Restriction enzyme
Encyclopedia
A Restriction Enzyme is an enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...

 that cuts double-stranded DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

 at specific recognition nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...

 sequences known as restriction sites. Such enzymes, found in bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...

 and archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...

, are thought to have evolved to provide a defense mechanism against invading virus
Virus
A virus is a small infectious agent that can replicate only inside the living cells of organisms. Viruses infect all types of organisms, from animals and plants to bacteria and archaea...

es. Inside a bacterial host, the restriction enzymes selectively cut up foreign DNA in a process called restriction; host DNA is methylated
Methylation
In the chemical sciences, methylation denotes the addition of a methyl group to a substrate or the substitution of an atom or group by a methyl group. Methylation is a form of alkylation with, to be specific, a methyl group, rather than a larger carbon chain, replacing a hydrogen atom...

 by a modification enzyme (a methylase
Methylase
A methylase is an enzyme that attaches a methyl group to a molecule.These are found in prokaryotes and eukaryotes. Bacteria use methylase to differentiate between foreign genetic material and their own, thus protecting their DNA from their own immune system...

) to protect it from the restriction enzyme’s activity. Collectively, these two processes form the restriction modification system
Restriction modification system
The restriction modification system is used by bacteria, and perhaps other prokaryotic organisms to protect themselves from foreign DNA, such as the one borne by bacteriophages. This phenomenon was first noticed in the 1950s. Certain bacteria strains were found to inhibit the growth of viruses...

. To cut the DNA, a restriction enzyme makes two incisions, once through each sugar-phosphate backbone (i.e. each strand) of the DNA double helix.

Over 3000 restriction enzymes have been studied in detail, and more than 600 of these are available commercially and are routinely used for DNA modification and manipulation in laboratories.

History

For the first isolation of a restriction enzyme, HindII
HindII
H.O. Smith, K.W. Wilcox, and T.J. Kelley, working at Johns Hopkins University in 1968, isolated and characterized the first restriction nuclease whose functioning depended on a specific DNA nucleotide sequence...

, in 1970, and the subsequent discovery and characterization of numerous restriction endonucleases, the 1978 Nobel Prize for Physiology or Medicine was awarded to Daniel Nathans
Daniel Nathans
Daniel Nathans was an American microbiologist.He was born in Wilmington, Delaware, the last of nine children born to Russian Jewish immigrant parents. During the Great Depression his father lost his small business and was unemployed for a long period of time...

, Werner Arber
Werner Arber
Werner Arber is a Swiss microbiologist and geneticist. Along with American researchers Hamilton Smith and Daniel Nathans, Werner Arber shared the 1978 Nobel Prize in Physiology or Medicine for the discovery of restriction endonucleases...

, and Hamilton O. Smith
Hamilton O. Smith
Hamilton Othanel Smith is an American microbiologist and Nobel laureate.Smith was born on August 23, 1931, and graduated from University Laboratory High School of Urbana, Illinois. He attended the University of Illinois at Urbana-Champaign, but in 1950 transferred to the University of California,...

. Their discovery led to the development of recombinant DNA
Recombinant DNA
Recombinant DNA molecules are DNA sequences that result from the use of laboratory methods to bring together genetic material from multiple sources, creating sequences that would not otherwise be found in biological organisms...

 technology that allowed, for example, the large scale production of human insulin
Insulin
Insulin is a hormone central to regulating carbohydrate and fat metabolism in the body. Insulin causes cells in the liver, muscle, and fat tissue to take up glucose from the blood, storing it as glycogen in the liver and muscle....

 for diabetics using E. coli bacteria.

Recognition site


5'-GTATAC-3'
::::::
3'-CATATG-5'
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 and produce a double-stranded cut in the DNA. While recognition sequences vary between 4 and 8 nucleotides, many of them are palindromic
Palindrome
A palindrome is a word, phrase, number, or other sequence of units that can be read the same way in either direction, with general allowances for adjustments to punctuation and word dividers....

, which correspond to nitrogenous base sequences that read the same backwards and forwards. 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 backwards on a single strand of DNA strand, as in GTAATG. The inverted repeat palindrome is also a sequence that reads the same forward and backwards, but the forward and backward sequences are found in complementary DNA strands (i.e., of double-stranded DNA), as in GTATAC (GTATAC being complementary
Complementarity (molecular biology)
In molecular biology, complementarity is a property of double-stranded nucleic acids such as DNA, as well as DNA:RNA duplexes. Each strand is complementary to the other in that the base pairs between them are non-covalently connected via two or three hydrogen bonds...

 to CATATG). Inverted repeat palindromes are more common and have greater biological importance than mirror-like palindromes.

EcoRI
EcoRI
EcoRI is an endonuclease enzyme isolated from strains of E. coli, and is part of the restriction modification system.In molecular biology it is used as a restriction enzyme. It creates sticky ends with 5' end overhangs...

 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 the 3' end) of a sticky-end
DNA end
DNA end or sticky end refers to the properties of the end of a molecule of DNA or a recombinant DNA molecule. The concept is important in molecular biology, especially in cloning or when subcloning inserts DNA into vector DNA. All the terms can also be used in reference to RNA. The sticky ends or...

 "overhang" of an enzyme restriction.

Different restriction enzymes that recognize the same sequence are known as neoschizomer
Neoschizomer
Neoschizomers are restriction enzymes that recognize the same nucleotide sequence as their prototype but cleave at a different site. In some special applications this is a very helpful feature....

s. These often cleave in different locales of the sequence. Different enzymes that recognize and cleave in the same location are known as isoschizomer
Isoschizomer
Isoschizomers are pairs of restriction enzymes specific to the same recognition sequence. For example, Sph I and Bbu I are isoschizomers of each other. The first enzyme to recognize and cut a given sequence is known as the prototype, all subsequent enzymes that recognize and cut that sequence...

s.

Types

Restriction endonucleases are categorized into three or four general groups (Types I, II and III) 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. There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements, as summarised below:
  • Type I enzymes cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase activities.
  • Type II enzymes cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.
  • Type III enzymes cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exist as part of a complex with a modification methylase .
  • Type IV enzymes target methylated DNA.

Type I

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
Escherichia coli
Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...

. 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 and modification activities, depending upon the methylation status of the target DNA. The cofactors S-Adenosyl methionine
S-Adenosyl methionine
S-Adenosyl methionine is a common cosubstrate involved in methyl group transfers. SAM was first discovered in Italy by G. L. Cantoni in 1952. It is made from adenosine triphosphate and methionine by methionine adenosyltransferase . Transmethylation, transsulfuration, and aminopropylation are the...

 (AdoMet), hydrolyzed adenosine triphosphate (ATP
Adenosine triphosphate
Adenosine-5'-triphosphate is a multifunctional nucleoside triphosphate used in cells as a coenzyme. It is often called the "molecular unit of currency" of intracellular energy transfer. ATP transports chemical energy within cells for metabolism...

), and magnesium
Magnesium
Magnesium is a chemical element with the symbol Mg, atomic number 12, and common oxidation number +2. It is an alkaline earth metal and the eighth most abundant element in the Earth's crust and ninth in the known universe as a whole...

 (Mg2+) ion
Ion
An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge. The name was given by physicist Michael Faraday for the substances that allow a current to pass between electrodes in a...

s, are required for their full activity. Type I restriction enzymes possess three subunits called HsdR, HsdM, and HsdS; HsdR is required for restriction; 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 (DNA cleavage) and modification (DNA methyltransferase) activity.

Type II

Typical type II restriction enzymes differ from type I restriction enzymes in several ways. They are a dimer
Protein dimer
In biochemistry, a dimer is a macromolecular complex formed by two, usually non-covalently bound, macromolecules like proteins or nucleic acids...

 of only one type of subunit; their recognition sites 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. 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
Nomenclature
Nomenclature is a term that applies to either a list of names or terms, or to the system of principles, procedures and terms related to naming - which is the assigning of a word or phrase to a particular object or property...

 was developed to divide this large family into subcategories based on deviations from typical characteristics of type II enzymes. These subgroups are defined using a letter suffix.

Type IIB restriction enzymes (e.g. BcgI and BplI) are multimers, containing more than one subunit. 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. One recognition site acts as the target for cleavage, while the other acts as an allosteric effector
Allosteric regulation
In biochemistry, allosteric regulation is the regulation of an enzyme or other protein by binding an effector molecule at the protein's allosteric site . Effectors that enhance the protein's activity are referred to as allosteric activators, whereas those that decrease the protein's activity are...

 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. Type IIG restriction endonucleases (Eco57I) do have a single subunit, like classical Type II restriction enzymes, but require the cofactor AdoMet to be active. Type IIM restriction endonucleases, such as DpnI, are able to recognize and cut methylated DNA. Type IIS restriction endonucleases (e.g. FokI) cleave DNA at a defined distance from their non-palindromic asymmetric recognition sites. These enzymes may function as dimer
Protein dimer
In biochemistry, a dimer is a macromolecular complex formed by two, usually non-covalently bound, macromolecules like proteins or nucleic acids...

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.

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. These enzymes contain more than one subunit and require AdoMet and ATP cofactors for their roles in DNA methylation and restriction, respectively. They are components of prokaryotic
Prokaryote
The prokaryotes are a group of organisms that lack a cell nucleus , or any other membrane-bound organelles. The organisms that have a cell nucleus are called eukaryotes. Most prokaryotes are unicellular, but a few such as myxobacteria have multicellular stages in their life cycles...

 DNA restriction-modification mechanism
Mechanism
Mechanism may refer to:*Mechanism , rigid bodies connected by joints in order to accomplish a desired force and/or motion transmission*Mechanism , explaining how a feature is created...

s that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional proteins
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

 composed of two subunits, Res and Mod. The Mod subunit recognises the DNA sequence specific for the system and is a modification methyltransferase
Methyltransferase
A methyltransferase is a type of transferase enzyme that transfers a methyl group from a donor to an acceptor.Methylation often occurs on nucleic bases in DNA or amino acids in protein structures...

; as such it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction, although it has no enzymatic
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...

 activity on its own. Type III enzymes recognise short 5-6 bp long asymmetric DNA sequences and cleave 25-27 bp downstream
Upstream and downstream (DNA)
In molecular biology and genetics, upstream and downstream both refer to a relative position in DNA or RNA. Each strand of DNA or RNA has a 5' end and a 3' end, so named for the carbons on the deoxyribose ring. Relative to the position on the strand, downstream is the region towards the 3' end of...

 to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction 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. Type III enzymes belong to the beta-subfamily of N6 adenine methyltransferases, containing the nine motifs that characterise this family, including motif
Sequence motif
In genetics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance...

 I, the AdoMet binding pocket (FXGXG), and motif IV, the catalytic region (S/D/N (PP) Y/F).

Artificial Restriction Enzymes

Artificial restriction enzymes can be generated by fusing a natural or engineered DNA binding domain to a nuclease
Nuclease
A nuclease is an enzyme capable of cleaving the phosphodiester bonds between the nucleotide subunits of nucleic acids. Older publications may use terms such as "polynucleotidase" or "nucleodepolymerase"....

 domain (often the cleavage domain of the type IIS restriction enzyme FokI
FokI
The enzyme FokI, naturally found in Flavobacterium okeanokoites, is a bacterial type IIS restriction endonuclease consisting of an N-terminal DNA-binding domain and a non-specific DNA cleavage domain at the C-terminal...

). Such artificial restriction enzymes can target large DNA sites (up to 36 bp) and can be engineered to bind to desired DNA sequences. Zinc finger nucleases are the most commonly used artificial restriction enzymes and are generally used in genetic engineering
Genetic engineering
Genetic engineering, also called genetic modification, is the direct human manipulation of an organism's genome using modern DNA technology. It involves the introduction of foreign DNA or synthetic genes into the organism of interest...

 applications, but can also be used for more standard gene cloning applications. Other artificial restriction enzymes are based on the DNA binding domain of TAL effector
TAL effector
TAL effectors are proteins secreted by Xanthomonas bacteria via their type III secretion system when they infect various plant species...

s.

Nomenclature

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

Since their discovery in the 1970s, more than 100 different restriction enzymes have been identified in different bacteria. Each enzyme is named after the bacterium from which it was isolated using a naming system based on bacterial genus
Genus
In biology, a genus is a low-level taxonomic rank used in the biological classification of living and fossil organisms, which is an example of definition by genus and differentia...

, species
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...

 and strain
Strain (biology)
In biology, a strain is a low-level taxonomic rank used in three related ways.-Microbiology and virology:A strain is a genetic variant or subtype of a micro-organism . For example, a "flu strain" is a certain biological form of the influenza or "flu" virus...

. For example, the name of the EcoRI
EcoRI
EcoRI is an endonuclease enzyme isolated from strains of E. coli, and is part of the restriction modification system.In molecular biology it is used as a restriction enzyme. It creates sticky ends with 5' end overhangs...

 restriction enzyme was derived as shown in the box.

Applications

See the main article on restriction digest
Restriction digest
A restriction digest is a procedure used in molecular biology to prepare DNA for analysis or other processing. It is sometimes termed DNA fragmentation...

s.

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

They are used to assist insertion of genes into plasmid
Plasmid
In microbiology and genetics, a plasmid is a DNA molecule that is separate from, and can replicate independently of, the chromosomal DNA. They are double-stranded and, in many cases, circular...

 vectors during gene cloning and protein expression
Protein expression
Protein expression is a subcomponent of gene expression. It consists of the stages after DNA has been translated into polypeptide chains, which are ultimately folded into proteins...

 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
Multiple cloning site
A multiple cloning site , also called a polylinker, is a short segment of DNA which contains many restriction sites - a standard feature of engineered plasmids. Restriction sites within an MCS are typically unique, occurring only once within a given plasmid. MCSs are commonly used during...

, 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
DNA ligase
In molecular biology, DNA ligase is a specific type of enzyme, a ligase, that repairs single-stranded discontinuities in double stranded DNA molecules, in simple words strands that have double-strand break . Purified DNA ligase is used in gene cloning to join DNA molecules together...

.

Restriction enzymes can also be used to distinguish gene allele
Allele
An allele is one of two or more forms of a gene or a genetic locus . "Allel" is an abbreviation of allelomorph. Sometimes, different alleles can result in different observable phenotypic traits, such as different pigmentation...

s by specifically recognizing single base changes in DNA known as single nucleotide polymorphism
Single nucleotide polymorphism
A single-nucleotide polymorphism is a DNA sequence variation occurring when a single nucleotide — A, T, C or G — in the genome differs between members of a biological species or paired chromosomes in an individual...

s (SNPs). This is only possible if a SNP alters the restriction site present in the allele. In this method, the restriction enzyme can be used to genotype
Genotype
The genotype is the genetic makeup of a cell, an organism, or an individual usually with reference to a specific character under consideration...

 a DNA sample without the need for expensive gene sequencing
Gene sequencing
Gene Sequencing may refer to:* DNA sequencing* or a comprehensive variant of it: Full genome sequencing...

. The sample is first digested with the restriction enzyme to generate DNA fragments, and then the different sized fragments separated by gel electrophoresis
Gel electrophoresis
Gel electrophoresis is a method used in clinical chemistry to separate proteins by charge and or size and in biochemistry and molecular biology to separate a mixed population of DNA and RNA fragments by length, to estimate the size of DNA and RNA fragments or to separate proteins by charge...

. 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. The number of bands reveals the sample subject's genotype, an example of restriction mapping.

In a similar manner, restriction enzymes are used to digest genomic DNA for gene analysis by Southern blot
Southern blot
A Southern blot is a method routinely used in molecular biology for detection of a specific DNA sequence in DNA samples. Southern blotting combines transfer of electrophoresis-separated DNA fragments to a filter membrane and subsequent fragment detection by probe hybridization. The method is named...

. 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 mutation
Mutation
In molecular biology and genetics, mutations are changes in a genomic sequence: the DNA sequence of a cell's genome or the DNA or RNA sequence of a virus. They can be defined as sudden and spontaneous changes in the cell. Mutations are caused by radiation, viruses, transposons and mutagenic...

s (polymorphisms
Polymorphism (biology)
Polymorphism in biology occurs when two or more clearly different phenotypes exist in the same population of a species — in other words, the occurrence of more than one form or morph...

) have occurred within a population. The latter example is called restriction fragment length polymorphism
Restriction fragment length polymorphism
In molecular biology, restriction fragment length polymorphism, or RFLP , is a technique that exploits variations in homologous DNA sequences. It refers to a difference between samples of homologous DNA molecules that come from differing locations of restriction enzyme sites, and to a related...

 (RFLP).

Examples

See the main article on list of restriction enzyme cutting sites.


Examples of restriction enzymes include:
Enzyme Source Recognition Sequence Cut
EcoRI
EcoRI
EcoRI is an endonuclease enzyme isolated from strains of E. coli, and is part of the restriction modification system.In molecular biology it is used as a restriction enzyme. It creates sticky ends with 5' end overhangs...

Escherichia coli
Escherichia coli
Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...


5'GAATTC
3'CTTAAG

5'---G AATTC---3'
3'---CTTAA G---5'
EcoRII Escherichia coli
Escherichia coli
Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...


5'CCWGG
3'GGWCC

5'--- CCWGG---3'
3'---GGWCC ---5'
BamHI
BamHI
BamHI is a restriction enzyme, derived from Bacillus amyloliquefaciens. It has the recognition site , and leaves a sticky end. One of the earlier enzymes to be used, it is popular for historical reasons, but also because digestion leaves a GATC overhang compatible with many other enzymes...

Bacillus amyloliquefaciens
Bacillus amyloliquefaciens
Bacillus amyloliquefaciens is a species of bacteria that is the source of the BamH1 restriction enzyme. It also synthesizes a natural antibiotic protein barnase, a widely studied ribonuclease that forms a famously tight complex with its intracellular inhibitor barstar.-Discovery and name:B...


5'GGATCC
3'CCTAGG

5'---G GATCC---3'
3'---CCTAG G---5'
HindIII
HindIII
HindIII is a type II site-specific deoxyribonuclease restriction enzyme isolated from Haemophilus influenzae that cleaves the palindromic DNA sequence AAGCTT in the presence of the cofactor Mg2+ via hydrolysis....

Haemophilus influenzae
Haemophilus influenzae
Haemophilus influenzae, formerly called Pfeiffer's bacillus or Bacillus influenzae, Gram-negative, rod-shaped bacterium first described in 1892 by Richard Pfeiffer during an influenza pandemic. A member of the Pasteurellaceae family, it is generally aerobic, but can grow as a facultative anaerobe. H...


5'AAGCTT
3'TTCGAA

5'---A AGCTT---3'
3'---TTCGA A---5'
TaqI
TaqI
TaqI is a restriction enzyme isolated from the bacterium Thermus aquaticus in 1978. It has a recognition sequence of 5'TCGA 3'AGCTand makes the cut 5'---T CGA---3' 3'---AGC T---5'...

Thermus aquaticus
Thermus aquaticus
Thermus aquaticus is a species of bacterium that can tolerate high temperatures, one of several thermophilic bacteria that belong to the Deinococcus-Thermus group...


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
Haemophilus influenzae
Haemophilus influenzae, formerly called Pfeiffer's bacillus or Bacillus influenzae, Gram-negative, rod-shaped bacterium first described in 1892 by Richard Pfeiffer during an influenza pandemic. A member of the Pasteurellaceae family, it is generally aerobic, but can grow as a facultative anaerobe. H...


5'GANTCA
3'CTNAGT

5'---G ANTC---3'
3'---CTNA G---5'
Sau3A Staphylococcus aureus
Staphylococcus aureus
Staphylococcus aureus is a facultative anaerobic Gram-positive coccal bacterium. It is frequently found as part of the normal skin flora on the skin and nasal passages. It is estimated that 20% of the human population are long-term carriers of S. aureus. S. aureus is the most common species of...


5'GATC
3'CTAG

5'--- GATC---3'
3'---CTAG ---5'
PovII* Proteus vulgaris
Proteus vulgaris
Proteus vulgaris is a rod-shaped, Gram negative bacterium that inhabits the intestinal tracts of humans and animals. It can be found in soil, water and fecal matter. It is grouped with the enterobacteriaceae and is an opportunistic pathogen of humans...


5'CAGCTG
3'GTCGAC

5'---CAG CTG---3'
3'---GTC GAC---5'
SmaI* Serratia marcescens
Serratia marcescens
Serratia marcescens is a species of Gram-negative, rod-shaped bacterium in the family Enterobacteriaceae. A human pathogen, S. marcescens is involved in nosocomial infections, particularly catheter-associated bacteremia, urinary tract infections and wound infections, and is responsible for 1.4% of...


5'CCCGGG
3'GGGCCC

5'---CCC GGG---3'
3'---GGG CCC---5'
HaeIII*
HaeIII
HaeIII is one of the 100+ restriction enzymes discovered since 1970. It was isolated from the Haemophilus aegyptius bacteria, and has a molecular weight of 37126. The enzyme's recognition site—the place where it cuts DNA molecules—is the GGCC nucleotide sequence...

Haemophilus aegyptius
5'GGCC
3'CCGG

5'---GG CC---3'
3'---CC GG---5'
HgaI 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*
EcoRV
EcoRV is a type II restriction endonuclease isolated from certain strains of Escherichia coli. It has the alternative name Eco32I.In molecular biology, it is a commonly used restriction enzyme. It creates blunt ends. The enzyme recognizes the palindromic 6-base DNA sequence 5'-GAT|ATC-3' and makes...

Escherichia coli
Escherichia coli
Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...


5'GATATC
3'CTATAG

5'---GAT ATC---3'
3'---CTA TAG---5'
EcoP15I Escherichia coli
Escherichia coli
Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...


5'CAGCAGN25NN
3'GTCGTCN25NN

5'---CAGCAGN25NN ---3'
3'---GTCGTCN25 NN---5'
KpnI
KPNI
KPNI - SMU Radio is the student-run radio station of Southern Methodist University in Dallas, Texas....

Klebsiella pneumoniae
Klebsiella pneumoniae
Klebsiella pneumoniae is a Gram-negative, non-motile, encapsulated, lactose fermenting, facultative anaerobic, rod shaped bacterium found in the normal flora of the mouth, skin, and intestines....


5'GGTACC
3'CCATGG

5'---GGTAC C---3'
3'---C CATGG---5'
PstI
PstI
PstI, is a Type II restriction endonuclease from Providencia stuartii. PstI recognition and cut site are as follows:...

Providencia stuartii
Providencia stuartii
Providencia stuartii , is a Gram negative bacterium that is commonly found in soil, water, and sewage. P. stuartii is the most common of the 5 species found in the genus Providencia, with Providencia rettgeri, Providencia alcalifaciens, Providencia rustigianii, P heimbachae...


5'CTGCAG
3'GACGTC

5'---CTGCA G---3'
3'---G ACGTC---5'
SacI
Saci
Saci may be:* An alternative spelling for the Hindu goddess Sachi* Saci , an impish mythical character of Brazilian folk tales* SacI, a restriction enzyme with the restriction site GAGCTC* Wellington Saci, Brazilian footballer...

Streptomyces achromogenes
Streptomyces achromogenes
Streptomyces achromogenes is a species of gram-positive bacterium that belongs in the genus Streptomyces. S. achromogenes can be grown at 28°C in a medium of yeast and malt extract with glucose....


5'GAGCTC
3'CTCGAG

5'---GAGCT C---3'
3'---C TCGAG---5'
SalI
Sali
Sali is a village and a municipality in Croatia in the Zadar County. Sali is a small town but still the largest on the island of Dugi otok. The total population of Sali is 1,688 inhabitants...

Streptomyces albus
Streptomyces albus
Streptomyces albus is a bacterial species from which the pseudodisaccharide aminoglycoside salbostatin was isolated....


5'GTCGAC
3'CAGCTG

5'---G TCGAC---3'
3'---CAGCT G---5'
ScaI
SCAI
SCAI may refer to:*SCAI, the Fraunhofer-Institute for Algorithms and Scientific Computing, see Fraunhofer Society#Institutes*Students Confronting Apartheid in Israel*Society for Cardiovascular Angiography and Interventions...

Streptomyces caespitosus
Streptomyces caespitosus
Streptomyces caespitosus is a species of actinobacteria. It produces chemotherapeutic drug mitomycin C....


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 Streptomyces phaeochromogenes
5'GCATGC
3'CGTACG

5'---GCATG C---3'
3'---C GTACG---5'
StuI Streptomyces tubercidicus
5'AGGCCT
3'TCCGGA

5'---AGG CCT---3'
3'---TCC GGA---5'
XbaI 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

See also

  • Detailed articles about certain restriction enzymes: EcoRI
    EcoRI
    EcoRI is an endonuclease enzyme isolated from strains of E. coli, and is part of the restriction modification system.In molecular biology it is used as a restriction enzyme. It creates sticky ends with 5' end overhangs...

    , HindIII
    HindIII
    HindIII is a type II site-specific deoxyribonuclease restriction enzyme isolated from Haemophilus influenzae that cleaves the palindromic DNA sequence AAGCTT in the presence of the cofactor Mg2+ via hydrolysis....

    , BglII
    BglII
    BglII is a type II restriction endonuclease enzyme isolated from certain strains of Bacillus globigii. The principal function of restriction enzymes is the protection of the host genome against foreign DNA but they may also have some involvement in recombination and transposition...

    .
  • List of restriction enzyme cutting sites
  • Homing endonuclease
    Homing endonuclease
    The homing endonucleases are a type of restriction enzymes typically encoded by introns or inteins. They act on the cellular DNA of the cells that synthesize them, in the opposite alleles of the genes that encode them.- Origin and mechanism :...

  • List of homing endonuclease cutting sites
  • Isoschizomer
    Isoschizomer
    Isoschizomers are pairs of restriction enzymes specific to the same recognition sequence. For example, Sph I and Bbu I are isoschizomers of each other. The first enzyme to recognize and cut a given sequence is known as the prototype, all subsequent enzymes that recognize and cut that sequence...

    .
  • Star activity
    Star activity
    Star activity is a relaxation or alteration of the specificity of restriction enzyme mediated cleavage of DNA that can occur under reaction conditions that differ significantly from those optimum for the enzyme...

  • Molecular weight size marker
    Molecular weight size marker
    A molecular weight size marker is used to identify the approximate size of a molecule run on a gel, using the principle that molecular weight is inversely proportional to migration rate through a gel matrix...


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