Lecture 33: DNA Repair

Question 1

Types of DNA repair

Answer 1

1. Direct repair of damaged base
2. Excision repair (NER, BER)
3. Mismatch repair
   (4. Double strand break repair (homologous recombination, non-homologous end joining))

Question 2

Key “R” stages of DNA repair

Answer 2

1. Recognize
2. Remove
3. Replace

Question 3

Direct repair of damaged base (example)

Answer 3

O6-alkylG repair by O6-methylguanine DNA methyltransferase (MGMT). MGMT single self-alkylation, takes methyl for itself to restore guanine. Otherwise, high chance of O6-aG to base-pair w/ thymine.

Question 4

Nucleotide Excision Repair process (prokaryotes)

Answer 4

e.g. intra-strand thymine dimers
1. Recognition by UvrAB complex; stall at damage, bend DNA, UvrA displaced by UvrC
2. Endonuclease 2 cuts 3’ then 5’ to damage
3. DNA poly I replaces excised DNA, DNA ligase seals backbone nick

Question 5

Nucleotide Excision Repair mechanisms (eukaryotes)

Answer 5

1. Transcription-coupled NER
2. Global genome NER
   Clinical: xeroderma pigmentosum (EXTREME sensitivity to UV)

Question 6

Base Excision Repair process (prokaryotes)

Answer 6

e.g. BER mismatched U by U DNA-N-glycosylase
1. Recognition by U DNA-N-g
2. Removal of base by U-DNA-N-g
3. Apyridimic endonuclease cuts backbone 5’ to damage
4. DNA polym. I nick translation
5. DNA ligase seals nick

Question 7

Base Excision Repair general scheme (prokaryotes)

Answer 7

DNA-N-glycosylases remove incorrect bases in DNA (recognition, removal), allowing DNA poly I to add correct base (repair) e.g. uracil mismatch due to cytosine deamination

Question 8

Base Excision Repair pathways (eukaryotes)

Answer 8

1. Short patch BER
2. Long patch BER

Question 9

Mismatch repair process (prokaryotes)

Answer 9

MutHLS system
1. MutS recognition and complex formation
2. MutHLS searches for nearest GATC sequence
3. MutL (endonuclease) cuts backbone 5’ to G of GATC
4. Helicase unwinds DNA past the damage
5. Exonuclease removes DNA past damage
6. DNA polym. III fills gap

Question 10

Mismatch repair general scheme

Answer 10

DNA polymerase III proofreading via ε subunit
+ nascent DNA scanning for base mismatch/single base insert./deletion