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Cells often use the base excision repair pathway to repair DNA that has deaminated adenine.Identifying a deaminated foundation is due to the presence of hypoxanthine, which is uncommon in DNA.

Base excision repair is carried out by enzymes called DNA glycosylases. They repair DNA by removing and replacing damaged nucleotides. The damaged nitrogenous base is excised by glycosyltransferases, leaving the sugar-phosphate backbone intact. A purine/a pyrimidine site is created by this method. This is accomplished by removing the damaged base from the double helix and cleaving the N-glycosidic link. Through the base excision-repair mechanism, glycosylases aid DNA demethylation. At the purine/a pyrimidine site, the S-methylcytosine base is removed, followed by the breakage of the DNA backbone.

A gap is formed due to the cleavage, which is then filled by an unmethylated cytosine nucleotide. Active DNA demethylation is also carried out in mammalian cells, at least in part, via the base excision repair process. Deaminase converts 5-methylcylosine to thymine in this process, followed by G/T mismatch repair by DNA glycosylase enzymes. The base excision repair mechanism can repair damaged DNA throughout the cell cycle. It cleans the DNA of minor, non-helix-distorting base defects.