Table 1.

Enzymes for identifying clustered and isolated damages and their substrates

Enzyme	Principal lesion class recognized	Lesions recognized*
Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg protein)	Oxidized purines	FaPy, 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine FaPy-adenine, FaPy-guanine, C8-oxoguanine, some abasic sites, C8-oxoadenine, and to a lesser extent, other modified purines (45–49)
E. coli Nth protein (endonuclease III)	Oxidized pyrimidines	Thymine residues damaged by ring saturation, fragmentation, or ring contraction, including 5,6-dihydrothymine, thymine glycol, urea, 5-hydroxy-5-methyl hydantoin, DNA damaged at guanine sites, and some abasic sites (48–51)
E. coli Nfo protein (endonuclease IV)	Abasic sites	Several types of abasic sites, including oxidized abasic sites, abasic sites modified with alkoxyamines, and DNA containing urea residues (34, 52)

^*5-Hydroxycyctosine and 5-hydroxy-2′-deoxyuridine are substrates for Fpg protein and Nth protein, but neither is formed at significant levels during aerobic irradiation.