In-Depth Notes on DNA Repair Mechanisms

Biological Repair Mechanisms

  • Organisms, including bacteria and humans, can efficiently repair their DNA rather than replace it.
  • Key Repair Mechanisms:
    • Mismatch Repair
    • Base Excision Repair
    • Nucleotide Excision Repair

Reversal of UV Damage

  • Cells can repair UV-induced damage when exposed to blue light.
  • The photoreactivation enzyme (Photolyase) cleaves bonds between thymine dimers, reversing the effects of UV radiation.
  • Direct Reversal of Damage: Photolyase reverses damage caused by cyclobutane pyrimidine dimer formation.

Base Excision Repair (BER)

  • BER is responsible for the removal and replacement of damaged or inappropriate bases.
  • If damage cannot be repaired by single-step reversal, a multi-step pathway is utilized:
    1. N-glycosyl bond cleavage, forming an abasic site (initiated by DNA glycosylase).
  • The abasic DNA then undergoes further processing:
    • AP Lyase function can also cleave the bond between the sugar and phosphate, leading to further repair action if necessary.

Mechanism of Base Excision Repair

  1. Recognition of altered base by DNA glycosylase.
  2. Cleavage of the glycosidic bond between the base and the sugar.
  3. AP Endonuclease recognizes the missing base and cuts the phosphodiester backbone, generating a 5'-deoxyribose phosphate end and a free 3'-OH end.
  4. Short Patch Repair:
    • Replaces only one nucleotide using DNA polymerase β followed by DNA ligase.
  5. Involvement of Enzymes:
    • Various DNA glycosylases exist, some are monofunctional while others have additional functions (like AP lyase).

Nucleotide Excision Repair (NER)

  • NER is critical for removing bulky distortions in DNA.
  • Process involves:
    1. Damage Recognition by specific proteins (e.g., UvrA, UvrB in E. coli).
    2. Cutting DNA on either side of the lesion.
    3. Excision of the oligonucleotide containing the lesion.
    4. Synthesis of new DNA using the undamaged strand as a template.
    5. Ligation of the remaining nick.
  • Individuals with Xeroderma Pigmentosum (XP) have defects in NER, leading to severe skin abnormalities and increased skin cancer risk.

Mismatch Repair (MMR)

  • MMR corrects errors occurring during DNA replication and is essential for maintaining genomic stability.
  • Major functions include:
    1. Recognition of mismatched base pairs.
    2. Determining the correct base among mismatched bases.
    3. Excision of the incorrect base and carrying out repair synthesis.
  • E. coli distinguishes between parental and new DNA based on methylation (parental strand is methylated at GATC sequences).

E. coli Mismatch Repair System

  • Involves:
    • MutH Endonuclease: Cleaves the nearest unmethylated GATC sequence, allowing exonucleases to digest the nicked strand.
    • MutS and MutL: Form a complex that activates MMR.

Inherited Human Syndromes with Defects in DNA Repair

  • Disorders linked to defective DNA repair mechanisms include:
    • Xeroderma Pigmentosum (XP): Nucleotide excision repair defect; linked to skin cancer and UV sensitivity.
    • Ataxia Telangiectasia (AT): Involves repair by homologous recombination.
    • BRCA1/2 mutations: Associated with breast and ovarian cancer due to impaired double-strand break repair.

Common Types of DNA Damage and Repair Mechanisms

  • Various types of DNA damage can occur, leading to need for specific repair systems:
    • Mismatch Repair: Addresses replication errors.
    • Nucleotide Excision Repair: Fundamental for bulky adducts and pyrimidine dimers.
    • Base Excision Repair: Replaces damaged bases directly.
    • Translesion DNA Synthesis (TLS): Helps bypass DNA lesions during replication.

Repair Overview in Diploid Mammalian Cells

  • Cells repair various endogenous DNA lesions daily, incorporating different repair mechanisms tailored to the type of damage.
  • List of common DNA lesions and their repair rates in 24 hours highlights the efficiency of DNA repair systems.