DNA Repair Measured by the Comet Assay

The stability of the genome is of crucial importance, and yet the DNA molecule is prone to spontaneous loss of bases, and damage from exogenous and endogenous sources – with potentially mutagenic consequences. Damage can take the form of small alterations to bases (alkylation or oxidation); breaks in the sugar-phosphate backbone involving one or both strands (single or double strand breaks – SSBs or DSBs); bulky adducts combined with bases; and covalent bonds between adjacent bases (intra-strand cross-links), across the double helix (inter-strand cross-links), or between DNA and protein. These lesions can disrupt replication, or cause incorporation of the wrong base. Cells possess repair enzymes that correct almost all the damage before it can result in permanent change to the genome. Different pathways deal with the various kinds of damage. Repair of SSBs is in most cells a rapid process, consisting of little more than ligation. DSBs are more complicated (and potentially more serious) since the continuity of the double helix is disrupted. Homologous recombination ensures restoration of the correct DNA sequence by using the DNA of the sister chromatid or homologous chromosome as a template, while non-homologous end-rejoining is less precise and can entail loss of sequence. Base excision repair (BER) is concerned with small base alterations and starts with removal of the damaged base by a more or less specific glycosylase, leaving a base-less sugar or AP-site (apurinic/apyrimidinic site). An AP endonuclease or lyase cleaves the DNA at this site, and – after trimming of the broken ends of DNA – the one-nucleotide gap is filled by DNA polymerase ┚. Ligation is the final stage. Nucleotide excision repair (NER) is a more complex affair, involving recognition of a bulky adduct or helix distortion (such as is caused by the dimerisation of adjacent pyrimidines by UV(C) radiation), endonucleolytic incision on each side of the lesion, and removal of an oligonucleotide containing the damage. This is then filled in by DNA polymerase ├, κ or ┝ and the new patch of nucleotides is ligated into the DNA, completing the repair. NER enzymes are also involved in repair of inter-strand cross-links, removing the linking molecule from one strand, leaving it attached to the other strand as a mono-adduct to be removed in a second NER reaction (according to the simplest, and possibly simplistic, model). Individual DNA repair capacity is regarded as a biomarker of susceptibility to mutation and cancer. A person with high repair rate is assumed to be at lower risk than one with low repair rate. DNA repair is partially determined genetically, and polymorphisms in repair