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Mechanism for Recognition and Excision of Oxidized Adenine by Thymine DNA Glycosylase

Servius, Hardler W.
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2025
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dissertation
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DNA oxidation is implicated in human diseases and neurodegenerative disorders and may result from normal cellular metabolism or exogenous sources. Base excision repair (BER) is one of the major pathways in cells to repair DNA damage that results from oxidation, deamination, and alkylation. It primarily removes small, non-helix distorting damaged nucleobase lesions that otherwise could cause mutations by mispairing or lead to breaks in DNA during synthesis or replication. One such oxidized DNA lesion is 7,8-dihydro-8-oxoadenine (oxoA). It is the major adenine oxidation product and is poorly characterized with regard to how it arises in and is eliminated from the genome. Direct damage of adenine by reactive oxygen species (ROS) is the most common source of oxoA arising within the DNA. DNA glycosylases such as human thymine DNA glycosylase (TDG) initiate BER by locating modified bases and removing them in DNA through hydrolysis of the N-glycosyl bond. TDG was originally discovered to be responsible for the removal of T from G•T mismatches, however it also contains key functions in epigenetic regulation. It performs a critical step in the ten-eleven translocation (TET) initiated pathway for active DNA demethylation, where it removes 5-formylcytosine (fC) and 5-carboxylcytosine (caC), which are oxidized derivatives of 5-methylcytosine (5mC). Previously, the confirmed targets of TDG were all modified pyrimidines paired across a guanine base (T, U, fC, caC). My studies demonstrated that TDG not only excises oxoA from DNA, but it does so at a rate that is much faster than the previously established pyrimidine substrates. When compared with the previously confirmed TDG targets (T, U, fC, and caC), hydrolytic activity for oxoA is approximately 303-, 18-, 86, and 346-fold higher, respectively. This finding is remarkable given that oxoA is substantially bulkier than the established pyrimidine substrates and before this, TDG had been reported to have very minimal activity against purine bases. This work addresses the mechanism by which TDG removes oxoA and the significant difference in catalytic activity between the smaller pyrimidine substrates and the bulker oxoA purine lesion. By mutating key active site residues, we quantified the importance of certain residues for cleavage of oxoA by TDG. We addressed the possibility that oxoA may be undergoing acid catalyzed excision (as observed for TDG excision of caC) through pH dependent studies. We performed single turnover kinetics experiments at multiple enzyme concentrations ([E]) and found that the hyperbolic dependence of activity (kobs) on [E] yielded the maximal glycosylase activity (kmax), the enzyme concentration giving half-maximal activity (K0.5), and the catalytic efficiency (kmax/K0.5). Lastly, we found that the prokaryotic ortholog E.coli mismatched uracil glycosylase (MUG) depicts remarkably slow cleavage of oxoA from DNA. The MUG enzyme has no detectable activity for removing oxoA from T⋅oxoA pairs and that its activity is exceedingly low for G⋅oxoA, A⋅oxoA, and C⋅oxoA pairs. These results have advanced the understanding of how TDG removes mutagenic oxoA lesions from DNA.

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University of Maryland, Baltimore. Biochemistry & Molecular Biology, Ph.D. 2025.
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