Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain. Some of them have no regard to sequence when cutting DNA, but many others do so only at specific nucleotide sequences. The latter group is often called restriction endonucleases or restriction enzymes. Endonucleases can be distinguished from exonucleases, which cut the ends of recognition sequences and not the middle portion, unlike endonucleases. It is also possible for an enzyme to display both functions, and these are known as exo-endonucleases. Comparing endonuclease activity to exonuclease activity, the evidence suggests that the former experiences a lag compared to the latter.
Restriction enzymes are endonucleases from eubacteria and archaea that recognize a specific DNA sequence. The restriction site is the nucleotide sequence that is recognized for cleavage by a restriction enzyme, and it is usually a palindromic sequence of four to six nucleotides. Cleaving is often performed unevenly, which leaves single-stranded ends (called sticky ends) which can use hybridization to reconnect. The phosphodiester bonds of the fragments can be joined through DNA ligase when they have been paired. Every restriction endonuclease that is known attacks a different restriction site, which means there are hundreds of restriction sites for hundreds of restriction endonucleases. The origin of the DNA has no impact on the ability of the DNA fragments that have been cleaved can join together. This is known as recombinant DNA, which is formed by the joining of genes in new combinations.
There are three categories of restriction endonucleases: Type I, Type II and Type III. They are categorized based on their mechanism of action. They are regularly used in genetic engineering to create recombinant DNA, which can be introduced into different cells of bacterial, plant or animal origin. They can also be used in synthetic biology. Cas9 (CRISPR associated protein 9) is one notable example of an endonuclease. It is a protein which plays an important role in the immunological defense of certain bacteria against DNA viruses. It has become more well-known due to its uses in genetic engineering.
Type I and Type II restriction endonucleases are multisubunit complexes that include endonucleases and methylase activities. Type I restriction enzymes are capable of cleaving a random sites of approximately 1,000 base pairs from the recognition sequence. Type II enzymes are simpler and don't require ATP as an energy source, unlike Type I. Type III cleaves the DNA at approximately 25 base pairs from the recognition sequence and, like Type I, requires ATP.
Endonucleases contribute to DNA repair. The incision of DNA at AP sites is catalyzed by AP endonuclease, which readies DNA for excision, repair synthesis and DNA litigation. There are two AP endonucleases in E.coli cells, which eukaryotes have just one AP endonuclease. Mutations can also occur in endonucleases. A defect in a UV-specific endonuclease causes the rare autosomal recessive disease xeroderma pigmentosa, which means that DNA damage caused by sunlight can't be repaired. Sickle Cell anemia is another result of a mutation, when the recognition site for the restriction endonuclease that recognizes the nucleotide sequences is eliminated.