Date of Award

12-2014

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Chemical and Biomolecular Engineering

Committee Member

Dr. Weiguo Cao, Committee Chair

Committee Member

Dr. Abbott Bert

Committee Member

Dr. Brian Dominy

Committee Member

Dr. Liangjiang Wang

Abstract

DNA can be damaged by several kinds of endogenous and exogenous reactive nitrogen species. Under nitosative stress, uracil (U), hypoxanthine (I), xanthine (X) and oxanine (O) are four major deaminated DNA bases derived from cytosine (C), adenine (A) and guanine (G) respectively. To repair this type of DNA damage, several different repair pathways are involved.

My dissertation work mainly focused on the uracil-DNA glycosylase (UDG) superfamily, which includes several groups of enzymes that recognize the damaged DNA bases and initiate the base excision repair (BER) pathway, one of the most important repair pathways to deal with deaminated DNA bases. Chapter 1 is a general introduction of different kinds of DNA damage and their corresponding repair pathways. Chapter 2 presents a detailed functional and structural analysis of family 5 UDGb from Thermus thermophilus HB8 in order to understand the specificity and catalytic mechanism of family 5 UDGb. Chapter 3 describes the biochemical properties and catalytic mechanism of family 4 UDGa from Thermus thermophilus HB8. A special double mutant has been identified with increased enzyme activity compared to single mutants. Chapter 4 is about a potential new group of enzymes within the UDG superfamily. Members from this new group of enzymes showed robust xanthine DNA glycosylase activities with unique catalytic mechanism and protein sequences. In summary, these functional and structural analyses provide new insights into substrate specificity and catalytic mechanism of UDG superfamily.

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