Nicking enzyme explained

A nicking enzyme (or nicking endonuclease) is an enzyme that cuts one strand of a double-stranded DNA or RNA^[1] at a specific recognition nucleotide sequences known as a restriction site. Such enzymes hydrolyse (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, exonucleotyic 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 13 of these are available commercially^[8] and are routinely used for research and in commercial products.

External links

• New England Biolabs Nicking Enzymes
• Fermentas Nicking Enzymes

Notes and References

1. Wang X, Zhu B. SARS-CoV-2 nsp15 preferentially degrades AU-rich dsRNA via its dsRNA nickase activity. Nucleic Acids Research. 52. 9. 22 May 2024. 5257–5272.
2. Ando T . etal . Isolation and characterization of enzymes with nicking action from phage T4-infected Escherichia coli . J. Biochem. . 66 . 1 . 1–10 . July 1969 . 4309718 . 10.1093/oxfordjournals.jbchem.a129107.
3. Morgan RD, Kong H, etal . Characterization of the specific DNA nicking activity of restriction endonuclease N.BstNBI. Biol. Chem. . 381 . 11 . 1123–5 . November 2000 . 11154070 . 10.1515/BC.2000.137. 22472698.
4. Walker GT, Little MC, Nadeau JG, Shank DD . 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 . 1309614 . 48243. 10.1073/pnas.89.1.392. 1992PNAS...89..392W . free .
5. Wang H, Hays JB . Simple and rapid preparation of gapped plasmid DNA for incorporation of oligomers containing specific DNA lesions . Mol. Biotechnol. . 19 . 2 . 133–40 . October 2001 . 11725483 . 10.1385/MB:19:2:133. 22156627 .
6. Rigby PW, Dieckmann M, Rhodes C, Berg P . 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 . 881736 . 10.1016/0022-2836(77)90052-3.
7. Jo K, Dhingra DM, Odijk T, de Pablo JJ, Graham MD, Runnheim R, Forrest D, Schwartz DC . A single-molecule barcoding system using nanoslits for DNA analysis . Proc. Natl. Acad. Sci. U.S.A. . 104 . 8 . 2673–8 . 2007 . 17296933 . 10.1073/pnas.0611151104 . 1815240. 2007PNAS..104.2673J . free .
8. Encyclopedia: REBASE Enzymes . Encyclopedia of restriction and nicking enzymes . 2009-06-01 .