At the core of preservation and sustenance of life is the need to preserve the genomic sequence in living organisms. Since DNA is the repository of genetic information, the integrity and stability of DNA are crucial. However, DNA is a reactive molecule and is thus subjected to damage caused by several endogenous and exogenous factors leading to mutagenesis.
Endogenous factors causing DNA damage include errors in DNA replication, DNA base mismatch, topoisomerase-DNA complexes that are formed by topoisomerase enzymes to eliminate tension in DNA helix during replication and transcription processes. Other exogenous factors include spontaneous base deamination, creation of abasic or apurinic/apyrimidinic sites within DNA, oxidative DNA damage by reactive oxygen species (ROS), and erroneous methylation of DNA by S-adenosylmethionine (SAM). Endogenous factors that can lead to DNA damage include ionising and ultraviolet (UV) radiation (particularly UV-C radiation induces dimerization of adjacent pyrimidine bases via covalent bond formation), alkylating agents, aromatic amines, polycyclic aromatic hydrocarbon (PAH), reactive electrophiles, toxins, and environmental stress.
Although mutagenesis plays an indispensible role in evolution, if the DNA damage is not repaired it can lead to diseases including cancer. For example, exposure to excessive UV radiation from the sun can cause DNA damage that can result in skin cancer.
DNA in both prokaryotic and eukaryotic species is naturally capable of repairing any damage. A host of cellular pathways have evolved such as DNA repair, DNA damage tolerance, cell cycle checkpoints, and apoptosis, to protect the body from adverse effects of DNA damage. In fact, the cell cycle employs a checkpoint mechanism to make sure that the DNA of the cell is intact before the replication process is initiated. This prevents the accumulation of DNA damage that can increase cell burden leading to potentially undesirable mutations capable of causing diseases.
There exist at least five robust DNA damage repair (DDR) pathways throughout the cell cycle as explained below:
(i) Base excision repair (BER): This mechanism allows the correction of DNA base damages caused by oxidation, deamination, alkylation, and creation of abasic sites within DNA. These damages do not significantly distort the helical conformation of DNA. BER mechanism is involved in the G1 phase of the cell division cycle. Different DNA glycosylases involved in the process identify and excise damaged bases from the DNA helix. They can also identify bases that have been flipped out of the major groove of the helical structure of DNA.
(ii) Nucleotide excision repair (NER): This method is used to repair multiple and bulky base damages within DNA caused by UV radiation or ionising radiation. NER can proceed via two distinct mechanisms- global genome NER (GG−NER) and transcription−coupled NER (TC−NER). In the case of the former mechanism (i.e., GG−NER), the site of base-pair disruption (i.e., the formation of transient single-stranded DNA) is searched and repaired by the XPC protein-RAD23B complex (XPC: Xeroderma Pigmentosum, complementation group C and RAD23B: UV excision repair protein Radiation sensitive 23B). The TC-NER mechanism, on the other hand, employs the CSA-CSB complex (CSA: Cockayne syndrome WD repeat protein A and CSB: Cockayne syndrome protein B) and lesion-bound RNA polymerase II to identify and remove the DNA lesion.
(iii) Mismatch repair (MMR): This pathway operates to repair DNA damage post replication in the cell cycle. MMR is generally involved in repairing DNA damages that arise during replication and from the insertion-deletion loops (IDLs) caused by strand slippage. MMR mechanism proceeds via chromatin modification to locate the DNA lesion and launch repair.
(iv) Homologous recombination (HR): The HR pathway consists of a set of DNA repair mechanisms, namely, double strand break repair (DSBR), synthesis-dependent strand annealing (SDSA), and break-induced repair (BIR) pathways. It involves template-directed DNA repair to produce a high-fidelity repair and is the earliest homology directed repair (HDR) pathway studied. The HDR pathway will be discussed in detail in the next section.
(v) Non-homologous end joining (NHEJ): This pathway is initiated to repair DNA damages arising out of nucleolytic degradation, recombination, etc. via end-to-end fusion. The NHEJ pathway is primarily involved in the repair of double strand breaks (DSBs) and damages to telomeres caused by declining activity of telomerase with age and diseases. In the repair of DSBs via NHEJ, p53-binding protein 1 (53BP1) activates checkpoint signalling and assists in end-to-end fusion. The NHEJ pathway will be further elaborated in the next section.
In addition to these DDR pathways, a few DNA lesions can also be repaired via direct chemical reversal and interstrand crosslink (ICL) repair mechanisms. Single stranded break repair (SSBR) mechanisms can help to repair SSBs caused by oxidation, the aberrant activity of topoisomerase, and the creation of abasic sites.