Synthesis of fluorinated nucleosides for probing DNA conformations via 19F NMR spectroscopy
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Work described in this thesis explored the synthesis of 5-fluoro-2’-deoxycytidine and 8-fluoro-2’-deoxyguanosine, and subsequent incorporation of these modified nucleosides into d(CG) repeat oligonucleotides through the phosphoramidite chemistry-based solid phase synthesis, in order to investigate the B-Z junction through 19F NMR spectroscopy. Toward this goal, 5-fluoro-2’-deoxycytidine was successfully synthesized from 5-fluoro-2’-deoxyuridine. Choices of protecting groups for the exocyclic amine of 5-fluoro-2’-deoxycytidine were examined, and N-acetyl was found to be most suitable in terms of the stability of the protected nucleoside and the readiness of its removal. 8-Fluoro-2’-deoxyguanosine was prepared by fluorination of suitably protected 2’-deoxyguanosine using N-fluorobenzenesulfonimide as the fluorinating agent. Circular dichroism and UV/vis spectroscopic studies showed that the fluoro-modification does not affect the overall conformation of the oligonucleotides, both in the B- and Z-form. 19F NMR spectra of single fluoro-modified d(CG)6 sequence at 3’-end (11-FdC) were recorded in solution containing 0.1 – 4 M NaCl. The results supported a theoretical model for B-/Z-DNA transition, where initiation starts from the ends, progressing to eventual transition.