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Saturday, May 16, 2015

Base Excision Repair Mechanism

Base Excision Repair Mechanism, is a DNA repair mechanism, where in the altered bases of the DNA, is removed or replaced. In Base Excision repair, glycosylase recognizes and removes the damaged base by hydrolysing the glycosidic bond.

The resulting abasic sugar, is removed from the backbone by endonucleolytic action.
Endonucleolytic cleavage also removes a-purinc or a-pyrimidinic sugars that arise by spontaneous hydrolysis.
After the removal of damaged nucleotide, DNA polymerase and DNA ligase act upon the damaged strand to restore.

Cells have different DNA glycosylases, with different specificities. For example Uracil glycosylase which specifically removes the damaged uracil.

Lets see How Does Glycosylase Detects damaged base?

Glycosylases, diffuse through the minor groove of the DNA until a specific kind of lesion is detected. Glycosylases removes, the damaged base by a mechanism called Base Flipping.
The damaged base project out or flip out of the DNA double helix, glycosylase goes and binds to that base and removes it.

Glycosylase can selectively cleave the nucleotide without cleaving the DNA backbone. When the nucleotide is removed, a gap is created. To repair the strand with the gap, the strand need to be cut out and that short stretch removed need to be synthesized. The site at which the gap is present is called as the AP site. apurinic site or the apyrimidinic site .

Once the gap is recognized on the DNA strand, AP Endonuclease comes into the scene to nick the strand. This is because for the DNA Polymerase one to act on the strand, DNA need to be nicked then only DNA polymerase start its function, that’s the reason AP endonuclease acts on the damaged strand to create a nick.

DNA Polymerase has two activities, exonuclease activity and the polymerase activity. In this case, DNA polymerase makes use of three prime to five prime exonuclease activity, to chew off some the bases, and at the same time DNA polymerase, starts adding up the chewed off bases by its polymerase activity.

Once polymerase completes its action Ligase, seals the nick and completes the process.