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.

• Nucleotide excision repair (NER) is a DNA repair mechanism that removes UV-induced thymine dimers and other bulky lesions.

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

• NER is essential for maintaining genome integrity, especially in XP patients where repair is defective.

Base excision repair (BER) is another pathway that repairs small, non-helix-distorting base lesions.

• BER removes damaged bases by glycosylases, followed by endonuclease cleavage and DNA synthesis.

Replication Error Repair: Proofreading and Mismatch Repair

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

• Proofreading by DNA polymerase III detects and removes incorrect nucleotides during DNA synthesis.

• Mismatch repair corrects errors that escape proofreading, using proteins to recognize and excise mismatched bases.

• Key enzymes: DNA polymerases and DNA ligase fill in and seal the corrected DNA.

Postreplication Repair

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

• Involves recombination mechanisms to fill gaps opposite damaged DNA.

• RecA protein directs recombinational repair by facilitating strand exchange.

Photoreactivation Repair

Photoreactivation directly reverses thymine dimers using photolyase and visible light.

• Enzyme binds to dimer and uses light energy to break the cyclobutane ring.

Double-Stranded Breaks (DSBs) in DNA

Consequences of Double-Stranded Breaks

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

• DSBs can occur during replication or due to external 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 template.

• HR involves strand invasion, DNA synthesis, and resolution of joint molecules.

• Key proteins: RecA (in bacteria), Rad51 (in eukaryotes).

Steps in Homologous Recombination Repair

1. DSB recognition and processing to generate 3' single-stranded overhangs.

2. Strand invasion into homologous template.

3. DNA synthesis using the template.

4. Resolution and ligation to restore DNA integrity.

Nonhomologous End-Joining (NHEJ)

Nonhomologous end-joining is an alternative DSB repair pathway that directly ligates broken DNA ends without a homologous template.

• NHEJ is error-prone and can lead to mutations or chromosomal rearrangements.

• Key proteins: Ku complex, DNA-PKcs, Ligase IV.

Steps in NHEJ

1. Recognition of DSB ends by Ku proteins.

2. Processing of DNA ends if necessary.

3. Direct ligation by DNA ligase IV.

Occurrence of Double-Strand Breaks

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

Summary Table: DNA Repair Pathways

Repair Pathway	Main Function	Key Enzymes/Proteins	Fidelity
NER (Nucleotide Excision Repair)	Removes bulky DNA lesions (e.g., thymine dimers)	XPA-XPG, DNA polymerase, DNA ligase	High
BER (Base Excision Repair)	Repairs small, non-helix-distorting base lesions	DNA glycosylase, AP endonuclease, DNA polymerase, DNA ligase	High
HR (Homologous Recombination)	Repairs double-stranded breaks using homologous template	RecA/Rad51, DNA polymerase, DNA ligase	High
NHEJ (Nonhomologous End-Joining)	Repairs double-stranded breaks without template	Ku, DNA-PKcs, Ligase IV	Low
Photoreactivation	Directly reverses thymine dimers	Photolyase	High

Key Equations

• DNA synthesis during repair: $DNA_{new} = DNA_{template} + DNA_{polymerase}$

• General reaction for ligation: $DNA_{nicks} + DNA_{ligase} \rightarrow DNA_{intact}$

Additional info: Some diagrams and steps were inferred based on standard textbook knowledge of DNA repair pathways and their molecular mechanisms.