Date of Award

7-3-1989

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Chemistry

Abstract

Phosphate-modified oligodeoxyribonucleotide analogs have been extensively investigated for the sequence hybridization arrest of mRNA translation and as biochemical probes of nucleic acid-protein interaction. The goal of our research was to synthesize a new class of nonionic oligodeoxyribonucleotides which structurally closely resembled natural DNA.Our initial research concentrated on the synthesis of bis(deoxythymidine) difluoromethylphosphonate, a dinucleotide analog of 5$\sp\prime$-deoxythymidyl-3$\sp\prime$-deoxythymidine in which a CF$\sb2$H group replaces a phosphate OH. The difluoromethyl group is isosteric and isopolar to an oxygen atom. We chose to model our approach after a scheme devised for conventional phosphodiester synthesis via the protected hydroxybenzotriazole of phosphonic acid. The difluoromethylphosphonate group was introduced as a 3$\sp\prime$-5$\sp\prime$ linkage between deoxythymidines by the sequential reaction of difluoromethyl-O,O-bis(1-benzotriazolyl) phosphonate with 5$\sp\prime$-O-4,4$\sp\prime$-dimethoxytrityldeoxythymidine and 3$\sp\prime$-O-levulinyldeoxythymidine. Two diastereomers differing in configuration at phosphorus were formed, but could be separated by column chromatography.There are substantial differences in the $\sp{19}$F NMR spectra of the two diastereomers. The $\sp{19}$F signals of the two diastereomers are strongly solvent and temperature dependent. A $\sp{19}$F temperature dependent NMR experiment was performed in order to understand the conformation of the two diastereomers in different media. Results from the experiment illustrated that the two fluorine atoms resided in chemically distinct environments, which suggested that this might be a significant and useful parameter in structure and binding studies. The absolute configurations of the two diastereomers were determined by an NOESY experiment.The synthesis of bis(deoxyadenosine) difluoromethylphosphonate was also attempted. Unfortunately, the difluoromethylphosphonate was unstable under the conditions required to remove the N$\sp6$-amino protecting group.The incorporation of the difluoromethylphosphonate linkage into an oligodeoxyribonucleotide via the phosphite triester method was also investigated. Preliminary studies showed that the difluoromethylphosphonate linkage was unstable under the conditions required to synthesize the phosphoramidite. Further work is needed to fully understand this observation.

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