DNA Repair Mechanisms and Double-Stranded Break Repair in Genetics

DNA Repair Mechanisms

Xeroderma Pigmentosum and Nucleotide Excision Repair

Xeroderma pigmentosum (XP) is a recessive genetic disorder that predisposes individuals to UV-induced DNA damage and skin cancer. Mutations in at least 7 genes (XPA-XPG) involved in nucleotide excision repair (NER) can cause this disorder.

• NER (Nucleotide Excision Repair): Repairs UV-induced thymine dimers and other bulky DNA lesions.

• Involves removal of a short single-stranded DNA segment containing the lesion, followed by DNA synthesis to fill the gap.

• Occurs in both prokaryotes and eukaryotes.

• XP genes: Encode proteins essential for NER; mutations lead to defective repair and disease.

Base Excision Repair (BER): Repairs small, non-helix-distorting base lesions, such as deaminated or oxidized bases.

• DNA glycosylases recognize and remove damaged bases.

• AP endonuclease cleaves the DNA backbone at the abasic site.

• DNA polymerase and ligase fill and seal the gap.

Replication Error Repair: Proofreading and Mismatch Repair

Errors during DNA replication are corrected by proofreading and mismatch repair mechanisms.

• Proofreading: DNA polymerase III (in prokaryotes) and DNA polymerases δ and ε (in eukaryotes) possess 3'→5' exonuclease activity to remove misincorporated nucleotides.

• Mismatch Repair (MMR): Corrects base mismatches that escape proofreading. Involves recognition of the mismatch, excision of the error-containing strand, and resynthesis.

• Key enzymes: MutS, MutL, MutH in prokaryotes; MSH and MLH proteins in eukaryotes.

Postreplication Repair

Postreplication repair fixes replication errors not corrected by normal proofreading and mismatch repair.

• Involves recombination-based mechanisms to bypass lesions and restore DNA integrity.

• RecA protein (in bacteria) promotes strand exchange and repair.

Photoreactivation

Photoreactivation repair uses photolyase enzyme to directly reverse UV-induced thymine dimers in the presence of visible light.

• Common in prokaryotes and some eukaryotes.

• Not present in placental mammals.

Double-Stranded Breaks (DSBs) in DNA

Consequences of Double-Stranded Breaks

Double-stranded breaks are severe DNA lesions that can lead to chromosomal rearrangements, cell death, and cancer if not properly repaired.

• DSBs can result from ionizing radiation, replication errors, or oxidative damage.

• Redundant repair pathways exist to address DSBs.

Homologous Recombination (HR) Repair

Homologous recombination is a high-fidelity repair pathway for DSBs, using a homologous DNA sequence as a template.

• Occurs primarily during late S and G2 phases of the cell cycle when sister chromatids are available.

• Key steps: End resection, strand invasion, DNA synthesis, and resolution.

• Proteins involved: RAD51, BRCA1/2, and others.

Homologous Recombination Repair Pathway Table

Step	Key Proteins	Description
End Resection	MRN complex, CtIP	DSB ends are processed to generate 3' single-stranded DNA overhangs.
Strand Invasion	RAD51	Single-stranded DNA invades homologous duplex DNA to form a displacement loop (D-loop).
DNA Synthesis	DNA polymerase	DNA is synthesized using the homologous template.
Resolution	Resolvases	Holliday junctions are resolved to restore intact DNA.

Nonhomologous End-Joining (NHEJ)

Nonhomologous end-joining (NHEJ) is an error-prone repair pathway that directly ligates the broken DNA ends without a homologous template.

• Occurs throughout the cell cycle, especially in G1 phase.

• Key proteins: Ku70/80, DNA-PKcs, XRCC4, Ligase IV.

• Can result in small insertions or deletions at the repair site.

NHEJ Repair Pathway Table

Step	Key Proteins	Description
End Recognition	Ku70/80	Ku proteins bind to DSB ends and recruit other factors.
End Processing	Artemis, DNA-PKcs	Ends are processed to make them compatible for ligation.
Ligation	XRCC4, Ligase IV	DNA ends are ligated to restore continuity.

Occurrence of Double-Strand Breaks

Double-strand breaks can occur normally during DNA replication, especially when replication forks encounter DNA lesions or secondary structures.

• DSBs are also intentionally generated during meiotic recombination and immune system development (V(D)J recombination).

Key Terms and Definitions

• Excision Repair: General term for DNA repair mechanisms that remove damaged nucleotides and replace them with correct ones.

• Mismatch Repair: System for correcting base-pair mismatches that escape proofreading during DNA replication.

• Double-Stranded Break (DSB): A type of DNA damage where both strands of the DNA double helix are severed.

• Homologous Recombination: Accurate repair of DSBs using a homologous DNA template.

• Nonhomologous End-Joining: Direct ligation of DSB ends without a template, often error-prone.

Relevant Equations

• DNA Repair Rate Equation:

$\text{Repair Rate} = k[\text{Damaged DNA}]$

• Probability of Error After Repair:

$P_{\text{error}} = 1 - \text{Repair Efficiency}$

Summary Table: DNA Repair Pathways

Pathway	Type of Damage	Key Enzymes	Fidelity
NER	Bulky adducts, thymine dimers	XPA-XPG	High
BER	Small base lesions	DNA glycosylases, AP endonuclease	High
MMR	Base mismatches	MutS, MutL, MutH	High
HR	Double-stranded breaks	RAD51, BRCA1/2	High
NHEJ	Double-stranded breaks	Ku70/80, Ligase IV	Moderate/Low

Additional info: Some context and terminology were expanded for clarity and completeness, including the summary tables and definitions of key proteins and steps in repair pathways.