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.
^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.
^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.
^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.
^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.
^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.
^ abRigby 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.
^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.
^"REBASE Enzymes". Encyclopedia of restriction and nicking enzymes. Retrieved 2009-06-01.
A nickingenzyme (or nicking endonuclease) is an enzyme that cuts one strand of a double-stranded DNA or RNA at a specific recognition nucleotide sequences...
NickingEnzyme Amplification Reaction (NEAR) is a method for in vitro DNA amplification like the polymerase chain reaction (PCR). NEAR is isothermal, replicating...
Registry (NEAR), a patient registry for intubations in the United States Nickingenzyme amplification reaction (NEAR), a method of DNA amplification NEAR Protocol...
nalA gene product and its relationship to DNA gyrase and a novel nicking-closing enzyme". Proceedings of the National Academy of Sciences of the United...
Taylor AF, Schultz DW, Ponticelli AS, Smith GR (May 1985). "RecBC enzymenicking at Chi sites during DNA unwinding: location and orientation-dependence...
amplification is a similar idea, but done with a strand-displacing polymerase. Nickingenzyme amplification reaction (NEAR) and its cousin strand displacement amplification...
Paul Tardif. Ionian's proprietary isothermal technology, termed the NickingEnzyme Amplification Reaction Assay, is claimed to be capable of amplifying...
Turberfield AJ (July 2005). "A free-running DNA motor powered by a nickingenzyme". Angewandte Chemie. 44 (28): 4358–4361. doi:10.1002/anie.200501262...
portion of the fusion protein to nick the unedited strand at a nearby site, opposite to the original nick. Nicking the non-edited strand causes the cell's...
techniques include LAMP, NASBA, helicase-dependent amplification (HDA), and nickingenzyme amplification reaction (NEAR). The techniques differ in the specifics...
produces 230 recombinant and 30 native restriction enzymes for genomic research, as well as nickingenzymes and DNA methylases. It pursues research in areas...
S2CID 85446523. Bath J (July 11, 2005). "A free-running DNA motor powered by a nickingenzyme". Angewandte Chemie International Edition. 117 (28): 4432–4435. Bibcode:2005AngCh...
conjugation with chemicals that mimic an intermediate step of this second nicking event. If the F-plasmid that is transferred has previously been integrated...
activity. Proprietary enzyme mixes are available commercially to perform all steps in the procedure in a single incubation. Nick translation could cause...
Deamination is the removal of an amino group from a molecule. Enzymes that catalyse this reaction are called deaminases. In the human body, deamination...
and bright sides of an enzyme: a three dimensional structure of the N-terminal domain of Zophobas morio luciferase-like enzyme, inferences on the biological...
which are synthesized discontinuously and later linked together by the enzyme DNA ligase to create the lagging strand during DNA replication. They were...
single-stranded DNA for cleavage. DNase I catalyzes nonspecific DNA cleavage by nicking phosphodiester linkages in one of the strands. Its cleavage site lies between...
drive the enzyme-catalyzed reaction. In DNA replication, for example, formation of the phosphodiester bonds is catalyzed by a DNA polymerase enzyme, using...
single-strand DNA transesterase enzyme produced by some prokaryotes and viruses. Relaxases are responsible for site- and strand-specific nicks in unwound double-stranded...
assay relies on the use of terminal deoxynucleotidyl transferase (TdT), an enzyme that catalyzes attachment of deoxynucleotides, tagged with a fluorochrome...
protein design principles. It has been used to improve the function of many enzymes for industrial catalysis. It is also a product and services market, with...
DNA polymerase III holoenzyme is the primary enzyme complex involved in prokaryotic DNA replication. It was discovered by Thomas Kornberg (son of Arthur...
In molecular biology, endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain (namely DNA or RNA). Some, such as deoxyribonuclease...
equivalents of ATP through substrate phosphorylation catalyzed by two enzymes, phosphoglycerate kinase (PGK) and pyruvate kinase. Two equivalents of...
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