During replication, DNA polymerase proofreads the newly synthesized strand, and improperly incorporated bases are removed by its 3' to 5’ exonuclease activity. In addition to proofreading, replication errors are corrected by the mismatch repair system. Mismatched bases change the conformation of the helix. In the mismatch repair system, the distortion is recognized and the region around the newly synthesized strand is excised. Some bacteria use methylase to differentiate between the old and newly synthesized strand. DNA polymerase then fills in the gap, using the older strand as a template. Other global systems commonly repair DNA in cells: base excision, photolyase, and nucleotide excision repair. In base excision repair, DNA glycosylase recognizes specific faulty bases, and hydrolyzes the glycosidic bond between the base and the deoxyribose backbone. AP endo/exonuclease then excises the single deoxyribose, and DNA polymerase fills in the gap. In photoreactivation, DNA photolyase recognizes and binds to thymine dimers, which cause a conformational change in the DNA helix. When light activates this enzyme, it breaks the covalent bonds of the ring, reversing UV damage. The nucleotide excision repair, helicases melt the duplex at the site of distortions, and a 12-13 residue long single-stranded DNA segment at this site is excised. DNA polymerase then fills in the gap left behind.
DNA damage can involve more than just wrongly incorporated bases. When double strand breaks or gaps occur, they are repaired either by non-homologous end joining (before replication) or homologous recombination (after replication, when sister chromatids can provide a template). In NHEJ, an exonuclease process the single stranded ends of the broken DNA, and ligases then directly join them together. The digestion of ends may result in the loss of nucleotides and mutations. Homologous recombination is less mutagenic because sister chromatids or other homologous regions are used as a template for repairing the gap.
Some mutations are induced as part of a cell’s response to stress and DNA damage. The presence of ssDNA induces the SOS response in E. coli. RecA binds to ssDNA filaments and ATP, activating RecA. Active RecA induces self-cleavage of the repressor of din genes, LexA, and the din genes, including the umuDC operon, are transcribed. The umuD and umuC gene products form a heterotrimer UmuD’(2)C, DNA Pol V, which will synthesize DNA across lesions irrespective of the residues on the template strand. For example, DNA Pol V may insert guanines opposite a thymine dimer or a cytosine opposite an apurinic site, something DNA Pol III cannot do. Thus, the SOS response and DNA Pol V allow the cell to continue replication of its genome despite DNA damage. Additionally, DNA Pol V’s mutagenic nature allows cells to mutate specifically when they are maladapted to their environment.