5-Fluoro-2′-deoxycytidine as a Probe for the Study of B/Z-DNA Transition by 19F NMR Spectroscopy

5-Fluoro-2'-deoxycytidine was synthesized by treating 5-fluoro-2'-deoxyuridine with 2,4,6-trimethylphenol in the presence of 1-methylpyrrolidine and trifluoroacetic anhydride, followed by aminolysis. Among N -acetyl, pivaloyl, and benzoyl, N -acetyl was found to be suitable for the protection of the exocyclic amine of 5-fluoro-2'-deoxycytidine because of the stability of the N 4 -protected nucleoside under acidic conditions and its ease of removal after solid-phase synthesis. This modified nucleoside was incorporated into d(CG) 6 sequences through the phosphoramidite chemistry-based solid-phase synthesis. Circular dichroism experiments suggest that replacement of 2'-deoxycytidine with 5-fluoro-2'-deoxycytidine does not lead to detectable conformational changes, either in the B- or Z-form. 19 F NMR spectroscopy of d(CG) 6 containing 5-fluoro-2'-deoxycytidine revealed that B/Z-DNA transition induced by sodium chloride is likely initiated at terminal ends, leading to unwinding at the middle of duplexes, and eventual switch of handedness when sodium chloride concentration reaches a threshold value.