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The Effect of 2′F-RNA on I-Motif Structure and Stability

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Titel: The Effect of 2′F-RNA on I-Motif Structure and Stability
Autoren: Cristina Ugedo, Arnau Domínguez, Irene Gómez-Pinto, Ramon Eritja, Carlos González, Anna Aviñó
Quelle: Molecules, Vol 30, Iss 17, p 3561 (2025)
Verlagsinformationen: MDPI AG, 2025.
Publikationsjahr: 2025
Bestand: LCC:Organic chemistry
Schlagwörter: i-motif, NMR, non-canonical nucleic acids, XNA, fluorine substitution, Organic chemistry, QD241-441
Beschreibung: I-motifs are non-canonical, cytosine-rich DNA structures stabilized by hemiprotonated C•C+ base pairs, whose formation is highly pH-dependent. While certain chemical modifications can enhance i-motif stability, modifications at the sugar moiety often disrupt essential inter-strand contacts. In this study, we examine the structural and thermodynamic impact of incorporating 2′-fluoro-ribocytidine (2′F-riboC) into i-motif-forming sequences derived from d(TCCCCC). Using a combination of UV, 1H NMR, and 19F NMR spectroscopy, we demonstrate that full substitution with 2′F-riboC strongly destabilizes i-motif, whereas partial substitutions (one or two substitutions per strand) support well-folded structures at acidic pH (pH 5). High-resolution NMR structures reveal well-defined i-motif architectures with conserved C•C+ pairing and characteristic interstrand NOEs. Sugar conformational analysis reveals a predominant North pucker for cytosines, which directs the fluorine substituent toward the minor groove of the i-motif. 19F NMR further confirms slow exchange between folded and unfolded species, enabling the simultaneous detection of both under identical experimental conditions and, consequently, highlighting the utility of fluorine at the 2′ sugar position as a spectroscopic probe. These findings provide insights into fluorine-mediated modulation of i-motif stability and further extend the utility of 19F NMR in nucleic acid research.
Publikationsart: article
Dateibeschreibung: electronic resource
Sprache: English
ISSN: 1420-3049
Relation: https://www.mdpi.com/1420-3049/30/17/3561; https://doaj.org/toc/1420-3049
DOI: 10.3390/molecules30173561
Zugangs-URL: https://doaj.org/article/b1036bd1512e4b4a80db0ea8054df92c
Dokumentencode: edsdoj.b1036bd1512e4b4a80db0ea8054df92c
Datenbank: Directory of Open Access Journals
Beschreibung
Abstract:I-motifs are non-canonical, cytosine-rich DNA structures stabilized by hemiprotonated C•C+ base pairs, whose formation is highly pH-dependent. While certain chemical modifications can enhance i-motif stability, modifications at the sugar moiety often disrupt essential inter-strand contacts. In this study, we examine the structural and thermodynamic impact of incorporating 2′-fluoro-ribocytidine (2′F-riboC) into i-motif-forming sequences derived from d(TCCCCC). Using a combination of UV, 1H NMR, and 19F NMR spectroscopy, we demonstrate that full substitution with 2′F-riboC strongly destabilizes i-motif, whereas partial substitutions (one or two substitutions per strand) support well-folded structures at acidic pH (pH 5). High-resolution NMR structures reveal well-defined i-motif architectures with conserved C•C+ pairing and characteristic interstrand NOEs. Sugar conformational analysis reveals a predominant North pucker for cytosines, which directs the fluorine substituent toward the minor groove of the i-motif. 19F NMR further confirms slow exchange between folded and unfolded species, enabling the simultaneous detection of both under identical experimental conditions and, consequently, highlighting the utility of fluorine at the 2′ sugar position as a spectroscopic probe. These findings provide insights into fluorine-mediated modulation of i-motif stability and further extend the utility of 19F NMR in nucleic acid research.
ISSN:14203049
DOI:10.3390/molecules30173561