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

[Image: see text] 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.