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The Effect of 2'F-RNA on I-Motif Structure and Stability
Cristina Ugedo1, Arnau Domínguez2, Irene Gómez-Pinto1
1Instituto de Química Física Blas Cabrera (IQF), CSIC, Serrano 119, 28006 Madrid, Spain.
Molecules (Basel, Switzerland)
|September 13, 2025
Summary
Incorporating 2'-fluoro-ribocytidine into DNA i-motifs can destabilize or stabilize the structure depending on the substitution level. Partial substitution supports stable i-motif formation at acidic pH, with fluorine acting as a useful spectroscopic probe.
Area of Science:
- Nucleic Acid Chemistry
- Structural Biology
- Biophysical Chemistry
Background:
- I-motifs are pH-dependent DNA structures stabilized by C•C+ base pairs.
- Chemical modifications can alter i-motif stability, but sugar modifications often disrupt structure.
Purpose of the Study:
- To investigate the structural and thermodynamic effects of 2 -fluoro-ribocytidine (2 F-riboC) incorporation into i-motif-forming DNA sequences.
- To explore the utility of 2 F-riboC as a spectroscopic probe for i-motif dynamics.
Main Methods:
- UV spectroscopy
- Proton Nuclear Magnetic Resonance (1H NMR) spectroscopy
- Fluorine-19 Nuclear Magnetic Resonance (19F NMR) spectroscopy
- High-resolution NMR structure determination
Main Results:
- Full substitution with 2 F-riboC destabilized i-motifs.
- Partial substitutions (1-2 per strand) yielded stable i-motif structures at acidic pH (pH 5).
- NMR structures showed well-defined i-motifs with conserved C•C+ pairing and characteristic NOEs.
- Cytosine sugars adopted a North pucker, directing fluorine to the minor groove.
- 19F NMR confirmed slow exchange between folded and unfolded states, enabling simultaneous detection.
Conclusions:
- 2 F-riboC incorporation modulates i-motif stability in a substitution-dependent manner.
- Partial 2 F-riboC substitution supports i-motif formation at acidic pH.
- Fluorine at the 2 sugar position serves as an effective spectroscopic probe for nucleic acid studies, particularly for i-motif dynamics.
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