In contrast to the general repair systems that recognize distortions in the DNA double helix, there are a variety of repair systems that recognize specific chemical changes in DNA. In particular, methylation and deamination give rise to unnatural bases that are not normally found in DNA (see Ch. 13). In such cases, there is no question which member of a mismatched base pair is wrong. Obviously the non-DNA base should be removed and a variety of enzymes exist that do just this.
Deamination generates hypoxanthine (from adenine), xanthine (from guanine) and uracil from cytosine (see Ch. 13). These three bases are all removed by DNA glycosylases that break the bond between the base and the deoxyribose sugar of
DNA glycosylase Enzyme that breaks the bond between a base and the deoxyribose of the DNA backbone
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