Base Excision Repair

The most common way to repair damaged DNA is to cut out the damaged part, recopy the undamaged complementary strand and ligate, or “re-seal”, the nick. This general scheme of cut, copy, and paste follows in all types of excision mechanism.

Base excision repair, or BER, corrects small base damages caused by deamination, oxidation, or alkylation that occur spontaneously or are caused by environmental toxins.

In BER, a group of around 11 different enzymes called DNA glycosylases recognize different altered bases and catalyze their removal. The modified bases make weak base pairs that are detected by the glycolases. 

Upon encountering such a weak base pair, DNA glycosylase wedges apart the neighboring base pairs and flips out the modified base. This flip allows the enzyme to interact with all facets of the base to accurately identify it.

Upon recognition, DNA glycosylase cleaves the bond between the modified DNA base and the deoxyribose, releasing the free base and leaving a gap in the DNA helix. This gap is recognized by an enzyme called AP endonuclease, or APE, which, along with another enzyme called phosphodiesterase, cuts the phosphodiester backbone within the polynucleotide chain.

The missing base in the DNA helix is filled by DNA polymerase β, which copies the correct base from the complementary strand at that position. Next, an enzyme called DNA ligase seals the remaining nick to give an intact, repaired DNA molecule.