Date of Award

7-1-1991

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Chemistry

Abstract

Oligonucleotides based on methyl phosphonate linkages between nucleoside units have been of particular interest as anti-sense molecules for inhibiting mRNA function. The focus of our research has been on the development of new construction techniques for anti-sense oligonucleotides. Specifically we have been investigating new methods for generating iron and cobalt-modified linkages in oligonucleotides during the course of automated synthesis.We have found that (dicarbonyl)($\eta\sp5$-cyclopentadienyl)($\eta\sp2$-ethylene)iron reacts with 5$\sp\prime$-O-dimethoxytritylnucleoside 3$\sp\prime$-phosphite esters to yield (dicarbonyl)($\eta\sp5$-cyclopentadienyl)iron(ethyl)phosphonates. These phosphonates appear to be stable to the conditions commonly used to construct oligonucleotides by phosphoramidite methodology. This chemistry has been extended to the formation of a dimer on the automated DNA synthesizer. This reaction could not be extended to the modification of nucleoside derived H-phosphonates, due to the reactivity of dicarbonyl($\eta\sp5$-cyclopentadienyl)($\eta\sp2$-ethylene)iron towards pyridine, which is required in the H-phosphonate coupling reaction.We have shown that $\eta\sp5$-cyclopentadienyl(1,2-dicyano-1,2-dithiolato)cobaltphosphite trialkyl esters appear to be stable to all conditions commonly used to construct oligonucleotides by phosphoramidite methodology, except the detritylation conditions. We have also found that $\eta\sp5$-cyclopentadienyl(1,2-dicyano-1,2-dithiolato)cobalt reacts with 5$\sp\prime$-O-dimethoxytritylnucleoside 3$\sp\prime$-phosphite esters to yield a mixture of phosphito and phosphonato complexes.The phosphonato-cobalt complex is formed by an H-phosphonate reaction, due to hydrolysis of the phosphoramidite under the reaction conditions used. All attempts to separate the phosphonato-cobalt complex from the phosphito-cobalt complex led to cleavage of the cobalt-phosphorus bond. The cobalt-phosphorus bond is cleaved under inert conditions over time in the phosphonato-cobalt complexes, therefore an H-phosphonate reaction is not applicable to the $\eta\sp5$-cyclopentadienyl(1,2-dicyano-1,2-dithiolato)cobalt complex. This chemistry was extended to the formation of a dimer on the automated DNA synthesizer, with the idea that it would eliminate the formation of the phosphonato complex. Cleavagte conditions, however, partially deprotected the phosphorus atom yielding a mixture of phosphito- and phosphonato-cobalt complexes.

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