In eukaryotic cells, both normal metabolism and exogenous factors, such as UV light and radiation, can cause DNA damage, resulting in as many as 105 spontaneous molecular lesions per cell per day. To respond to these threats, mammals have evolved the DNA damage response (DDR). This response controls DNA repair, a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome.

The rate of DNA repair is dependent on many factors, including the cell type, the age of the cell, and the extracellular environment. A cell that has accumulated a large amount of DNA damage, or one that no longer effectively repairs damage incurred to its DNA, can enter one of three possible states: senescence, apoptosis, or tumor.

The DNA repair ability of a cell is dependent on the coordination of DNA repair processes, which play a critical role in allowing the proper development and survival of organisms. DDR pathways have the ability to prevent numerous human diseases and conditions, such as tumor and senescence.

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DNA Strand Crosslink Repair

The problem of crosslink repair was addressed many years ago in experiments in E. coli. This work resulted in the well-known “Cole” model, which accounted for the sensitivity of strains deficient in NER and HR to crosslinking agents and the virtual intolerance of strains with deficiencies in both pathways.

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Nonhomologous End-Joining

In NHEJ, DNA Ligase IV, a specialized DNA ligase that forms a complex with cofactor XRCC4, directly joins the two ends. To guide accurate repair, NHEJ relies on short homologous sequences called microhomologies present on the single-stranded tails of the DNA ends to be joined. If these overhangs are compatible, repair is usually accurate. NHEJ can also introduce mutations during repair. Loss of damaged nucleotides at the break site can lead to deletions, and joining of nonmatching termini forms translocations. NHEJ is especially important before the cell has replicated its DNA because there is no template available for repair by homologous recombination.

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Nucleotide excision repair

Nucleotide excision repair (NER) repairs damaged DNA, which commonly consists of bulky, helix-distorting damage, such as pyrimidine dimerization caused by UV light. Damaged regions are removed in 12-24 nucleotide-long strands in a three-step process consisting of damage recognition, the excision of damaged DNA by endonucleases both upstream and downstream of damage, and resynthesis of the removed DNA. NER is a highly evolutionarily conserved repair mechanism and is used in nearly all eukaryotic and prokaryotic cells. In prokaryotes, NER is mediated by Uvr proteins. In eukaryotes, many more proteins are involved, though the general strategy is the same.

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Mismatch repair

Mismatch repair systems are present in essentially all cells to correct errors that are not corrected by proofreading. These systems consist of at least two proteins. One detects the mismatch, and the other recruits an endonuclease that cleaves the newly synthesized DNA strand close to the region of damage. In E. coli, the proteins involved are the Mut proteins. This is followed by removal of the damaged region by an exonuclease, resynthesis by DNA polymerase, and nick sealing by DNA ligase.

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Homologous recombination

Mismatch repair systems are present in essentially all cells to correct errors that are not corrected by proofreading. These systems consist of at least two proteins. One detects the mismatch, and the other recruits an endonuclease that cleaves the newly synthesized DNA strand close to the region of damage. In E. coli , the proteins involved are the Mut class
proteins. This is followed by removal of damaged region by an exonuclease, resynthesis by DNA polymerase, and nick sealing by DNA ligase.

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