Restriction enzyme: Difference between revisions

Type II site-specific deoxyribonuclease-like
Type II site-specific deoxyribonuclease-like
	Structure of the homodimeric restriction enzyme EcoRI (cyan and green cartoon diagram) bound to double stranded DNA (brown tubes). Two catalytic magnesium ions (one from each monomer) are shown as magenta spheres and are adjacent to the cleaved sites in the DNA made by the enzyme (depicted as gaps in the DNA backbone).
Identifiers
Symbol	Restrct_endonuc-II-like
Pfam clan	CL0236
InterPro	IPR011335
SCOP2	1wte / SCOPe / SUPFAM

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A restriction enzyme, restriction endonuclease, REase, ENase or restrictase is an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites.^[1]^[2]^[3] Restriction enzymes are one class of the broader endonuclease group of enzymes. Restriction enzymes are commonly classified into five types, which differ in their structure and whether they cut their DNA substrate at their recognition site, or if the recognition and cleavage sites are separate from one another. To cut DNA, all restriction enzymes make two incisions, once through each sugar-phosphate backbone (i.e. each strand) of the DNA double helix.

These enzymes are found in bacteria and archaea and provide a defense mechanism against invading viruses.^[4]^[5] Inside a prokaryote, the restriction enzymes selectively cut up foreign DNA in a process called restriction digestion; meanwhile, host DNA is protected by a modification enzyme (a methyltransferase) that modifies the prokaryotic DNA and blocks cleavage. Together, these two processes form the restriction modification system.^[6]

More than 3,600 restriction endonucleases are known which represent over 250 different specificities.^[7] Over 3,000 of these have been studied in detail, and more than 800 of these are available commercially.^[8] These enzymes are routinely used for DNA modification in laboratories, and they are a vital tool in molecular cloning.^[9]^[10]^[11]

History

The term restriction enzyme originated from the studies of phage λ, a virus that infects bacteria, and the phenomenon of host-controlled restriction and modification of such bacterial phage or bacteriophage.^[12] The phenomenon was first identified in work done in the laboratories of Salvador Luria, Jean Weigle and Giuseppe Bertani in the early 1950s.^[13]^[14] It was found that, for a bacteriophage λ that can grow well in one strain of Escherichia coli, for example E. coli C, when grown in another strain, for example E. coli K, its yields can drop significantly, by as much as three to five orders of magnitude. The host cell, in this example E. coli K, is known as the restricting host and appears to have the ability to reduce the biological activity of the phage λ. If a phage becomes established in one strain, the ability of that phage to grow also becomes restricted in other strains. In the 1960s, it was shown in work done in the laboratories of Werner Arber and Matthew Meselson that the restriction is caused by an enzymatic cleavage of the phage DNA, and the enzyme involved was therefore termed a restriction enzyme.^[4]^[15]^[16]^[17]

The restriction enzymes studied by Arber and Meselson were type I restriction enzymes, which cleave DNA randomly away from the recognition site.^[18] In 1970, Hamilton O. Smith, Thomas Kelly and Kent Wilcox isolated and characterized the first type II restriction enzyme, HindII, from the bacterium Haemophilus influenzae.^[19]^[20] Restriction enzymes of this type are more useful for laboratory work as they cleave DNA at the site of their recognition sequence and are the most commonly used as a molecular biology tool.^[21] Later, Daniel Nathans and Kathleen Danna showed that cleavage of simian virus 40 (SV40) DNA by restriction enzymes yields specific fragments that can be separated using polyacrylamide gel electrophoresis, thus showing that restriction enzymes can also be used for mapping DNA.^[22] For their work in the discovery and characterization of restriction enzymes, the 1978 Nobel Prize for Physiology or Medicine was awarded to Werner Arber, Daniel Nathans, and Hamilton O. Smith.^[23] The discovery of restriction enzymes allows DNA to be manipulated, leading to the development of recombinant DNA technology that has many applications, for example, allowing the large scale production of proteins such as human insulin used by diabetic patients.^[13]^[24]

Origins

Restriction enzymes likely evolved from a common ancestor and became widespread via horizontal gene transfer.^[25]^[26] In addition, there is mounting evidence that restriction endonucleases evolved as a selfish genetic element.^[27]

Recognition site

A palindromic recognition site reads the same on the reverse strand as it does on the forward strand when both are read in the same orientation

Restriction enzymes recognize a specific sequence of nucleotides^[2] and produce a double-stranded cut in the DNA. The recognition sequences can also be classified by the number of bases in its recognition site, usually between 4 and 8 bases, and the number of bases in the sequence will determine how often the site will appear by chance in any given genome, e.g., a 4-base pair sequence would theoretically occur once every 4^4 or 256bp, 6 bases, 4^6 or 4,096bp, and 8 bases would be 4^8 or 65,536bp.^[28] Many of them are palindromic, meaning the base sequence reads the same backwards and forwards.^[29] In theory, there are two types of palindromic sequences that can be possible in DNA. The mirror-like palindrome is similar to those found in ordinary text, in which a sequence reads the same forward and backward on a single strand of DNA, as in GTAATG. The inverted repeat palindrome is also a sequence that reads the same forward and backward, but the forward and backward sequences are found in complementary DNA strands (i.e., of double-stranded DNA), as in GTATAC (GTATAC being complementary to CATATG).^[30] Inverted repeat palindromes are more common and have greater biological importance than mirror-like palindromes.

EcoRI digestion produces "sticky" ends,

whereas SmaI restriction enzyme cleavage produces "blunt" ends:

Recognition sequences in DNA differ for each restriction enzyme, producing differences in the length, sequence and strand orientation (5' end or 3' end) of a sticky-end "overhang" of an enzyme restriction.^[31]

Different restriction enzymes that recognize the same sequence are known as neoschizomers. These often cleave in different locales of the sequence. Different enzymes that recognize and cleave in the same location are known as isoschizomers.

Types

Naturally occurring restriction endonucleases are categorized into five groups (Types I, II, III, IV, and V) based on their composition and enzyme cofactor requirements, the nature of their target sequence, and the position of their DNA cleavage site relative to the target sequence.^[32]^[33]^[34] DNA sequence analysis of restriction enzymes however show great variations, indicating that there are more than four types.^[35] All types of enzymes recognize specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements,^[36]^[37] as summarised below:

Type I enzymes (EC 3.1.21.3) cleave at sites remote from a recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction digestion and methylase (EC 2.1.1.72) activities.
Type II enzymes (EC 3.1.21.4) cleave within or at short specific distances from a recognition site; most require magnesium; single function (restriction digestion) enzymes independent of methylase.
Type III enzymes (EC 3.1.21.5) cleave at sites a short distance from a recognition site; require ATP (but do not hydrolyse it); S-adenosyl-L-methionine stimulates the reaction but is not required; exist as part of a complex with a modification methylase (EC 2.1.1.72).
Type IV enzymes target modified DNA, e.g. methylated, hydroxymethylated and glucosyl-hydroxymethylated DNA
Type V enzymes utilize guide RNAs (gRNAs)

Type l

Type I restriction enzymes were the first to be identified and were first identified in two different strains (K-12 and B) of E. coli.^[38] These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions—one containing 3–4 nucleotides, and another containing 4–5 nucleotides—separated by a non-specific spacer of about 6–8 nucleotides. These enzymes are multifunctional and are capable of both restriction digestion and modification activities, depending upon the methylation status of the target DNA. The cofactors S-Adenosyl methionine (AdoMet), hydrolyzed adenosine triphosphate (ATP), and magnesium (Mg²⁺) ions, are required for their full activity. Type I restriction enzymes possess three subunits called HsdR, HsdM, and HsdS; HsdR is required for restriction digestion; HsdM is necessary for adding methyl groups to host DNA (methyltransferase activity), and HsdS is important for specificity of the recognition (DNA-binding) site in addition to both restriction digestion (DNA cleavage) and modification (DNA methyltransferase) activity.^[32]^[38]

Type II

Typical type II restriction enzymes differ from type I restriction enzymes in several ways. They form homodimers, with recognition sites that are usually undivided and palindromic and 4–8 nucleotides in length. They recognize and cleave DNA at the same site, and they do not use ATP or AdoMet for their activity—they usually require only Mg²⁺ as a cofactor.^[29] These enzymes cleave the phosphodiester bond of double helix DNA. It can either cleave at the center of both strands to yield a blunt end, or at a staggered position leaving overhangs called sticky ends.^[40] These are the most commonly available and used restriction enzymes. In the 1990s and early 2000s, new enzymes from this family were discovered that did not follow all the classical criteria of this enzyme class, and new subfamily nomenclature was developed to divide this large family into subcategories based on deviations from typical characteristics of type II enzymes.^[29] These subgroups are defined using a letter suffix.

Type IIB restriction enzymes (e.g., BcgI and BplI) are multimers, containing more than one subunit.^[29] They cleave DNA on both sides of their recognition to cut out the recognition site. They require both AdoMet and Mg²⁺ cofactors. Type IIE restriction endonucleases (e.g., NaeI) cleave DNA following interaction with two copies of their recognition sequence.^[29] One recognition site acts as the target for cleavage, while the other acts as an allosteric effector that speeds up or improves the efficiency of enzyme cleavage. Similar to type IIE enzymes, type IIF restriction endonucleases (e.g. NgoMIV) interact with two copies of their recognition sequence but cleave both sequences at the same time.^[29] Type IIG restriction endonucleases (e.g., RM.Eco57I) do have a single subunit, like classical Type II restriction enzymes, but require the cofactor AdoMet to be active.^[29] Type IIM restriction endonucleases, such as DpnI, are able to recognize and cut methylated DNA.^[29]^[41]^[42] Type IIS restriction endonucleases (e.g. FokI) cleave DNA at a defined distance from their non-palindromic asymmetric recognition sites;^[29] this characteristic is widely used to perform in-vitro cloning techniques such as Golden Gate cloning. These enzymes may function as dimers. Similarly, Type IIT restriction enzymes (e.g., Bpu10I and BslI) are composed of two different subunits. Some recognize palindromic sequences while others have asymmetric recognition sites.^[29]

Type III

Type III restriction enzymes (e.g., EcoP15) recognize two separate non-palindromic sequences that are inversely oriented. They cut DNA about 20–30 base pairs after the recognition site.^[43] These enzymes contain more than one subunit and require AdoMet and ATP cofactors for their roles in DNA methylation and restriction digestion, respectively.^[44] They are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional proteins composed of two subunits, Res (P08764) and Mod (P08763). The Mod subunit recognises the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction digestion, although it has no enzymatic activity on its own. Type III enzymes recognise short 5–6 bp-long asymmetric DNA sequences and cleave 25–27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction digestion to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenine residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction digestion. Type III enzymes belong to the beta-subfamily of N6 adenine methyltransferases, containing the nine motifs that characterise this family, including motif I, the AdoMet binding pocket (FXGXG), and motif IV, the catalytic region (S/D/N (PP) Y/F).^[36]^[45]

Type IV

Type IV enzymes recognize modified, typically methylated DNA and are exemplified by the McrBC and Mrr systems of E. coli.^[35]

Type V

Type V restriction enzymes (e.g., the cas9-gRNA complex from CRISPRs^[46]) utilize guide RNAs to target specific non-palindromic sequences found on invading organisms. They can cut DNA of variable length, provided that a suitable guide RNA is provided. The flexibility and ease of use of these enzymes make them promising for future genetic engineering applications.^[46]^[47]

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).^[48] Such artificial restriction enzymes can target large DNA sites (up to 36 bp) and can be engineered to bind to desired DNA sequences.^[49] Zinc finger nucleases are the most commonly used artificial restriction enzymes and are generally used in genetic engineering applications,^[50]^[51]^[52]^[53] but can also be used for more standard gene cloning applications.^[54] Other artificial restriction enzymes are based on the DNA binding domain of TAL effectors.^[55]^[56]

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.^[57] 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.^[58]

Artificial ribonucleases that act as restriction enzymes for RNA have also been developed. A PNA-based system, called a PNAzyme, has a Cu(II)-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.^[59]

Nomenclature

Derivation of the EcoRI name
Abbreviation	Meaning	Description
E	Escherichia	genus
co	coli	specific species
R	RY13	strain
I	First identified	order of identification in the bacterium

Since their discovery in the 1970s, many restriction enzymes have been identified; for example, more than 3500 different Type II restriction enzymes have been characterized.^[60] Each enzyme is named after the bacterium from which it was isolated, using a naming system based on bacterial genus, species and strain.^[61]^[62] For example, the name of the EcoRI restriction enzyme was derived as shown in the box.

Applications

Isolated restriction enzymes are used to manipulate DNA for different scientific applications.

They are used to assist insertion of genes into plasmid vectors during gene cloning and protein production experiments. For optimal use, plasmids that are commonly used for gene cloning are modified to include a short polylinker sequence (called the multiple cloning site, or MCS) rich in restriction recognition sequences. This allows flexibility when inserting gene fragments into the plasmid vector; restriction sites contained naturally within genes influence the choice of endonuclease for digesting the DNA, since it is necessary to avoid restriction of wanted DNA while intentionally cutting the ends of the DNA. To clone a gene fragment into a vector, both plasmid DNA and gene insert are typically cut with the same restriction enzymes, and then glued together with the assistance of an enzyme known as a DNA ligase.^[63]^[64]

Restriction enzymes can also be used to distinguish gene alleles by specifically recognizing single base changes in DNA known as single-nucleotide polymorphisms (SNPs).^[65]^[66] This is however only possible if a SNP alters the restriction site present in the allele. In this method, the restriction enzyme can be used to genotype a DNA sample without the need for expensive gene sequencing. The sample is first digested with the restriction enzyme to generate DNA fragments, and then the different sized fragments separated by gel electrophoresis. In general, alleles with correct restriction sites will generate two visible bands of DNA on the gel, and those with altered restriction sites will not be cut and will generate only a single band. A DNA map by restriction digest can also be generated that can give the relative positions of the genes.^[67] The different lengths of DNA generated by restriction digest also produce a specific pattern of bands after gel electrophoresis, and can be used for DNA fingerprinting.

In a similar manner, restriction enzymes are used to digest genomic DNA for gene analysis by Southern blot. This technique allows researchers to identify how many copies (or paralogues) of a gene are present in the genome of one individual, or how many gene mutations (polymorphisms) have occurred within a population. The latter example is called restriction fragment length polymorphism (RFLP).^[68]

Artificial restriction enzymes created by linking the FokI DNA cleavage domain with an array of DNA binding proteins or zinc finger arrays, denoted zinc finger nucleases (ZFN), are a powerful tool for host genome editing due to their enhanced sequence specificity. ZFN work in pairs, their dimerization being mediated in-situ through the FokI domain. Each zinc finger array (ZFA) is capable of recognizing 9–12 base pairs, making for 18–24 for the pair. A 5–7 bp spacer between the cleavage sites further enhances the specificity of ZFN, making them a safe and more precise tool that can be applied in humans. A recent Phase I clinical trial of ZFN for the targeted abolition of the CCR5 co-receptor for HIV-1 has been undertaken.^[69]

Others have proposed using the bacteria R-M system as a model for devising human anti-viral gene or genomic vaccines and therapies since the RM system serves an innate defense-role in bacteria by restricting tropism by bacteriophages.^[70] There is research on REases and ZFN that can cleave the DNA of various human viruses, including HSV-2, high-risk HPVs and HIV-1, with the ultimate goal of inducing target mutagenesis and aberrations of human-infecting viruses.^[71]^[72]^[73] The human genome already contains remnants of retroviral genomes that have been inactivated and harnessed for self-gain. Indeed, the mechanisms for silencing active L1 genomic retroelements by the three prime repair exonuclease 1 (TREX1) and excision repair cross complementing 1(ERCC) appear to mimic the action of RM-systems in bacteria, and the non-homologous end-joining (NHEJ) that follows the use of ZFN without a repair template.^[74]^[75]

Examples

Examples of restriction enzymes include:^[76]

Enzyme	Source	Recognition Sequence	Cut
EcoRI	Escherichia coli	5'GAATTC 3'CTTAAG	5'---G AATTC---3' 3'---CTTAA G---5'
EcoRII	Escherichia coli	5'CCWGG 3'GGWCC	5'--- CCWGG---3' 3'---GGWCC ---5'
BamHI	Bacillus amyloliquefaciens	5'GGATCC 3'CCTAGG	5'---G GATCC---3' 3'---CCTAG G---5'
HindIII	Haemophilus influenzae	5'AAGCTT 3'TTCGAA	5'---A AGCTT---3' 3'---TTCGA A---5'
TaqI	Thermus aquaticus	5'TCGA 3'AGCT	5'---T CGA---3' 3'---AGC T---5'
NotI	Nocardia otitidis	5'GCGGCCGC 3'CGCCGGCG	5'---GC GGCCGC---3' 3'---CGCCGG CG---5'
HinFI	Haemophilus influenzae	5'GANTC 3'CTNAG	5'---G ANTC---3' 3'---CTNA G---5'
Sau3AI	Staphylococcus aureus	5'GATC 3'CTAG	5'--- GATC---3' 3'---CTAG ---5'
PvuII*	Proteus vulgaris	5'CAGCTG 3'GTCGAC	5'---CAG CTG---3' 3'---GTC GAC---5'
SmaI*	Serratia marcescens	5'CCCGGG 3'GGGCCC	5'---CCC GGG---3' 3'---GGG CCC---5'
HaeIII*	Haemophilus aegyptius	5'GGCC 3'CCGG	5'---GG CC---3' 3'---CC GG---5'
HgaI^[77]	Haemophilus gallinarum	5'GACGC 3'CTGCG	5'---NN NN---3' 3'---NN NN---5'
AluI*	Arthrobacter luteus	5'AGCT 3'TCGA	5'---AG CT---3' 3'---TC GA---5'
EcoRV*	Escherichia coli	5'GATATC 3'CTATAG	5'---GAT ATC---3' 3'---CTA TAG---5'
EcoP15I	Escherichia coli	5'CAGCAGN₂₅NN 3'GTCGTCN₂₅NN	5'---CAGCAGN₂₅ NN---3' 3'---GTCGTCN₂₅NN ---5'
KpnI^[78]	Klebsiella pneumoniae	5'GGTACC 3'CCATGG	5'---GGTAC C---3' 3'---C CATGG---5'
PstI^[78]	Providencia stuartii	5'CTGCAG 3'GACGTC	5'---CTGCA G---3' 3'---G ACGTC---5'
SacI^[78]	Streptomyces achromogenes	5'GAGCTC 3'CTCGAG	5'---GAGCT C---3' 3'---C TCGAG---5'
SalI^[78]	Streptomyces albus	5'GTCGAC 3'CAGCTG	5'---G TCGAC---3' 3'---CAGCT G---5'
ScaI*^[78]	Streptomyces caespitosus	5'AGTACT 3'TCATGA	5'---AGT ACT---3' 3'---TCA TGA---5'
SpeI	Sphaerotilus natans	5'ACTAGT 3'TGATCA	5'---A CTAGT---3' 3'---TGATC A---5'
SphI^[78]	Streptomyces phaeochromogenes	5'GCATGC 3'CGTACG	5'---GCATG C---3' 3'---C GTACG---5'
StuI*^[79]^[80]	Streptomyces tubercidicus	5'AGGCCT 3'TCCGGA	5'---AGG CCT---3' 3'---TCC GGA---5'
XbaI^[78]	Xanthomonas badrii	5'TCTAGA 3'AGATCT	5'---T CTAGA---3' 3'---AGATC T---5'

Key:
* = blunt ends
N = C or G or T or A
W = A or T

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^ ^a ^b Sistla S, Rao DN (2004). "S-Adenosyl-L-methionine-dependent restriction enzymes". Critical Reviews in Biochemistry and Molecular Biology. 39 (1): 1–19. doi:10.1080/10409230490440532. PMID 15121719. S2CID 1929381.
^ Williams RJ (March 2003). "Restriction endonucleases: classification, properties, and applications". Molecular Biotechnology. 23 (3): 225–43. doi:10.1385/MB:23:3:225. PMID 12665693. S2CID 29672999.
^ ^a ^b Murray NE (June 2000). "Type I restriction systems: sophisticated molecular machines (a legacy of Bertani and Weigle)". Microbiology and Molecular Biology Reviews. 64 (2): 412–34. doi:10.1128/MMBR.64.2.412-434.2000. PMC 98998. PMID 10839821.
^ PDB: 1qps Gigorescu A, Morvath M, Wilkosz PA, Chandrasekhar K, Rosenberg JM (2004). "The integration of recognition and cleavage: X-ray structures of pre-transition state complex, post-reactive complex, and the DNA-free endonuclease". In Alfred M. Pingoud (ed.). Restriction Endonucleases (Nucleic Acids and Molecular Biology, Volume 14). Berlin: Springer. pp. 137–178. ISBN 3-540-20502-0.
^ Ninfa JP, Balou DP, Benore M (2010). Fundamental Laboratory Approaches for Biochemistry and Biotechnology. Hoboken, NJ: John Wiley & Sons. p. 341. ISBN 978-0-470-08766-4.
^ Siwek W, Czapinska H, Bochtler M, Bujnicki JM, Skowronek K (August 2012). "Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI". Nucleic Acids Research. 40 (15): 7563–72. doi:10.1093/nar/gks428. PMC 3424567. PMID 22610857.
^ Mierzejewska K, Siwek W, Czapinska H, Kaus-Drobek M, Radlinska M, Skowronek K, et al. (July 2014). "Structural basis of the methylation specificity of R.DpnI". Nucleic Acids Research. 42 (13): 8745–54. doi:10.1093/nar/gku546. PMC 4117772. PMID 24966351.
^ Dryden DT, Murray NE, Rao DN (September 2001). "Nucleoside triphosphate-dependent restriction enzymes". Nucleic Acids Research. 29 (18): 3728–41. doi:10.1093/nar/29.18.3728. PMC 55918. PMID 11557806.
^ Meisel A, Bickle TA, Krüger DH, Schroeder C (January 1992). "Type III restriction enzymes need two inversely oriented recognition sites for DNA cleavage". Nature. 355 (6359): 467–9. Bibcode:1992Natur.355..467M. doi:10.1038/355467a0. PMID 1734285. S2CID 4354056.
^ Bourniquel AA, Bickle TA (November 2002). "Complex restriction enzymes: NTP-driven molecular motors". Biochimie. 84 (11): 1047–59. doi:10.1016/S0300-9084(02)00020-2. PMID 12595133.
^ ^a ^b Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, et al. (March 2007). "CRISPR provides acquired resistance against viruses in prokaryotes". Science. 315 (5819): 1709–12. Bibcode:2007Sci...315.1709B. doi:10.1126/science.1138140. hdl:20.500.11794/38902. PMID 17379808. S2CID 3888761.
^ Horvath P, Barrangou R (January 2010). "CRISPR/Cas, the immune system of bacteria and archaea". Science. 327 (5962): 167–70. Bibcode:2010Sci...327..167H. doi:10.1126/science.1179555. PMID 20056882. S2CID 17960960.
^ Kim YG, Cha J, Chandrasegaran S (February 1996). "Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain". Proceedings of the National Academy of Sciences of the United States of America. 93 (3): 1156–60. Bibcode:1996PNAS...93.1156K. doi:10.1073/pnas.93.3.1156. PMC 40048. PMID 8577732.
^ Urnov FD, Rebar EJ, Holmes MC, Zhang HS, Gregory PD (September 2010). "Genome editing with engineered zinc finger nucleases". Nature Reviews. Genetics. 11 (9): 636–46. doi:10.1038/nrg2842. PMID 20717154. S2CID 205484701.
^ Townsend JA, Wright DA, Winfrey RJ, Fu F, Maeder ML, Joung JK, Voytas DF (May 2009). "High-frequency modification of plant genes using engineered zinc-finger nucleases". Nature. 459 (7245): 442–5. Bibcode:2009Natur.459..442T. doi:10.1038/nature07845. PMC 2743854. PMID 19404258.
^ Shukla VK, Doyon Y, Miller JC, DeKelver RC, Moehle EA, Worden SE, et al. (May 2009). "Precise genome modification in the crop species Zea mays using zinc-finger nucleases". Nature. 459 (7245): 437–41. Bibcode:2009Natur.459..437S. doi:10.1038/nature07992. PMID 19404259. S2CID 4323298.
^ Ekker SC (2008). "Zinc finger-based knockout punches for zebrafish genes". Zebrafish. 5 (2): 121–3. doi:10.1089/zeb.2008.9988. PMC 2849655. PMID 18554175.
^ Geurts AM, Cost GJ, Freyvert Y, Zeitler B, Miller JC, Choi VM, et al. (July 2009). "Knockout rats via embryo microinjection of zinc-finger nucleases". Science. 325 (5939): 433. Bibcode:2009Sci...325..433G. doi:10.1126/science.1172447. PMC 2831805. PMID 19628861.
^ Tovkach A, Zeevi V, Tzfira T (January 2011). "Expression, purification and characterization of cloning-grade zinc finger nuclease". Journal of Biotechnology. 151 (1): 1–8. doi:10.1016/j.jbiotec.2010.10.071. PMID 21029755.
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External links

Library resources about
Restriction enzymes

DNA Restriction Enzymes at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
Firman K (2007-11-24). "Type I Restriction-Modification". University of Portsmouth. Archived from the original on 2008-07-06. Retrieved 2008-06-06.
Goodsell DS (2000-08-01). "Restriction Enzymes". Molecule of the Month. RCSB Protein Data Bank. Archived from the original on 2008-05-31. Retrieved 2008-06-06.
Simmer M, Secko D (2003-08-01). "Restriction Endonucleases: Molecular Scissors for Specifically Cutting DNA". The Science Creative Quarterly. Retrieved 2008-06-06.
Roberts RJ, Vincze T, Posfai, J, Macelis D. "REBASE". Archived from the original on 2015-02-16. Retrieved 2008-06-06. Restriction Enzyme Database.

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[urlMedicine_1978-23] "The Nobel Prize in Physiology or Medicine". The Nobel Foundation. 1978. Retrieved 2008-06-07. for the discovery of restriction enzymes and their application to problems of molecular genetics

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[28] Cooper S (2003). "Restriction Map". bioweb.uwlax.edu. University of Wisconsin. Retrieved 10 May 2021.

[pmid11557805-29] ^ ^a ^b ^c ^d ^e ^f ^g ^h ⁱ ^j Pingoud A, Jeltsch A (September 2001). "Structure and function of type II restriction endonucleases". Nucleic Acids Research. 29 (18): 3705–27. doi:10.1093/nar/29.18.3705. PMC 55916. PMID 11557805.

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[pmid6267988-34] Yuan R (1981). "Structure and mechanism of multifunctional restriction endonucleases". Annual Review of Biochemistry. 50: 285–319. doi:10.1146/annurev.bi.50.070181.001441. PMID 6267988.

[neb-35] Types of Restriction Endonucleases | NEB

[pmid15121719-36] Sistla S, Rao DN (2004). "S-Adenosyl-L-methionine-dependent restriction enzymes". Critical Reviews in Biochemistry and Molecular Biology. 39 (1): 1–19. doi:10.1080/10409230490440532. PMID 15121719. S2CID 1929381.

[PUB00035707-37] Williams RJ (March 2003). "Restriction endonucleases: classification, properties, and applications". Molecular Biotechnology. 23 (3): 225–43. doi:10.1385/MB:23:3:225. PMID 12665693. S2CID 29672999.

[pmid10839821-38] Murray NE (June 2000). "Type I restriction systems: sophisticated molecular machines (a legacy of Bertani and Weigle)". Microbiology and Molecular Biology Reviews. 64 (2): 412–34. doi:10.1128/MMBR.64.2.412-434.2000. PMC 98998. PMID 10839821.

[pdb_1qps-39] PDB: 1qps Gigorescu A, Morvath M, Wilkosz PA, Chandrasekhar K, Rosenberg JM (2004). "The integration of recognition and cleavage: X-ray structures of pre-transition state complex, post-reactive complex, and the DNA-free endonuclease". In Alfred M. Pingoud (ed.). Restriction Endonucleases (Nucleic Acids and Molecular Biology, Volume 14). Berlin: Springer. pp. 137–178. ISBN 3-540-20502-0.

[40] Ninfa JP, Balou DP, Benore M (2010). Fundamental Laboratory Approaches for Biochemistry and Biotechnology. Hoboken, NJ: John Wiley & Sons. p. 341. ISBN 978-0-470-08766-4.

[41] Siwek W, Czapinska H, Bochtler M, Bujnicki JM, Skowronek K (August 2012). "Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI". Nucleic Acids Research. 40 (15): 7563–72. doi:10.1093/nar/gks428. PMC 3424567. PMID 22610857.

[42] Mierzejewska K, Siwek W, Czapinska H, Kaus-Drobek M, Radlinska M, Skowronek K, et al. (July 2014). "Structural basis of the methylation specificity of R.DpnI". Nucleic Acids Research. 42 (13): 8745–54. doi:10.1093/nar/gku546. PMC 4117772. PMID 24966351.

[pmid11557806-43] Dryden DT, Murray NE, Rao DN (September 2001). "Nucleoside triphosphate-dependent restriction enzymes". Nucleic Acids Research. 29 (18): 3728–41. doi:10.1093/nar/29.18.3728. PMC 55918. PMID 11557806.

[pmid1734285-44] Meisel A, Bickle TA, Krüger DH, Schroeder C (January 1992). "Type III restriction enzymes need two inversely oriented recognition sites for DNA cleavage". Nature. 355 (6359): 467–9. Bibcode:1992Natur.355..467M. doi:10.1038/355467a0. PMID 1734285. S2CID 4354056.

[pmid12595133-45] Bourniquel AA, Bickle TA (November 2002). "Complex restriction enzymes: NTP-driven molecular motors". Biochimie. 84 (11): 1047–59. doi:10.1016/S0300-9084(02)00020-2. PMID 12595133.

[:0-46] Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, et al. (March 2007). "CRISPR provides acquired resistance against viruses in prokaryotes". Science. 315 (5819): 1709–12. Bibcode:2007Sci...315.1709B. doi:10.1126/science.1138140. hdl:20.500.11794/38902. PMID 17379808. S2CID 3888761.

[pmid20056882-47] Horvath P, Barrangou R (January 2010). "CRISPR/Cas, the immune system of bacteria and archaea". Science. 327 (5962): 167–70. Bibcode:2010Sci...327..167H. doi:10.1126/science.1179555. PMID 20056882. S2CID 17960960.

[kim1996-48] Kim YG, Cha J, Chandrasegaran S (February 1996). "Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain". Proceedings of the National Academy of Sciences of the United States of America. 93 (3): 1156–60. Bibcode:1996PNAS...93.1156K. doi:10.1073/pnas.93.3.1156. PMC 40048. PMID 8577732.

[pmid20717154-49] Urnov FD, Rebar EJ, Holmes MC, Zhang HS, Gregory PD (September 2010). "Genome editing with engineered zinc finger nucleases". Nature Reviews. Genetics. 11 (9): 636–46. doi:10.1038/nrg2842. PMID 20717154. S2CID 205484701.

[pmid19404258-50] Townsend JA, Wright DA, Winfrey RJ, Fu F, Maeder ML, Joung JK, Voytas DF (May 2009). "High-frequency modification of plant genes using engineered zinc-finger nucleases". Nature. 459 (7245): 442–5. Bibcode:2009Natur.459..442T. doi:10.1038/nature07845. PMC 2743854. PMID 19404258.

[pmid19404259-51] Shukla VK, Doyon Y, Miller JC, DeKelver RC, Moehle EA, Worden SE, et al. (May 2009). "Precise genome modification in the crop species Zea mays using zinc-finger nucleases". Nature. 459 (7245): 437–41. Bibcode:2009Natur.459..437S. doi:10.1038/nature07992. PMID 19404259. S2CID 4323298.

[pmid18554175-52] Ekker SC (2008). "Zinc finger-based knockout punches for zebrafish genes". Zebrafish. 5 (2): 121–3. doi:10.1089/zeb.2008.9988. PMC 2849655. PMID 18554175.

[pmid19628861-53] Geurts AM, Cost GJ, Freyvert Y, Zeitler B, Miller JC, Choi VM, et al. (July 2009). "Knockout rats via embryo microinjection of zinc-finger nucleases". Science. 325 (5939): 433. Bibcode:2009Sci...325..433G. doi:10.1126/science.1172447. PMC 2831805. PMID 19628861.

[pmid21029755-54] Tovkach A, Zeevi V, Tzfira T (January 2011). "Expression, purification and characterization of cloning-grade zinc finger nuclease". Journal of Biotechnology. 151 (1): 1–8. doi:10.1016/j.jbiotec.2010.10.071. PMID 21029755.

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@@ Line 1: / Line 1: @@
 {{Short description|Class of enzymes that divide DNA}}
 {{Restriction enzyme glossary}}
 A '''restriction enzyme''', '''restriction endonuclease''', '''REase''', '''ENase''' or'' '''restrictase''' '' is an [[enzyme]] that cleaves [[DNA]] into fragments at or near specific recognition sites within molecules known as [[restriction site]]s.<ref name="pmid795607">{{cite journal | vauthors = Roberts RJ | title = Restriction endonucleases | journal = CRC Critical Reviews in Biochemistry | volume = 4 | issue = 2 | pages = 123–64 | date = November 1976 | pmid = 795607 | doi = 10.3109/10409237609105456 }}</ref><ref name="pmid2172084">{{cite journal | vauthors = Kessler C, Manta V | title = Specificity of restriction endonucleases and DNA modification methyltransferases a review (Edition 3) | journal = Gene | volume = 92 | issue = 1–2 | pages = 1–248 | date = August 1990 | pmid = 2172084 | doi = 10.1016/0378-1119(90)90486-B }}</ref><ref name="isbn0-89603-234-5">{{cite book |vauthors=Pingoud A, Alves J, Geiger R | editor = Burrell M | title = Enzymes of Molecular Biology | publisher = Humana Press | location = Totowa, NJ | series= Methods of Molecular Biology | volume= 16 | year = 1993 | pages = 107–200 | chapter = Chapter 8: Restriction Enzymes | isbn = 0-89603-234-5}}</ref>   Restriction enzymes are one class of the broader [[endonuclease]] group of enzymes. Restriction enzymes are commonly classified into five types, which differ in their structure and whether they cut their DNA [[enzyme substrate (biology)|substrate]] at their recognition site, or if the recognition and cleavage sites are separate from one another. To cut DNA, all restriction enzymes make two incisions, once through each [[backbone chain|sugar-phosphate backbone]] (i.e. each strand) of the [[DNA double helix]].
 These enzymes are found in [[bacteria]] and [[archaea]] and provide a defense mechanism against invading [[virus]]es.<ref name="pmid4897066">{{cite journal | vauthors = Arber W, Linn S | title = DNA modification and restriction | journal = Annual Review of Biochemistry | volume = 38 | pages = 467–500 | year = 1969 | pmid = 4897066 | doi = 10.1146/annurev.bi.38.070169.002343 }}</ref><ref name="pmid6314109">{{cite journal | vauthors = Krüger DH, Bickle TA | title = Bacteriophage survival: multiple mechanisms for avoiding the deoxyribonucleic acid restriction systems of their hosts | journal = Microbiological Reviews | volume = 47 | issue = 3 | pages = 345–60 | date = September 1983 | pmid = 6314109 | pmc = 281580 | doi = 10.1128/MMBR.47.3.345-360.1983 }}</ref> Inside a [[prokaryote]], the restriction enzymes selectively cut up ''foreign'' DNA in a process called ''restriction digestion''; meanwhile, host DNA is protected by a modification enzyme (a [[methyltransferase]]) that [[DNA methylation|modifies]] the prokaryotic DNA and blocks cleavage. Together, these two processes form the [[restriction modification system]].<ref name="pmid11557807">{{cite journal | vauthors = Kobayashi I | title = Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution | journal = Nucleic Acids Research | volume = 29 | issue = 18 | pages = 3742–56 | date = September 2001 | pmid = 11557807 | pmc = 55917 | doi = 10.1093/nar/29.18.3742 }}</ref>
-More than 3,600 restriction endonucleases are known which represent over 250 different specificities.<ref>{{cite journal | vauthors = Roberts RJ | title = How restriction enzymes became the workhorses of molecular biology | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 102 | issue = 17 | pages = 5905–8 | date = April 2005 | pmid = 15840723 | pmc = 1087929 | doi = 10.1073/pnas.0500923102 | bibcode = 2005PNAS..102.5905R | doi-access = free }}</ref> Over 3,000 of these have been studied in detail, and more than 800 of these are available commercially.<ref name="pmid17202163">{{cite journal | vauthors = Roberts RJ, Vincze T, Posfai J, Macelis D | title = REBASE--enzymes and genes for DNA restriction and modification | journal = Nucleic Acids Research | volume = 35 | issue = Database issue | pages = D269-70 | date = January 2007 | pmid = 17202163 | pmc = 1899104 | doi = 10.1093/nar/gkl891 }}</ref> These enzymes are routinely used for DNA modification in laboratories, and they are a vital tool in [[molecular cloning]].<ref name="isbn0-632-03712-1">{{cite book | vauthors = Primrose SB, Old RW | title = Principles of gene manipulation: an introduction to genetic engineering | publisher = Blackwell Scientific | location = Oxford | year = 1994 | isbn = 0-632-03712-1 | url = https://archive.org/details/principlesofgene00oldr }}</ref><ref name="isbn0-8053-3040-2">{{cite book |vauthors=Micklos DA, Bloom MV, Freyer GA | title = Laboratory DNA science: an introduction to recombinant DNA techniques and methods of genome analysis |publisher = Benjamin/Cummings Pub. Co | location = Menlo Park, Calif | year = 1996 | isbn = 0-8053-3040-2}}</ref><ref name="isbn1-55581-176-0">{{cite book |vauthors=Massey A, Kreuzer H | title = Recombinant DNA and Biotechnology: A Guide for Students | publisher = ASM Press | location = Washington, D.C | year = 2001 | isbn = 1-55581-176-0}}</ref>structure and whether they cut their DNA substrate at their recognition site, or if the recognition and cleavage sites are separate from one another. To cut DNA, all restriction enzymes make two incisions, once through each sugar-phosphate backbone (i.e. each strand) of the DNA double helix.
+More than 3,600 restriction endonucleases are known which represent over 250 different specificities.<ref>{{cite journal | vauthors = Roberts RJ | title = How restriction enzymes became the workhorses of molecular biology | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 102 | issue = 17 | pages = 5905–8 | date = April 2005 | pmid = 15840723 | pmc = 1087929 | doi = 10.1073/pnas.0500923102 | bibcode = 2005PNAS..102.5905R | doi-access = free }}</ref> Over 3,000 of these have been studied in detail, and more than 800 of these are available commercially.<ref name="pmid17202163">{{cite journal | vauthors = Roberts RJ, Vincze T, Posfai J, Macelis D | title = REBASE--enzymes and genes for DNA restriction and modification | journal = Nucleic Acids Research | volume = 35 | issue = Database issue | pages = D269-70 | date = January 2007 | pmid = 17202163 | pmc = 1899104 | doi = 10.1093/nar/gkl891 }}</ref> These enzymes are routinely used for DNA modification in laboratories, and they are a vital tool in [[molecular cloning]].<ref name="isbn0-632-03712-1">{{cite book | vauthors = Primrose SB, Old RW | title = Principles of gene manipulation: an introduction to genetic engineering | publisher = Blackwell Scientific | location = Oxford | year = 1994 | isbn = 0-632-03712-1 | url = https://archive.org/details/principlesofgene00oldr }}</ref><ref name="isbn0-8053-3040-2">{{cite book |vauthors=Micklos DA, Bloom MV, Freyer GA | title = Laboratory DNA science: an introduction to recombinant DNA techniques and methods of genome analysis |publisher = Benjamin/Cummings Pub. Co | location = Menlo Park, Calif | year = 1996 | isbn = 0-8053-3040-2}}</ref><ref name="isbn1-55581-176-0">{{cite book |vauthors=Massey A, Kreuzer H | title = Recombinant DNA and Biotechnology: A Guide for Students | publisher = ASM Press | location = Washington, D.C. | year = 2001 | isbn = 1-55581-176-0}}</ref>
-These enzymes are found in bacteria and archaea and provide a defense mechanism against invading viruses.[4][5] Inside a prokaryote, the restriction enzymes selectively cut up foreign DNA in a process called restriction digestion; meanwhile, host DNA is protected by a modification enzyme (a methyltransferase) that modifies the prokaryotic DNA and blocks cleavage. Together, these two processes form the restriction modification system.[6]
-More than 3,600 restriction endonucleases are known which represent over 250 different specificities.[7] Over 3,000 of these have been studied in detail, and more than 800 of these are available commercially.[8] These enzymes are routinely used for DNA modification in laboratories, and they are a vital tool in molecular cloning.[9][10][11]
 == History ==
-The term restriction enzyme originated from the studies of [[lambda phage|phage λ]], a virus that infects bacteria, and the phenomenon of host-controlled restriction and modification of such bacterial phage or [[bacteriophage]].<ref>{{cite book |title=From Genes to Clones |author=Winnacker E-L |publisher=VCH |year=1987 |chapter=Chapter 2: Isolation, Identification, and Characterisation of DNA fragments |isbn=0-89573-614-4 |chapter-url=https://archive.org/details/fromgenestoclone0000winn }}</ref> The phenomenon was first identified in work done in the laboratories of [[Salvador Luria]], [[Jean Weigle]] and Giuseppe Bertani in the early 1950s.<ref name="Luria_Human_1952">{{cite journal | vauthors = Luria SE, Human ML | title = A nonhereditary, host-induced variation of bacterial viruses | journal = Journal of Bacteriology | volume = 64 | issue = 4 | pages = 557–69 | date = October 1952 | pmid = 12999684 | pmc = 169391 | doi = 10.1128/JB.64.4.557-569.1952 }}</ref><ref name="pmid13034700">{{cite journal | vauthors = Bertani G, Weigle JJ | title = Host controlled variation in bacterial viruses | journal = Journal of Bacteriology | volume = 65 | issue = 2 | pages = 113–21 | date = February 1953 | pmid = 13034700 | pmc = 169650 | doi = 10.1128/JB.65.2.113-121.1953 }}</ref>  It was found that, for a bacteriophage λ that can grow well in one strain of ''Escherichia coli'', for example ''E. coli'' C, when grown in another strain, for example ''E. coli'' K, its yields can drop significantly, by as much as 3-5 orders of magnitude. The host cell, in this example ''E. coli'' K, is known as the restricting host and appears to have the ability to reduce the biological activity of the phage λ. If a phage becomes established in one strain, the ability of that phage to grow also becomes restricted in other strains. In the 1960s, it was shown in work done in the laboratories of [[Werner Arber]] and [[Matthew Meselson]] that the restriction is caused by an enzymatic cleavage of the phage DNA, and the enzyme involved was therefore termed a restriction enzyme.<ref name="pmid4897066" /><ref name="pmid4868368">{{cite journal | vauthors = Meselson M, Yuan R | title = DNA restriction enzyme from E. coli | journal = Nature | volume = 217 | issue = 5134 | pages = 1110–4 | date = March 1968 | pmid = 4868368 | doi = 10.1038/2171110a0 | bibcode = 1968Natur.217.1110M | s2cid = 4172829 }}</ref><ref name="pmid13888713">{{cite journal | vauthors = Dussoix D, Arber W | title = Host specificity of DNA produced by Escherichia coli. II. Control over acceptance of DNA from infecting phage lambda | journal = Journal of Molecular Biology | volume = 5 | issue = 1 | pages = 37–49 | date = July 1962 | pmid = 13888713 | doi = 10.1016/S0022-2836(62)80059-X }}</ref><ref name="pmid14187389">{{cite journal | vauthors = Lederberg S, Meselson M | title = Degradation of non-replicating bacteriophage dna in non-accepting cells | journal = Journal of Molecular Biology | volume = 8 | issue = 5 | pages = 623–8 | date = May 1964 | pmid = 14187389 | doi = 10.1016/S0022-2836(64)80112-1 }}</ref>
+The term restriction enzyme originated from the studies of [[lambda phage|phage λ]], a virus that infects bacteria, and the phenomenon of host-controlled restriction and modification of such bacterial phage or [[bacteriophage]].<ref>{{cite book |title=From Genes to Clones |author=Winnacker E-L |publisher=VCH |year=1987 |chapter=Chapter 2: Isolation, Identification, and Characterisation of DNA fragments |isbn=0-89573-614-4 |chapter-url=https://archive.org/details/fromgenestoclone0000winn }}</ref> The phenomenon was first identified in work done in the laboratories of [[Salvador Luria]], [[Jean Weigle]] and Giuseppe Bertani in the early 1950s.<ref name="Luria_Human_1952">{{cite journal | vauthors = Luria SE, Human ML | title = A nonhereditary, host-induced variation of bacterial viruses | journal = Journal of Bacteriology | volume = 64 | issue = 4 | pages = 557–69 | date = October 1952 | pmid = 12999684 | pmc = 169391 | doi = 10.1128/JB.64.4.557-569.1952 }}</ref><ref name="pmid13034700">{{cite journal | vauthors = Bertani G, Weigle JJ | title = Host controlled variation in bacterial viruses | journal = Journal of Bacteriology | volume = 65 | issue = 2 | pages = 113–21 | date = February 1953 | pmid = 13034700 | pmc = 169650 | doi = 10.1128/JB.65.2.113-121.1953 }}</ref>  It was found that, for a bacteriophage λ that can grow well in one strain of ''Escherichia coli'', for example ''E. coli'' C, when grown in another strain, for example ''E. coli'' K, its yields can drop significantly, by as much as three to five orders of magnitude. The host cell, in this example ''E. coli'' K, is known as the restricting host and appears to have the ability to reduce the biological activity of the phage λ. If a phage becomes established in one strain, the ability of that phage to grow also becomes restricted in other strains. In the 1960s, it was shown in work done in the laboratories of [[Werner Arber]] and [[Matthew Meselson]] that the restriction is caused by an enzymatic cleavage of the phage DNA, and the enzyme involved was therefore termed a restriction enzyme.<ref name="pmid4897066" /><ref name="pmid4868368">{{cite journal | vauthors = Meselson M, Yuan R | title = DNA restriction enzyme from E. coli | journal = Nature | volume = 217 | issue = 5134 | pages = 1110–4 | date = March 1968 | pmid = 4868368 | doi = 10.1038/2171110a0 | bibcode = 1968Natur.217.1110M | s2cid = 4172829 }}</ref><ref name="pmid13888713">{{cite journal | vauthors = Dussoix D, Arber W | title = Host specificity of DNA produced by Escherichia coli. II. Control over acceptance of DNA from infecting phage lambda | journal = Journal of Molecular Biology | volume = 5 | issue = 1 | pages = 37–49 | date = July 1962 | pmid = 13888713 | doi = 10.1016/S0022-2836(62)80059-X }}</ref><ref name="pmid14187389">{{cite journal | vauthors = Lederberg S, Meselson M | title = Degradation of non-replicating bacteriophage dna in non-accepting cells | journal = Journal of Molecular Biology | volume = 8 | issue = 5 | pages = 623–8 | date = May 1964 | pmid = 14187389 | doi = 10.1016/S0022-2836(64)80112-1 }}</ref>
-The restriction enzymes studied by Arber and Meselson were type I restriction enzymes, which cleave DNA randomly away from the recognition site.<ref name="pmid15840723">{{cite journal | vauthors = Roberts RJ | title = How restriction enzymes became the workhorses of molecular biology | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 102 | issue = 17 | pages = 5905–8 | date = April 2005 | pmid = 15840723 | pmc = 1087929 | doi = 10.1073/pnas.0500923102 | bibcode = 2005PNAS..102.5905R | doi-access = free }}</ref> In 1970, [[Hamilton O. Smith]], [[Thomas J. Kelly (scientist)|Thomas Kelly]] and Kent Wilcox isolated and characterized the first type II restriction enzyme, [[HindII]], from the bacterium ''[[Haemophilus influenzae]]''.<ref name="pmid5312500">{{cite journal | vauthors = Smith HO, Wilcox KW | title = A restriction enzyme from Hemophilus influenzae. I. Purification and general properties | journal = Journal of Molecular Biology | volume = 51 | issue = 2 | pages = 379–91 | date = July 1970 | pmid = 5312500 | doi = 10.1016/0022-2836(70)90149-X }}</ref><ref name="pmid5312501">{{cite journal | vauthors = Kelly TJ, Smith HO | title = A restriction enzyme from Hemophilus influenzae. II | journal = Journal of Molecular Biology | volume = 51 | issue = 2 | pages = 393–409 | date = July 1970 | pmid = 5312501 | doi = 10.1016/0022-2836(70)90150-6 }}</ref> Restriction enzymes of this type are more useful for laboratory work as they cleave DNA at the site of their recognition sequence and are the most commonly used as a molecular biology tool.<ref>{{cite journal | vauthors = Loenen WA, Dryden DT, Raleigh EA, Wilson GG, Murray NE | title = Highlights of the DNA cutters: a short history of the restriction enzymes | journal = Nucleic Acids Research | volume = 42 | issue = 1 | pages = 3–19 | date = January 2014 | pmid = 24141096 | pmc = 3874209 | doi = 10.1093/nar/gkt990 }}</ref> Later, [[Daniel Nathans]] and Kathleen Danna showed that cleavage of [[simian virus 40]] (SV40) DNA by restriction enzymes yields specific fragments that can be separated using [[polyacrylamide gel electrophoresis]], thus showing that restriction enzymes can also be used for mapping DNA.<ref name="pmid4332003">{{cite journal | vauthors = Danna K, Nathans D | title = Specific cleavage of simian virus 40 DNA by restriction endonuclease of Hemophilus influenzae | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 68 | issue = 12 | pages = 2913–7 | date = December 1971 | pmid = 4332003 | pmc = 389558 | doi = 10.1073/pnas.68.12.2913 | bibcode = 1971PNAS...68.2913D | doi-access = free }}</ref> For their work in the discovery and characterization of restriction enzymes, the 1978 [[Nobel Prize for Physiology or Medicine]] was awarded to [[Werner Arber]], [[Daniel Nathans]], and [[Hamilton O. Smith]].<ref name="urlMedicine 1978">{{cite web | url = http://nobelprize.org/nobel_prizes/medicine/laureates/1978/ | title = The Nobel Prize in Physiology or Medicine | year = 1978 | publisher = The Nobel Foundation | quote = for the discovery of restriction enzymes and their application to problems of molecular genetics | access-date = 2008-06-07}}</ref> The discovery of restriction enzymes allows DNA to be manipulated, leading to the development of [[recombinant DNA]] technology that has many applications, for example, allowing the large scale production of proteins such as human [[insulin]] used by [[diabetes|diabetic]] patients.<ref name="Luria_Human_1952"/><ref name="pmid358198">{{cite journal | vauthors = Villa-Komaroff L, Efstratiadis A, Broome S, Lomedico P, Tizard R, Naber SP, Chick WL, Gilbert W | display-authors = 6 | title = A bacterial clone synthesizing proinsulin | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 75 | issue = 8 | pages = 3727–31 | date = August 1978 | pmid = 358198 | pmc = 392859 | doi = 10.1073/pnas.75.8.3727 | bibcode = 1978PNAS...75.3727V | doi-access = free }}</ref>The term restriction enzyme originated from the studies of phage λ, a virus that infects bacteria, and the phenomenon of host-controlled restriction and modification of such bacterial phage or bacteriophage.[12] The phenomenon was first identified in work done in the laboratories of Salvador Luria, Jean Weigle and Giuseppe Bertani in the early 1950s.[13][14] It was found that, for a bacteriophage λ that can grow well in one strain of Escherichia coli, for example E. coli C, when grown in another strain, for example E. coli K, its yields can drop significantly, by as much as 3-5 orders of magnitude. The host cell, in this example E. coli K, is known as the restricting host and appears to have the ability to reduce the biological activity of the phage λ. If a phage becomes established in one strain, the ability of that phage to grow also becomes restricted in other strains. In the 1960s, it was shown in work done in the laboratories of Werner Arber and Matthew Meselson that the restriction is caused by an enzymatic cleavage of the phage DNA, and the enzyme involved was therefore termed a restriction enzyme.[4][15][16][17]
+The restriction enzymes studied by Arber and Meselson were type I restriction enzymes, which cleave DNA randomly away from the recognition site.<ref name="pmid15840723">{{cite journal | vauthors = Roberts RJ | title = How restriction enzymes became the workhorses of molecular biology | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 102 | issue = 17 | pages = 5905–8 | date = April 2005 | pmid = 15840723 | pmc = 1087929 | doi = 10.1073/pnas.0500923102 | bibcode = 2005PNAS..102.5905R | doi-access = free }}</ref> In 1970, [[Hamilton O. Smith]], [[Thomas J. Kelly (scientist)|Thomas Kelly]] and Kent Wilcox isolated and characterized the first type II restriction enzyme, [[HindII]], from the bacterium ''[[Haemophilus influenzae]]''.<ref name="pmid5312500">{{cite journal | vauthors = Smith HO, Wilcox KW | title = A restriction enzyme from Hemophilus influenzae. I. Purification and general properties | journal = Journal of Molecular Biology | volume = 51 | issue = 2 | pages = 379–91 | date = July 1970 | pmid = 5312500 | doi = 10.1016/0022-2836(70)90149-X }}</ref><ref name="pmid5312501">{{cite journal | vauthors = Kelly TJ, Smith HO | title = A restriction enzyme from Hemophilus influenzae. II | journal = Journal of Molecular Biology | volume = 51 | issue = 2 | pages = 393–409 | date = July 1970 | pmid = 5312501 | doi = 10.1016/0022-2836(70)90150-6 }}</ref> Restriction enzymes of this type are more useful for laboratory work as they cleave DNA at the site of their recognition sequence and are the most commonly used as a molecular biology tool.<ref>{{cite journal | vauthors = Loenen WA, Dryden DT, Raleigh EA, Wilson GG, Murray NE | title = Highlights of the DNA cutters: a short history of the restriction enzymes | journal = Nucleic Acids Research | volume = 42 | issue = 1 | pages = 3–19 | date = January 2014 | pmid = 24141096 | pmc = 3874209 | doi = 10.1093/nar/gkt990 }}</ref> Later, [[Daniel Nathans]] and Kathleen Danna showed that cleavage of [[simian virus 40]] (SV40) DNA by restriction enzymes yields specific fragments that can be separated using [[polyacrylamide gel electrophoresis]], thus showing that restriction enzymes can also be used for mapping DNA.<ref name="pmid4332003">{{cite journal | vauthors = Danna K, Nathans D | title = Specific cleavage of simian virus 40 DNA by restriction endonuclease of Hemophilus influenzae | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 68 | issue = 12 | pages = 2913–7 | date = December 1971 | pmid = 4332003 | pmc = 389558 | doi = 10.1073/pnas.68.12.2913 | bibcode = 1971PNAS...68.2913D | doi-access = free }}</ref> For their work in the discovery and characterization of restriction enzymes, the 1978 [[Nobel Prize for Physiology or Medicine]] was awarded to [[Werner Arber]], [[Daniel Nathans]], and [[Hamilton O. Smith]].<ref name="urlMedicine 1978">{{cite web | url = http://nobelprize.org/nobel_prizes/medicine/laureates/1978/ | title = The Nobel Prize in Physiology or Medicine | year = 1978 | publisher = The Nobel Foundation | quote = for the discovery of restriction enzymes and their application to problems of molecular genetics | access-date = 2008-06-07}}</ref> The discovery of restriction enzymes allows DNA to be manipulated, leading to the development of [[recombinant DNA]] technology that has many applications, for example, allowing the large scale production of proteins such as human [[insulin]] used by [[diabetes|diabetic]] patients.<ref name="Luria_Human_1952"/><ref name="pmid358198">{{cite journal | vauthors = Villa-Komaroff L, Efstratiadis A, Broome S, Lomedico P, Tizard R, Naber SP, Chick WL, Gilbert W | display-authors = 6 | title = A bacterial clone synthesizing proinsulin | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 75 | issue = 8 | pages = 3727–31 | date = August 1978 | pmid = 358198 | pmc = 392859 | doi = 10.1073/pnas.75.8.3727 | bibcode = 1978PNAS...75.3727V | doi-access = free }}</ref>
-The restriction enzymes studied by Arber and Meselson were type I restriction enzymes, which cleave DNA randomly away from the recognition site.[18] In 1970, Hamilton O. Smith, Thomas Kelly and Kent Wilcox isolated and characterized the first type II restriction enzyme, HindII, from the bacterium Haemophilus influenzae.[19][20] Restriction enzymes of this type are more useful for laboratory work as they cleave DNA at the site of their recognition sequence and are the most commonly used as a molecular biology tool.[21] Later, Daniel Nathans and Kathleen Danna showed that cleavage of simian virus 40 (SV40) DNA by restriction enzymes yields specific fragments that can be separated using polyacrylamide gel electrophoresis, thus showing that restriction enzymes can also be used for mapping DNA.[22] For their work in the discovery and characterization of restriction enzymes, the 1978 Nobel Prize for Physiology or Medicine was awarded to Werner Arber, Daniel Nathans, and Hamilton O. Smith.[23] The discovery of restriction enzymes allows DNA to be manipulated, leading to the development of recombinant DNA technology that has many applications, for example, allowing the large scale production of proteins such as human insulin used by diabetic patients.[13][24]
 ==Origins==
-Restriction enzymes likely evolved from a common ancestor and became widespread via [[horizontal gene transfer]].<ref name="Jeltsch_1995">{{cite journal | vauthors = Jeltsch A, Kröger M, Pingoud A | title = Evidence for an evolutionary relationship among type-II restriction endonucleases | journal = Gene | volume = 160 | issue = 1 | pages = 7–16 | date = July 1995 | pmid = 7628720 | doi = 10.1016/0378-1119(95)00181-5 }}</ref><ref name="Jeltsch_1996">{{cite journal | vauthors = Jeltsch A, Pingoud A | title = Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems | journal = Journal of Molecular Evolution | volume = 42 | issue = 2 | pages = 91–6 | date = February 1996 | pmid = 8919860 | doi = 10.1007/BF02198833 | bibcode = 1996JMolE..42...91J | s2cid = 19989648 }}</ref> In addition, there is mounting evidence that restriction [[endonuclease]]s evolved as a [[Selfish DNA|selfish]] genetic element.<ref name="Naito_1995">{{cite journal | vauthors = Naito T, Kusano K, Kobayashi I | title = Selfish behavior of restriction-modification systems | journal = Science | volume = 267 | issue = 5199 | pages = 897–9 | date = February 1995 | pmid = 7846533 | doi = 10.1126/science.7846533 | bibcode = 1995Sci...267..897N | s2cid = 31128438 }}</ref>Restriction enzymes likely evolved from a common ancestor and became widespread via horizontal gene transfer.[25][26] In addition, there is mounting evidence that restriction endonucleases evolved as a selfish genetic element.[27]
+Restriction enzymes likely evolved from a common ancestor and became widespread via [[horizontal gene transfer]].<ref name="Jeltsch_1995">{{cite journal | vauthors = Jeltsch A, Kröger M, Pingoud A | title = Evidence for an evolutionary relationship among type-II restriction endonucleases | journal = Gene | volume = 160 | issue = 1 | pages = 7–16 | date = July 1995 | pmid = 7628720 | doi = 10.1016/0378-1119(95)00181-5 }}</ref><ref name="Jeltsch_1996">{{cite journal | vauthors = Jeltsch A, Pingoud A | title = Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems | journal = Journal of Molecular Evolution | volume = 42 | issue = 2 | pages = 91–6 | date = February 1996 | pmid = 8919860 | doi = 10.1007/BF02198833 | bibcode = 1996JMolE..42...91J | s2cid = 19989648 }}</ref> In addition, there is mounting evidence that restriction [[endonuclease]]s evolved as a [[Selfish DNA|selfish]] genetic element.<ref name="Naito_1995">{{cite journal | vauthors = Naito T, Kusano K, Kobayashi I | title = Selfish behavior of restriction-modification systems | journal = Science | volume = 267 | issue = 5199 | pages = 897–9 | date = February 1995 | pmid = 7846533 | doi = 10.1126/science.7846533 | bibcode = 1995Sci...267..897N | s2cid = 31128438 }}</ref>
 == Recognition site ==
@@ Line 36: / Line 31: @@
 Different restriction enzymes that recognize the same sequence are known as [[neoschizomer]]s. These often cleave in different locales of the sequence. Different enzymes that recognize and cleave in the same location are known as [[isoschizomer]]s.
-A palindromic recognition site reads the same on the reverse strand as it does on the forward strand when both are read in the same orientation
-Restriction enzymes recognize a specific sequence of nucleotides[2] and produce a double-stranded cut in the DNA. The recognition sequences can also be classified by the number of bases in its recognition site, usually between 4 and 8 bases, and the number of bases in the sequence will determine how often the site will appear by chance in any given genome, e.g., a 4-base pair sequence would theoretically occur once every 4^4 or 256bp, 6 bases, 4^6 or 4,096bp, and 8 bases would be 4^8 or 65,536bp.[28] Many of them are palindromic, meaning the base sequence reads the same backwards and forwards.[29] In theory, there are two types of palindromic sequences that can be possible in DNA. The mirror-like palindrome is similar to those found in ordinary text, in which a sequence reads the same forward and backward on a single strand of DNA, as in GTAATG. The inverted repeat palindrome is also a sequence that reads the same forward and backward, but the forward and backward sequences are found in complementary DNA strands (i.e., of double-stranded DNA), as in GTATAC (GTATAC being complementary to CATATG).[30] Inverted repeat palindromes are more common and have greater biological importance than mirror-like palindromes.
-EcoRI digestion produces "sticky" ends,
-EcoRI restriction enzyme recognition site.svg
-whereas SmaI restriction enzyme cleavage produces "blunt" ends:
-SmaI restriction enzyme recognition site.svg
-Recognition sequences in DNA differ for each restriction enzyme, producing differences in the length, sequence and strand orientation (5' end or 3' end) of a sticky-end "overhang" of an enzyme restriction.[31]
-Different restriction enzymes that recognize the same sequence are known as neoschizomers. These often cleave in different locales of the sequence. Different enzymes that recognize and cleave in the same location are known as isoschizomers.
 == Types ==
 Naturally occurring restriction endonucleases are categorized into five groups (Types I, II, III, IV, and V) based on their composition and [[enzyme cofactor]] requirements, the nature of their target sequence, and the position of their DNA cleavage site relative to the target sequence.<ref name="pmid8336674">{{cite journal | vauthors = Bickle TA, Krüger DH | title = Biology of DNA restriction | journal = Microbiological Reviews | volume = 57 | issue = 2 | pages = 434–50 | date = June 1993 | pmid = 8336674 | pmc = 372918 | doi =  10.1128/MMBR.57.2.434-450.1993}}</ref><ref name="pmid4949033">{{cite journal | vauthors = Boyer HW | title = DNA restriction and modification mechanisms in bacteria | journal = Annual Review of Microbiology | volume = 25 | pages = 153–76 | year = 1971 | pmid = 4949033 | doi = 10.1146/annurev.mi.25.100171.001101 }}</ref><ref name="pmid6267988">{{cite journal | vauthors = Yuan R | title = Structure and mechanism of multifunctional restriction endonucleases | journal = Annual Review of Biochemistry | volume = 50 | pages = 285–319 | year = 1981 | pmid = 6267988 | doi = 10.1146/annurev.bi.50.070181.001441 }}</ref>  DNA sequence analysis of restriction enzymes however show great variations, indicating that there are more than four types.<ref name="neb"/> All types of enzymes recognize specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements,<ref name="pmid15121719">{{cite journal | vauthors = Sistla S, Rao DN | title = S-Adenosyl-L-methionine-dependent restriction enzymes | journal = Critical Reviews in Biochemistry and Molecular Biology | volume = 39 | issue = 1 | pages = 1–19 | year = 2004 | pmid = 15121719 | doi = 10.1080/10409230490440532 | s2cid = 1929381 }}</ref><ref name="PUB00035707">{{cite journal | vauthors = Williams RJ | title = Restriction endonucleases: classification, properties, and applications | journal = Molecular Biotechnology | volume = 23 | issue = 3 | pages = 225–43 | date = March 2003 | pmid = 12665693 | doi = 10.1385/MB:23:3:225 | s2cid = 29672999 }}</ref> as summarised below:
-* Type I enzymes ({{EC number|3.1.21.3}}) cleave at sites remote from a recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction digestion and methylase ({{EC number|2.1.1.72}}) activities.
+* Type I enzymes ({{EC number|3.1.21.3}}) cleave at sites remote from a recognition site; require both [[Adenosine triphosphate|ATP]] and [[S-Adenosyl methionine|S-adenosyl-L-methionine]] to function; multifunctional protein with both restriction digestion and methylase ({{EC number|2.1.1.72}}) activities.
-* Type II enzymes ({{EC number|3.1.21.4}}) cleave within or at short specific distances from a recognition site; most require magnesium; single function (restriction digestion) enzymes independent of methylase.
+* Type II enzymes ({{EC number|3.1.21.4}}) cleave within or at short specific distances from a recognition site; most require [[magnesium]]; single function (restriction digestion) enzymes independent of methylase.
 * Type III enzymes ({{EC number|3.1.21.5}}) cleave at sites a short distance from a recognition site; require ATP (but do not hydrolyse it); S-adenosyl-L-methionine stimulates the reaction but is not required; exist as part of a complex with a modification methylase ({{EC number|2.1.1.72}}).
 * Type IV enzymes target modified DNA, e.g. methylated, hydroxymethylated and glucosyl-hydroxymethylated DNA
-* Type V enzymes utilize guide RNAs (gRNAs)
+* Type V enzymes utilize [[Guide RNA|guide RNAs (gRNAs)]]
 === Type l ===
-Type I restriction enzymes were the first to be identified and were first identified in two different strains (K-12 and B) of ''[[Escherichia coli|E. coli]]''.<ref name="pmid10839821">{{cite journal | vauthors = Murray NE | title = Type I restriction systems: sophisticated molecular machines (a legacy of Bertani and Weigle) | journal = Microbiology and Molecular Biology Reviews | volume = 64 | issue = 2 | pages = 412–34 | date = June 2000 | pmid = 10839821 | pmc = 98998 | doi = 10.1128/MMBR.64.2.412-434.2000 }}</ref> These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions—one containing 3–4 nucleotides, and another containing 4–5 nucleotides—separated by a non-specific spacer of about 6–8 nucleotides. These enzymes are multifunctional and are capable of both restriction digestion and modification activities, depending upon the methylation status of the target DNA. The cofactors [[S-Adenosyl methionine]] (AdoMet), hydrolyzed adenosine triphosphate ([[Adenosine triphosphate|ATP]]), and [[magnesium]] (Mg<sup>2+</sup>) [[ion]]s, are required for their full activity. Type I restriction enzymes possess three subunits called HsdR, HsdM, and HsdS; HsdR is required for restriction digestion; HsdM is necessary for adding [[methyl]] groups to host DNA (methyltransferase activity), and HsdS is important for specificity of the recognition (DNA-binding) site in addition to both restriction digestion (DNA cleavage) and modification (DNA methyltransferase) activity.<ref name="pmid8336674"/><ref name="pmid10839821"/>Type I restriction enzymes were the first to be identified and were first identified in two different strains (K-12 and B) of E. coli.[38] These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions—one containing 3–4 nucleotides, and another containing 4–5 nucleotides—separated by a non-specific spacer of about 6–8 nucleotides. These enzymes are multifunctional and are capable of both restriction digestion and modification activities, depending upon the methylation status of the target DNA. The cofactors S-Adenosyl methionine (AdoMet), hydrolyzed adenosine triphosphate (ATP), and magnesium (Mg2+) ions, are required for their full activity. Type I restriction enzymes possess three subunits called HsdR, HsdM, and HsdS; HsdR is required for restriction digestion; HsdM is necessary for adding methyl groups to host DNA (methyltransferase activity), and HsdS is important for specificity of the recognition (DNA-binding) site in addition to both restriction digestion (DNA cleavage) and modification (DNA methyltransferase) activity.[32][38]Type I restriction enzymes were the first to be identified and were first identified in two different strains (K-12 and B) of E. coli.[38] These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions—one containing 3–4 nucleotides, and another containing 4–5 nucleotides—separated by a non-specific spacer of about 6–8 nucleotides. These enzymes are multifunctional and are capable of both restriction digestion and modification activities, depending upon the methylation status of the target DNA. The cofactors S-Adenosyl methionine (AdoMet), hydrolyzed adenosine triphosphate (ATP), and magnesium (Mg2+) ions, are required for their full activity. Type I restriction enzymes possess three subunits called HsdR, HsdM, and HsdS; HsdR is required for restriction digestion; HsdM is necessary for adding methyl groups to host DNA (methyltransferase activity), and HsdS is important for specificity of the recognition (DNA-binding) site in addition to both restriction digestion (DNA cleavage) and modification (DNA methyltransferase) activity.[32][38]
+Type I restriction enzymes were the first to be identified and were first identified in two different strains (K-12 and B) of ''[[Escherichia coli|E. coli]]''.<ref name="pmid10839821">{{cite journal | vauthors = Murray NE | title = Type I restriction systems: sophisticated molecular machines (a legacy of Bertani and Weigle) | journal = Microbiology and Molecular Biology Reviews | volume = 64 | issue = 2 | pages = 412–34 | date = June 2000 | pmid = 10839821 | pmc = 98998 | doi = 10.1128/MMBR.64.2.412-434.2000 }}</ref> These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions—one containing 3–4 nucleotides, and another containing 4–5 nucleotides—separated by a non-specific spacer of about 6–8 nucleotides. These enzymes are multifunctional and are capable of both restriction digestion and modification activities, depending upon the methylation status of the target DNA. The cofactors [[S-Adenosyl methionine]] (AdoMet), hydrolyzed adenosine triphosphate ([[Adenosine triphosphate|ATP]]), and [[magnesium]] (Mg<sup>2+</sup>) [[ion]]s, are required for their full activity. Type I restriction enzymes possess three subunits called HsdR, HsdM, and HsdS; HsdR is required for restriction digestion; HsdM is necessary for adding [[methyl]] groups to host DNA (methyltransferase activity), and HsdS is important for specificity of the recognition (DNA-binding) site in addition to both restriction digestion (DNA cleavage) and modification (DNA methyltransferase) activity.<ref name="pmid8336674"/><ref name="pmid10839821"/>
 === Type II ===
+{{Infobox protein family
-{{pfam box
 | Name = Type II site-specific deoxyribonuclease-like
 |Symbol= Restrct_endonuc-II-like
@@ Line 81: / Line 62: @@
 Type IIB restriction enzymes (e.g., BcgI and BplI) are [[multimer]]s, containing more than one subunit.<ref name="pmid11557805"/> They cleave DNA on both sides of their recognition to cut out the recognition site. They require both AdoMet and Mg<sup>2+</sup> cofactors. Type IIE restriction endonucleases (e.g., NaeI) cleave DNA following interaction with two copies of their recognition sequence.<ref name="pmid11557805"/> One recognition site acts as the target for cleavage, while the other acts as an [[Allosteric regulation|allosteric effector]] that speeds up or improves the efficiency of enzyme cleavage. Similar to type IIE enzymes, type IIF restriction endonucleases (e.g. NgoMIV) interact with two copies of their recognition sequence but cleave both sequences at the same time.<ref name="pmid11557805"/> Type IIG restriction endonucleases (e.g., RM.Eco57I) do have a single subunit, like classical Type II restriction enzymes, but require the cofactor AdoMet to be active.<ref name="pmid11557805"/> Type IIM restriction endonucleases, such as DpnI, are able to recognize and cut methylated DNA.<ref name="pmid11557805"/><ref>{{cite journal | vauthors = Siwek W, Czapinska H, Bochtler M, Bujnicki JM, Skowronek K | title = Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI | journal = Nucleic Acids Research | volume = 40 | issue = 15 | pages = 7563–72 | date = August 2012 | pmid = 22610857 | pmc = 3424567 | doi = 10.1093/nar/gks428 }}</ref><ref>{{cite journal | vauthors = Mierzejewska K, Siwek W, Czapinska H, Kaus-Drobek M, Radlinska M, Skowronek K, Bujnicki JM, Dadlez M, Bochtler M | display-authors = 6 | title = Structural basis of the methylation specificity of R.DpnI | journal = Nucleic Acids Research | volume = 42 | issue = 13 | pages = 8745–54 | date = July 2014 | pmid = 24966351 | pmc = 4117772 | doi = 10.1093/nar/gku546 }}</ref> Type IIS restriction endonucleases (e.g. FokI) cleave DNA at a defined distance from their non-palindromic asymmetric recognition sites;<ref name="pmid11557805"/> this characteristic is widely used to perform in-vitro cloning techniques such as [[Golden Gate Cloning|Golden Gate cloning]]. These enzymes may function as [[protein dimer|dimer]]s. Similarly, Type IIT restriction enzymes (e.g., Bpu10I and BslI) are composed of two different subunits. Some recognize palindromic sequences while others have asymmetric recognition sites.<ref name="pmid11557805"/>
-{{Further|BsuBI/PstI restriction endonuclease}}Type II site-specific deoxyribonuclease-like
+{{Further|BsuBI/PstI restriction endonuclease}}
-QPS.png
-Structure of the homodimeric restriction enzyme EcoRI (cyan and green cartoon diagram) bound to double stranded DNA (brown tubes).[39] Two catalytic magnesium ions (one from each monomer) are shown as magenta spheres and are adjacent to the cleaved sites in the DNA made by the enzyme (depicted as gaps in the DNA backbone).
-Identifiers
-Symbol
-Restrct_endonuc-II-like
-Pfam clan
-CL0236
-InterPro
-IPR011335
-SCOP2
-wte / SCOPe / SUPFAM
-Typical type II restriction enzymes differ from type I restriction enzymes in several ways. They form homodimers, with recognition sites that are usually undivided and palindromic and 4–8 nucleotides in length. They recognize and cleave DNA at the same site, and they do not use ATP or AdoMet for their activity—they usually require only Mg2+ as a cofactor.[29] These enzymes cleave the phosphodiester bond of double helix DNA. It can either cleave at the center of both strands to yield a blunt end, or at a staggered position leaving overhangs called sticky ends.[40] These are the most commonly available and used restriction enzymes. In the 1990s and early 2000s, new enzymes from this family were discovered that did not follow all the classical criteria of this enzyme class, and new subfamily nomenclature was developed to divide this large family into subcategories based on deviations from typical characteristics of type II enzymes.[29] These subgroups are defined using a letter suffix.
-Type IIB restriction enzymes (e.g., BcgI and BplI) are multimers, containing more than one subunit.[29] They cleave DNA on both sides of their recognition to cut out the recognition site. They require both AdoMet and Mg2+ cofactors. Type IIE restriction endonucleases (e.g., NaeI) cleave DNA following interaction with two copies of their recognition sequence.[29] One recognition site acts as the target for cleavage, while the other acts as an allosteric effector that speeds up or improves the efficiency of enzyme cleavage. Similar to type IIE enzymes, type IIF restriction endonucleases (e.g. NgoMIV) interact with two copies of their recognition sequence but cleave both sequences at the same time.[29] Type IIG restriction endonucleases (e.g., RM.Eco57I) do have a single subunit, like classical Type II restriction enzymes, but require the cofactor AdoMet to be active.[29] Type IIM restriction endonucleases, such as DpnI, are able to recognize and cut methylated DNA.[29][41][42] Type IIS restriction endonucleases (e.g. FokI) cleave DNA at a defined distance from their non-palindromic asymmetric recognition sites;[29] this characteristic is widely used to perform in-vitro cloning techniques such as Golden Gate cloning. These enzymes may function as dimers. Similarly, Type IIT restriction enzymes (e.g., Bpu10I and BslI) are composed of two different subunits. Some recognize palindromic sequences while others have asymmetric recognition sites.[29]
 === Type III ===
-Type III restriction enzymes (e.g., EcoP15) recognize two separate non-palindromic sequences that are inversely oriented. They cut DNA about 20–30 base pairs after the recognition site.<ref name="pmid11557806">{{cite journal | vauthors = Dryden DT, Murray NE, Rao DN | title = Nucleoside triphosphate-dependent restriction enzymes | journal = Nucleic Acids Research | volume = 29 | issue = 18 | pages = 3728–41 | date = September 2001 | pmid = 11557806 | pmc = 55918 | doi = 10.1093/nar/29.18.3728 }}</ref> These enzymes contain more than one subunit and require AdoMet and ATP cofactors for their roles in DNA methylation and restriction digestion, respectively.<ref name="pmid1734285">{{cite journal | vauthors = Meisel A, Bickle TA, Krüger DH, Schroeder C | title = Type III restriction enzymes need two inversely oriented recognition sites for DNA cleavage | journal = Nature | volume = 355 | issue = 6359 | pages = 467–9 | date = January 1992 | pmid = 1734285 | doi = 10.1038/355467a0 | bibcode = 1992Natur.355..467M | s2cid = 4354056 }}</ref> They are components of [[Prokaryote|prokaryotic]] DNA restriction-modification [[Mechanism (biology)|mechanisms]] that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional [[protein]]s composed of two subunits, Res ({{uniProt|P08764}}) and Mod ({{uniProt|P08763}}). The Mod subunit recognises the DNA sequence specific for the system and is a modification [[methyltransferase]]; as such, it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction digestion, although it has no [[enzyme|enzymatic]] activity on its own. Type III enzymes recognise short 5–6 bp-long asymmetric DNA sequences and cleave 25–27 bp [[Upstream and downstream (DNA)|downstream]] to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction digestion to occur. These enzymes [[DNA methylation|methylate]] only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction digestion. Type III enzymes belong to the beta-subfamily of [[DNA methyltransferase|N6 adenine methyltransferases]], containing the nine [[protein motif|motif]]s that characterise this family, including [[sequence motif|motif]] I, the [[S-adenosyl-L-methionine|AdoMet]] binding pocket (FXGXG), and motif IV, the [[catalytic]] region (S/D/N (PP) Y/F).<ref name="pmid15121719"/><ref name="pmid12595133">{{cite journal | vauthors = Bourniquel AA, Bickle TA | title = Complex restriction enzymes: NTP-driven molecular motors | journal = Biochimie | volume = 84 | issue = 11 | pages = 1047–59 | date = November 2002 | pmid = 12595133 | doi = 10.1016/S0300-9084(02)00020-2 }}</ref>Type III restriction enzymes (e.g., EcoP15) recognize two separate non-palindromic sequences that are inversely oriented. They cut DNA about 20–30 base pairs after the recognition site.[43] These enzymes contain more than one subunit and require AdoMet and ATP cofactors for their roles in DNA methylation and restriction digestion, respectively.[44] They are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional proteins composed of two subunits, Res (P08764) and Mod (P08763). The Mod subunit recognises the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction digestion, although it has no enzymatic activity on its own. Type III enzymes recognise short 5–6 bp-long asymmetric DNA sequences and cleave 25–27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction digestion to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction digestion. Type III enzymes belong to the beta-subfamily of N6 adenine methyltransferases, containing the nine motifs that characterise this family, including motif I, the AdoMet binding pocket (FXGXG), and motif IV, the catalytic region (S/D/N (PP) Y/F).[36][45]
+Type III restriction enzymes (e.g., EcoP15) recognize two separate non-palindromic sequences that are inversely oriented. They cut DNA about 20–30 base pairs after the recognition site.<ref name="pmid11557806">{{cite journal | vauthors = Dryden DT, Murray NE, Rao DN | title = Nucleoside triphosphate-dependent restriction enzymes | journal = Nucleic Acids Research | volume = 29 | issue = 18 | pages = 3728–41 | date = September 2001 | pmid = 11557806 | pmc = 55918 | doi = 10.1093/nar/29.18.3728 }}</ref> These enzymes contain more than one subunit and require AdoMet and ATP cofactors for their roles in DNA methylation and restriction digestion, respectively.<ref name="pmid1734285">{{cite journal | vauthors = Meisel A, Bickle TA, Krüger DH, Schroeder C | title = Type III restriction enzymes need two inversely oriented recognition sites for DNA cleavage | journal = Nature | volume = 355 | issue = 6359 | pages = 467–9 | date = January 1992 | pmid = 1734285 | doi = 10.1038/355467a0 | bibcode = 1992Natur.355..467M | s2cid = 4354056 }}</ref> They are components of [[Prokaryote|prokaryotic]] DNA restriction-modification [[Mechanism (biology)|mechanisms]] that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional [[protein]]s composed of two subunits, Res ({{uniProt|P08764}}) and Mod ({{uniProt|P08763}}). The Mod subunit recognises the DNA sequence specific for the system and is a modification [[methyltransferase]]; as such, it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction digestion, although it has no [[enzyme|enzymatic]] activity on its own. Type III enzymes recognise short 5–6 bp-long asymmetric DNA sequences and cleave 25–27 bp [[Upstream and downstream (DNA)|downstream]] to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction digestion to occur. These enzymes [[DNA methylation|methylate]] only one strand of the DNA, at the N-6 position of adenine residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction digestion. Type III enzymes belong to the beta-subfamily of [[DNA methyltransferase|N6 adenine methyltransferases]], containing the nine [[protein motif|motif]]s that characterise this family, including [[sequence motif|motif]] I, the [[S-adenosyl-L-methionine|AdoMet]] binding pocket (FXGXG), and motif IV, the [[catalytic]] region (S/D/N (PP) Y/F).<ref name="pmid15121719"/><ref name="pmid12595133">{{cite journal | vauthors = Bourniquel AA, Bickle TA | title = Complex restriction enzymes: NTP-driven molecular motors | journal = Biochimie | volume = 84 | issue = 11 | pages = 1047–59 | date = November 2002 | pmid = 12595133 | doi = 10.1016/S0300-9084(02)00020-2 }}</ref>
 === Type IV ===
-Type IV enzymes recognize modified, typically methylated DNA and are exemplified by the&nbsp;McrBC&nbsp;and Mrr systems of&nbsp;''E. coli''.<ref name="neb">[https://www.neb.com/products/restriction-endonucleases/restriction-endonucleases/types-of-restriction-endonucleases Types of Restriction Endonucleases | NEB<!-- Bot generated title -->]</ref>Type IV enzymes recognize modified, typically methylated DNA and are exemplified by the McrBC and Mrr systems of E. coli.[35]
+Type IV enzymes recognize modified, typically methylated DNA and are exemplified by the&nbsp;McrBC&nbsp;and Mrr systems of&nbsp;''E. coli''.<ref name="neb">[https://www.neb.com/products/restriction-endonucleases/restriction-endonucleases/types-of-restriction-endonucleases Types of Restriction Endonucleases | NEB<!-- Bot generated title -->]</ref>
 ===Type V===
@@ Line 113: / Line 80: @@
 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>Naturally occurring restriction endonucleases are categorized into five groups (Types I, II, III, IV, and V) based on their composition and enzyme cofactor requirements, the nature of their target sequence, and the position of their DNA cleavage site relative to the target sequence.[32][33][34] DNA sequence analysis of restriction enzymes however show great variations, indicating that there are more than four types.[35] All types of enzymes recognize specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements,[36][37] as summarised below:
+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>
-Type I enzymes (EC 3.1.21.3) cleave at sites remote from a recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction digestion and methylase (EC 2.1.1.72) activities.
-Type II enzymes (EC 3.1.21.4) cleave within or at short specific distances from a recognition site; most require magnesium; single function (restriction digestion) enzymes independent of methylase.
-Type III enzymes (EC 3.1.21.5) cleave at sites a short distance from a recognition site; require ATP (but do not hydrolyse it); S-adenosyl-L-methionine stimulates the reaction but is not required; exist as part of a complex with a modification methylase (EC 2.1.1.72).
-Type IV enzymes target modified DNA, e.g. methylated, hydroxymethylated and glucosyl-hydroxymethylated DNA
-Type V enzymes utilize guide RNAs (gRNAs)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).[48] Such artificial restriction enzymes can target large DNA sites (up to 36 bp) and can be engineered to bind to desired DNA sequences.[49] Zinc finger nucleases are the most commonly used artificial restriction enzymes and are generally used in genetic engineering applications,[50][51][52][53] but can also be used for more standard gene cloning applications.[54] Other artificial restriction enzymes are based on the DNA binding domain of TAL effectors.[55][56]
-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.[57] 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.[58]
-Artificial ribonucleases that act as restriction enzymes for RNA have also been developed. A PNA-based system, called a PNAzyme, has a Cu(II)-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.[59]
 == Nomenclature ==
@@ Line 144: / Line 99: @@
 | '''I''' || First identified || order of identification<br />in the bacterium
 |}
-Since their discovery in the 1970s, many restriction enzymes have been identified; for example, more than 3500 different Type II restriction enzymes have been characterized.<ref>{{cite book |url=https://books.google.com/books?id=i-HwCAAAQBAJ&pg=PA3 |title= Restriction Endonucleases (Nucleic Acids and Molecular Biology) |author=A. Pingoud |publisher=Springer |year= 2004|page= 3 |isbn= 9783642188510 }}</ref> Each enzyme is named after the bacterium from which it was isolated, using a naming system based on bacterial [[genus]], [[species]] and [[Strain (biology)|strain]].<ref name="pmid4588280">{{cite journal | vauthors = Smith HO, Nathans D | title = Letter: A suggested nomenclature for bacterial host modification and restriction systems and their enzymes | journal = Journal of Molecular Biology | volume = 81 | issue = 3 | pages = 419–23 | date = December 1973 | pmid = 4588280 | doi = 10.1016/0022-2836(73)90152-6 }}</ref><ref name="pmid12654995">{{cite journal | vauthors = Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, Bitinaite J, Blumenthal RM, Degtyarev SK, Dryden DT, Dybvig K, Firman K, Gromova ES, Gumport RI, Halford SE, Hattman S, Heitman J, Hornby DP, Janulaitis A, Jeltsch A, Josephsen J, Kiss A, Klaenhammer TR, Kobayashi I, Kong H, Krüger DH, Lacks S, Marinus MG, Miyahara M, Morgan RD, Murray NE, Nagaraja V, Piekarowicz A, Pingoud A, Raleigh E, Rao DN, Reich N, Repin VE, Selker EU, Shaw PC, Stein DC, Stoddard BL, Szybalski W, Trautner TA, Van Etten JL, Vitor JM, Wilson GG, Xu SY | display-authors = 6 | title = A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes | journal = Nucleic Acids Research | volume = 31 | issue = 7 | pages = 1805–12 | date = April 2003 | pmid = 12654995 | pmc = 152790 | doi = 10.1093/nar/gkg274 }}</ref> For example, the name of the [[EcoRI]] restriction enzyme was derived as shown in the box.Abbreviation	Meaning	Description
+Since their discovery in the 1970s, many restriction enzymes have been identified; for example, more than 3500 different Type II restriction enzymes have been characterized.<ref>{{cite book |url=https://books.google.com/books?id=i-HwCAAAQBAJ&pg=PA3 |title= Restriction Endonucleases (Nucleic Acids and Molecular Biology) |author=A. Pingoud |publisher=Springer |year= 2004|page= 3 |isbn= 9783642188510 }}</ref> Each enzyme is named after the bacterium from which it was isolated, using a naming system based on bacterial [[genus]], [[species]] and [[Strain (biology)|strain]].<ref name="pmid4588280">{{cite journal | vauthors = Smith HO, Nathans D | title = Letter: A suggested nomenclature for bacterial host modification and restriction systems and their enzymes | journal = Journal of Molecular Biology | volume = 81 | issue = 3 | pages = 419–23 | date = December 1973 | pmid = 4588280 | doi = 10.1016/0022-2836(73)90152-6 }}</ref><ref name="pmid12654995">{{cite journal | vauthors = Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, Bitinaite J, Blumenthal RM, Degtyarev SK, Dryden DT, Dybvig K, Firman K, Gromova ES, Gumport RI, Halford SE, Hattman S, Heitman J, Hornby DP, Janulaitis A, Jeltsch A, Josephsen J, Kiss A, Klaenhammer TR, Kobayashi I, Kong H, Krüger DH, Lacks S, Marinus MG, Miyahara M, Morgan RD, Murray NE, Nagaraja V, Piekarowicz A, Pingoud A, Raleigh E, Rao DN, Reich N, Repin VE, Selker EU, Shaw PC, Stein DC, Stoddard BL, Szybalski W, Trautner TA, Van Etten JL, Vitor JM, Wilson GG, Xu SY | display-authors = 6 | title = A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes | journal = Nucleic Acids Research | volume = 31 | issue = 7 | pages = 1805–12 | date = April 2003 | pmid = 12654995 | pmc = 152790 | doi = 10.1093/nar/gkg274 }}</ref> For example, the name of the [[EcoRI]] restriction enzyme was derived as shown in the box.
-E	Escherichia	genus
-co	coli	specific species
-R	RY13	strain
-I	First identified	order of identification
-in the bacterium
-Since their discovery in the 1970s, many restriction enzymes have been identified; for example, more than 3500 different Type II restriction enzymes have been characterized.[60] Each enzyme is named after the bacterium from which it was isolated, using a naming system based on bacterial genus, species and strain.[61][62] For example, the name of the EcoRI restriction enzyme was derived as shown in the
 ==Applications==
@@ Line 156: / Line 105: @@
 Isolated restriction enzymes are used to manipulate DNA for different scientific applications.
-They are used to assist insertion of genes into [[plasmid vector]]s during [[gene cloning]] and [[protein production]] experiments. For optimal use, plasmids that are commonly used for gene cloning are modified to include a short polylinker sequence (called the [[multiple cloning site]], or MCS) rich in restriction enzyme recognition sequences. This allows flexibility when inserting gene fragments into the plasmid vector; restriction sites contained naturally within genes influence the choice of endonuclease for digesting the DNA, since it is necessary to avoid restriction of wanted DNA while intentionally cutting the ends of the DNA. To clone a gene fragment into a vector, both plasmid DNA and gene insert are typically cut with the same restriction enzymes, and then glued together with the assistance of an enzyme known as a [[DNA ligase]].<ref name="urlCloning using restriction enzymes">{{cite web | url = http://www.embl.de/pepcore/pepcore_services/cloning/cloning_methods/restriction_enzymes/ | title = Cloning using restriction enzymes | author = Geerlof A | publisher = European Molecular Biology Laboratory - Hamburg | access-date = 2008-06-07}}</ref><ref name="isbn0-87969-576-5">{{cite book | vauthors = Russell DW, Sambrook J | title = Molecular cloning: a laboratory manual | publisher = Cold Spring Harbor Laboratory | location = Cold Spring Harbor, N.Y | year = 2001 | isbn = 0-87969-576-5 | url-access = registration | url = https://archive.org/details/molecularcloning0000samb_p7p5 }}</ref>
+They are used to assist insertion of genes into [[plasmid vector]]s during [[gene cloning]] and [[protein production]] experiments. For optimal use, plasmids that are commonly used for gene cloning are modified to include a short polylinker sequence (called the [[multiple cloning site]], or MCS) rich in restriction [[recognition sequence]]s. This allows flexibility when inserting gene fragments into the plasmid vector; restriction sites contained naturally within genes influence the choice of endonuclease for digesting the DNA, since it is necessary to avoid restriction of wanted DNA while intentionally cutting the ends of the DNA. To clone a gene fragment into a vector, both plasmid DNA and gene insert are typically cut with the same restriction enzymes, and then glued together with the assistance of an enzyme known as a [[DNA ligase]].<ref name="urlCloning using restriction enzymes">{{cite web | url = http://www.embl.de/pepcore/pepcore_services/cloning/cloning_methods/restriction_enzymes/ | title = Cloning using restriction enzymes | author = Geerlof A | publisher = European Molecular Biology Laboratory - Hamburg | access-date = 2008-06-07}}</ref><ref name="isbn0-87969-576-5">{{cite book | vauthors = Russell DW, Sambrook J | title = Molecular cloning: a laboratory manual | publisher = Cold Spring Harbor Laboratory | location = Cold Spring Harbor, N.Y | year = 2001 | isbn = 0-87969-576-5 | url-access = registration | url = https://archive.org/details/molecularcloning0000samb_p7p5 }}</ref>
 Restriction enzymes can also be used to distinguish gene [[allele]]s by specifically recognizing single base changes in DNA known as [[single-nucleotide polymorphism]]s (SNPs).<ref name="pmid18330346">{{cite journal | vauthors = Wolff JN, Gemmell NJ | title = Combining allele-specific fluorescent probes and restriction assay in real-time PCR to achieve SNP scoring beyond allele ratios of 1:1000 | journal = BioTechniques | volume = 44 | issue = 2 | pages = 193–4, 196, 199 | date = February 2008 | pmid = 18330346 | doi = 10.2144/000112719 | doi-access = free }}</ref><ref name="pmid15980518">{{cite journal | vauthors = Zhang R, Zhu Z, Zhu H, Nguyen T, Yao F, Xia K, Liang D, Liu C | display-authors = 6 | title = SNP Cutter: a comprehensive tool for SNP PCR-RFLP assay design | journal = Nucleic Acids Research | volume = 33 | issue = Web Server issue | pages = W489-92 | date = July 2005 | pmid = 15980518 | pmc = 1160119 | doi = 10.1093/nar/gki358 }}</ref> This is however only possible if a SNP alters the restriction site present in the allele. In this method, the restriction enzyme can be used to [[genotype]] a DNA sample without the need for expensive [[DNA sequencing|gene sequencing]]. The sample is first digested with the restriction enzyme to generate DNA fragments, and then the different sized fragments separated by [[gel electrophoresis]]. In general, alleles with correct restriction sites will generate two visible bands of DNA on the gel, and those with altered restriction sites will not be cut and will generate only a single band. A [[restriction map|DNA map]] by restriction digest can also be generated that can give the relative positions of the genes.<ref>{{cite web |url=http://www.nature.com/scitable/definition/mapping-282 |title=Mapping |work=Nature }}</ref>  The different lengths of DNA generated by restriction digest also produce a specific pattern of bands after gel electrophoresis, and can be used for [[DNA fingerprinting]].
@@ Line 374: / Line 323: @@
 == See also ==
 {{Portal|Biology|Technology}}
+* [[BglII]] – A restriction enzyme
+* [[EcoRI]] – A restriction enzyme
-* [[BglII]] – a restriction enzyme
+* [[HindIII]] – A restriction enzyme
-* [[EcoRI]] – a restriction enzyme
-* [[HindIII]] – a restriction enzyme
 * [[Homing endonuclease]]
 * [[List of homing endonuclease cutting sites]]
@@ Line 397: / Line 344: @@
 * {{MeshName|DNA+Restriction+Enzymes|3=DNA Restriction Enzymes}}
 * {{cite web | url = http://www.typei-rm.info | title = Type I Restriction-Modification | author = Firman K | date = 2007-11-24 | publisher = University of Portsmouth | access-date = 2008-06-06 | archive-url = https://web.archive.org/web/20080706085746/http://www.typei-rm.info/ | archive-date = 2008-07-06 | url-status = dead }}
-* {{cite web | url = http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb8_1.html | title = Restriction Enzymes | author = Goodsell DS | date = 2000-08-01 | work = Molecule of the Month | publisher = RCSB Protein Data Bank | access-date = 2008-06-06 | url-status = dead | archive-url = https://web.archive.org/web/20080531095339/http://www.rcsb.org/pdb/static.do?p=education_discussion%2Fmolecule_of_the_month%2Fpdb8_1.html | archive-date = 2008-05-31 }}
+* {{cite web | url = http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb8_1.html | title = Restriction Enzymes | author = Goodsell DS | date = 2000-08-01 | department = Molecule of the Month | publisher = RCSB Protein Data Bank | access-date = 2008-06-06 | url-status = dead | archive-url = https://web.archive.org/web/20080531095339/http://www.rcsb.org/pdb/static.do?p=education_discussion%2Fmolecule_of_the_month%2Fpdb8_1.html | archive-date = 2008-05-31 }}
 * {{cite web | url = http://www.scq.ubc.ca/?p=249 | title = Restriction Endonucleases: Molecular Scissors for Specifically Cutting DNA |vauthors=Simmer M, Secko D |date = 2003-08-01 | work = The Science Creative Quarterly |access-date=2008-06-06}}
-* {{cite web| url =http://rebase.neb.com| title =REBASE| vauthors =Roberts RJ, Vincze T, Posfai, J, Macelis D| archive-url =https://web.archive.org/web/20150216092957/http://rebase.neb.com/| archive-date =2015-02-16| quote =Restriction Enzyme Database| url-status =dead| access-date =2008-06-06}}
+* {{cite web| url =http://rebase.neb.com| title =REBASE| vauthors =Roberts RJ, Vincze T, Posfai, J, Macelis D| archive-url =https://web.archive.org/web/20150216092957/http://rebase.neb.com/| archive-date =2015-02-16| quote =Restriction Enzyme Database| url-status =dead| access-date =2008-06-06}}.
 {{Esterases}}
 {{enzymes}}
-{{Portal bar|Biology|border=no}}
 {{Authority control}}
 {{DEFAULTSORT:Restriction Enzyme}}
-[[Category:Molecular biology]]
+[[Category:Restriction enzymes| ]]
 [[Category:Biotechnology]]
-[[Category:Restriction enzymes| ]]
 [[Category:EC 3.1]]
 [[Category:Life sciences industry]]
+[[Category:Molecular biology]]

v t e Enzymes
Activity	Active site Binding site Catalytic triad Oxyanion hole Enzyme promiscuity Diffusion-limited enzyme Cofactor Enzyme catalysis
Regulation	Allosteric regulation Cooperativity Enzyme inhibitor Enzyme activator
Classification	EC number Enzyme superfamily Enzyme family List of enzymes
Kinetics	Enzyme kinetics Eadie–Hofstee diagram Hanes–Woolf plot Lineweaver–Burk plot Michaelis–Menten kinetics
Types	EC1 Oxidoreductases (list) EC2 Transferases (list) EC3 Hydrolases (list) EC4 Lyases (list) EC5 Isomerases (list) EC6 Ligases (list) EC7 Translocases (list)