**4. Base excision repair of oxidized bases**

 Base excision repair (BER) is responsible for repairing most oxidized base lesions, AP sites, and DNA SSBs. The basic mechanism of BER first elucidated in *Escherichia coli* is broadly conserved across all organisms, as highlighted in several reviews [43–46]. BER requiring only four or five enzymes in the basic reaction steps is initiated with excision of the damaged base by a monofunctional DNA glycosylase (DG), for example, uracil-DNA glycosylase (UDG) or 3-methyladenine-DNA glycosylase, generating an abasic apurinic/apyrimidinic (AP) site due to hydrolysis of the N-glycosidic bond of the damaged base. The AP endonuclease (APE1 in mammalian cells) cleaves the resulting AP site in the second step and generates 3′ OH and 5′ deoxyribose phosphate (dRP) termini. The DNA polymerase in the third step fills in the single nucleotide gap. In mammalian cells, DNA polymerase β (Pol β) also has intrinsic dRP lyase activity, which cleaves the dRP residue and generates 5′ phosphate; the resulting nick after incorporation of the correct base is sealed by DNA ligase III (Lig III) complexed with XRCC1 in the final step.

 The BER initiating DGs for oxidized bases, on the other hand, are bifunctional with intrinsic AP lyase activity. The bifunctional oxidized base-specific DGs further process the AP site via β or βδ lyase reaction. The Nth family of DGs, OGG1, and NTH1, via β eliminations generates 3′ phospho α,β-unsaturated aldehyde (3′ PUA; formally named 3′ phospho 4-hydroxylpentenal) and 5′ phosphate at the strand break. NTH1 prefers oxidized pyrimidines as substrates, and 8-oxoG and ring opened guanine, that is, formamidopyrimidine (Fapy-G), are preferred substrates for OGG1. The Fpg/Nei family DGs NEIL1, NEIL2, NEIL3, discovered by us and others [47–51] catalyze βδ elimination and remove the deoxyribose residue to produce a 3′ phosphate and 5′ phosphate at the strand break. NEILs prefer modified pyrimidine substrates, NEIL1 having preference for ring-opened purines, for example, Fapy-A and Fapy-G. The activity and substrate specificity of NEILs depend on the DNA structure, and NEILs have significant 5-OHU excision activity with single-stranded or bubble, forked DNA. In contrast, OGG1 and NTH1 prefer double-stranded DNA substrates. Usually, the base excision and lyase reactions act in a concerted sequence. However, due to weak lyase activity of OGG1, intact AP sites are the major product after OGG1 catalyzed cleavage of 8-oxoG [52, 53]. All these bifunctional DGs have broad and overlapping substrate range and possess backup activity for many base lesions. This accounts for the fact that only few DGs have been discovered so far for much larger number of oxidized bases and for the nonessentiality of individual DGs.

The 3′ phosphate generated by the NEILs by βδ elimination is a poor substrate for mammalian APE1 and is processed by polynucleotide kinase phosphatase (PNKP) [54–57]. Thus, for oxidized bases, the DGs actually define the subsequent steps. APE1 is responsible for processing the β elimination product of OGG1 and NTH1, whereas PNKP is required for generating 3′-OH termini from 3′ phosphate, a βδ elimination product of NEILs. Furthermore, AP sites and 3′ PUA generated by other DNA glycosylases can also be processed through a NEIL-PNKP-dependent pathway [53, 57]. This alternative repair route provides the functional redundancy in mammalian BER for genome safeguarding against a plethora of endogenous and induced oxidative damages.

*Regulation of Oxidized Base Repair in Human Chromatin by Posttranslational Modification DOI: http://dx.doi.org/10.5772/intechopen.81979* 

BER, in the simplistic model, generates a 1-nucleotide gap after excision of the damaged base and has been termed single nucleotide BER (SN-BER) or short-patch BER (SP-BER). In contrast, long-patch BER (LP-BER) involves repair synthesis of two to eight deoxynucleotides. The 5′ blocking group after oxidation of AP sites cannot be removed by Pol β via its dRP lyase activity. Instead it is removed by 5′-flap endonuclease 1 (FEN-1), which is normally required for removing the 5′ RNA primers from Okazaki fragments during DNA replication. Thus, the subsequent steps of LP-BER are identical to that of DNA replication, utilizing DNA replication machinery, involving DNA polymerases δ/ε (Pol δ/ε) and DNA ligase I (Lig I). These enzymes including FEN-1 are recruited by the sliding clamp PCNA, loaded by replication factor-C (RFC), as in replication [58]. Thus, the choice of LP-BER vs. SN-BER depends on the 5′-terminus at the base cleavage site. With unaltered aldehyde group in deoxyribose, Pol β could carry out SN-BER by excising the 5′-dRP. LP-BER becomes necessary for repairing the oxidized AP sites, which cannot be processed by the 5′ end cleaning lyase activity of Pol β. The nuclear replicative Pol δ/ε lack dRP lyase activity and thus repair synthesis by these enzymes have to follow the LP-BER subpathway. Because Pol β-depleted cells are resistant to oxidative stress, Pol δ/ε can substitute for DNA Pol β and carry out the preferred LP-BER. The BER subpathways are schematically shown in **Figure 1**, adapted from [44].

#### **Figure 1.**

*A schematic representation of oxidized base-specific BER subpathways. The damaged base is represented as . BER is initiated by the DGs: OGG1, NTH1, NEILs, and converge to common steps for end cleaning, followed by repair synthesis and ligation. See text for details.* 
