Date of Graduation

Summer 2014

Degree

Master of Science in Chemistry

Department

Chemistry and Biochemistry

Committee Chair

Gary Meints

Abstract

Base excision repair is thought to be the most commonly employed DNA repair mechanism. How DNA repair proteins detect DNA damage is not well understood, but a dynamic component (i.e. motion, flexibility) has been suggested. It was hypothesized that since many DNA damages disrupt stabilizing forces of the helix, greater dynamics would be observed at the damaged base. The damaged base chosen for this research was 1,N6-ethenodeoxyadenosine (εdA). Since the εdA lesion is not capable of hydrogen bonding with its base pairing partner, high angle, fast local motion was expected to be observed. To test this hypothesis, εdA with a deuterium label at the C2 position on the base was synthesized, incorporated into a well-known DNA sequence (the Dickerson dodecamer), and analyzed using solid-state NMR to provide information about the local flexibility and motion of the labeled site. When comparing simulated solid-state NMR spectra to the experimental spectra, it was found that the label on εdA experienced low angle, fast local motion. Earlier results from the Meints research group showed that the C3'-2H3' bond on the sugar ring of a thymidine paired with εdA experienced a significant increase in dynamics. If DNA repair proteins use the dynamics of the DNA helix to detect damage before base excision repair, this research indicates that the repair proteins detect dynamics of the undamaged base pairing partner nucleotide.

Keywords

solid-state nuclear magnetic resonance, base excision repair, ethenodeoxyadenosine, deoxyribonucleic acid, deuterium, oligonucleotide synthesis

Subject Categories

Chemistry

Copyright

© Aaron Daniel Proctor

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