Nearest-neighbour parameters optimized for melting temperature prediction of DNA/RNA hybrids at high and low salt concentrations

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dc.creatorVivianne Basilio Barbosa
dc.creatorErik de Oliveira Martins
dc.creatorGerald Weber
dc.date.accessioned2024-03-11T12:51:21Z
dc.date.accessioned2025-09-08T23:35:00Z
dc.date.available2024-03-11T12:51:21Z
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.bpc.2019.106189
dc.identifier.issn1873-4200
dc.identifier.urihttps://hdl.handle.net/1843/65618
dc.languageeng
dc.publisherUniversidade Federal de Minas Gerais
dc.relation.ispartofBiophysical Chemistry
dc.rightsAcesso Restrito
dc.subjectDNA
dc.subjectÁcido ribonucleico
dc.subject.otherDNA
dc.subject.otherDNA/RNA hybrid
dc.subject.otherRNA stability
dc.subject.otherLow sodium nearest-neighbour parameters
dc.titleNearest-neighbour parameters optimized for melting temperature prediction of DNA/RNA hybrids at high and low salt concentrations
dc.typeArtigo de periódico
local.citation.epage5
local.citation.spage1
local.citation.volume251
local.description.resumoGene editing technologies sparked a renewed interest in the hybridization of DNA/RNA duplexes, yet little improvement on nearest-neighbour parameters was made over the past two decades. For low sodium concentration no parameter set was yet calculated. Here, we revised the existing experimental datasets and used an expanded set of sequences from which we recalculated the nearest-neighbour parameters, reducing the average temperature prediction uncertainty to 1.6 °C. Two experimental sets using temperatures extracted via different methods were used with similar results, with the curve-fitting method achieving a slight advantage in prediction quality over other methods. Additionally, we obtained new parameters for low salt with an average uncertainty of 0.98 °C. We also tested several types of salt correction factors and concluded that it is advisable to use those originally developed for RNA/RNA rather than for DNA/DNA.
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://www.sciencedirect.com/science/article/pii/S0301462219301814?via%3Dihub

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