**2.2 Nucleotide excision repair (NER)**

568 DNA Repair

generally divided into single stand break (SSB) and double strand break (DSB) repair

The DNA base excision repair pathway deserves a detailed description since it is believed to be the major pathway for repairing DNA base modifications caused by oxidation, deamination and alkylation. DNA glycosylases catalyze the first step in the BER process by cleaving the N-glycosylic bond between a damaged base and the sugar moiety; after the cleavage the damaged base is released resulting in the formation of an abasic site which is then cleaved by an AP lyase activity or by the major mammalian apurinic/apyrimidinic endonuclease (APEX1). Repair can then proceed through short or long-patch BER. In shortpatch BER, which is the most common sub-pathway, a single nucleotide is incorporated into the gap by DNA polymerase β (Pol β) and ligated by the DNA ligase III/ X-ray repair crosscomplementing group 1 (XRCC1) complex. In long-patch BER several nucleotides (two to seven-eight) are incorporated, followed by cleavage of the resulting 5' flap structure and ligation. It has been suggested that after Pol β adds the first nucleotide into the gap, it is substituted by Pol δ/ε which continues long-patch BER. DNA ligase I completes the longpatch pathway. Several other proteins, including the proliferating cell nuclear antigen (PCNA), the RPA protein, and the 5'-flap endonuclease (FEN-1) participate in long-patch BER. Recent evidence suggests that XRCC1 acts as a scaffold protein in short-patch BER, regulating and coordinating the whole process. XRCC1 recruits DNA Pol β and DNA ligase III required for filling and sealing the damaged strand. Moreover, it also interacts with DNA glycosylases and APEX1, mediating their exchange at the damaged site. XRCC1 also interacts with PARP-1, which is one of the cellular sensors of DNA SSBs and DSBs. BER

SSB Modifications of DNA bases due to

SSB Repair of UV photoproducts, DNA crosslinks, and bulky lesions.

SSB Repair of mismatches and small insertions or deletions during replication.

DSB Repair of DNA DSBs, such as those caused by ionizing radiations, through

G2 phases of the cell cycle

DSB Repair of DNA DSBs, such as those induced

recombination with regions of homology (usually a sister chromatid) during late S or

by radiations, without recombination with regions of homology; it occurs during G0, G1, and early S phases of the cell cycle

oxidation, alkylation, and deamination

**Pathway Type of repair Type of damage** 

Table 1. Major DNA repair pathways in mammalian cells

pathways (Table 1).

Base excision repair

Nucleotide excision repair (NER)

Mismatch repair

Non homologous end joining (NHEJ)

**2.1 Base excision repair (BER)** 

Homologous recombination (HR)

(BER)

(MMR)

The nucleotide excision repair pathway (NER) is required for the removal of a wide variety of forms of DNA damage, including UV induced photoproducts, DNA crosslinks, and other bulky lesions. NER involves at least 20-30 proteins or complexes of proteins, and is divided into global genome repair (GGR) and transcription coupled repair (TCR). The two pathways mainly differ in the initial steps that recognize the DNA lesion, and different initial recognition factors are involved. NER senses the presence of a lesion through the distortion it causes to the DNA structure. In GGR DNA damage recognition requires the xeroderma pigmentosum (XP) complementing protein XPC-HR23B-centrin complex. The DNA damage is verified by opening of the DNA strands surrounding the lesion by the transcription factor TFIIH. This is followed by recruitment of XPA and other components of the transcription factor TFIIH to the lesion site. In TCR the recognition step is initiated when a RNA polymerase stalls at a lesion site and requires the Cockayne's syndrome proteins CSA and CSB. After a correct assembly of the NER complex, a fragment of 24-32 nucleotides is incised and removed from the damaged strand by the simultaneous action of the DNA excision repair cross complementing (ERCC) proteins ERCC5 (XPG; 3' endonuclease) and ERCC4 (XPF; 5' endonuclease) complexed with ERCC1. Repair is completed by new DNA synthesis mediated by DNA Pol δ/ε, DNA Pol κ, and ligation (DNA ligase I, DNA ligase III) of the nascent DNA to the parental strands using the undamaged strand as a template. The GGR pathway removes damages overall in the genome irrespective of genome location and point in the cell cycle, whereas TCR is required for the specific repair of bulky lesions in the transcribed strand of active genes. Mitochondria have been shown to lack NER, which operates in the nucleus removing the majority of DNA lesions (Fleck & Nielsen, 2004; Subba Rao, 2007).
