Mechanism used to repair damaged DNA
generally are devided in two:
Direct Repair
Photo reactivation
Prokaryotes use a direct approach to repair UV caused thymine dimerization. an enzyme called photolyase in combination with a cofactor and a blue photon repairs the thymine dimers. In this radical reactions a electron is used to break the cyclobutan ring of thymine dimers.
Methyl transferases
Sometimes DNA can be methylated with alkylating agents. In the next strategy an enzyme(paradoxically with one turnover) reverses the damage by transferring methyl group from DNA to one of it's own residue (Cys).an example is MGMT(Methyl Guanine Methyl Transferase).
Reductive cleavage
In this strategy an enzyme (AlkB) removes the methyl groups as an aldehyde.
Indirect repair
Base excision repair (BER)
In this strategy an enzyme called DNA glycosidase removes damaged base (Oxidized or chemically altered base) then an AP endonuclease and exonuclease removes the AP nucleoside. a dna polymerase (POL I / POL beta) refills the AP site. a dna ligase reseals the gap.
Nucleotide Excision repair (NER)
In this strategy several enzyme and protein complexes work together to remove a portion of damaged(lesion) stand. with aid of the other strand the removed nucleotides are replaced.Several congenital disease such as XP and Cocain syndrome are thought to be results of mutations in gene encoding NER repair pathway.
Mismatch repair
Some times healthy nucleotide can incorporate themselves to DNA in incorrect position(by DNA polymerase). there must be a mechanism to identify them and remove the incorrect base. mismatch repair pathway does this. Prokaryotic MutS,H,L together recognize the mismatch and remove incorrectly inserted nucleotides. mutations of human counterpart of these genes can cause HNPCC(A form of colon cancer).