Analysis of quadruplex propensity of aptamer sequences

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dc.contributor.authorCucchiarini, Annecs
dc.contributor.authorDobrovolná, Michaelacs
dc.contributor.authorBrázda, Václavcs
dc.contributor.authorMergny, Jean-Louiscs
dc.coverage.issue9cs
dc.coverage.volume53cs
dc.date.accessioned2025-07-17T08:59:21Z
dc.date.available2025-07-17T08:59:21Z
dc.date.issued2025-05-26cs
dc.description.abstractAptamers are short DNA or RNA sequences that can fold into unique three-dimensional structures, enabling them to bind specifically to target molecules with high affinity, similar to antibodies. A distinctive feature of many aptamers is their ability to adopt a G-quadruplex (G4) fold, a four-stranded structure formed by guanine-rich sequences. While G4 formation has been proposed or demonstrated for some aptamers, we aimed to investigate how frequently quadruplex-prone motifs emerge from the SELEX process. To achieve this, we examined quadruplex candidate sequences from the UTexas Aptamer Database, which contains over 1400 aptamer sequences extracted from 400 publications spanning several decades. We analyzed the G4 and i-motif propensity of these sequences. While no likely i-motif forming candidates were found, nearly 1/4 of DNA aptamers and 1/6 of RNA aptamers were predicted to form G4 structures. Interestingly, many motifs capable of forming G4 structures were not previously reported or suspected. Out of 311 sequences containing a potential stable G4 motif, only 53 of them (17%) reported the word "quadruplex" in the corresponding article. We experimentally tested G4 formation for 30 aptamer sequences and were able to confirm G4 formation for all the sequences with a G4Hunter score of 1.31 or more. These observations suggest the need to reevaluate G4 propensity among aptamer sequences.en
dc.formattextcs
dc.format.extent1-11cs
dc.format.mimetypeapplication/pdfcs
dc.identifier.citationNucleic Acids Research. 2025, vol. 53, issue 9, p. 1-11.en
dc.identifier.doi10.1093/nar/gkaf424cs
dc.identifier.issn1362-4962cs
dc.identifier.orcid0000-0003-2837-4226cs
dc.identifier.other198003cs
dc.identifier.researcheridF-9582-2011cs
dc.identifier.urihttps://hdl.handle.net/11012/255180
dc.language.isoencs
dc.publisherOXFORD UNIV PRESScs
dc.relation.ispartofNucleic Acids Researchcs
dc.relation.urihttps://pubmed.ncbi.nlm.nih.gov/40377215/cs
dc.rightsCreative Commons Attribution 4.0 Internationalcs
dc.rights.accessopenAccesscs
dc.rights.sherpahttp://www.sherpa.ac.uk/romeo/issn/1362-4962/cs
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/cs
dc.subjectAptameren
dc.subjectG-quadruplexen
dc.titleAnalysis of quadruplex propensity of aptamer sequencesen
dc.type.driverarticleen
dc.type.statusPeer-revieweden
dc.type.versionpublishedVersionen
sync.item.dbidVAV-198003en
sync.item.dbtypeVAVen
sync.item.insts2025.07.17 10:59:21en
sync.item.modts2025.07.17 10:33:57en
thesis.grantorVysoké učení technické v Brně. Fakulta chemická. Ústav chemie potravin a biotechnologiícs
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