Editing Restriction enzyme (section)

=== Artificial restriction enzymes ===
Artificial restriction enzymes can be generated by fusing a natural or engineered [[DNA-binding domain]] to a [[nuclease]] domain (often the cleavage domain of the type IIS restriction enzyme [[FokI]]).<ref name="kim1996">{{cite journal | vauthors = Kim YG, Cha J, Chandrasegaran S | title = Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 93 | issue = 3 | pages = 1156–60 | date = February 1996 | pmid = 8577732 | pmc = 40048 | doi = 10.1073/pnas.93.3.1156 | bibcode = 1996PNAS...93.1156K | doi-access = free }}</ref> Such artificial restriction enzymes can target large DNA sites (up to 36 bp) and can be engineered to bind to desired DNA sequences.<ref name="pmid20717154">{{cite journal | vauthors = Urnov FD, Rebar EJ, Holmes MC, Zhang HS, Gregory PD | title = Genome editing with engineered zinc finger nucleases | journal = Nature Reviews. Genetics | volume = 11 | issue = 9 | pages = 636–46 | date = September 2010 | pmid = 20717154 | doi = 10.1038/nrg2842 | s2cid = 205484701 }}</ref> [[Zinc finger nuclease]]s are the most commonly used artificial restriction enzymes and are generally used in [[genetic engineering]] applications,<ref name="pmid19404258">{{cite journal | vauthors = Townsend JA, Wright DA, Winfrey RJ, Fu F, Maeder ML, Joung JK, Voytas DF | title = High-frequency modification of plant genes using engineered zinc-finger nucleases | journal = Nature | volume = 459 | issue = 7245 | pages = 442–5 | date = May 2009 | pmid = 19404258 | pmc = 2743854 | doi = 10.1038/nature07845 | bibcode = 2009Natur.459..442T }}</ref><ref name="pmid19404259">{{cite journal | vauthors = Shukla VK, Doyon Y, Miller JC, DeKelver RC, Moehle EA, Worden SE, Mitchell JC, Arnold NL, Gopalan S, Meng X, Choi VM, Rock JM, Wu YY, Katibah GE, Zhifang G, McCaskill D, Simpson MA, Blakeslee B, Greenwalt SA, Butler HJ, Hinkley SJ, Zhang L, Rebar EJ, Gregory PD, Urnov FD | display-authors = 6 | title = Precise genome modification in the crop species Zea mays using zinc-finger nucleases | journal = Nature | volume = 459 | issue = 7245 | pages = 437–41 | date = May 2009 | pmid = 19404259 | doi = 10.1038/nature07992 | bibcode = 2009Natur.459..437S | s2cid = 4323298 }}</ref><ref name="pmid18554175">{{cite journal | vauthors = Ekker SC | title = Zinc finger-based knockout punches for zebrafish genes | journal = Zebrafish | volume = 5 | issue = 2 | pages = 121–3 | year = 2008 | pmid = 18554175 | pmc = 2849655 | doi = 10.1089/zeb.2008.9988 }}</ref><ref name="pmid19628861">{{cite journal | vauthors = Geurts AM, Cost GJ, Freyvert Y, Zeitler B, Miller JC, Choi VM, Jenkins SS, Wood A, Cui X, Meng X, Vincent A, Lam S, Michalkiewicz M, Schilling R, Foeckler J, Kalloway S, Weiler H, Ménoret S, Anegon I, Davis GD, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Jacob HJ, Buelow R | display-authors = 6 | title = Knockout rats via embryo microinjection of zinc-finger nucleases | journal = Science | volume = 325 | issue = 5939 | pages = 433 | date = July 2009 | pmid = 19628861 | pmc = 2831805 | doi = 10.1126/science.1172447 | bibcode = 2009Sci...325..433G }}</ref> but can also be used for more standard [[gene cloning]] applications.<ref name="pmid21029755">{{cite journal | vauthors = Tovkach A, Zeevi V, Tzfira T | title = Expression, purification and characterization of cloning-grade zinc finger nuclease | journal = Journal of Biotechnology | volume = 151 | issue = 1 | pages = 1–8 | date = January 2011 | pmid = 21029755 | doi = 10.1016/j.jbiotec.2010.10.071 }}</ref> Other artificial restriction enzymes are based on the DNA binding domain of [[TAL effector]]s.<ref name="pmid20660643">{{cite journal | vauthors = Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, Hummel A, Bogdanove AJ, Voytas DF | display-authors = 6 | title = Targeting DNA double-strand breaks with TAL effector nucleases | journal = Genetics | volume = 186 | issue = 2 | pages = 757–61 | date = October 2010 | pmid = 20660643 | pmc = 2942870 | doi = 10.1534/genetics.110.120717 }}</ref><ref name="pmid20699274">{{cite journal | vauthors = Li T, Huang S, Jiang WZ, Wright D, Spalding MH, Weeks DP, Yang B | title = TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain | journal = Nucleic Acids Research | volume = 39 | issue = 1 | pages = 359–72 | date = January 2011 | pmid = 20699274 | pmc = 3017587 | doi = 10.1093/nar/gkq704 }}</ref>

In 2013, a new technology CRISPR-Cas9, based on a prokaryotic viral defense system, was engineered for editing the genome, and it was quickly adopted in laboratories.<ref name=Hsu2014>{{cite journal | vauthors = Hsu PD, Lander ES, Zhang F | title = Development and applications of CRISPR-Cas9 for genome engineering | journal = Cell | volume = 157 | issue = 6 | pages = 1262–78 | date = June 2014 | pmid = 24906146 | pmc = 4343198 | doi = 10.1016/j.cell.2014.05.010 }}</ref> For more detail, read [[CRISPR]] (Clustered regularly interspaced short palindromic repeats).

In 2017, a group from University of Illinois reported using an [[Argonaute]] protein taken from ''[[Pyrococcus furiosus]]'' (PfAgo) along with guide DNA to edit DNA ''in vitro'' as artificial restriction enzymes.<ref>{{cite news |title=Revolutionizing Biotechnology with Artificial Restriction Enzymes |url=https://www.genengnews.com/topics/omics/revolutionizing-biotechnology-with-artificial-restriction-enzymes/ |access-date=27 May 2021 |work=Genetic Engineering and Biotechnology News |date=10 February 2017}} (reporting on [http://pubs.acs.org/doi/abs/10.1021/acssynbio.6b00324 Programmable DNA-Guided Artificial Restriction Enzymes])</ref>

Artificial ribonucleases that act as restriction enzymes for RNA have also been developed. A [[Peptide nucleic acid|PNA]]-based system, called a PNAzyme, has a Cu(II)-[[Neocuproine|2,9-dimethylphenanthroline]] group that mimics ribonucleases for specific RNA sequence and cleaves at a non-base-paired region (RNA bulge) of the targeted RNA formed when the enzyme binds the RNA. This enzyme shows selectivity by cleaving only at one site that either does not have a mismatch or is kinetically preferred out of two possible cleavage sites.<ref>{{cite journal | vauthors = Murtola M, Wenska M, Strömberg R | title = PNAzymes that are artificial RNA restriction enzymes | journal = Journal of the American Chemical Society | volume = 132 | issue = 26 | pages = 8984–90 | date = July 2010 | pmid = 20545354 | doi = 10.1021/ja1008739 }}</ref>