Endonuclease

Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain, in contrast to exonucleases, which cleave phosphodiester bonds at the end of a polynucleotide chain. Typically, a restriction site will be a palindromic sequence four to six nucleotides long. Most restriction endonucleases cleave the DNA strand unevenly, leaving complementary single-stranded ends. These ends can reconnect through hybridization and are termed "sticky ends." Once paired, the phosphodiester bonds of the fragments can be joined by DNA ligase. There are hundreds of restriction endonucleases known, each attacking a different restriction site. A given sample of DNA is likely to contain a recognition sequence for any restriction endonuclease. The DNA fragments cleaved by the same endonuclease can be joined together regardless of the origin of the DNA. Such DNA is called recombinant DNA; it has been artificially recombined. Restriction endonucleases (restriction enzymes) and are divided into three categories, Type I, Type II, and Type III, according to their mechanism of action. These enzymes are often used in genetic engineering to make recombinant DNA for introduction into bacterial, plant, or animal cells, as well as in synthetic biology.

The commonly used notation for restriction endonucleases is of the form "vwxyz", where "vwx" names the life form (bacteria) where this restriction endonuclease may be found, "y" names the strain (and is optional), and "z" (in Roman numerals) indicates different restriction endonucleases in the same life form (bacteria). Thus for example, "EcoRI" means that the restriction endonuclease is found in Escherichia coli ("Eco"); strain RY13 ("R"), restriction endonuclease number "I". Another example: "HaeII" and "HaeIII" refer to bacterium Haemophilus aegyptius, number II and number III, respectively.

Restriction endonucleases come in several types. A restriction endonuclease typically requires a recognition site and a cleavage pattern (typically of nucleotide bases: A, C, G, T). If the recognition site is outside the region of the cleavage pattern, then the restriction endonuclease is referred to as Type I. If the recognition sequence overlaps with the cleavage sequence, then the restriction endonuclease restriction enzyme is Type II.

Restriction endonucleases may be found that cleave standard dsDNA (double-stranded DNA), or ssDNA (single-stranded DNA), or even RNA. This discussion is restricted to dsDNA, however, the discussion can be extended:
 * Standard dsDNA
 * Non-standard DNA
 * 1) Holliday junctions Holliday junction
 * 2) Triple-stranded DNA triple-stranded DNA, quadruple-stranded DNA (G-quadruplex), etc.
 * 3) Double-stranded hybrids of DNA and RNA (one strand is DNA, the other strand is RNA)
 * 4) Synthetic or artificial DNA (for example, containing bases other than A, C, G, T, refer to the work of Eric T. Kool). Research with synthetic codons, refer to the research by S. Benner, and enlarging the amino acid set in polypeptides, thus enlarging the proteome or proteomics, see the research by P. Schultz.

In addition, research is now underway to construct synthetic or artificial restriction endonucleases, especially with recognition sites that are unique within a genome.

Restriction endonucleases or restriction enzymes typically cleave in two ways: blunt-ended or sticky-ended patterns. An example of a Type I restriction endonuclease, see

Common endonucleases
Restriction endonucleases (ENases) are most commonly produced by bacteria, and can be used to map a piece of DNA.

ENases are widespread amongst prokaryotes (bacteria and archaea), but are produced by some eukaryotic organisms as well, although this is very rare.

Some endonucleases have actions on RNA, such as the Dicer enzyme, which initiates the formation of RNA-induced silencing complexes. These may also be termed endoribonucleases.

Bacterial

 * 1) UvrABC endonuclease is a well-documented endonuclease found in E.coli.