Editing Endonuclease (section)

{{short description|Enzymes which cleave a nucleotide chain}}

In [[molecular biology]], '''endonucleases''' are [[enzyme]]s that [[Bond cleavage|cleave]] the [[phosphodiester bond]] within a [[polynucleotide]] chain (namely [[DNA]] or [[RNA]]). Some, such as [[deoxyribonuclease I]], cut DNA relatively nonspecifically (with regard to sequence), while many, typically called ''[[restriction endonucleases]]'' or ''restriction enzymes'', cleave only at very specific nucleotide sequences. Endonucleases differ from [[exonuclease]]s, which cleave the ends of recognition sequences instead of the middle (''endo'') portion. Some enzymes known as "'''exo-endonucleases'''", however, are not limited to either nuclease function, displaying qualities that are both endo- and exo-like.<ref>{{Cite web|url=https://www.neb.com/tools-and-resources/selection-charts/properties-of-exonucleases-and-endonucleases|title=Properties of Exonucleases and Endonucleases|date=2017|website=New England BioLabs|access-date=May 21, 2017}}</ref> Evidence suggests that endonuclease activity experiences a lag compared to exonuclease activity.<ref>{{Cite journal|last=Slor|first=Hanoch|date=April 14, 1975|title=Differentiation between exonucleases and endonucleases and between haplotomic and diplotomic endonucleases using 3-h-dna-coated wells of plastic depression plates as substrate|journal=Nucleic Acids Research|volume=2|issue=6|pages=897–903|doi=10.1093/nar/2.6.897|pmid=167356|pmc=343476}}</ref>

Restriction enzymes are endonucleases from [[eubacteria]] and [[archaea]] that recognize a specific DNA sequence.<ref>{{cite book |author1=Stephen T. Kilpatrick |author2=Jocelyn E. Krebs |author3=Lewin, Benjamin |author4=Goldstein, Elliott |title=Lewin's genes X |publisher=Jones and Bartlett |location=Boston |year=2011 |isbn=978-0-7637-6632-0 |url-access=registration |url=https://archive.org/details/lewinsgenesx0000unse }}</ref> The nucleotide sequence recognized for cleavage by a restriction enzyme is called the ''restriction site''. Typically, a restriction site will be a [[palindromic]] sequence about 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. The DNA fragments cleaved by the same endonuclease can be joined regardless of the origin of the DNA. Such DNA is called [[recombinant DNA]]; DNA formed by the joining of genes into new combinations.<ref name="Cox_Nelson_Lehninger_2005">{{cite book | vauthors = Cox M, Nelson DR, Lehninger AL | title = Lehninger principles of biochemistry | publisher = W.H. Freeman | location = San Francisco | year = 2005 | pages = [https://archive.org/details/lehningerprincip00lehn_0/page/952 952] | isbn = 978-0-7167-4339-2 | url-access = registration | url = https://archive.org/details/lehningerprincip00lehn_0/page/952 }}</ref> ''Restriction endonucleases'' ([[restriction enzyme]]s) 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]].<ref name="Simon_2010">{{cite book | author = Simon M | title = Emergent computation: Emphasizing Bioinformatics | year = 2010 |publisher = Springer | location =  New York | isbn = 978-1441919632 | pages = 437 }}</ref> One of the more famous endonucleases is [[Cas9]].