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DNA i-motif formation at physiological pH revealed by Raman spectroscopy

dc.contributor.authorPalacký, Jan
dc.contributor.authorŠkoláková, Petra
dc.contributor.authorRenčiuk, Daniel
dc.contributor.authorMojzeš, Peter
dc.contributor.authorRossi, Barbara
dc.contributor.authorMatroodi, Fatima
dc.contributor.authorVorlíčková, Michaela
dc.date.accessioned2025-03-03T06:12:19Z
dc.date.available2025-03-03T06:12:19Z
dc.date.issued2024
dc.identifier.urihttps://hdl.handle.net/20.500.14178/2919
dc.description.abstractThe intercalated motif (iM) is a four-stranded structure consisting of two parallel homoduplexes formed by hemiprotonated C.C+ pairs and intercalated antiparallel to each other. iM is generally formed at acidic pH, as cytosine protonation is required for its formation. However, sequences with long cytosine tracts can form iM at physiological pH conditions. Here, we use both off-resonant Raman and UV-resonant Raman (using synchrotron radiation) spectroscopy (RS) to study the sequence (C9T3)3C9, which has been recently thoroughly analysed by other spectroscopic methods (CD, 1H NMR). In line with these methods, RS has shown that (C9T3)3C9 adopts iM at neutral pH and the iM forms with slow kinetics, melts in multiple steps and exhibits a large thermal hysteresis between the folding and refolding processes. The presence of isosbestic points in the temperature-dependent Raman spectra (in line with the SVD analysis indicating just two independent spectral components) suggests that the (C9T3)3C9 is found as a mixture of disordered and ordered structures, the proportion of which is temperature dependent. The ordered iM species are believed to be composed of the same type of C.C+ pairs but differing in their number and arrangement along the cytosine tracts. The related sequence (C9A3)3C9 shows the same behaviour as (C9T3)3C9, indicating that the substitution of adenine bases for thymine bases has little effect. We apply off-resonant and UV-resonant Raman spectroscopies to study i-motif (iM) formation of the model C rich sequence (C9T3)3C9 at neutral pH. We show that different iM species with different thermal stability and different time kinetics are formed depending on the temperature. SVD analysis demonstrates that the studied sequence adopts (at each time and temperature) a variable proportion of disordered and perfectly ordered iM forms.imageen
dc.language.isoen
dc.relation.urlhttps://doi.org/10.1002/jrs.6606
dc.rightsCreative Commons Uveďte původ-Neužívejte dílo komerčně-Nezpracovávejte 4.0 Internationalcs
dc.rightsCreative Commons Attribution-NonCommercial-NoDerivativeWorks 4.0 Internationalen
dc.titleDNA i-motif formation at physiological pH revealed by Raman spectroscopyen
dcterms.accessRightsopenAccess
dcterms.licensehttps://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
dc.date.updated2025-03-03T06:12:19Z
dc.subject.keywordcytosine i-motif DNAen
dc.subject.keywordpHen
dc.subject.keywordRaman spectroscopyen
dc.subject.keywordsingular value decompositionen
dc.subject.keywordUV-resonant Ramanen
dc.identifier.eissn1097-4555
dc.relation.fundingReferenceinfo:eu-repo/grantAgreement/UK/COOP/COOP
dc.date.embargoStartDate2025-03-03
dc.type.obd73
dc.type.versioninfo:eu-repo/semantics/publishedVersion
dc.identifier.doi10.1002/jrs.6606
dc.identifier.utWos001088024900001
dc.identifier.eidScopus2-s2.0-85174602671
dc.identifier.obd642012
dc.subject.rivPrimary10000::10300::10301
dcterms.isPartOf.nameJournal of Raman Spectroscopy
dcterms.isPartOf.issn0377-0486
dcterms.isPartOf.journalYear2024
dcterms.isPartOf.journalVolume55
dcterms.isPartOf.journalIssue1
uk.faculty.primaryId116
uk.faculty.primaryNameMatematicko-fyzikální fakultacs
uk.faculty.primaryNameFaculty of Mathematics and Physicsen
uk.department.primaryId1191
uk.department.primaryNameFyzikální ústav UKcs
uk.department.primaryNameInstitute of Physics of Charles Universityen
dc.description.pageRange43-57
dc.type.obdHierarchyCsČLÁNEK V ČASOPISU::článek v časopisu::původní článekcs
dc.type.obdHierarchyEnJOURNAL ARTICLE::journal article::original articleen
dc.type.obdHierarchyCode73::152::206en
uk.displayTitleDNA i-motif formation at physiological pH revealed by Raman spectroscopyen


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