DNA Repair Mechanisms in Genetics

DNA Repair Mechanisms

Introduction to DNA Repair

DNA repair is essential for maintaining genetic stability and preventing mutations that can lead to diseases such as cancer. Cells possess multiple repair pathways to correct different types of DNA damage, ensuring the integrity of genetic information across generations.

Proofreading by DNA Polymerase

Mechanism of Proofreading

During DNA replication, DNA polymerase incorporates nucleotides complementary to the template strand. The enzyme possesses a proofreading function that detects and corrects misincorporated bases through its 3' to 5' exonuclease activity.

• Detection: DNA polymerase checks the newly added base for correct pairing.

• Excision: If a mismatch is detected, the incorrect nucleotide is removed.

• Replacement: The correct nucleotide is inserted, and replication continues.

Types of DNA Damage and Corresponding Repair Mechanisms

Overview of DNA Damage

Cells encounter various types of DNA damage, including non-bulky base modifications, bulky adducts, mismatches, and strand breaks. The repair mechanism chosen depends on the nature of the lesion.

• Non-bulky damage: Base excision repair (BER), direct repair

• Bulky damage: Nucleotide excision repair (NER)

• Base mismatch: Mismatch repair (MMR)

• Double-strand breaks: Non-homologous end joining (NHEJ), homologous recombination repair (HRR)

Direct Repair Mechanisms

Direct Reversal of DNA Damage

Direct repair mechanisms restore damaged DNA bases to their original state without removing the nucleotide or cleaving the DNA backbone. These processes are highly specific and enzyme-mediated.

• Photoreactivation: Repairs UV-induced thymine dimers using photolyase and visible light.

• Alkylation repair: O6-methylguanine methyltransferase (MGMT) removes methyl groups from guanine.

Base Excision Repair (BER)

Repair of Non-Bulky Base Lesions

BER corrects small, non-helix-distorting base lesions such as deaminated, oxidized, or alkylated bases. The process involves removal of the damaged base followed by replacement with the correct nucleotide.

• Recognition: DNA glycosylase identifies and removes the abnormal base, creating an abasic (AP) site.

• Incision: AP endonuclease cleaves the DNA backbone at the AP site.

• Repair synthesis: DNA polymerase fills the gap with the correct nucleotide.

• Ligation: DNA ligase seals the nick in the backbone.

Nucleotide Excision Repair (NER)

Repair of Bulky DNA Lesions

NER removes bulky, helix-distorting lesions such as thymine dimers and large chemical adducts. This pathway excises a short single-stranded DNA segment containing the lesion and fills the gap using the undamaged strand as a template.

• Damage recognition: NER machinery detects the distortion in the DNA helix.

• Excision: Endonucleases cut the DNA on both sides of the lesion, removing a short oligonucleotide.

• Repair synthesis: DNA polymerase synthesizes new DNA to fill the gap.

• Ligation: DNA ligase seals the final nick.

Clinical Relevance

• Xeroderma pigmentosum (XP): A genetic disorder caused by defective NER, leading to extreme sensitivity to UV light and increased risk of skin cancer.

Mismatch Repair (MMR)

Correction of Replication Errors

MMR corrects base-pair mismatches that escape proofreading during DNA replication. The system distinguishes the newly synthesized strand from the parental strand and removes the incorrect base.

• Recognition: MMR proteins (e.g., MutS in bacteria, MSH2/MSH6 in eukaryotes) detect the mismatch.

• Strand discrimination: In bacteria, the parental strand is methylated; in eukaryotes, nicks in the new strand serve as signals.

• Excision: Endonuclease removes a segment of the new strand containing the mismatch.

• Repair synthesis: DNA polymerase fills the gap.

• Ligation: DNA ligase seals the nick.

Double-Strand Break Repair

Non-Homologous End Joining (NHEJ)

NHEJ repairs double-strand breaks by directly ligating the broken DNA ends. This process does not require a homologous template and can occur throughout the cell cycle, but may result in small insertions or deletions.

• Recognition: End-binding proteins detect and stabilize the break.

• Processing: Nucleases may trim DNA ends, creating overhangs.

• Filling and ligation: DNA polymerase fills gaps, and DNA ligase joins the ends.

Homologous Recombination Repair (HRR)

HRR uses a homologous DNA sequence (usually a sister chromatid) as a template to accurately repair double-strand breaks. This mechanism is most active during the S and G2 phases of the cell cycle.

• End resection: Exonucleases generate 3' single-stranded overhangs at the break site.

• Strand invasion: The overhang invades the homologous template, forming a displacement loop (D-loop).

• DNA synthesis: DNA polymerase extends the invading strand using the template.

• Resolution: Holliday junctions are formed and resolved, resulting in crossover or non-crossover products.

Outcomes of Homologous Recombination

• SDSA (Synthesis-dependent strand annealing): Non-crossover repair, the invading strand returns to its original DNA.

• DSBR (Double-strand break repair): Can result in crossover or non-crossover products depending on how Holliday junctions are resolved.

Summary Table: DNA Repair Mechanisms

Type of Damage	Repair Mechanism	Key Enzymes/Proteins	Template Required?
Non-bulky base modifications	Base Excision Repair (BER)	DNA glycosylase, AP endonuclease, DNA polymerase, DNA ligase	No
Bulky adducts, thymine dimers	Nucleotide Excision Repair (NER)	Excision nuclease, DNA polymerase, DNA ligase	No
Base mismatches	Mismatch Repair (MMR)	MutS/MutL/MutH (bacteria), MSH2/MSH6 (eukaryotes), exonuclease, DNA polymerase, DNA ligase	No
Double-strand breaks	NHEJ, HRR	Ku proteins, DNA ligase IV (NHEJ); Rad51, BRCA1/2 (HRR)	Yes (HRR only)
UV-induced thymine dimers	Direct repair (photoreactivation)	Photolyase	No