Date of Award

Spring 1-1-2018

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

First Advisor

Marvin H. Caruthers

Second Advisor

Robert Kuchta

Third Advisor

Natalie Ahn

Fourth Advisor

David Walba

Fifth Advisor

Doug Dellinger

Abstract

Antisense oligonucleotides are synthetic DNAs that bind to RNA and alter or reduce the biological activity of the target RNA. Studies performed in recent years have demonstrated that an antisense strategy can be utilized to address various issues in fundamental biomedical research and have additionally shown that this approach can be used to create novel therapeutic drugs. For example, IONIS Pharmaceuticals has so far commercialized three drugs using antisense oligonucleotides. These drugs target spinal muscular atrophy, homozygous familial hypercholesterolemia, and pouchitis. Antisense oligonucleotides targeting several other diseases are in various stages of clinical study at IONIS and elsewhere.

My research focuses on synthesizing a new DNA analogue called phosphoramidimidate DNA that has nitrogen joined covalently to phosphorus at both nonlinking internucleotide positions. The analogue was prepared using phosphoramidite chemistry that has been modified to facilitate the synthesis. The resulting phosphoramidimidate DNA is positively charged, nuclease resistant, forms duplexes with complementary, unmodified oligonucleotides and is stable to neutral and basic conditions. Most importantly, this new analogue is RNase H1 active and can be transfected into cells in culture where it is located in the cytoplasm. These attributes are essential for any analogue that has antisense activity. Additionally, a very unique attribute of this analogue is that the phosphoramidimidate linkage is tolerated in the RNase H1 cleavage domain. Moreover, phosphoramidimidate antisense oligonucleotides are expected to be more stable toward cellular nucleases and consequently have significantly longer half-lives when used as therapeutic drugs.

The synthesis of phosphoramidate DNA using a similar chemistry generates this analogue by a new methodology that is far superior to previously developed chemistries. This analogue is also efficiently transfected, via passive transfection, into the cytoplasm of HeLa cells.

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