DNA Repair

Damage Tolerance

• Function
  • can allow DNA replication to continue despite presence of DNA damage (e.g. thymidine dimer)
• Process
  • DNA polymerase stalls at dimer
  • sliding clamp releases regular DNA polymerase and binds the one of two translesion polymerases
    • error free
      • recognizes that the dimer is normally a thymidine and the polymerase adds an adenosine opposite and continues replication
    • error prone
• polymerase adds any base opposite the lesion and continues replication

Mismatch Repair

• Process 
  • repairs G/T or A/C pairing
    • sometimes misincorporated due to tautomerization of the nucleotide
  • involves MutS, MutH, MutL enzymes
  • strand specific
    • recognizes which is the new strand because it is unmethylated and the old strand is methylated
• Deficiency
  • hereditary nonpolyposis colorectal cancer 
    • aka Lynch syndrome
    • cause
      • hereditary absence of one copy of enzyme hMLH1 or hMSH2
        • second copy lost due to somatic mutation
          • known as the two-hit model
          • common to many DNA repair deficiencies
    • presentation
      • microsatellite instability
        • di-, tri-, tetranucleotide repeats that can be amplified
          • constant in number in normal cells
        • diagnostic in Lynch syndrome
      • ↑↑ risk of colorectal cancer
• NOT preceded by benign polyps

Base Excision Repair

• Function
  • specific endonucleases (glycosylases) remove bases that have been modified by several common mechanisms of damage 
    • e.g. deaminated cytosines (C → U) removed by uracil glycosylase
  • can take place anytime during the cell cycle but occurs primarily in G1
• Process 
  • glycosylase specific for the damaged nucleotide removed damaged base by breaking glycosidic bond
  • damaged base removed
    • sugar remains but base removed
    • creates an apurinic/apyrimidinic (AP) site
  • gap filled by DNA polymerase I
    • this protein has 5′ to 3′ exonuclease activity 
• ligation of strand nick by DNA ligase III

Nucleotide Excision Repair

• Function 
  • removes thymidine dimers caused by UV-B light
  • removes damaged bases caused by chemicals
• Process 
  • maintenance repair
    • XPC recognises DNA lesion and recruits XPA
    • XPB-G binds DNA and removes a chunk spanning the damaged segment
    • DNA polymerase fills the gap
    • DNA ligase seals the nick
  • transcription-coupled repair
    • RNA polymerase stalls at DNA lesion
    • CSB and XPG recognize stalled RNA polymerase
    • CSA joins complex and removes damaged site and allows transcription to continue
• Deficiency 
  • xeroderma pigmentosum (XP)
    • cause
      • lack any enzyme XPA – XPG
    • presentation
      • cannot repair UV damage
        • sunlight sensitivity
        • ↑↑↑ prevalence of skin cancer 
        • corneal ulcers
    • diagnosis
      • measurement of repair mechanisms in white blood cells
    • treatment
      • avoidance of sunlight
  • Cockayne syndrome
    • cause
      • lack of CSA or CSB
    • AR
    • presentation
      • growth failure
      • photosensitivity
      • nervous system abnormalities
• can affect any organ system

Homologous Recombination

• Function 
  • repair double-strand breaks
  • requires a sister chromatid to use as a template
    • therefore must occur after S phase of cell cycle
• Process
  • double-strand break recognized by MRN complex
  • BRCA and BLM enzymes involved in end processing
  • Holliday junctions are formed
    • cross-shaped structures that mediate strand rejoining
  • junctions are resolved
    • may result in loss of heterozygosity
    • due to the use of the opposite strand as a template
• Deficiency
  • Bloom syndrome
    • cause
      • lack of BLM helicase enzyme
    • presentation
      • short stature
      • rash from sun exposure
      • café-au-lait spot
      • leukemias, lymphomas, carcinomas
  • BRCA-1 involved in 
    • breast, prostate, and ovarian cancer
  • BRCA-2 involved in
• breast cancer

Non-Homologous End Joining

• Function 
  • repair double-strand break 
    • these breaks may be caused by ionizing radiation or oxidative free radicals 
    • mechanism of cancer radiation therapy 
  • occurs when a sister chromatid is not available to use as a template (prior to S phase of cell cycle)
• Process
  • break recognized by MRN complex
  • additional enzymes (Artemis, XLF, Pol μ) cut ends so they can bind
  • DNA ligase IV joins ends together
• Deficiency
  • severe combined immunodeficiency disease (SCID)
• one of many causes