DNA Repair Pathways

• DNA repair is an essential process to prevent the accumulation of mutations.
• Failure to repair DNA could lead to cell death, dysregulation, or uncontrolled growth.
• DNA repair mechanisms can be valuable targets for drug development, especially in cancer therapeutics.

Specific Repair Pathways

• Recognizes specific alterations to the DNA.
• Base Excision Repair (BER).
• Deamination repair.
• Oxidative damage repair.
• Alkylation repair.

General Repair Pathways

• Recognizes distortions in DNA caused by a wide range of damage.
• DNA Proofreading.
• Mismatch Repair (MMR).
• Nucleotide Excision Repair (NER).
• Translesion Synthesis.
• Post-replication/Recombination Repair.
• Non-homologous end joining.
• Microhomology-mediated end joining.
• Homologous recombination.

Base Excision Repair (BER)

• BER involves a damage-specific DNA glycosylase removes damaged base, resulting in an AP site.
• AP-endonuclease I cleaves DNA backbone at the 5' side of the sugar group.
• Accessory factors bind to promote repair.
• Short Patch repair involves DNA polymerase ẞ or λ removes 5'-sugar residue, gap filling DNA synthesis, and ligation of backbone nick by DNA ligase I or III.
• Long Patch repair involves DNA polymerase ẞ performing strand-displacement DNA synthesis, removal of the 5'-flap by flap endonuclease 1 (FEN1), and ligation of backbone nick by DNA ligase I or III.
• BER removes small and often non-helix-distorting base lesions.

DNA Proofreading

• During replication, DNA polymerase sometimes adds the wrong base.
• Pol ɛ (leading) and Pol δ (lagging) have 3' → 5' proofreading exonuclease activity.

Mismatch Repair (MMR)

• Repairs mismatches present in the DNA after replication has occurred.
• Recognizes damage due to minor distortions in the DNA helix: mismatches, frameshifts, base analog incorporation, alkylation, and small insertions/deletions (up to ~13 nt).
• Mismatch and surrounding DNA are removed, and replacement DNA is synthesized by Pol 8.

Nucleotide Excision Repair (NER)

• NER is the most versatile mechanism of DNA repair.
• Removes a wide variety of structurally unrelated DNA lesions that distort the DNA helix.
• NER repairs UV-induced damage, including cyclobutane-pyrimidine dimers (CPDs) and 6-4 pyrimidine-pyrimidone photoproducts (6–4PPs).
• NER also repairs Bulky chemical adducts, Intrastrand crosslinking (e.g. due to cisplatin treatment), and ROS-generated cyclopurines.

Translesion Synthesis

• The cell can swap out standard DNA Pol (Pol δ / Pol ε) for a translesion polymerase (Rev1 / Pol ζ/η/κ/ι) to power through DNA damage in the template strand that blocks DNA synthesis.
• Translesion synthesis is error-prone due to error prone insertion of bases across lesion, different polymerases for different damage types, and differing levels of accuracy.

Double-Stranded Break Repair

• DNA double-strand breaks are the most lethal form of DNA damage.
• Repair of broken ends must occur for cell survival.
• Causes include: Topoisomerase II, Antibody maturation, Site-specific endonucleases, Ionizing radiation, Chemical crosslinks, Strain due to blockages (replication / transcription).
• Two major pathways: End-joining and Homologous Recombination.

Non-homologous End Joining (NHEJ)

• Break ends are directly ligated without the need for a homologous template via juxtaposition and ligation using little (1–4 nt) or no complementary base pairing.
• NHEJ leads to small sequence insertions or deletions (indels) at the breakpoint junction.
• If more than two breaks occur simultaneously, improper joining can produce chromosomal translocations and rearrangements.

Microhomology-Mediated End Joining (MMEJ)

• MMEJ repairs DNA double-stranded breaks by annealing 2-4 bp stretches of overlapping bases flanking the break.
• Causes mutations because one of the two micro homology (MH) regions, and the inter-MH region, will be deleted from the repair product.
• MMEJ is may be an attractive anti-cancer drug target.

Single-Strand Annealing (SSA)

• A type of end joining which results in medium to large deletions.
• Requires identical or highly similar sequences in the crossover region, with ~30 bp in common, with homologous chromosomes, transposable elements, and multi-copy genes.
• Process involves Break, End resection, Alignment, Flap removal, and Gap filling and ligation.