Biology:Nicking enzyme

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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[1] 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.[2][3]

They can be used for strand-displacement amplification,[4] Nicking Enzyme Amplification Reaction, exonucleolytic degradation, the creation of small gaps,[5] or nick translation.[6] 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.[6][7] Over 200 nicking enzymes have been studied, and 15 of these are available commercially[8] and are routinely used for research and in commercial products.

The nicking enzyme Nb.BbvCI has been successfully used to incorporate fluorochrome-labeled nucleotides into specific spots of a DNA sequence via nick translation.[9]

References

  1. ↑ "SARS-CoV-2 nsp15 preferentially degrades AU-rich dsRNA via its dsRNA nickase activity". Nucleic Acids Research 52 (9): 5257–5272. 22 May 2024. doi:10.1093/nar/gkae290. PMID 38634805. 
  2. ↑ Ando T (July 1969). "Isolation and characterization of enzymes with nicking action from phage T4-infected Escherichia coli". J. Biochem. 66 (1): 1–10. doi:10.1093/oxfordjournals.jbchem.a129107. PMID 4309718. 
  3. ↑ "Characterization of the specific DNA nicking activity of restriction endonuclease N.BstNBI". Biol. Chem. 381 (11): 1123–5. November 2000. doi:10.1515/BC.2000.137. PMID 11154070. 
  4. ↑ "Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system". Proc. Natl. Acad. Sci. U.S.A. 89 (1): 392–6. Jan 1992. doi:10.1073/pnas.89.1.392. PMID 1309614. Bibcode: 1992PNAS...89..392W. 
  5. ↑ "Simple and rapid preparation of gapped plasmid DNA for incorporation of oligomers containing specific DNA lesions". Mol. Biotechnol. 19 (2): 133–40. October 2001. doi:10.1385/MB:19:2:133. PMID 11725483. 
  6. ↑ 6.0 6.1 "Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I". J. Mol. Biol. 113 (1): 237–51. June 1977. doi:10.1016/0022-2836(77)90052-3. PMID 881736. 
  7. ↑ "A single-molecule barcoding system using nanoslits for DNA analysis". Proc. Natl. Acad. Sci. U.S.A. 104 (8): 2673–8. 2007. doi:10.1073/pnas.0611151104. PMID 17296933. Bibcode: 2007PNAS..104.2673J. 
  8. ↑ "REBASE Enzymes". Encyclopedia of restriction and nicking enzymes. https://rebase.neb.com/rebase/azlist.nick.html. Retrieved 2009-06-01. 
  9. ↑ "A single-molecule barcoding system using nanoslits for DNA analysis". PNAS 104 (8): 2673–8. 2007. doi:10.1073/pnas.0611151104. PMID 17296933. Bibcode: 2007PNAS..104.2673J. 



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