The Pathways of Double-Strand Break Repair

1.1 Induction and repair of double-strand breaks (DSBs) in the DNA DNA encodes and transmits genetic information into the progeny of cells and organisms. As a result, processes associated with DNA replication, repair and recombination are at the center of biological research. Although the double-stranded nature of the DNA molecule is not a requirement for its replication or transcription, it is essential for the repair of practically all forms of damage that are limited to one DNA strand. Thus, in the base excision repair (BER) pathway, the damaged base is excised by the appropriate DNA glycosylase and the resulting apurinic/apyrimidinic site is recognized by the APendonuclease (APE1) which opens the sugar phosphate backbone and removes the sugar residue (Fig. 1A). The resulting single nucleotide gap is filled-in using information from the complementary strand with the help of DNA polymerase pol) and the sugar phosphate backbone is resealed with the help of XRCC1/DNA LigaseIII (LigIII) complex (Sancar et al., 2004). In an alternative form of this repair pathway, more nucleotides are removed from the vicinity of the damaged base and are subsequently replaced by the DNA polymerase, hence the name long-patch base excision repair. A further example of a repair pathway relying exclusively on the complementarity of the DNA strands for the faithful restoration of the DNA molecule is the nucleotide excision repair pathway (NER) (Fig. 1B). In this repair pathway gross structural distortions are recognized in the DNA rather than altered bases. Such structural alterations can be generated by pyrimidine dimers forming after exposure to UV light, as well as by several other forms of DNA lesions, including DNA crosslinks and DNA “bulky” adducts. Upon their recognition by a multi-protein complex (see Fig. 1B for details) and with the help of two independently acting 3’and 5’excision nucleases XPG and XPF/ERCC1 respectively, an incision is placed 6 ±3 and 20 ±5 nucleotides upstream and downstream of the pyrimidine dimer ultimately removing an approximately 24-32 nt single stranded DNA segment including the lesion. The resulting gap is filled in, again using information available on the complementary strand with the help of a polymerase. The continuity of the DNA is finally restored by ligation with DNA Ligase I (LigI) (Sancar et al., 2004). This fundamental concept of DNA repair, i.e. the use of a complementary strand to restore sequence information in the damaged strand, fails when complex damage is generated in the DNA consisting of multiple lesions distributed on both strands of the DNA in close proximity (Fig. 1C). Such forms of DNA damage are generated after exposure of cells to