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Please use this identifier to cite or link to this item: http://hdl.handle.net/1843/65617
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dc.creatorTauanne Dias Amarantept_BR
dc.creatorGerald Weberpt_BR
dc.date.accessioned2024-03-11T11:58:19Z-
dc.date.available2024-03-11T11:58:19Z-
dc.date.issued2016-
dc.citation.volume56pt_BR
dc.citation.issue1pt_BR
dc.citation.spage101pt_BR
dc.citation.epage109pt_BR
dc.identifier.doihttps://doi.org/10.1021/acs.jcim.5b00571pt_BR
dc.identifier.issn1549-960xpt_BR
dc.identifier.urihttp://hdl.handle.net/1843/65617-
dc.description.resumoGuanine−Uracil (GU) mismatches are crucial to the stability of the RNA double helix and need to be considered in RNA folding algorithms for numerous biotechnological applications. Yet despite its importance, many aspects of GU base pairs are still poorly understood. There is also a lack of parametrization which prevents it to be considered in mesoscopic models. Here, we adapted the mesoscopic Peyrard–Bishop model to deal with context-dependent hydrogen bonds of GU mismatches and calculated the model parameters related to hydrogen bonding and base stacking from available experimental melting temperatures. The context-dependence causes a proliferation of parameters which made the problem computationally very demanding. We were able to overcome this problem by systematically regrouping the parameters during the minimization procedure. Our results not only provide the much needed parametrization but also answer several questions about the general properties of GU base pairs, as they can be associated straightforwardly to hydrogen bonding and base stacking. In particular, we found a very small Morse potential for tandem 5′-GU-3′, which confirms a single hydrogen bond for this configuration, answering a long-standing question over conflicting experimental findings. Terminal GU base pairs are known to increase the duplex stability, but it is not clear why. Our results suggest that the increased terminal stability is mostly due to stronger hydrogen bonding.pt_BR
dc.description.sponsorshipCNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológicopt_BR
dc.description.sponsorshipFAPEMIG - Fundação de Amparo à Pesquisa do Estado de Minas Geraispt_BR
dc.description.sponsorshipCAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superiorpt_BR
dc.languageengpt_BR
dc.publisherUniversidade Federal de Minas Geraispt_BR
dc.publisher.countryBrasilpt_BR
dc.publisher.departmentICX - DEPARTAMENTO DE FÍSICApt_BR
dc.publisher.initialsUFMGpt_BR
dc.relation.ispartofJournal of Chemical Information and Modeling-
dc.rightsAcesso Restritopt_BR
dc.subjectEstabilidade térmica de RNApt_BR
dc.subjectModelos Peyrard-Bishoppt_BR
dc.subject.otherÁcido ribonucleicopt_BR
dc.titleEvaluating hydrogen bonds and base stacking of single, tandem and terminal GU mismatches in RNA with a mesoscopic modelpt_BR
dc.typeArtigo de Periódicopt_BR
dc.url.externahttps://pubs.acs.org/doi/10.1021/acs.jcim.5b00571pt_BR
dc.identifier.orcidhttps://orcid.org/0000-0002-1999-9753pt_BR
dc.identifier.orcidhttp://orcid.org/0000-0002-2935-1571pt_BR
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