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

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.