Naveen Sooknanan McGill Fall 2011
DNA Repair and Recombination:
Over the course of evolution, errors in DNA replication can introduce permanent, transmissible
changes into a daughter cell of organism. This is known as a mutation to DNA. This causes the
encoding for different mRNA molecules after translation, and, eventually, different amino acids
coded during translation.
Mutagens, on the other hand, are chemical compounds, ultraviolet radiation, or ionizing
radiation (X-rays and atomic particles) which can increase the frequency of mutation.
A carcinogen is an agent that causes cancer. All carcinogens are mutagens. Carcinogens can
introduce the following changes into a normal cell:
Self-sufficiency in growth signals
Insensitivity to antigrowth signals
Evasion of apoptosis
Limitless replicative potential
Tissue invasion and metastasis
There are multiple methods of DNA repair through which the cell can prevent the occurrence of
mutations. Each of the mechanisms can take place at different times after transcription in order to
maximize effectiveness. Note that we will use a eukaryotic model to explain DNA repair.
E. coli DNA polymerase can introduce 1 error in every 10,000 nucleotides incorporated
into new polynucleotide strands. An error incorporation rate like this would cause too
many mutations to allow for our survival.
Due to the effectiveness of DNA repair mechanisms, the actual rate of error incorporation
is in fact 1 in every 1,000,000 nucleotides after measures of correction.
Some DNA polymerases have a proofreading activity which reads the newly synthesized strand
in the 5’ 3’ direction.
DNA polymerase δ, and not α, is able to read the new
strand with an exonuclease activity
o This is why Pol δ takes over for Pol α in DNA
When there is a mistake, Pol δ chews off the 3’ end of the
new strand and repolymerizes it with the correct base pairing.
Another mechanism, called base excision repair is able to fix errors after replication. It is used to
fix errors caused by mutagens.
De-amination of cytosine into uracil can occur spontaneously in the cell, for example
during cell metabolism
o This is not good if it happens in DNA and must be repairs by base excision repair
Cytosine can also be methylated on carbon 5 via and enzyme called DNA
o This is not necessarily a bad thing, in fact it is necessary for gene regulation,
transposon silencing and chromatin remodelling (gene compacting)
o Methylated cytosine can also be transformed into thymine by de-amination
(part of DNA Pol B)
T T DNA Pol B
LGL DNA ligase
Template strand MsH2 MSH6 3
polymerase and ligase
DNA glycosylase APEI endonuclease AP lyase (part of DNA Pol B) T T DNA Pol B LGL DNA ligase Repaired wild-type DNA Template strand MsH2 MSH6 3 endonuclease 3 by DNA polymerase and ligaseNaveen Sooknanan McGill Fall 2011
Base excision repair undergoes a multitude of steps involving gap repair in order to repair one
nucleotide in a polynucleotide strand.
DNA glycosylase hydrolyzes the bond between the
mispaired base and the sugar phosphate backbone, leaving
the backbone attached to the sequence and removing only
the T in this example
Apurininc/Apyrimidinic Endonuclease 1 (APE1) cuts the
sugar phosphate backbone at the 5’ end
AP lysase associates with DNA Polymerase β cuts the 3’
end of the sugar phosphate backbone (deoxyribose
phosphate), removing it from the sequence
The new, correct nucleotide is brought in as a dNTP and is
synthesized into the sequence by DNA polymerase β and the sugar phosphate backbone
is ligated by DNA ligase (called gap repair).
Mismatch excision repair is coupled with DNA replication; it happens shortly after replication
takes place. This mechanism is used on newly synthesized strands where errors were
incorporated and missed by proofreading.
Once an error is introduced, a series of steps is taken out to carry out mismatch excision repair.
This mechanism also involves gap repair.
Proteins MSH2 and MSH6 bind to the daughter strand and associate with the erroneous
o It’s not known how these complexes recognize which is
the newly synthesized strand, but it must be able to in
order for this mechanism to work
Endonuclease MLH1 and PMS2 bind to the complex and are
DNA helicase and DNA exonuclease then unwind and digest
the area around the erroneous base.
Pol δ then synthesizes the removed area of the daughter strand,