DNA is not chemically inert. Every single human cell experiences approximately $10,000text{–}100,000$ molecular lesions per day caused by endogenous oxidative free radicals (ROS), thermal depurination, deamination, environmental ultraviolet (UV) radiation, and cosmic rays. Without robust, multi-pathway repair mechanisms, genomic entropy would inexorably degrade biological life into senescence, oncogenesis, and death.
1. Base Excision Repair (BER) & Abasic Sites
Small, non-helix-distorting base modifications—such as cytosine deamination into uracil ($text{C} to text{U}$) or 8-oxoguanine formation from reactive oxygen species—are targeted by Base Excision Repair (BER):
- Lesion Recognition: A lesion-specific DNA glycosylase (e.g., Uracil-DNA glycosylase, UDG) flips the damaged base completely out of the double helix into its active-site pocket and cleaves the $N$-glycosidic bond, leaving an apurinic/apyrimidinic (AP, abasic) site.
- Backbone Cleavage: AP endonuclease (APE1) cleaves the phosphodiester backbone immediately $5’$ to the abasic site, generating a $3’text{-OH}$ and a $5’text{-deoxyribose phosphate (dRP)}$ terminus.
- Synthesis & Ligation: DNA polymerase $beta$ inserts the single correct nucleotide and excises the dRP flap via its lyase domain, followed by sealing by DNA Ligase III / XRCC1.
2. Nucleotide Excision Repair (NER) & Bulky Adducts
Bulky, helix-distorting DNA adducts—most notably ultraviolet light-induced cyclobutane pyrimidine dimers (CPD) and 6-4 photoproducts—are resolved by Nucleotide Excision Repair (NER):
- Global Genome NER (GG-NER): XPC-RAD23B detects helical distortions throughout the entire genome.
- Transcription-Coupled NER (TC-NER): Stalled RNA Polymerase II directly recruits CSB and CSA proteins at actively transcribed genes.
- Dual Incision Mechanics: The multi-subunit TFIIH complex (containing XPB and XPD ATP-dependent helicases) unwinds a $25text{–}30 text{ bp}$ bubble around the lesion. Structure-specific endonucleases XPF-ERCC1 and XPG cleave the damaged strand $5’$ and $3’$ of the adduct, respectively, releasing an oligonucleotide fragment of $24text{–}32 text{ nt}$. The gap is resynthesized by $text{Pol } delta/epsilon$ and sealed by Ligase I.
3. Double-Strand Break Repair: NHEJ vs Homologous Recombination
Double-strand breaks (DSBs) represent the most cytotoxic chromosomal lesion: a single unrepaired DSB triggers cell cycle arrest or apoptotic demise. Cells possess two distinct mechanisms to repair DSBs:
A. Non-Homologous End Joining (NHEJ)
Operating throughout all phases of the cell cycle (predominantly G0 and G1), NHEJ is a fast, error-prone direct ligation pathway:
[
text{DSB} xrightarrow{text{Ku70/Ku80 ring binding}} text{DNA-PKcs recruitment} xrightarrow{text{Artemis processing}} text{Ligase IV / XRCC4 end sealing}
]
Because damaged ends are enzymatically chewed back or filled in before blunt-end ligation, NHEJ frequently introduces small insertions or deletions (indels).
B. Homologous Recombination (HR)
Restricted strictly to S and G2 phases when an identical sister chromatid is available as a donor template, HR is an error-free, high-fidelity repair pathway:
- Resection: The MRN complex (Mre11-Rad50-Nbs1) and Exo1 generate long single-stranded $3’$ tails.
- Rad51 Nucleoprotein Filament: Rad51 polymerizes onto the single-stranded DNA, forming a helical nucleoprotein filament that hydrolyzes ATP.
- Homology Search & Strand Invasion: The Rad51 filament interrogates the intact sister duplex, driving D-loop (Displacement loop) invasion when homologous sequence is found.
- Synthesis & Holliday Junction Resolution: DNA synthesis extends across the break. The resulting double Holliday junctions ($text{dHJ}$) are resolved by structure-specific resolvases (Gen1, Brca2-complex) or dissolved by BLM-Topoisomerase III$alpha$, restoring chromosomal integrity without loss of a single base pair.
