Mesoscopic modelling of Cy3 and Cy5 dyes attached to DNA duplexes

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dc.creatorPâmella Miranda de Moura
dc.creatorLuciana Márcia de Oliveira
dc.creatorGerald Weber
dc.date.accessioned2024-02-21T17:17:27Z
dc.date.accessioned2025-09-08T22:59:49Z
dc.date.available2024-02-21T17:17:27Z
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/10.1016/j.bpc.2017.08.007
dc.identifier.issn1873-4200
dc.identifier.urihttps://hdl.handle.net/1843/64414
dc.languageeng
dc.publisherUniversidade Federal de Minas Gerais
dc.relation.ispartofBiophysical Chemistry
dc.rightsAcesso Restrito
dc.subjectBiofísica
dc.subjectDNA
dc.subjectHidrogênio
dc.subject.otherCyanine dyes
dc.subject.otherPeyrard-Bishop DNA models
dc.subject.otherDNA
dc.subject.otherHydrogen bonds
dc.subject.otherStacking interactions
dc.titleMesoscopic modelling of Cy3 and Cy5 dyes attached to DNA duplexes
dc.typeArtigo de periódico
local.citation.epage67
local.citation.spage62
local.citation.volume230
local.description.resumoCy3 and Cy5 dyes linked to the 5′ end of a double stranded DNA molecule are known to attach to both strands in a way that is very similar to an additional base pair and has a stabilizing effect on the oligonucleotide. Here we adapt the Peyrard-Bishop mesoscopic model to incorporate cyanine dyes and use the technique of thermal equivalence to obtain the appropriate parameters from existing melting temperatures. We have found that the stacking parameters are in the same range of ordinary AT and CG base pairs, in particular Cy3-A was found to be most rigidly stacked. While the cyanines stabilize the AT hydrogen bonds quite strongly the CG bonds are mostly unaffected.
local.identifier.orcidhttps://orcid.org/0000-0001-8876-1864
local.identifier.orcidhttps://orcid.org/0000-0002-0300-5232
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/S0301462217302831?via%3Dihub

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