Download MendeleyThe Effect of 2'F-RNA on I-Motif Structure and Stability.
Ugedo, C., Dominguez, A., Gomez-Pinto, I., Eritja, R., Gonzalez, C., Avino, A.(2025) Molecules 30
- PubMed: 40942089 Search on PubMedSearch on PubMed Central
- DOI: https://doi.org/10.3390/molecules30173561
- Primary Citation Related Structures:
9S6I, 9S6Z - PubMed 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, 1 H NMR, and 19 F 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. 19 F 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 19 F NMR in nucleic acid research.
- Instituto de Química Física Blas Cabrera (IQF), CSIC, Serrano 119, 28006 Madrid, Spain.
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