Nicking enzyme

A nicking enzyme (or nicking endonuclease) is an enzyme that cuts only one strand of a double-stranded DNA or RNA molecule 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.

They can be used for strand-displacement amplification, Nicking Enzyme Amplification Reaction, exonucleolytic degradation, the creation of small gaps, or nick translation. 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. Over 200 nicking enzymes have been studied, and 15 of these are available commercially 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.

References

  1. ↑ Wang X, Zhu B (22 May 2024). "SARS-CoV-2 nsp15 preferentially degrades AU-rich dsRNA via its dsRNA nickase activity". Nucleic Acids Research. 52 (9): 5257–5272. doi:10.1093/nar/gkae290. PMC 11109939. PMID 38634805.
  2. ↑ Ando T; et al. (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. ↑ Morgan RD, Kong H, et al. (November 2000). "Characterization of the specific DNA nicking activity of restriction endonuclease N.BstNBI". Biol. Chem. 381 (11): 1123–5. doi:10.1515/BC.2000.137. PMID 11154070. S2CID 22472698.
  4. ↑ Walker GT, Little MC, Nadeau JG, Shank DD (Jan 1992). "Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system". Proc. Natl. Acad. Sci. U.S.A. 89 (1): 392–6. Bibcode:1992PNAS...89..392W. doi:10.1073/pnas.89.1.392. PMC 48243. PMID 1309614.
  5. ↑ Wang H, Hays JB (October 2001). "Simple and rapid preparation of gapped plasmid DNA for incorporation of oligomers containing specific DNA lesions". Mol. Biotechnol. 19 (2): 133–40. doi:10.1385/MB:19:2:133. PMID 11725483. S2CID 22156627.
  6. 1 2 Rigby PW, Dieckmann M, Rhodes C, Berg P (June 1977). "Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I". J. Mol. Biol. 113 (1): 237–51. doi:10.1016/0022-2836(77)90052-3. PMID 881736.
  7. ↑ Jo K, Dhingra DM, Odijk T, de Pablo JJ, Graham MD, Runnheim R, Forrest D, Schwartz DC (2007). "A single-molecule barcoding system using nanoslits for DNA analysis". Proc. Natl. Acad. Sci. U.S.A. 104 (8): 2673–8. Bibcode:2007PNAS..104.2673J. doi:10.1073/pnas.0611151104. PMC 1815240. PMID 17296933.
  8. ↑ "REBASE Enzymes". Encyclopedia of restriction and nicking enzymes. Retrieved 2009-06-01.
  9. ↑ Jo K, Dhingra DM, Odijk T, de Pablo JJ, Graham MD, Runnheim R, Forrest D, Schwartz DC (2007). "A single-molecule barcoding system using nanoslits for DNA analysis". PNAS. 104 (8): 2673–8. Bibcode:2007PNAS..104.2673J. doi:10.1073/pnas.0611151104. PMC 1815240. PMID 17296933.