secondary structures. Here we derived the conditions for the Peyrard-Bishop mesoscopic model to overcome these limitations and applied it to the calculation of single bulges, the smallest and simplest of these asymmetric structures. We found that these theoretical conditions can indeed be applied to any situation where stacking asymmetry needs to be considered. The full set of parameters for group I RNA bulges was determined from experimental melting temperatures using an optimization procedure, and we also calculated average opening profiles for several RNA sequences. We found that guanosine bulges show the strongest perturbation on their neighboring base pairs, considerably reducing the on-site interactions of their neighboring base pairs.
local.identifier.orcidhttps://orcid.org/0000-0002-4480-6298
local.identifier.orcidhttps://orcid.org/0000-0002-2935-1571
local.publisher.countryBrasil
local.publisher.departmentICX - DEPARTAMENTO DE FÍSICA
local.publisher.initialsUFMG
local.url.externahttps://pubs.aip.org/aip/jcp/article/147/15/155102/196704/An-asymmetric-mesoscopic-model-for-single-bulges

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