Melting temperature measurement and mesoscopic evaluation of single, double and triple DNA mismatches

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dc.creatorLuciana Márcia de Oliveira
dc.creatorAdam S. Long
dc.creatorTom Brown
dc.creatorKeith R. Fox
dc.creatorGerald Weber
dc.date.accessioned2025-02-25T18:19:12Z
dc.date.accessioned2025-09-09T00:04:59Z
dc.date.available2025-02-25T18:19:12Z
dc.date.issued2020
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.format.mimetypepdf
dc.identifier.doihttps://doi.org/10.1039/D0SC01700K
dc.identifier.issn2041-6539
dc.identifier.urihttps://hdl.handle.net/1843/80433
dc.languageeng
dc.publisherUniversidade Federal de Minas Gerais
dc.relation.ispartofChemical Science
dc.rightsAcesso Aberto
dc.subjectDNA
dc.subjectMedição de temperatura
dc.subject.otherDNA
dc.subject.otherMelting temperature measurement
dc.subject.otherMesoscopic evaluation
dc.titleMelting temperature measurement and mesoscopic evaluation of single, double and triple DNA mismatches
dc.typeArtigo de periódico
local.citation.epage8287
local.citation.issue31
local.citation.spage8273
local.citation.volume11
local.description.resumoUnlike the canonical base pairs AT and GC, the molecular properties of mismatches such as hydrogen bonding and stacking interactions are strongly dependent on the identity of the neighbouring base pairs. As a result, due to the sheer number of possible combinations of mismatches and flanking base pairs, only a fraction of these have been studied in varying experiments or theoretical models. Here, we report on the melting temperature measurement and mesoscopic analysis of contiguous DNA mismatches in nearest-neighbours and next-nearest neighbour contexts. A total of 4032 different mismatch combinations, including single, double and triple mismatches were covered. These were compared with 64 sequences containing all combinations of canonical base pairs in the same location under the same conditions. For a substantial number of single mismatch configurations, 15%, the measured melting temperatures were higher than the least stable AT base pair. The mesoscopic calculation, using the Peyrard–Bishop model, was performed on the set of 4096 sequences, and resulted in estimates of on- site and nearest-neighbour interactions that can be correlated to hydrogen bonding and base stacking. Our results confirm many of the known properties of mismatches, including the peculiar sheared stacking of tandem GA mismatches. More intriguingly, it also reveals that a number of mismatches present strong hydrogen bonding when flanked on both sites by other mismatches. To highlight the applicability of our results, we discuss a number of practical situations such as enzyme binding affinities, thymine DNA glycosylase repair activity, and trinucleotide repeat expansions.
local.identifier.orcidhttps://orcid.org/0000-0002-0300-5232
local.identifier.orcidhttps://orcid.org/0000-0002-7826-4060
local.identifier.orcidhttps://orcid.org/0000-0002-6538-3036
local.identifier.orcidhttps://orcid.org/0000-0002-2925-7315
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.rsc.org/en/content/articlelanding/2020/SC/D0SC01700K

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