Base damage recognition is performed by a monofunctional or bifunctional DNA glycosylase. The damaged base is removed by hydrolyzing the N-glycosidic bond thereby leaving an abasic site. Strand incision occurs at the abasic site primarily through the action of APE1, or alternatively via the lyase activity of a bifunctional DNA glycosylase. The ends of the phosphodiester backbone are processed to render them suitable for DNA repair synthesis. POLβ fills the gap for short-patch repair while a processive polymerase fills the gap in long-patch repair. XRCC1 and DNA ligase 3 seal the phosphodiester backbone in short-ptach BER while DNA ligase 1 completes the repair process in long-patch BER.

Relationship between damaged bases, DNA structure and recognition by specific DNA glycosylases. While each DNA glycosylase has a limited substrate repertoire, there is redundancy in damage recognition among the DNA glycosylases. Damaged bases, deaminated, alkylated or oxidized, are shown in double-stranded DNA, bubble DNA or newly replicated DNA in conjunction with the DNA glycosylases that recognize the damaged base in the particular DNA structure. DNA glycosylases are shown in blue with arrows to the damaged base(s) recognized. Modified bases shown are in red and include U=uracil, X=xanthine, HX=hypoxanthine, 3-meA=3-methyladenine, 7-meG=7 methylguanine, Tg=thymine glycol, foU=5-formyl uracil, 8-oxG=8-oxoguanine; Sp=spiroiminodihydantoin, Gh=guanidinohydantoin, Oa=oxaluric acid, Oz=oxazolone, Ca=cyanuric acid, FapyG=formamidopyrimidine derivative of guanine; FapyA=formamidopyrimidine derivative of adenine, 5oU=5 hydroxy uracil, fluorU= 5 fluorouracil, 5-meCpG= 5-methyl cytosine in the CpG context. The cytosine to uracil and 5-methyl cytosine to thymine reactions catalyzed by activation induced cytosine deaminase, AID, are shown in grey (Bransteitter et al., 2006).
Selected references for the glycosylase repair of mispairs include: G/U, (Akbari et al., 2004; Barrett et al., 1998), CpG/GpU, (Krokan et al., 2002); X/C, HX/T, 3meA/T, 7meG/C, (Chakravarti et al., 1991; Engelward et al., 1997); G/Tg, (Bandaru et al., 2002; Ikeda et al., 1998; Marenstein et al., 2003; Yoon et al., 2003); Tg/A, (Dianov et al., 2001; Hazra et al., 2002b; Marenstein et al., 2003; Rosenquist et al., 2003); foU/G, (Liu et al., 2003); foU/A, (Ikeda et al., 1998; Matsubara et al., 2003; Miyabe et al., 2002); foU/A, (Liu et al., 2003; Miyabe et al., 2002); 8-oxG, (Asagoshi et al., 2000; Laval et al., 1998); oxidized 8-oxG bases Sp, Gh, Oa, Oz, Ca, (Dherin et al., 2004; Hailer et al., 2005); FapyA/T, (Hazra et al., 2002a; Rosenquist et al., 2003); FapyG/C; (Asagoshi et al., 2000; Hazra et al., 2002a; Ide, 2001); TpG/GpC, (Krokan et al., 2002; Sousa et al., 2007); TG in bubbles, (Englander and Ma, 2006; Hazra and Mitra, 2006); 5oU in bubble DNA, (Englander and Ma, 2006; Hazra and Mitra, 2006; Matsubara et al., 2004); fluorU/A, (An et al., 2007); U/A post-replicative, (Nilsen et al., 2000; Parlanti et al., 2007); 8-oxG/A and G/A post replicative, (Ide and Kotera, 2004; McGoldrick et al., 1995).