Characterizing the excision of 7,8-dihydro-8-oxoadenine by thymine DNA glycosylase

Oxidation of DNA yields mutagenic and cytotoxic lesions that threaten genomic integrity, cause cancer and other diseases, and contribute to aging. Oxidative damage is countered by base excision repair, a pathway initiated by DNA glycosylases, which cleave bases through N-glycosyl bond hydrolysis. The major adenine oxidative lesion, 7,8-dihydro-8-oxoadenine (oxoA), is mutagenic in mammalian cells, but repair mechanisms are poorly understood. Thymine DNA glycosylase (TDG) removes T from mutagenic G⋅T mispairs arising through 5-methylcytosine deamination and mediates active DNA demethylation by excising 5-formylcytosine and 5-carboxylcytosine (caC). TDG excises oxoA from G⋅oxoA, A⋅oxoA, or C⋅oxoA pairs with remarkably high activity and from T⋅oxoA pairs with lower activity, comparable to that for established pyrimidine substrates. To further characterize TDG excision of oxoA, single-turnover experiments were collected with varying enzyme concentration, revealing vast differences in catalytic efficiency (k_max/K_0.5) among oxoA pairs, reflecting large variances in both substrate affinity (K_0.5) and maximal activity (k_max). TDG excision of oxoA depends strongly on the 3' base, as seen for excision of T from G⋅T pairs. Unlike MutY excision of adenine or TDG excision of caC, TDG excision of oxoA is not acid catalyzed, indicating that TDG stabilizes an anionic oxoA leaving group. A conserved TDG residue, H151, strongly promotes oxoA excision, whereas it antagonizes excision of T and uracil. The hydroxyl of Y152 catalyzes excision of oxoA and T, but not uracil, 5-formylcytosine, or caC, whereas its aromatic ring is essential for all substrates. Our results inform the catalytic requirements for enzymatic excision of oxoA from DNA.