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Access Type

WSU Access

Date of Award

January 2017

Degree Type

Dissertation

Degree Name

Ph.D.

Department

Chemistry

First Advisor

Ashok S. Bhagwat

Abstract

Uracils are incorporated into DNA by several mechanisms. They are by dUMP incorporation during DNA replication and by hydrolytic and enzymatic DNA cytosine deamination. AID/APOBEC family of single stranded DNA specific DNA cytosine deaminases has several important functions during the innate and adaptive immune response in mammals. However, recent studies have observed the presence of AID/APOBEC derived mutational signature in multiple human cancers including B cell lymphoma, breast cancer, lung cancer, cervical cancer ect. Some studies have reported an AID/APOBEC dependent increase in genomic uracils in human cancers. Therefore, accurate quantification and mapping of genomic uracils could provide valuable insights about the role of AID/APOBEC family of enzymes in human cancer. During this study we introduce a novel technique to map uracils in genomes. Our studies used APOBEC3A expression in a repair deficient E. coli strain BH212. By mapping of the uracils in the E. coli genome we have found evidence about a mechanism APOBEC3A uses to target into genomic regions. We have also developed a LC/MS/MS based method to quantify genomic uracils and introduced a novel technique that can be used to separately quantify uracils in U:A pairs and U:G mispairs. We expect that these methods would continue to provide insights about AID/APOBEC targeting during human cancer.

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