Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain. Some of them do not take sequence into account when cutting DNA, but many others do so only at specific nucleotide sequences. The latter group is often referred to as restriction endonucleases or restriction enzymes.
Endonucleases can be distinguished from exonucleases, which cut the ends of the recognition sequences and not the middle, unlike endonucleases. It is also possible for one enzyme to display both functions, and these are known as exoendonucleases. When comparing the activity of the endonuclease with the activity of the exonuclease, the evidence suggests that the former experiences a delay 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 is typically a palindromic sequence of four to six nucleotides. Cleavage is often done unevenly, leaving single-stranded ends (called sticky ends) that can use hybridization to reconnect. The phosphodiester bonds of the fragments can be joined via DNA ligase when they have paired.
Each known restriction endonuclease attacks a different restriction site, which means that there are hundreds of restriction sites for hundreds of restriction endonucleases. The origin of the DNA does not influence the ability of the DNA fragments that have been cleaved to join together. This is known as recombinant DNA, which is formed by joining genes together in new combinations. There are three categories of restriction endonucleases: Type I, Type II, and Type III. They are classified according to their mechanism of action.
They are commonly 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 a notable example of an endonuclease. It is a protein that plays an important role in the immune defence of certain bacteria against DNA viruses. It has become better known due to its uses in genetic engineering.
Type I and type II restriction endonucleases are multi-subunit complexes that include endonuclease and methylase activities. Type I restriction enzymes are capable of cleaving random sites approximately 1000 base pairs from the recognition sequence. Type II enzymes are simpler and do not require ATP as an energy source, unlike type I. Type III enzymes cut DNA at approximately 25 base pairs from the recognition sequence and, like type I They require ATP.
Endonucleases contribute to DNA repair. DNA cleavage at AP sites is catalyzed by AP endonuclease, which prepares DNA for DNA cleavage, repair synthesis, and litigation. There are two AP endonucleases in E.coli cells, while eukaryotes have only one AP endonuclease. Mutations can also occur in endonucleases. A defect in a UV-specific endonuclease causes the rare autosomal recessive disease xeroderma pigmentosum, which means that DNA damage caused by sunlight cannot be repaired. Sickle cell anaemia is another result of a mutation when the recognition site for the restriction endonuclease that recognizes nucleotide sequences is removed.