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Molecular Scissors Introduction Do You Know That

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Class of enzymes that carve up 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 equally restriction sites.[1] [two] [3] Restriction enzymes are 1 form of the broader endonuclease grouping of enzymes. Restriction enzymes are commonly classified into v 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 ane another. To cut DNA, all restriction enzymes make two incisions, once through each sugar-phosphate backbone (i.e. each strand) of the Deoxyribonucleic acid double helix.

These enzymes are found in bacteria and archaea and provide a defense mechanism confronting invading viruses.[4] [5] Within a prokaryote, the restriction enzymes selectively cutting up foreign DNA in a process called restriction digestion; meanwhile, host Deoxyribonucleic acid 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.[six]

More than iii,600 restriction endonucleases are known which stand for over 250 different specificities.[7] Over iii,000 of these have been studied in item, and more 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] [xi]

History [edit]

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 get-go identified in work done in the laboratories of Salvador Luria, Jean Weigle and Giuseppe Bertani in the early 1950s.[13] [fourteen] Information technology was institute that, for a bacteriophage λ that tin grow well in i strain of Escherichia coli, for example East. coli C, when grown in another strain, for example East. coli K, its yields can drop significantly, past as much as 3-5 orders of magnitude. The host prison cell, in this example E. coli Thou, is known every bit 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 power of that phage to grow likewise becomes restricted in other strains. In the 1960s, it was shown in piece of 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.[4] [15] [16] [17]

The restriction enzymes studied past Arber and Meselson were type I restriction enzymes, which cleave DNA randomly away from the recognition site.[xviii] In 1970, Hamilton O. Smith, Thomas Kelly and Kent Wilcox isolated and characterized the first blazon 2 brake enzyme, Hind2, from the bacterium Haemophilus influenzae.[xix] [twenty] Restriction enzymes of this type are more useful for laboratory work as they carve 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) Deoxyribonucleic acid by restriction enzymes yields specific fragments that can exist separated using polyacrylamide gel electrophoresis, thus showing that restriction enzymes can as well exist used for mapping Deoxyribonucleic acid.[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 Deoxyribonucleic acid technology that has many applications, for instance, allowing the large scale product of proteins such as human insulin used by diabetic patients.[thirteen] [24]

Origins [edit]

Restriction enzymes likely evolved from a common ancestor and became widespread via horizontal factor transfer.[25] [26] In improver, there is mounting evidence that restriction endonucleases evolved every bit 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 frontward 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 past the number of bases in its recognition site, usually between iv and 8 bases, and the number of bases in the sequence will determine how often the site volition announced past take chances in any given genome, eastward.g., a four-base pair sequence would theoretically occur once every 4^4 or 256bp, 6 bases, 4^6 or 4,096bp, and 8 bases would be iv^eight or 65,536bp.[28] Many of them are palindromic, meaning the base sequence reads the aforementioned backwards and forrad.[29] In theory, at that place are 2 types of palindromic sequences that can exist possible in Deoxyribonucleic acid. The mirror-like palindrome is similar to those found in ordinary text, in which a sequence reads the same forrard and backward on a single strand of Deoxyribonucleic acid, as in GTAATG. The inverted repeat palindrome is too a sequence that reads the same forward and backward, but the forrad and astern sequences are found in complementary DNA strands (i.eastward., of double-stranded Deoxyribonucleic acid), as in GTATAC (GTATAC being complementary to CATATG).[xxx] Inverted echo palindromes are more than 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 brake enzyme, producing differences in the length, sequence and strand orientation (v' end or 3' end) of a gluey-finish "overhang" of an enzyme brake.[31]

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

Types [edit]

Naturally occurring brake endonucleases are categorized into iv groups (Types I, Ii III, and 4) 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 analyses of restriction enzymes nonetheless evidence great variations, indicating that there are more than four types.[35] All types of enzymes recognize specific short Deoxyribonucleic acid sequences and carry out the endonucleolytic cleavage of Deoxyribonucleic acid to give specific fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements,[36] [37] every bit summarised beneath:

  • Blazon I enzymes (EC 3.1.21.iii) cleave at sites remote from a recognition site; require both ATP and Due south-adenosyl-50-methionine to function; multifunctional protein with both restriction digestion and methylase (EC ii.1.ane.72) activities.
  • Type II enzymes (EC three.1.21.4) cleave within or at brusque specific distances from a recognition site; nigh require magnesium; single function (restriction digestion) enzymes independent of methylase.
  • Type III enzymes (EC 3.i.21.v) cleave at sites a short altitude from a recognition site; require ATP (only exercise non hydrolyse it); Southward-adenosyl-L-methionine stimulates the reaction merely is not required; exist as part of a complex with a modification methylase (EC 2.i.1.72).
  • Blazon Iv enzymes target modified DNA, e.thou. methylated, hydroxymethylated and glucosyl-hydroxymethylated DNA
  • Blazon V enzymes utilize guide RNAs (gRNAs)

Type l [edit]

Type I restriction enzymes were the first to exist identified and were kickoff identified in ii different strains (1000-12 and B) of E. coli.[38] These enzymes cutting 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 too molecular motors. The recognition site is asymmetrical and is equanimous of two specific portions—one containing three–four nucleotides, and another containing 4–5 nucleotides—separated past a non-specific spacer of near 6–eight nucleotides. These enzymes are multifunctional and are capable of both restriction digestion and modification activities, depending upon the methylation condition of the target DNA. The cofactors S-Adenosyl methionine (AdoMet), hydrolyzed adenosine triphosphate (ATP), and magnesium (Mgtwo+) ions, are required for their full activity. Type I restriction enzymes possess three subunits chosen HsdR, HsdM, and HsdS; HsdR is required for restriction digestion; HsdM is necessary for calculation 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) action.[32] [38]

Blazon II [edit]

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

Structure of the homodimeric brake enzyme EcoRI (cyan and dark-green cartoon diagram) bound to double stranded Dna (brown tubes).[39] 2 catalytic magnesium ions (one from each monomer) are shown as magenta spheres and are adjacent to the cleaved sites in the DNA fabricated by the enzyme (depicted as gaps in the DNA backbone).
Identifiers
Symbol Restrct_endonuc-2-similar
Pfam clan CL0236
InterPro IPR011335
SCOP2 1wte / Scope / SUPFAM

Typical type 2 restriction enzymes differ from blazon I restriction enzymes in several ways. They form homodimers, with recognition sites that are unremarkably undivided and palindromic and iv–viii nucleotides in length. They recognize and cleave DNA at the same site, and they practice non apply ATP or AdoMet for their activity—they ordinarily require only Mgii+ 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.[twoscore] These are the near normally bachelor 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 course, and new subfamily nomenclature was developed to divide this big family into subcategories based on deviations from typical characteristics of blazon Two enzymes.[29] These subgroups are defined using a letter of the alphabet suffix.

Type IIB restriction enzymes (eastward.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 brake endonucleases (e.g., NaeI) cleave DNA post-obit interaction with ii 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 upwardly or improves the efficiency of enzyme cleavage. Similar to type IIE enzymes, type IIF brake endonucleases (eastward.g. NgoMIV) interact with two copies of their recognition sequence but cleave both sequences at the same time.[29] Type IIG restriction endonucleases (e.thou., RM.Eco57I) exercise accept a single subunit, similar classical Type II restriction enzymes, but require the cofactor AdoMet to exist active.[29] Blazon IIM brake endonucleases, such as DpnI, are able to recognize and cut methylated Deoxyribonucleic acid.[29] [41] [42] Blazon IIS restriction endonucleases (east.g., FokI) carve Dna at a defined altitude from their non-palindromic disproportionate recognition sites;[29] this characteristic is widely used to perform in-vitro cloning techniques such every bit Golden Gate cloning. These enzymes may function as dimers. Similarly, Type IIT brake enzymes (eastward.thou., Bpu10I and BslI) are composed of two different subunits. Some recognize palindromic sequences while others have asymmetric recognition sites.[29]

Type III [edit]

Blazon 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 comprise more than one subunit and require AdoMet and ATP cofactors for their roles in DNA methylation and brake digestion, respectively.[44] They are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading strange Deoxyribonucleic acid. Type III enzymes are hetero-oligomeric, multifunctional proteins equanimous of 2 subunits, Res (P08764) and Mod (P08763). The Modernistic subunit recognises the Dna sequence specific for the organization and is a modification methyltransferase; equally such, it is functionally equivalent to the M and S subunits of blazon I brake endonuclease. Res is required for brake digestion, although it has no enzymatic activeness on its own. Type 3 enzymes recognise short 5–6 bp-long asymmetric DNA sequences and cleave 25–27 bp downstream to exit short, single-stranded 5' protrusions. They require the presence of 2 inversely oriented unmethylated recognition sites for brake digestion to occur. These enzymes methylate but ane strand of the DNA, at the Northward-six position of adenosyl residues, and then newly replicated DNA will have only 1 strand methylated, which is sufficient to protect against brake digestion. Type III enzymes vest to the beta-subfamily of N6 adenine methyltransferases, containing the 9 motifs that characterise this family, including motif I, the AdoMet bounden pocket (FXGXG), and motif IV, the catalytic region (S/D/N (PP) Y/F).[36] [45]

Type IV [edit]

Type 4 enzymes recognize modified, typically methylated Deoxyribonucleic acid and are exemplified by the McrBC and Mrr systems ofE. coli.[35]

Type V [edit]

Type 5 restriction enzymes (due east.g., the cas9-gRNA circuitous from CRISPRs[46]) utilize guide RNAs to target specific non-palindromic sequences found on invading organisms. They tin cut Deoxyribonucleic acid of variable length, provided that a suitable guide RNA is provided. The flexibility and ease of use of these enzymes make them promising for time to come genetic engineering applications.[46] [47]

Artificial brake enzymes [edit]

Artificial brake enzymes tin can be generated by fusing a natural or engineered Dna-binding domain to a nuclease domain (oft the cleavage domain of the blazon IIS restriction enzyme FokI).[48] Such bogus brake enzymes tin can target big Dna sites (upward to 36 bp) and tin can be engineered to bind to desired DNA sequences.[49] Zinc finger nucleases are the most commonly used artificial brake enzymes and are generally used in genetic technology applications,[50] [51] [52] [53] merely 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 force organisation, was engineered for editing the genome, and it was chop-chop adopted in laboratories.[57] For more detail, read CRISPR (Clustered regularly interspaced short palindromic repeats).

In 2017, a grouping from Academy of Illinois reported using an Argonaute protein taken from Pyrococcus furiosus (PfAgo) along with guide Deoxyribonucleic acid to edit Dna in vitro as artificial restriction enzymes.[58]

Artificial ribonucleases that act as restriction enzymes for RNA have besides been developed. A PNA-based system, called a PNAzyme, has a Cu(II)-two,9-dimethylphenanthroline grouping that mimics ribonucleases for specific RNA sequence and cleaves at a not-base of operations-paired region (RNA bulge) of the targeted RNA formed when the enzyme binds the RNA. This enzyme shows selectivity by cleaving only at ane site that either does not have a mismatch or is kinetically preferred out of two possible cleavage sites.[59]

Classification [edit]

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

Since their discovery in the 1970s, many brake enzymes have been identified; for case, more 3500 unlike Type Ii brake enzymes have been characterized.[lx] Each enzyme is named later 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 every bit shown in the box.

Applications [edit]

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

They are used to assist insertion of genes into plasmid vectors during factor cloning and poly peptide production experiments. For optimal use, plasmids that are unremarkably 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 independent naturally within genes influence the option of endonuclease for digesting the Dna, since it is necessary to avert restriction of wanted Deoxyribonucleic acid 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, then glued together with the assistance of an enzyme known as a DNA ligase.[63] [64]

Brake enzymes tin can too be used to distinguish gene alleles past specifically recognizing unmarried base changes in Deoxyribonucleic acid known as single-nucleotide polymorphisms (SNPs).[65] [66] This is however merely possible if a SNP alters the brake site nowadays in the allele. In this method, the restriction enzyme tin can be used to genotype a DNA sample without the need for expensive gene sequencing. The sample is starting time digested with the restriction enzyme to generate Dna fragments, and and so 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 non be cut and will generate only a unmarried band. A Deoxyribonucleic acid map past brake assimilate can also be generated that can requite the relative positions of the genes.[67] The different lengths of DNA generated past restriction digest also produce a specific design of bands after gel electrophoresis, and can exist used for DNA fingerprinting.

In a similar manner, brake enzymes are used to digest genomic DNA for gene analysis past Southern absorb. 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 brake 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 beingness 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 five–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 accept proposed using the bacteria R-M system as a model for devising human being anti-viral gene or genomic vaccines and therapies since the RM system serves an innate defence-role in leaner by restricting tropism past bacteriophages.[70] In that location is inquiry on REases and ZFN that tin carve the DNA of diverse human being viruses, including HSV-two, high-adventure HPVs and HIV-i, with the ultimate goal of inducing target mutagenesis and aberrations of homo-infecting viruses.[71] [72] [73] The human genome already contains remnants of retroviral genomes that have been inactivated and harnessed for cocky-proceeds. Indeed, the mechanisms for silencing active L1 genomic retroelements past the three prime repair exonuclease 1 (TREX1) and excision repair cross complementing 1(ERCC) appear to mimic the action of RM-systems in leaner, and the not-homologous end-joining (NHEJ) that follows the apply 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                
v'---1000     AATTC---three' 3'---CTTAA     G---v'
EcoRII Escherichia coli 
5'CCWGG 3'GGWCC                
5'---     CCWGG---3' 3'---GGWCC     ---5'
BamHI Bacillus amyloliquefaciens 
v'GGATCC three'CCTAGG                
5'---G     GATCC---3' 3'---CCTAG     G---5'
HindIII Haemophilus influenzae 
5'AAGCTT iii'TTCGAA                
5'---A     AGCTT---3' iii'---TTCGA     A---5'
TaqI Thermus aquaticus 
5'TCGA iii'AGCT                
5'---T   CGA---3' iii'---AGC   T---5'
NotI Nocardia otitidis 
v'GCGGCCGC 3'CGCCGGCG                
5'---GC   GGCCGC---3' iii'---CGCCGG   CG---5'
HinFI Haemophilus influenzae 
5'GANTC iii'CTNAG                
5'---G   ANTC---3' 3'---CTNA   Thou---5'
Sau3AI Staphylococcus aureus 
5'GATC iii'CTAG                
5'---     GATC---3' three'---CTAG     ---v'
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' iii'---GGG  CCC---5'
HaeIII* Haemophilus aegyptius 
5'GGCC 3'CCGG                
v'---GG  CC---3' 3'---CC  GG---5'
HgaI[77] Haemophilus gallinarum 
5'GACGC 3'CTGCG                
v'---NN  NN---iii' 3'---NN  NN---5'
AluI* Arthrobacter luteus 
5'AGCT 3'TCGA                
5'---AG  CT---three' 3'---TC  GA---five'
EcoRV* Escherichia coli 
v'GATATC three'CTATAG                
five'---GAT  ATC---3' 3'---CTA  TAG---5'
EcoP15I Escherichia coli 
5'CAGCAGN25NN three'GTCGTCN25NN                
5'---CAGCAGN25                  NN---3' 3'---GTCGTCN25NN   ---five'
KpnI[78] Klebsiella pneumoniae 
v'GGTACC 3'CCATGG                
5'---GGTAC  C---3' 3'---C  CATGG---5'
PstI[78] Providencia stuartii 
5'CTGCAG 3'GACGTC                
5'---CTGCA  G---three' 3'---Thousand  ACGTC---5'
SacI[78] Streptomyces achromogenes 
v'GAGCTC 3'CTCGAG                
5'---GAGCT  C---3' iii'---C  TCGAG---five'
SalI[78] Streptomyces albus 
5'GTCGAC three'CAGCTG                
5'---G  TCGAC---3' iii'---CAGCT  G---v'
ScaI*[78] Streptomyces caespitosus 
5'AGTACT 3'TCATGA                
5'---AGT  ACT---3' 3'---TCA  TGA---5'
SpeI Sphaerotilus natans 
v'ACTAGT 3'TGATCA                
five'---A  CTAGT---3' 3'---TGATC  A---five'
SphI[78] Streptomyces phaeochromogenes 
5'GCATGC 3'CGTACG                
five'---GCATG  C---iii' 3'---C  GTACG---5'
StuI*[79] [lxxx] Streptomyces tubercidicus 
five'AGGCCT 3'TCCGGA                
five'---AGG  CCT---iii' 3'---TCC  GGA---5'
XbaI[78] Xanthomonas badrii 
5'TCTAGA three'AGATCT                
5'---T  CTAGA---iii' 3'---AGATC  T---five'

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

See too [edit]

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

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External links [edit]

  • DNA Restriction Enzymes at the US National Library of Medicine Medical Subject Headings (MeSH)
  • Firman K (2007-11-24). "Blazon I Brake-Modification". Academy 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 Information Bank. Archived from the original on 2008-05-31. Retrieved 2008-06-06 .
  • Simmer Chiliad, 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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Source: https://en.wikipedia.org/wiki/Restriction_enzyme

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