Excision repair is one of the types of DNA repair systems, which is an enzymatic process and follows a cut, copy and paste mechanism. A cutting mechanism involves, removal of the damaged part or unusual bases by the specific enzymes like glycosylases and helicases. Then a copying mechanism consists of an enzyme DNA-polymerase I, uses the template DNA to form a copy of new DNA from 3′-OH primer site which replaces the damaged portion of the DNA. At last, the pasting mechanism makes the use of DNA ligase to paste the disjointed fragments of the DNA.
After a cut, copy and paste process, a DNA appears to be fully intact and repaired. It is named as Excision repair because, in this type of DNA repair mechanism, the unwanted base is directly excised by the combination of enzymes and replaced by the new DNA. The excision repair can be employed for the DNA of different lengths like, Very short, short and long patch of DNA.
An excision repair involves two methods, namely BER (base excision repair) and NER (nucleotide excision repair). When there is a single unwanted base present in the DNA, it refers as very short patch DNA and to repair this the base excision repair system is employed. When more than one unwanted bases are present in the DNA, it refers as short and long patch DNA and requires nucleotide excision repair system.
Content: Excision Repair
Definition of Excision Repair
An excision repair can define as the DNA repair mechanism which deals with the damaged part of the DNA, by excising either a single unwanted base or a nucleotide sequence with the new DNA bases. Excision repair makes the use of enzymes for the removal of the mutated or the damaged part of the DNA.
Excision repair is of two types:
BER stands for “Base Excision Repair” which can define as the excision repair mechanism which removes the small base adducts in DNA. In simple words, it is a type of short patch excision repair mechanism. This repair system does not cause distortion in the configuration of the DNA helix. BER mainly repairs the mutated DNA, caused by the endogenous mutagens. Base excision repair can correct the chemical changes in the DNA.
Hydrolysis and oxidation are the two leading causes of DNA damage. Hydrolysis cause depurination or depyrimidination in the DNA, which then forms an AP-site. The AP-site will indicate the damaged part of the DNA. BER can also cause deamination of cytosine into uracil, which leads to the transition mutation in the DNA.
Oxidation changes the guanine base to 8-Oxo-G, which pairs with A instead of C and results into the formation of two daughter duplexes (8-Oxo-G: A and T: A).
BER uses a combination of enzymes like DNA glycosylases, AP-endonuclease, DNA polymerase-I and DNA-ligase.
- DNA glycosylases: Its function is to recognize the unwanted base pair and formation of AP-site in the DNA.
- AP-endonuclease: Its function is to create a nick in the AP-site or damaged part of the DNA.
- DNA polymerase-I: It performs a functional role in the base excision repair by performing two activities. Through first, it cut out the AP-site through its 3’-5’ exonuclease activity. Secondly, it synthesizes new DNA base pair through its 5’-3’ polymerization activity to fill the gap created by the AP-endonuclease.
- DNA ligase: It seals the gap or joins the DNA fragments. DNA ligase-I with the cofactor (XR C1) seals the gap in short patch BER.
In BER, unwanted bases like uracil, hypoxanthine, 3-methyl Adenosine occur in the base sequence of DNA as a result of chemical change. Uracil is not a part of DNA, but when it pairs with the usual base sequence of DNA, cause transitional mutation in the DNA.
Similarly, when hypoxanthine is present in the DNA, it will mislead the DNA for the synthesis of some essential proteins. 3-methyl Adenosine will cause an error in the replication of DNA. The process of base excision repair involves the following steps:
Glycosylase is used to first recognize the presence of an unwanted base in the DNA and then cleaves the unwanted base. The enzyme glycosylase will only remove the unwanted base, not the DNA backbone.
After, the action of glycosylase, a gap appears at the site where the unwanted base has been removed. This site will refer as “AP-site” or Apurinic/Apyrimidinic site.
The AP-site represents the damaged part of the DNA. Thus, an AP-endonuclease enzyme will create a nick in the damaged section.
DNA polymerase-I then cleaves the AP-site, through its 3’-5’ exonuclease activity. Along with the exonuclease activity, it also fulfils the gap created by AP-endonuclease by adding new base pairs through its 5’-3’ polymerization activity. At last, DNA ligase seals the gap between the DNA fragments.
NER stands for “Nucleotide Excision Repair” which can define as the excision repair mechanism which removes the long base adducts in DNA or the whole nucleotide sequence. It is a type of long patch excision repair mechanism. This repair system cause distortion in the configuration of the DNA helix. NER mainly repairs the damage of DNA, caused by the exogenous mutagens. NER repairs the damage induced by the UV-light in a DNA, oxidative damage and large chemical adducts.
NER makes the use of Uvr-BC, Uvr-D and DNA polymerase-I and DNA-ligase enzymes.
- Uvr-BC: It is the multisubunit enzyme complex, where the Uvr-BC complex is encoded by the uvr-B and uvr-C genes, respectively. Uvr-BC functions in recognition of the damage in the DNA segment, induced by the UV-radiation. This complex attaches with the T=T dimer.
- Uvr-D: It also refers as helicase enzyme which unwinds the DNA and chops the damaged DNA segment.
- DNA polymerase-I: It fills the gap by synthesizing new DNA base pairs through its 5’-3’ polymerization activity.
- DNA ligase: It seals the gap between the DNA fragments.
In NER, the formation of pyrimidine dimer occurs in the base sequence of DNA as a result of physical change or UV-rays. The method of nucleotide excision repair involves the following steps:
A thymine=thymine dimer forms as a result of UV-radiation. Uvr-B enzyme unites with the Uvr-C and forms Uvr-BC complex, to remove the dimer. The formation of Uvr-BC complex gets energy by the hydrolysis of ATP molecule. Uvr-BC subunit scans and recognizes the damage in the DNA segment.
Then, Uvr-B enzyme loads the Uvr-C enzyme, which will act as an endonuclease enzyme. Thus, Uvr-C enzyme will form a cleavage site for the further processing of DNA. This process also requires the utilization of energy.
Uvr-D then binds to the cleavage site and unwinds and cleaves the damaged DNA segment. An enzyme Uvr-D works like helicase-II, as it performs unwinding of the mutated portion. It also makes the use of ATP.
DNA polymerase-I then fulfils the gap created by the Uvr-D helicase enzyme, by adding new DNA through its 5’-3’ polymerization activity. At last, DNA ligase seals the gap between the DNA fragments.