Difference between Base Excision Repair and Nucleotide Excision Repair

Base excision repair (BER) and nucleotide excision repair (NER) are two major DNA excision repair systems. They follow a complex repair pathway in eukaryotes whereas a prototype system exists in prokaryotes. The two pathways of BER and NER have four steps: (1) recognition of damaged DNA, (2) excision of damaged DNA, (3) DNA synthesis to fill the nucleotide gap, and (4) sealing of nicks in the DNA.

Base Excision Repair

Base excision repair (BER) is a repair pathway that repairs the replicating DNA throughout the cell cycle. It ensures that mutations are not incorporated into the newly replicating DNA strands. Adenine, cytosine, guanine and thymine are prone to alkylation (addition of an alkyl group), deamination (removal of an amine group) and oxidation (damage by reactive oxygen species). These activities can cause substitution or deletion in the base pairs of DNA that can lead to perpetuation of mutation.

The process of base excision repair begins by identification and removal of the mutated base by the DNA glycosylase enzyme. It catalyses the N-glycosidic bond between the sugar and a base. This creates an apurinic/apyrimidinic (AP) site. Next, another enzyme called AP endonuclease nicks the abasic site, creating a break in the strand of DNA. In the next two steps, DNA polymerase fills in the gap created by endonuclease and DNA ligase seals it.

Nucleotide Excision Repair

Nucleotide excision repair (NER) is a damage repair pathway that exists in all organisms. It repairs damages made by UV light, chemicals adducts, radiations and other mutagens. The resulting damages can cause distortion to the DNA helix.

The pathway of nucleotide excision repair is complex, but can be simplified as: removal of damaged stretch of DNA, resynthesis of the removed fragment by taking undamaged fragments as template and finally ligation of the fragments.

Xeroderma pigmentosum is a genetic disease caused by a defect in the XPC enzyme. The enzyme XPC removes UV lesions caused by daily exposure of UV rays from the sun.


Base Excision Repair Nucleotide Excision Repair
Base excision repair is a pathway that repairs replicating DNA throughout the cell cycle. Nucleotide excision repair is a pathway that repairs constantly damaging DNA due to UV rays, radiation and mutagens.
Removal of Damaged DNA
A single base is removed which creates an abasic site in the DNA strand. A short, single-stranded stretch of the affected DNA strand is removed.
Cause of DNA Damage
It repairs DNA that is damaged by endogenous mutagens. It repairs DNA that is damaged by exogenous mutagens.
Initial Cleavage Site
The initial cleavage is directed at the glycosidic bond that joins the purine or pyrimidine base to the deoxyribose sugar of the DNA. In NER, the initial cleavage is directed towards the phosphodiester bond that connects the 3’ end of one sugar to the 5’ end of another sugar.
Nature of Repair
It repairs small damages that do not distort the helix lesion of a genome. It repairs bulky helix-distorting lesions in a genome.
First Enzyme that Recognises the Damaged Site
DNA Glycosylase XPC in eukaryotes and UvrABC in prokaryotes
What Type of Modifications Does It Repair?
It repairs bases that are prone to alkylation, deamination and oxidation. The NER pathway can repair a wide spectrum of damaged DNA. It can remove structurally unrelated base modifications such as those caused by UV light (pyrimidine dimers), benzopyrenes, aflatoxins and other chemotherapeutic agents.
Clinical Manifestation
Defects in this pathway can lead to cancer. Defects in this pathway cause xeroderma pigmentosum, Cockayne syndrome and also cancer predispositions.

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Frequently Asked Questions


How does nucleotide excision repair differ from base excision repair?

The nucleotide excision repair system recognises bulky and DNA-helix distorting damages, while the base excision repair system recognises small, non-distorting damages in the DNA helix.

What enzymes are involved in nucleotide excision repair?

Repair by the nucleotide excision repair system is accomplished by a set of multisubunit enzymes referred to as excision nuclease or exinuclease.

What DNA polymerase is used in nucleotide excision repair?

Nucleotide excision repair uses delta or epsilon DNA polymerase for the resynthesis of the DNA, whereas base excision uses beta DNA polymerase for the same.