Endonuclease - Categories of Endonucleases

Categories of Endonucleases

Ultimately, there are three categories of restriction endonucleases (restriction endonucleases). The types I and III are large multisubunit complexes that include both the endonucleases and methylase activities. Type I can cleave at random sites of about 1000 base pairs or more from the recognition sequence and it requires ATP as source of energy. The type II behaves slightly different and was first isolated by Hamilton Smith in 1970. They are simpler versions of the endonucleases and requires no ATP in its degradation processes. Some examples of the type II restriction endonucleases include BamHI, EcoRI, EcoRV, and Haelll. The type III, however, cleaves the DNA at about 25 base pairs from the recognition sequence and also requires ATP in the process.

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.. The restriction enzymes used in molecular biology usually recognize short target sequences of about 4 – 8 base pairs. For instance, the EcoRI enzyme recognizes and cleaves the sequence 5' – GAATTC – 3'.

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 to the following:

• 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