DNA Repair
Direct reversal of DNA damage
- Alkyltransferase (methylguanine methyl transferase) (MGMT)
o directly transfers alkyl group from O6 guanine to self
o suicide – can only do this once
o actually can probably get different kinds of alkyl groups too
o influence of MGMT in chemotherapy
- photolyase
o directly reverses pyrimidine dimers
o using UV light as an energy source
o not in mammals
Removing damaged nucleotides
Base excision repair
- Recognizes certain types of damage to base (or depurination)
- Starts with DNA glycosylase chopping off base
o Uracil glycosylase just to recognize deaminated cytosines
- Then AP endonuclease makes single stranded cut
- Then DNA polymerase puts in new nucleotide(s) and DNA ligase makes last phosphodiester bond
Nucleotide excision repair
- recognizes other types of damage that distort helix
- DNA damage is recognized
o Bacteria it is UvrA+UvrB that senses damage
o Eukaryotes still trying to figure that out
- Proteins cut out a short oligonucleotide (around 30 nt or so)
o Bacteria it is UvrB+ UvrC
o Eukaryotes lots of proteins involved
- Replaced by DNAP and DNA ligase
- Lots of proteins/genes involved in this named XP
o Xeroderma pigmentosum
o Genetic disease, people who have this have mutations in these proteins
o So can’t do this type of repair
o So get melanoma if not protected from sun
o Says that the primary carcinogen for these people is UV light?
- Methyl-directed Mismatch repair
o repairs mismatches that DNA polymerase makes
o protein binds mismatch
§ MutL + MutS in bacteria
§ eukaryotes have homologous genes/proteins
o excise a chunk of new strand
§ MutH in bacteria
o replacemen by some DNA polymerase + DNA ligase
o how to know which strand is right and which is wrong?
- DNA is methylated on GATC, on N6 of A by dam methylase
- takes a bit of time after synthesis for this to be methylated
- so for a while, only old strand is methylated
- so nt in unmethylated strand is excised and replaced
- People with inherited mutations of genes for some of these proteins are prone to colon cancer (HNPCC)
Error prone repair
- Last resort
- When previous systems are overwhelmed, this kicks in
- The worst is unrepaired damage
o Might cause replication stalling, leading to double strand breaks, leading to cell death
- So use an alternative DNA polymerase that can replicate opposite damaged bases
o Usually not as accurate as normal DNA polymerases, so lots of mistakes
o SOS system in E. coli
o Lots (10-15?) of alternative DNA polymerases in human cells