Aptamer sequences as potentional formers of G-quadruplex

Aptamer sequences as potentional formers of G-quadruplex

Abstract

Aptamers are short DNA or RNA sequences that fold into unique three-dimensional structures, allowing them to bind target molecules with high specificity and affinity, similar to antibodies. A notable structural motif in many aptamers is the G-quadruplex (G4), a four-stranded fold formed by guanine-rich sequences. While G4 formation has been proposed for select aptamers, we investigated how frequently G4-prone motifs emerge through the SELEX process. We analyzed over 1,400 sequences from the UTexas Aptamer Database, sourced from 400 publications, to assess their potential to form G4 and i-motif structures. No strong i-motif candidates were identified, but nearly one-quarter of DNA aptamers and one-sixth of RNA aptamers showed potential for G4 formation. Interestingly, many of these G4-capable motifs were previously unrecognized; only 17% of sequences with predicted stable G4s mentioned "quadruplex" in the corresponding publications. We experimentally tested 30 aptamers and confirmed G4 formation in all sequences with a G4Hunter score of 1.31 or higher. These results indicate that G4 motifs may be an underappreciated structural feature in aptamer design. Greater awareness and analysis of G4-forming potential could enhance aptamer discovery and functional interpretation.

Aptamers are short DNA or RNA sequences that fold into unique three-dimensional structures, allowing them to bind target molecules with high specificity and affinity, similar to antibodies. A notable structural motif in many aptamers is the G-quadruplex (G4), a four-stranded fold formed by guanine-rich sequences. While G4 formation has been proposed for select aptamers, we investigated how frequently G4-prone motifs emerge through the SELEX process. We analyzed over 1,400 sequences from the UTexas Aptamer Database, sourced from 400 publications, to assess their potential to form G4 and i-motif structures. No strong i-motif candidates were identified, but nearly one-quarter of DNA aptamers and one-sixth of RNA aptamers showed potential for G4 formation. Interestingly, many of these G4-capable motifs were previously unrecognized; only 17% of sequences with predicted stable G4s mentioned "quadruplex" in the corresponding publications. We experimentally tested 30 aptamers and confirmed G4 formation in all sequences with a G4Hunter score of 1.31 or higher. These results indicate that G4 motifs may be an underappreciated structural feature in aptamer design. Greater awareness and analysis of G4-forming potential could enhance aptamer discovery and functional interpretation.

aptamers, G-quadruplex, DNA secondary structures, Bioinformatics, CD spectroscopy, FRET-MC

aptamers, G-quadruplex, DNA secondary structures, Bioinformatics, CD spectroscopy, FRET-MC

DOBROVOLNÁ, M.; CUCCHIARINI, A.; BRÁZDA, V.; MERGNY, J.-L.

01.09.2025

1336-7242

ChemZi – Chemické Zvesti

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http://hdl.handle.net/