Abstract

Discrimination by DNA polymerases controls the fidelity of DNA replication, and reduced fidelity results in mutations essential in the etiology of cancer. Polymerase discrimination operates at both dNTP insertion and subsequent elongation steps, and involves several energetic and structural factors that are as yet incompletely understood. While base pairing interactions have been studied extensively, substantially less is known about the role of sugar structure and conformation for polymerase incorporation and extension. In these studies we examined, systematically, the role of sugar structure and conformation on polymerase selection of the dNTP for insertion and polymerase elongation. To accomplish these goals, we have developed methods for the synthesis of oligonucleotides with nucleoside analogues with biased sugar conformations at the 3'-end (growing end) as well as at internucleotide positions. Through a series of thermodynamic, structural and functional studies, we reveal how sugar structure and conformational properties impact polymerase incorporation and extension behavior. The analogues proposed for this study allow an examination of structural and conformational properties, but also, this group of analogues comprises an important class of cytotoxic, antitumor and antiviral agents. The results of these studies will likely provide a clearer understanding of the role of sugar conformation in the fidelity of DNA synthesis and replication as well as reveal important insights into the activity and toxicity of several nucleoside analogues and allow prediction of the biological properties of future analogues.

LLU Discipline

Biochemistry

Department

Basic Sciences

School

School of Medicine

First Advisor

Sowers, Lawrence C.

Second Advisor

Buchholz, John

Third Advisor

Duerksen-Hughes, Penelope

Fourth Advisor

Neidigh, Jonathan

Fifth Advisor

Zhang, Kangling

Degree Name

Doctor of Philosophy (PhD)

Degree Level

Ph.D.

Year Degree Awarded

January 2012

Date (Title Page)

3-1-2012

Language

English

Library of Congress/MESH Subject Headings

DNA -- Synthesis; DNA -- Biosynthesis; Glycoproteins; DNA Polymerases;

Subject - Local

Nucleoside Sugar Modification; Biochemical DNA Transactions; DNA Replication; Polymerase Discrimination; DNA Synthesis

Type

Dissertation

Page Count

168 p.

Digital Format

Application/PDF

Digital Publisher

Loma Linda University Libraries

Usage Rights

This title appears here courtesy of the author, who has granted Loma Linda University a limited, non-exclusive right to make this publication available to the public. The author retains all other copyrights.

Collection

Loma Linda University Electronic Theses & Dissertations

Collection Website

http://scholarsrepository.llu.edu/etd/

Repository

Loma Linda University. Del E. Webb Memorial Library. University Archives

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