DNA Replication and Repair

DNA replication is a semi-conservative process that duplicates the genome before cell division, with an intrinsic error rate reduced to approximately 1 error per 10^9 bases by proofreading and repair mechanisms. When replication errors or DNA damage escape correction, multiple repair pathways (mismatch repair, nucleotide excision repair, base excision repair, and double-strand break repair) serve as critical safeguards against mutagenesis.

• Semi-conservative replication: Each daughter DNA molecule contains one parental strand and one newly synthesized strand. DNA polymerase synthesizes in the 5' to 3' direction, with the leading strand synthesized continuously and the lagging strand as Okazaki fragments.
• Proofreading: DNA polymerase has 3' to 5' exonuclease activity that detects and removes misincorporated nucleotides during synthesis. Reduces error rate by ~100-fold.
• Mismatch repair (MMR): Corrects base-base mismatches and insertion/deletion loops that escape proofreading. Key proteins: MSH2/MSH6 (MutS alpha, recognizes mismatches), MSH2/MSH3 (MutS beta, recognizes insertion/deletion loops), MLH1/PMS2 (MutL alpha, coordinates repair). The system identifies the newly synthesized strand for correction.
• Nucleotide excision repair (NER): Removes bulky, helix-distorting lesions such as thymine dimers (from UV radiation) and chemical adducts. Involves recognition, dual incision flanking the lesion (~24-32 nucleotides excised), and gap filling. Two sub-pathways: global genome NER (GG-NER) surveys the entire genome; transcription-coupled NER (TC-NER) repairs lesions on actively transcribed strands.
• Base excision repair (BER): Removes small, non-helix-distorting base modifications such as oxidized bases (8-oxoguanine), deaminated bases (uracil from cytosine deamination), and alkylated bases. DNA glycosylases recognize and remove the damaged base, creating an abasic (AP) site. AP endonuclease then cleaves the backbone for repair.
• Double-strand break (DSB) repair: The most dangerous type of DNA damage. Two main pathways: homologous recombination (HR) uses the sister chromatid as a template for error-free repair (requires BRCA1, BRCA2, RAD51) and operates in S/G2 phase; non-homologous end joining (NHEJ) ligates broken ends directly (error-prone, can cause small insertions/deletions) and operates throughout the cell cycle.
• DNA damage checkpoints: Cell cycle checkpoints (G1/S, intra-S, G2/M) halt progression when damage is detected. ATM responds to DSBs; ATR responds to replication stress. Both activate p53 (TP53), which can trigger cell cycle arrest, DNA repair, or apoptosis.

• Lynch syndrome (MMR deficiency: MLH1, MSH2, MSH6, PMS2): Autosomal dominant cancer predisposition. Defective mismatch repair leads to microsatellite instability (MSI). High risk of colorectal cancer (lifetime risk 40-80%), endometrial cancer (40-60%), and other cancers (ovarian, gastric, urinary tract). Tumors show MSI-high phenotype and respond to immune checkpoint inhibitors.
• Xeroderma pigmentosum (XP: XPA through XPG, POLH): Autosomal recessive. Defective nucleotide excision repair causes extreme UV sensitivity and >1,000-fold increased risk of skin cancers. Patients must strictly avoid sun exposure. Neurodegeneration in some complementation groups due to defective TC-NER.
• Hereditary breast/ovarian cancer (BRCA1/BRCA2): Defective homologous recombination. Tumors show genomic instability and are sensitive to PARP inhibitors (synthetic lethality: blocking BER in HR-deficient cells is lethal because both repair pathways are compromised).
• Ataxia-telangiectasia (ATM): Autosomal recessive. Defective DSB signaling leads to cerebellar ataxia, oculocutaneous telangiectasias, immunodeficiency, radiosensitivity, and cancer predisposition (especially lymphoid malignancies). Elevated alpha-fetoprotein is a diagnostic clue.
• MUTYH-associated polyposis (MAP): Autosomal recessive. MUTYH is a BER glycosylase that corrects 8-oxoguanine:adenine mispairs. Deficiency leads to increased G:C to T:A transversions and colorectal polyposis/cancer.