DNA repair

DNA repair is the collection of processes employed by the cell that recognises and corrects damage to the genome (i.e. mutation), either caused by endogenous agents such as metabolic damage or exogenous agents such as ionising radiation.

Types of DNA repair include:

  • Proof-reading is an intrinsic function of DNA polymerase III: it has a 3'-->5' exonucleolytic activity enabling it to 'look over its shoulder' for mismatched bases, exonucleolytically remove them, and then insert the correct base. Sometimes this mechanism fails, however, and the post-replication correction (mismatch repair) involves a series of protein interactions with the unmethylated template strand. MutS recognises and binds to mismatched bases. MutL associates with MutS. MutH binds to hemimethylated DNA and cleaves the non-methylated strand. An exonuclease digests the nicked strand in the direction of the mismatched base, and terminates shortly after passing the base. DNA polymerase I and DNA ligase replace the nucleotides and ligate the phosphodiester backbone back together.

  • Base excision repair (BER) recognises and corrects minor chemical modifications to DNA bases. Minor modifications are defined as those that do not impede DNA replication from occuring.
    • A family of DNA glycosylases recognise bases with a range of modifications, and upon recognition, will cleave the glycosidic bond between the sugar and the base to leave an apurinic or apyrimidinic site.
    • AP endonucleases recognise AP sites and will cleave the phosphodiester backbone at such sites.
    • DNA polymerase I (E.coli) or DNA polymerase beta (Eukaryotes) adds the appropriate complementary nucleotide to the exposed 3'OH end. DNA ligase ligates the backbone together.

    It is worth noting that DNA polymerase beta does not possess any proof-reading capability, and therefore inserts the incorrect base once in every 4000 insertions. Fidelity is maintained because unless the correct base has been inserted, DNA ligase cannot ligate the backbone together (3'OH and 5'P are in an incorrect orientation). This leaves the base exposed to AP endonuclease activity (3' --> 5'), which removes the base and allows for DNA polymerase beta to insert the correct base.

  • Nucleotide excision repair (NER) repairs leisons that distort the DNA double-helix (e.g. pyrimidine dimers). The DNA including the leison is removed as an oligonucleotide fragment. This fragment is 12-13 nucleotides long in prokaryotes, and 27-29 nucleotides long in eukaryotes. Below is a description of the E.coli model. There is a similar mechanism that occurs in humans, although it is more complicated with other 17 proteins and enzymes involved in the process.
    • UvrA recognises and binds to damaged DNA. This recruits UvrB which melts the strands apart, and causes UvrA to dissociate.
    • UvrB recruits UvrC, which cuts the DNA 8 nucleotides 5' of the leison, and 5 nucleotides 3' of the leison.
    • Oligonucleotide fragment is removed with the help of UvrD helicase.
    • DNA polymerase I and DNA ligase refil and seal the gap.