DNA repair mechanisms correct damage to the genetic material caused by environmental agents, replication errors, and normal metabolic processes. Without these systems, the mutation rate would be thousands of times higher, and genome instability would lead to cancer and other diseases.

Types of DNA Damage

DNA damage arises from multiple sources. Endogenous damage includes depurination, where the glycosidic bond between the base and deoxyribose is hydrolyzed, occurring thousands of times per cell per day. Deamination converts cytosine to uracil, and oxidative damage from reactive oxygen species produces 8-oxoguanine and other modified bases. Exogenous damage includes ultraviolet light causing cyclobutane pyrimidine dimers, ionizing radiation causing single and double-strand breaks, and chemical agents such as alkylating agents and polycyclic aromatic hydrocarbons.

Base Excision Repair

Base excision repair corrects small, non-helix-distorting lesions such as oxidized or alkylated bases. DNA glycosylases recognize and remove the damaged base by cleaving the glycosidic bond, creating an abasic site. AP endonuclease then cuts the backbone at the apurinic or apyrimidinic site. DNA polymerase beta fills the single-nucleotide gap, and DNA ligase seals the nick. The process is initiated by damage-specific glycosylases, providing specificity for different types of base damage. OGG1 recognizes 8-oxoguanine, and UNG recognizes uracil in DNA.

Nucleotide Excision Repair

Nucleotide excision repair removes bulky, helix-distorting lesions such as pyrimidine dimers and chemical adducts. In humans, the XPC protein detects the distortion, and TFIIH unwinds the DNA around the lesion. XPG and XPF-ERCC1 make incisions on the 3-prime and 5-prime sides of the lesion, removing a 24 to 32 nucleotide oligonucleotide. DNA polymerase delta or epsilon fills the gap, and DNA ligase seals the nick. Defects in NER proteins cause xeroderma pigmentosum, a genetic disorder characterized by extreme sensitivity to sunlight and a thousand-fold increased risk of skin cancer.

Mismatch Repair

Mismatch repair corrects DNA replication errors that escape proofreading, including misincorporated bases and insertion-deletion loops from polymerase slippage. In E. coli, MutS recognizes the mismatch, MutL recruits the repair machinery, and MutH nicks the newly synthesized strand at hemi-methylated GATC sites. The eukaryotic system is more complex, with multiple MutS and MutL homologs. MSH2-MSH6 recognizes base mismatches and small loops, while MSH2-MSH3 recognizes larger loops. Defects in mismatch repair cause microsatellite instability and are responsible for Lynch syndrome, also known as hereditary non-polyposis colorectal cancer.

Double-Strand Break Repair

Double-strand breaks are the most dangerous type of DNA damage, capable of causing chromosomal rearrangements and cell death. Two main pathways repair DSBs. Non-homologous end joining directly ligates the broken ends without requiring sequence homology. These repair pathways are exploited by CRISPR-Cas9 for genome editing. The Ku70-Ku80 heterodimer binds the broken ends and recruits DNA-PKcs, which brings the ends together. Artemis processes damaged ends, and DNA ligase IV seals the break. NHEJ is error-prone and can introduce small deletions or insertions. It operates throughout the cell cycle and is the dominant DSB repair pathway in mammalian cells.

Homologous recombination uses the sister chromatid as a template for accurate repair. The MRN complex senses DSBs and initiates resection of the 5-prime ends, generating 3-prime single-stranded tails. RPA coats the single-stranded DNA, and BRCA2 loads RAD51 onto the tail, forming a nucleoprotein filament that invades the homologous duplex DNA. DNA synthesis extends the invading strand, and the repaired DNA is resolved by cleavage of Holliday junctions. HR is restricted to S and G2 phases when sister chromatids are available. Defects in HR genes, including BRCA1 and BRCA2, predispose to breast and ovarian cancer.

DNA Damage Checkpoints

Cell cycle checkpoints coordinate DNA repair with cell cycle progression. The ATM and ATR kinases are master regulators of the DNA damage response. ATM is activated primarily by double-strand breaks, while ATR responds to replication stress and single-stranded DNA. These kinases phosphorylate CHK1 and CHK2, which in turn phosphorylate the CDC25 phosphatases and p53, leading to cell cycle arrest. p53 activation induces expression of p21, which inhibits cyclin-dependent kinases and arrests the cell cycle, allowing time for repair or triggering apoptosis if damage is extensive.