Nicking enzyme

{{Short description|Endonuclease that cuts a single DNA strand}}

A nicking enzyme (or nicking endonuclease) is an enzyme that cuts only one strand of a double-stranded DNA or RNA molecule{{cite journal|vauthors=Wang X, Zhu B|title=SARS-CoV-2 nsp15 preferentially degrades AU-rich dsRNA via its dsRNA nickase activity|journal=Nucleic Acids Research|volume=52|issue=9|date=22 May 2024|pages=5257–5272|doi=10.1093/nar/gkae290 |pmid=38634805 |pmc=11109939 }} at a specific recognition nucleotide sequence known as the restriction site. Such enzymes hydrolyze (cut) only one strand of the DNA duplex, to produce DNA molecules that are “nicked”, rather than cleaved.{{cite journal |author1=Ando T |display-authors=etal | title = Isolation and characterization of enzymes with nicking action from phage T4-infected Escherichia coli | journal = J. Biochem. | volume = 66 | issue = 1 | pages = 1–10 |date=July 1969 | pmid = 4309718 | doi = 10.1093/oxfordjournals.jbchem.a129107}}{{cite journal |vauthors=Morgan RD, Kong H, etal | title = Characterization of the specific DNA nicking activity of restriction endonuclease N.BstNBI| journal = Biol. Chem. | volume = 381 | issue = 11 | pages = 1123–5 |date=November 2000 | pmid = 11154070 | doi = 10.1515/BC.2000.137| s2cid = 22472698}}

They can be used for strand-displacement amplification,{{cite journal |vauthors=Walker GT, Little MC, Nadeau JG, Shank DD | title = Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system | journal = Proc. Natl. Acad. Sci. U.S.A. | volume = 89 | issue = 1 | pages = 392–6 |date=Jan 1992 | pmid = 1309614 | pmc = 48243| doi = 10.1073/pnas.89.1.392| bibcode = 1992PNAS...89..392W | doi-access = free }} Nicking Enzyme Amplification Reaction, exonucleolytic degradation, the creation of small gaps,{{cite journal |vauthors=Wang H, Hays JB | title = Simple and rapid preparation of gapped plasmid DNA for incorporation of oligomers containing specific DNA lesions | journal = Mol. Biotechnol. | volume = 19 | issue = 2 | pages = 133–40 |date=October 2001 | pmid = 11725483 | doi = 10.1385/MB:19:2:133| s2cid = 22156627 }} or nick translation.{{cite journal |vauthors=Rigby PW, Dieckmann M, Rhodes C, Berg P |title=Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I |journal=J. Mol. Biol. |volume=113 |issue=1 |pages=237–51 |date=June 1977 |pmid=881736 |doi= 10.1016/0022-2836(77)90052-3}} The latter process has been successfully used to incorporate both radioactively labelled nucleotides and fluorescent nucleotides allowing specific regions on a double stranded DNA to be studied.{{cite journal |vauthors=Jo K, Dhingra DM, Odijk T, de Pablo JJ, Graham MD, Runnheim R, Forrest D, Schwartz DC |title=A single-molecule barcoding system using nanoslits for DNA analysis |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=104 |issue=8 |pages=2673–8 |year=2007 |pmid=17296933 |doi=10.1073/pnas.0611151104 |pmc=1815240|bibcode=2007PNAS..104.2673J |doi-access=free }} Over 200 nicking enzymes have been studied, and 13 of these are available commercially{{cite encyclopedia |title=REBASE Enzymes |encyclopedia=Encyclopedia of restriction and nicking enzymes |url= http://rebase.neb.com/cgi-bin/azlist?nick |access-date=2009-06-01 }} and are routinely used for research and in commercial products.