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What Are Restriction Enzymes Used For In Nature

Written By Tuesday, May 10, 2022 Add Comment Edit

Class of enzymes that divide DNA

A restriction enzyme, restriction endonuclease, or restrictase is an enzyme that cleaves Dna into fragments at or near specific recognition sites within molecules known every bit restriction sites.[one] [two] [3] Brake enzymes are one class of the broader endonuclease group of enzymes. Brake 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 some other. To cut DNA, all restriction enzymes brand 2 incisions, once through each saccharide-phosphate courage (i.east. each strand) of the DNA double helix.

These enzymes are found in bacteria and archaea and provide a defence force mechanism confronting invading viruses.[4] [v] Inside a prokaryote, the restriction enzymes selectively cut upward foreign Deoxyribonucleic acid in a process called restriction digestion; meanwhile, host DNA is protected past 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 stand for over 250 different specificities.[7] Over three,000 of these have been studied in detail, and more than 800 of these are available commercially.[viii] These enzymes are routinely used for Dna modification in laboratories, and they are a vital tool in molecular cloning.[nine] [10] [11]

History [edit]

The term restriction enzyme originated from the studies of phage λ, a virus that infects leaner, and the phenomenon of host-controlled brake and modification of such bacterial phage or bacteriophage.[12] The phenomenon was offset identified in work done in the laboratories of Salvador Luria, Jean Weigle and Giuseppe Bertani in the early 1950s.[13] [fourteen] Information technology was plant that, for a bacteriophage λ that tin can abound well in one strain of Escherichia coli, for example E. coli C, when grown in another strain, for case E. coli K, its yields tin drop significantly, by equally much every bit 3-5 orders of magnitude. The host prison cell, in this case Due east. coli G, is known as the restricting host and appears to have the ability to reduce the biological activeness of the phage λ. If a phage becomes established in ane strain, the ability of that phage to grow besides 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 past an enzymatic cleavage of the phage DNA, and the enzyme involved was therefore termed a restriction enzyme.[four] [15] [16] [17]

The restriction enzymes studied by Arber and Meselson were type I brake enzymes, which cleave Deoxyribonucleic acid randomly abroad from the recognition site.[18] In 1970, Hamilton O. Smith, Thomas Kelly and Kent Wilcox isolated and characterized the first type II brake enzyme, HindII, from the bacterium Haemophilus influenzae.[19] [20] Restriction enzymes of this blazon are more than useful for laboratory piece of work as they carve Dna at the site of their recognition sequence and are the most usually used as a molecular biological science 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 Deoxyribonucleic acid to be manipulated, leading to the evolution of recombinant DNA technology that has many applications, for example, allowing the large scale production of proteins such as homo insulin used by diabetic patients.[13] [24]

Origins [edit]

Restriction enzymes probable evolved from a mutual ancestor and became widespread via horizontal factor transfer.[25] [26] In addition, there is mounting evidence that restriction endonucleases evolved equally a selfish genetic chemical element.[27]

Recognition site [edit]

A palindromic recognition site reads the same on the reverse strand as it does on the forwards 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 tin as well 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 volition appear past risk in whatsoever given genome, e.g., a 4-base pair sequence would theoretically occur once every 4^4 or 256bp, vi bases, four^half-dozen or iv,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 2 types of palindromic sequences that tin can exist possible in DNA. The mirror-similar palindrome is similar to those found in ordinary text, in which a sequence reads the aforementioned forward and astern on a unmarried strand of DNA, as in GTAATG. The inverted repeat palindrome is also a sequence that reads the same forward and backward, but the forrard and backward sequences are plant in complementary Dna strands (i.east., of double-stranded DNA), as in GTATAC (GTATAC beingness complementary to CATATG).[30] Inverted echo palindromes are more than mutual and accept greater biological importance than mirror-similar 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 mucilaginous-end "overhang" of an enzyme brake.[31]

Different brake 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 every bit isoschizomers.

Types [edit]

Naturally occurring restriction endonucleases are categorized into five groups (Types I, 2, 3, 4, and V) based on their composition and enzyme cofactor requirements, the nature of their target sequence, and the position of their Deoxyribonucleic acid cleavage site relative to the target sequence.[32] [33] [34] DNA sequence analyses of restriction enzymes all the same 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 Deoxyribonucleic acid to give specific fragments with terminal v'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements,[36] [37] every bit summarised below:

  • Type I enzymes (EC 3.ane.21.iii) cleave at sites remote from a recognition site; crave both ATP and S-adenosyl-L-methionine to office; multifunctional protein with both restriction digestion and methylase (EC 2.1.1.72) activities.
  • Type II enzymes (EC 3.1.21.iv) cleave within or at brusque specific distances from a recognition site; about require magnesium; unmarried office (restriction digestion) enzymes independent of methylase.
  • Type III enzymes (EC 3.one.21.5) cleave at sites a brusk distance from a recognition site; require ATP (but do non hydrolyse it); S-adenosyl-Fifty-methionine stimulates the reaction simply is non required; exist as role of a complex with a modification methylase (EC two.1.ane.72).
  • Type 4 enzymes target modified DNA, eastward.thou. methylated, hydroxymethylated and glucosyl-hydroxymethylated DNA
  • Type Five enzymes utilise guide RNAs (gRNAs)

Type l [edit]

Type I restriction enzymes were the first to be identified and were commencement identified in 2 different strains (G-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 equanimous of two specific portions—one containing iii–4 nucleotides, and another containing 4–five nucleotides—separated by a non-specific spacer of nearly 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 total activity. Type I brake 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 activeness), and HsdS is important for specificity of the recognition (Dna-binding) site in addition to both brake digestion (DNA cleavage) and modification (DNA methyltransferase) activeness.[32] [38]

Type 2 [edit]

Blazon Ii site-specific deoxyribonuclease-like
1QPS.png

Structure of the homodimeric brake enzyme EcoRI (cyan and green cartoon diagram) bound to double stranded Deoxyribonucleic acid (chocolate-brown tubes).[39] Two catalytic magnesium ions (one from each monomer) are shown as magenta spheres and are side by side to the broken sites in the Deoxyribonucleic acid made by the enzyme (depicted every bit gaps in the Deoxyribonucleic acid backbone).
Identifiers
Symbol Restrct_endonuc-II-similar
Pfam clan CL0236
InterPro IPR011335
SCOP2 1wte / SCOPe / SUPFAM

Typical blazon 2 restriction enzymes differ from type I restriction enzymes in several ways. They course homodimers, with recognition sites that are usually undivided and palindromic and 4–8 nucleotides in length. They recognize and cleave Deoxyribonucleic acid at the same site, and they do not utilise ATP or AdoMet for their activity—they usually require only Mgtwo+ as a cofactor.[29] These enzymes cleave the phosphodiester bond of double helix Deoxyribonucleic acid. It can either cleave at the center of both strands to yield a edgeless end, or at a staggered position leaving overhangs called mucilaginous ends.[40] These are the nigh 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 adult to divide this large family into subcategories based on deviations from typical characteristics of blazon 2 enzymes.[29] These subgroups are defined using a letter suffix.

Blazon IIB restriction enzymes (e.k., 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 crave both AdoMet and Mg2+ cofactors. Blazon IIE brake endonucleases (e.g., NaeI) cleave Deoxyribonucleic acid post-obit interaction with 2 copies of their recognition sequence.[29] Ane 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. Like 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] Blazon IIG brake endonucleases (eastward.yard., RM.Eco57I) practice have a unmarried subunit, similar classical Type Two restriction enzymes, but crave the cofactor AdoMet to be agile.[29] Type IIM restriction endonucleases, such as DpnI, are able to recognize and cut methylated Dna.[29] [41] [42] Type IIS brake endonucleases (e.g., FokI) cleave Deoxyribonucleic acid at a defined altitude 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 office as dimers. Similarly, Blazon IIT restriction enzymes (eastward.thousand., Bpu10I and BslI) are composed of two different subunits. Some recognize palindromic sequences while others have asymmetric recognition sites.[29]

Type III [edit]

Type Three restriction enzymes (east.chiliad., EcoP15) recognize two separate non-palindromic sequences that are inversely oriented. They cut DNA almost 20–30 base pairs afterward the recognition site.[43] These enzymes contain more than than one subunit and crave 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 Deoxyribonucleic acid. 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 organization and is a modification methyltransferase; as such, information technology is functionally equivalent to the Yard and Due south subunits of type I brake endonuclease. Res is required for brake digestion, although it has no enzymatic activity on its own. Blazon Three enzymes recognise short 5–6 bp-long asymmetric DNA sequences and cleave 25–27 bp downstream to leave short, single-stranded five' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction digestion to occur. These enzymes methylate but 1 strand of the DNA, at the N-6 position of adenosyl residues, then newly replicated DNA will have only 1 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 unit, including motif I, the AdoMet binding pocket (FXGXG), and motif IV, the catalytic region (Southward/D/N (PP) Y/F).[36] [45]

Type IV [edit]

Type 4 enzymes recognize modified, typically methylated DNA and are exemplified past the McrBC and Mrr systems ofDue east. coli.[35]

Type V [edit]

Type 5 restriction enzymes (east.k., the cas9-gRNA complex from CRISPRs[46]) use guide RNAs to target specific not-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 employ of these enzymes brand them promising for futurity genetic engineering applications.[46] [47]

Artificial brake enzymes [edit]

Artificial restriction enzymes tin be generated by fusing a natural or engineered Deoxyribonucleic acid-binding domain to a nuclease domain (often the cleavage domain of the type IIS restriction enzyme FokI).[48] Such bogus 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 almost usually used artificial restriction enzymes and are generally used in genetic engineering applications,[50] [51] [52] [53] only tin also exist 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 organization, was engineered for editing the genome, and it was rapidly adopted in laboratories.[57] For more detail, read CRISPR (Clustered regularly interspaced short palindromic repeats).

In 2017, a group from Academy of Illinois reported using an Argonaute protein taken from Pyrococcus furiosus (PfAgo) along with guide DNA to edit DNA in vitro every bit artificial restriction enzymes.[58]

Artificial ribonucleases that act equally restriction enzymes for RNA have too been adult. A PNA-based system, called a PNAzyme, has a Cu(II)-2,9-dimethylphenanthroline grouping 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 past cleaving merely at one site that either does not have a mismatch or is kinetically preferred out of ii possible cleavage sites.[59]

Classification [edit]

Derivation of the EcoRI proper name
Abridgement Pregnant Clarification
E Escherichia genus
co coli specific species
R RY13 strain
I First identified lodge of identification
in the bacterium

Since their discovery in the 1970s, many restriction enzymes have been identified; for instance, more than 3500 different Blazon 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 [edit]

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

They are used to aid insertion of genes into plasmid vectors during gene cloning and protein production experiments. For optimal use, plasmids that are usually used for gene cloning are modified to include a short polylinker sequence (chosen 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 cutting with the same restriction enzymes, so glued together with the assistance of an enzyme known every bit a Deoxyribonucleic acid ligase.[63] [64]

Restriction enzymes can also be used to distinguish gene alleles past specifically recognizing unmarried base changes in Dna known every bit unmarried-nucleotide polymorphisms (SNPs).[65] [66] This is nevertheless merely possible if a SNP alters the restriction site nowadays 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 kickoff digested with the restriction enzyme to generate Deoxyribonucleic acid 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 contradistinct restriction sites volition non be cutting and will generate merely 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 past restriction digest also produce a specific blueprint of bands after gel electrophoresis, and can be used for DNA fingerprinting.

In a similar manner, brake enzymes are used to digest genomic DNA for factor assay past Southern absorb. This technique allows researchers to identify how many copies (or paralogues) of a gene are nowadays in the genome of i individual, or how many gene mutations (polymorphisms) have occurred inside a population. The latter example is called restriction fragment length polymorphism (RFLP).[68]

Bogus restriction enzymes created by linking the FokI Deoxyribonucleic acid cleavage domain with an assortment 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 eighteen–24 for the pair. A 5–vii bp spacer between the cleavage sites further enhances the specificity of ZFN, making them a condom and more than precise tool that can exist 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 leaner R-1000 system as a model for devising human anti-viral gene or genomic vaccines and therapies since the RM organization serves an innate defense-role in bacteria past restricting tropism by bacteriophages.[lxx] In that location is enquiry on REases and ZFN that can cleave the DNA of various human viruses, including HSV-2, high-adventure HPVs and HIV-one, 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 i(ERCC) appear to mimic the action of RM-systems in bacteria, and the not-homologous end-joining (NHEJ) that follows the utilize of ZFN without a repair template.[74] [75]

Examples [edit]

Examples of restriction enzymes include:[76]

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

Key:
* = edgeless ends
N = C or K or T or A
W = A or T

See as well [edit]

  • BglII – a restriction enzyme
  • EcoRI – a restriction enzyme
  • HindIII – a restriction enzyme
  • Homing endonuclease
  • Listing of homing endonuclease cutting sites
  • List of brake enzyme cutting sites
  • Molecular-weight size mark
  • REBASE (database)
  • Star activity

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External links [edit]

  • Dna Restriction Enzymes at the Usa National Library of Medicine Medical Bailiwick Headings (MeSH)
  • Firman Grand (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 Banking company. Archived from the original on 2008-05-31. Retrieved 2008-06-06 .
  • Simmer Grand, Secko D (2003-08-01). "Restriction Endonucleases: Molecular Scissors for Specifically Cutting Deoxyribonucleic acid". 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 . Brake Enzyme Database

What Are Restriction Enzymes Used For In Nature,

Source: https://en.wikipedia.org/wiki/Restriction_enzyme

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