Updated: 9/30/2020

DNA Repair

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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 breaks
      • 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

References

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(M1.BC.15.73) A 3-year-old male child is found to have a disease involving DNA repair. Specifically, he is found to have a defect in the endonucleases involved in the nucleotide excision repair of pyrimidine dimers. Which of the following is a unique late-stage complication of this child's disease? Tested Concept

QID: 106551
1

Colorectal cancer

12%

(28/233)

2

Endometrial cancer

1%

(2/233)

3

Lymphomas

7%

(16/233)

4

Telangiectasia

11%

(25/233)

5

Malignant melanoma

68%

(158/233)

M 4 D

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(M1.BC.14.27) A 5-month-old male infant from a consanguineous marriage presents with severe sunburns and freckling in sun exposed areas. The mother explains that the infant experiences these sunburns every time the infant goes outside despite applying copious amounts of sunscreen. Which of the following DNA repair mechanisms is defective in this child? Tested Concept

QID: 107023
1

Nucleotide excision repair

67%

(35/52)

2

Base excision repair

12%

(6/52)

3

Mismatch repair

6%

(3/52)

4

Homologous recombination

6%

(3/52)

5

Non-homologous end joining

0%

(0/52)

M 2 E

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(M1.BC.13.26) A 65-year-old male is treated for anal carcinoma with therapy including external beam radiation. How does radiation affect cancer cells? Tested Concept

QID: 100091
1

Induces the formation of thymidine dimers

17%

(49/296)

2

Induces the formation of disulfide bonds

2%

(6/296)

3

Induces G/T and A/C pair formation

4%

(11/296)

4

Induces deamination of cytosine

5%

(15/296)

5

Induces breaks in double-stranded DNA

71%

(210/296)

M 1 E

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EXPERT COMMENTS (27)
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