Synthesis and application of a F-labeled fluorescent nucleoside as a dual-mode probe for i-motif DNAs

Because of their stable orientations and their minimal interference with native DNA interactions and folding, emissive isomorphic nucleoside analogues are versatile tools for the accurate analysis of DNA structural heterogeneity. Here, we report on a bifunctional trifluoromethylphenylpyrrolocytidine derivative ( FP dC ) that displays an unprecedented quantum yield and highly sensitive 19 F NMR signal. This is the first report of a cytosine-based dual-purpose probe for both fluorescence and 19 F NMR spectroscopic DNA analysis. FP dC and FP dC -containing DNA were synthesized and characterized; our robust dual probe was successfully used to investigate the noncanonical DNA structure, i-motifs, through changes in fluorescence intensity and 19 F chemical shift in response to i-motif formation. The utility of FP dC was exemplified through reversible fluorescence switching of an FP dC -containing i-motif oligonucleotide in the presence of Ag( i ) and cysteine. We report on the first bifunctional cytidine-based probe (FPdC) that displays high quantum yield and sensitive 19 F NMR signal. FPdC was used to investigate a noncanonical DNA structure, and displayed significant response to i-motif formation.