Key DNA Repair Mechanisms

Why This Matters

Your cells face an onslaught of DNA damage every single day—estimates suggest 10,000 to 100,000 lesions per cell daily from replication errors, reactive oxygen species, UV radiation, and chemical exposure. The repair mechanisms you'll study here aren't just molecular housekeeping; they're the reason your genome doesn't collapse into chaos. When these systems fail, the consequences are severe: cancer predisposition syndromes, premature aging, neurodegeneration, and immunodeficiency.

You're being tested on more than pathway names and protein players. Exams will ask you to match damage types to appropriate repair mechanisms, explain why certain pathways are error-prone while others maintain fidelity, and predict what happens when specific repair proteins are mutated. Don't just memorize the steps—know when each pathway activates, what triggers it, and why cells sometimes choose a less accurate repair route over a precise one.

---

Excision-Based Repair: Cut It Out and Start Fresh

These pathways share a common logic: recognize the damage, excise it, and use the undamaged strand as a template for accurate repair. The key difference lies in the size of what gets removed.

Base Excision Repair (BER)

• Targets small, non-helix-distorting lesions—oxidized bases, deaminated cytosines, and alkylated bases that don't dramatically warp the DNA structure
• DNA glycosylases initiate repair by flipping the damaged base out of the helix and cleaving the glycosidic bond, creating an abasic (AP) site
• AP endonuclease and DNA polymerase β complete short-patch repair; this pathway handles the most common daily damage from reactive oxygen species

Nucleotide Excision Repair (NER)

• Removes bulky, helix-distorting adducts—UV-induced pyrimidine dimers, chemical crosslinks, and large covalent modifications that bend or unwind the double helix
• Excises a 24-32 nucleotide segment in eukaryotes using a multi-protein complex including XPA, XPC, and the TFIIH helicase; this is why it's called "nucleotide" excision—it removes a whole chunk
• Defects cause xeroderma pigmentosum (XP)—patients are extremely UV-sensitive and develop skin cancers at young ages, making NER a classic example of repair-disease connections

---

Replication Quality Control: Catching Mistakes Before They Stick

Mismatch repair operates specifically during and after DNA replication to correct errors that escaped polymerase proofreading. The challenge: distinguishing the newly synthesized (error-containing) strand from the template strand.

Mismatch Repair (MMR)

• Corrects base-pair mismatches and small insertion/deletion loops that occur during replication—these errors don't distort the helix enough for NER recognition
• MutS recognizes the mismatch, MutL coordinates the response, and in E. coli, MutH nicks the unmethylated (new) strand; eukaryotes use strand discontinuities instead of methylation for strand discrimination
• Defective MMR causes Lynch syndrome—hereditary nonpolyposis colorectal cancer (HNPCC) with characteristic microsatellite instability, a hallmark tested frequently on exams

---

Double-Strand Break Repair: The Most Dangerous Lesion

Double-strand breaks (DSBs) are catastrophic—there's no intact template strand for guidance. Cells have two main options: accurate but slow (homologous recombination) or fast but error-prone (non-homologous end joining). The choice depends on cell cycle phase and template availability.

Homologous Recombination (HR)

• Uses a homologous sequence (sister chromatid) as a template—this makes HR essentially error-free but restricts it to S and G2 phases when a sister chromatid is available
• Rad51 forms nucleoprotein filaments on resected single-stranded DNA and catalyzes strand invasion into the homologous duplex; BRCA1 and BRCA2 are critical regulators
• BRCA1/BRCA2 mutations impair HR and cause hereditary breast and ovarian cancer—these tumors become dependent on error-prone repair, which is why PARP inhibitors are effective therapeutics

Non-Homologous End Joining (NHEJ)

• Directly ligates broken DNA ends without a template—faster than HR but often causes small insertions or deletions at the junction site
• Ku70/Ku80 heterodimer rapidly binds broken ends and recruits DNA-PKcs; DNA ligase IV seals the break after minimal end processing
• Active throughout the cell cycle and is the dominant DSB repair pathway in G1; essential for V(D)J recombination in immune cells, where controlled imprecision generates antibody diversity

---

Direct Reversal: No Excision Required

Some damage types can be fixed by simply reversing the chemical modification. These pathways are fast and don't require DNA synthesis, but they're limited to specific lesion types.

Direct Reversal Repair

• O6-methylguanine-DNA methyltransferase (MGMT) transfers the methyl group from $O^6$-methylguanine to a cysteine residue on itself—this is a suicide reaction that inactivates the enzyme
• Alkylation damage from environmental carcinogens and chemotherapy drugs (like temozolomide) is the primary target; high MGMT expression in tumors causes drug resistance
• No template needed, no strand breaks created—the fastest possible repair, but each enzyme molecule can only act once

Photoreactivation

• Photolyase directly cleaves UV-induced pyrimidine dimers using energy absorbed from visible light (300-500 nm)—a light-dependent mechanism
• Contains flavin and folate cofactors that absorb photons and transfer electrons to break the cyclobutane ring of the dimer
• Present in bacteria, plants, and many animals but absent in placental mammals—humans rely entirely on NER for UV damage repair

---

Damage Tolerance: When You Can't Fix It, Work Around It

Sometimes repair must wait—replication forks can't stall indefinitely. These mechanisms allow DNA synthesis to continue past unrepaired lesions, prioritizing genome duplication over perfect repair.

Translesion Synthesis (TLS)

• Specialized Y-family polymerases (Pol η, Pol ι, Pol κ, Rev1) have open active sites that accommodate damaged bases but lack proofreading activity
• Pol η accurately bypasses thymine dimers—inserting AA opposite the lesion; mutations in Pol η cause the XP variant form, where patients are UV-sensitive despite functional NER
• Inherently mutagenic because TLS polymerases have low fidelity; this is a last resort mechanism that trades accuracy for survival

Interstrand Crosslink Repair

• Covalent links between complementary strands block both replication and transcription—neither strand can serve as a clean template
• Requires coordination of multiple pathways—unhooking by NER-like nucleases, bypass by TLS, and restoration by HR; the Fanconi anemia pathway coordinates this complex process
• Fanconi anemia mutations cause bone marrow failure and cancer predisposition; these patients are hypersensitive to crosslinking agents like cisplatin and mitomycin C

---

Quick Reference Table

---

Self-Check Questions

1. A patient presents with extreme UV sensitivity and early-onset skin cancers but has normal NER function. Which repair pathway is most likely defective, and what is this condition called?

2. Compare and contrast how cells distinguish the error-containing strand in mismatch repair between E. coli (using MutH) and eukaryotes.

3. Why is homologous recombination restricted to S and G2 phases of the cell cycle, while NHEJ can operate in G1? What molecular requirement explains this difference?

4. Both BER and NER use excision-based strategies. If a cell is exposed to cigarette smoke containing bulky polycyclic aromatic hydrocarbons, which pathway responds—and why can't the other pathway handle this damage?

5. A tumor shows high MGMT expression and is resistant to temozolomide chemotherapy. Explain the molecular basis of this resistance and why MGMT is called a "suicide enzyme."