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 N4-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. 19F 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.

3 ,5 -O-Bis(tert-butyldimethylsilyl)-8-fluoro-N-2-isobutyryl-2 -deoxyguanosine was synthesized from 3 ,5 -O-bis(tert-butyldimethylsilyl)-N-2-isobutyryl-2 -deoxyguanosine by the treatment with N-fluorobenzenesulfonimide. A similar fluorination reaction with 3 ,5 -O-bis(tert-butyldimethylsilyl)-N-2-(N,N-dimethylformamidine)-2 -deoxyguanosine, however, failed to give the corresponding fluorinated product. It was found that 8-fluoro-N-2-isobutyryl-2 -deoxyguanosine is labile under acidic conditions, but sufficiently stable in dichloroacetic acid used in solid phase synthesis. Incorporation of 8-fluoro-N-2-isobutyryl-2 -deoxyguanosine into oligonucleotides through the phosphoramidite chemistry-based solid phase synthesis failed to give the desired products. Furthermore, treatment of 8-fluoro-N-2-isobutyryl-2 -deoxyguanosine with aqueous ammonium hydroxide did not give 8-fluoro-2 -deoxyguanosine, but led to the formation of a mixture consisting of 8-amino-N-2-isobutyryl-2 -deoxyguanosine and C8:5 -O-cyclo-2 -deoxyguanosine. Taken together, an alternative N-protecting group and possibly modified solid phase synthetic cycle conditions will be required for the incorporation of 8-fluoro-2 -deoxyguanosine into oligonucleotides through the phosphoramidite chemistry-based solid phase synthesis.