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Enhanced i-Motif Stability through Consecutive 2',2'-Difluorocytidine Incorporation.

Arnau Domínguez^1,2,3, Cristina Cabrero⁴, Irene Gómez-Pinto⁴

¹Department of Surfactants and Nanobiotechnology, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, Barcelona, 08034, Spain.

Chemistry (Weinheim an Der Bergstrasse, Germany)

|November 19, 2025

Summary

This summary is machine-generated.

Gemcitabine (dFdC) modifications enhance the stability of DNA i-motif structures, particularly when multiple consecutive residues are incorporated. These findings suggest dFdC can be used to engineer more robust i-motifs for biotechnology and therapeutics.

Keywords:

I‐motif NMR Structure fluorine modifications gemcitabine thermal stability

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Published on: July 26, 2018

Area of Science:

Biochemistry
Molecular Biology
Chemical Biology

Background:

Chemical modifications of nucleic acids are crucial for tuning stability and function in therapeutics and nanotechnology.
Fluorinated cytidine derivatives like 2'-fluoro-arabinocytidine (2'F-araC) and 2'-fluoro-ribocytidine (2'F-riboC) differentially affect i-motif stability.

Purpose of the Study:

To investigate the impact of gemcitabine (2'-deoxy-2',2'-difluorocytidine, dFdC) on the stability of DNA i-motif structures.
To understand the structural basis for dFdC's effect on i-motif folding.

Main Methods:

Synthesis and characterization of nucleic acid sequences containing dFdC modifications.
Thermal and pH-dependent analyses (e.g., UV-Vis spectroscopy, differential scanning calorimetry) to assess i-motif stability.
Structural analysis to elucidate the molecular mechanisms of stabilization.

Main Results:

Single or double dFdC substitutions show minor effects on i-motif stability.
Multiple consecutive dFdC substitutions lead to pronounced stabilization of i-motif structures.
Sequences with fully substituted dFdC maintain i-motif folding at neutral pH and exhibit enhanced thermal stability.
Structural factors including hyperconjugative interactions, hydrogen bonding, and adaptable sugar conformation contribute to stabilization.

Conclusions:

Gemcitabine (dFdC) uniquely enhances i-motif robustness through strategic difluoro substitutions.
The adaptable sugar conformation of dFdC mitigates destabilizing interactions seen with other modifications.
Exploiting dFdC modifications can lead to the design of more stable i-motifs for biotechnological and therapeutic applications.