Biology:Restriction enzyme

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Short description: Class of enzymes that divide DNA

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 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.[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,

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.[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

Type II site-specific deoxyribonuclease-like
1QPS.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
SymbolRestrct_endonuc-II-like
Pfam clanCL0236
InterProIPR011335
SCOP21wte / 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.[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 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

Main page: Biology:Restriction digest

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 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.[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

See also

References

  1. ↑ "Restriction endonucleases". CRC Critical Reviews in Biochemistry 4 (2): 123–64. November 1976. doi:10.3109/10409237609105456. PMID 795607. 
  2. ↑ 2.0 2.1 "Specificity of restriction endonucleases and DNA modification methyltransferases a review (Edition 3)". Gene 92 (1–2): 1–248. August 1990. doi:10.1016/0378-1119(90)90486-B. PMID 2172084. 
  3. ↑ Burrell M, ed (1993). "Chapter 8: Restriction Enzymes". Enzymes of Molecular Biology. Methods of Molecular Biology. 16. Totowa, NJ: Humana Press. pp. 107–200. ISBN 0-89603-234-5. 
  4. ↑ 4.0 4.1 "DNA modification and restriction". Annual Review of Biochemistry 38: 467–500. 1969. doi:10.1146/annurev.bi.38.070169.002343. PMID 4897066. 
  5. ↑ "Bacteriophage survival: multiple mechanisms for avoiding the deoxyribonucleic acid restriction systems of their hosts". Microbiological Reviews 47 (3): 345–60. September 1983. doi:10.1128/MMBR.47.3.345-360.1983. PMID 6314109. 
  6. ↑ "Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution". Nucleic Acids Research 29 (18): 3742–56. September 2001. doi:10.1093/nar/29.18.3742. PMID 11557807. 
  7. ↑ "How restriction enzymes became the workhorses of molecular biology". Proceedings of the National Academy of Sciences of the United States of America 102 (17): 5905–8. April 2005. doi:10.1073/pnas.0500923102. PMID 15840723. Bibcode: 2005PNAS..102.5905R. 
  8. ↑ "REBASE--enzymes and genes for DNA restriction and modification". Nucleic Acids Research 35 (Database issue): D269-70. January 2007. doi:10.1093/nar/gkl891. PMID 17202163. 
  9. ↑ Principles of gene manipulation: an introduction to genetic engineering. Oxford: Blackwell Scientific. 1994. ISBN 0-632-03712-1. https://archive.org/details/principlesofgene00oldr. 
  10. ↑ Laboratory DNA science: an introduction to recombinant DNA techniques and methods of genome analysis. Menlo Park, Calif: Benjamin/Cummings Pub. Co. 1996. ISBN 0-8053-3040-2. 
  11. ↑ Recombinant DNA and Biotechnology: A Guide for Students. Washington, D.C: ASM Press. 2001. ISBN 1-55581-176-0. 
  12. ↑ Winnacker E-L (1987). "Chapter 2: Isolation, Identification, and Characterisation of DNA fragments". From Genes to Clones. VCH. ISBN 0-89573-614-4. https://archive.org/details/fromgenestoclone0000winn. 
  13. ↑ 13.0 13.1 "A nonhereditary, host-induced variation of bacterial viruses". Journal of Bacteriology 64 (4): 557–69. October 1952. doi:10.1128/JB.64.4.557-569.1952. PMID 12999684. 
  14. ↑ "Host controlled variation in bacterial viruses". Journal of Bacteriology 65 (2): 113–21. February 1953. doi:10.1128/JB.65.2.113-121.1953. PMID 13034700. 
  15. ↑ "DNA restriction enzyme from E. coli". Nature 217 (5134): 1110–4. March 1968. doi:10.1038/2171110a0. PMID 4868368. Bibcode: 1968Natur.217.1110M. 
  16. ↑ "Host specificity of DNA produced by Escherichia coli. II. Control over acceptance of DNA from infecting phage lambda". Journal of Molecular Biology 5 (1): 37–49. July 1962. doi:10.1016/S0022-2836(62)80059-X. PMID 13888713. 
  17. ↑ "Degradation of non-replicating bacteriophage dna in non-accepting cells". Journal of Molecular Biology 8 (5): 623–8. May 1964. doi:10.1016/S0022-2836(64)80112-1. PMID 14187389. 
  18. ↑ "How restriction enzymes became the workhorses of molecular biology". Proceedings of the National Academy of Sciences of the United States of America 102 (17): 5905–8. April 2005. doi:10.1073/pnas.0500923102. PMID 15840723. Bibcode: 2005PNAS..102.5905R. 
  19. ↑ "A restriction enzyme from Hemophilus influenzae. I. Purification and general properties". Journal of Molecular Biology 51 (2): 379–91. July 1970. doi:10.1016/0022-2836(70)90149-X. PMID 5312500. 
  20. ↑ "A restriction enzyme from Hemophilus influenzae. II". Journal of Molecular Biology 51 (2): 393–409. July 1970. doi:10.1016/0022-2836(70)90150-6. PMID 5312501. 
  21. ↑ "Highlights of the DNA cutters: a short history of the restriction enzymes". Nucleic Acids Research 42 (1): 3–19. January 2014. doi:10.1093/nar/gkt990. PMID 24141096. 
  22. ↑ "Specific cleavage of simian virus 40 DNA by restriction endonuclease of Hemophilus influenzae". Proceedings of the National Academy of Sciences of the United States of America 68 (12): 2913–7. December 1971. doi:10.1073/pnas.68.12.2913. PMID 4332003. Bibcode: 1971PNAS...68.2913D. 
  23. ↑ "The Nobel Prize in Physiology or Medicine". The Nobel Foundation. 1978. http://nobelprize.org/nobel_prizes/medicine/laureates/1978/. "for the discovery of restriction enzymes and their application to problems of molecular genetics" 
  24. ↑ "A bacterial clone synthesizing proinsulin". Proceedings of the National Academy of Sciences of the United States of America 75 (8): 3727–31. August 1978. doi:10.1073/pnas.75.8.3727. PMID 358198. Bibcode: 1978PNAS...75.3727V. 
  25. ↑ "Evidence for an evolutionary relationship among type-II restriction endonucleases". Gene 160 (1): 7–16. July 1995. doi:10.1016/0378-1119(95)00181-5. PMID 7628720. 
  26. ↑ "Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems". Journal of Molecular Evolution 42 (2): 91–6. February 1996. doi:10.1007/BF02198833. PMID 8919860. Bibcode: 1996JMolE..42...91J. 
  27. ↑ "Selfish behavior of restriction-modification systems". Science 267 (5199): 897–9. February 1995. doi:10.1126/science.7846533. PMID 7846533. Bibcode: 1995Sci...267..897N. 
  28. ↑ "Restriction Map". University of Wisconsin. 2003. http://bioweb.uwlax.edu/genweb/molecular/seq_anal/restriction_map/restriction_map.htm. 
  29. ↑ 29.0 29.1 29.2 29.3 29.4 29.5 29.6 29.7 29.8 29.9 "Structure and function of type II restriction endonucleases". Nucleic Acids Research 29 (18): 3705–27. September 2001. doi:10.1093/nar/29.18.3705. PMID 11557805. 
  30. ↑ Clark DP (2005). Molecular biology. Amsterdam: Elsevier Academic Press. ISBN 0-12-175551-7. 
  31. ↑ "The molecular perspective: restriction endonucleases". Stem Cells 20 (2): 190–1. 2002. doi:10.1634/stemcells.20-2-190. PMID 11897876. http://theoncologist.alphamedpress.org/content/7/1/82.full.pdf. 
  32. ↑ 32.0 32.1 "Biology of DNA restriction". Microbiological Reviews 57 (2): 434–50. June 1993. doi:10.1128/MMBR.57.2.434-450.1993. PMID 8336674. 
  33. ↑ "DNA restriction and modification mechanisms in bacteria". Annual Review of Microbiology 25: 153–76. 1971. doi:10.1146/annurev.mi.25.100171.001101. PMID 4949033. 
  34. ↑ "Structure and mechanism of multifunctional restriction endonucleases". Annual Review of Biochemistry 50: 285–319. 1981. doi:10.1146/annurev.bi.50.070181.001441. PMID 6267988. 
  35. ↑ 35.0 35.1 Types of Restriction Endonucleases | NEB
  36. ↑ 36.0 36.1 "S-Adenosyl-L-methionine-dependent restriction enzymes". Critical Reviews in Biochemistry and Molecular Biology 39 (1): 1–19. 2004. doi:10.1080/10409230490440532. PMID 15121719. 
  37. ↑ "Restriction endonucleases: classification, properties, and applications". Molecular Biotechnology 23 (3): 225–43. March 2003. doi:10.1385/MB:23:3:225. PMID 12665693. 
  38. ↑ 38.0 38.1 "Type I restriction systems: sophisticated molecular machines (a legacy of Bertani and Weigle)". Microbiology and Molecular Biology Reviews 64 (2): 412–34. June 2000. doi:10.1128/MMBR.64.2.412-434.2000. PMID 10839821. 
  39. ↑ PDB: 1qps​ Alfred M. Pingoud, ed (2004). "The integration of recognition and cleavage: X-ray structures of pre-transition state complex, post-reactive complex, and the DNA-free endonuclease". Restriction Endonucleases (Nucleic Acids and Molecular Biology, Volume 14). Berlin: Springer. pp. 137–178. ISBN 3-540-20502-0. 
  40. ↑ Fundamental Laboratory Approaches for Biochemistry and Biotechnology. Hoboken, NJ: John Wiley & Sons. 2010. pp. 341. ISBN 978-0-470-08766-4. 
  41. ↑ "Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI". Nucleic Acids Research 40 (15): 7563–72. August 2012. doi:10.1093/nar/gks428. PMID 22610857. 
  42. ↑ "Structural basis of the methylation specificity of R.DpnI". Nucleic Acids Research 42 (13): 8745–54. July 2014. doi:10.1093/nar/gku546. PMID 24966351. 
  43. ↑ "Nucleoside triphosphate-dependent restriction enzymes". Nucleic Acids Research 29 (18): 3728–41. September 2001. doi:10.1093/nar/29.18.3728. PMID 11557806. 
  44. ↑ "Type III restriction enzymes need two inversely oriented recognition sites for DNA cleavage". Nature 355 (6359): 467–9. January 1992. doi:10.1038/355467a0. PMID 1734285. Bibcode: 1992Natur.355..467M. 
  45. ↑ "Complex restriction enzymes: NTP-driven molecular motors". Biochimie 84 (11): 1047–59. November 2002. doi:10.1016/S0300-9084(02)00020-2. PMID 12595133. 
  46. ↑ 46.0 46.1 "CRISPR provides acquired resistance against viruses in prokaryotes". Science 315 (5819): 1709–12. March 2007. doi:10.1126/science.1138140. PMID 17379808. Bibcode: 2007Sci...315.1709B. 
  47. ↑ "CRISPR/Cas, the immune system of bacteria and archaea". Science 327 (5962): 167–70. January 2010. doi:10.1126/science.1179555. PMID 20056882. Bibcode: 2010Sci...327..167H. 
  48. ↑ "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. February 1996. doi:10.1073/pnas.93.3.1156. PMID 8577732. Bibcode: 1996PNAS...93.1156K. 
  49. ↑ "Genome editing with engineered zinc finger nucleases". Nature Reviews. Genetics 11 (9): 636–46. September 2010. doi:10.1038/nrg2842. PMID 20717154. 
  50. ↑ "High-frequency modification of plant genes using engineered zinc-finger nucleases". Nature 459 (7245): 442–5. May 2009. doi:10.1038/nature07845. PMID 19404258. Bibcode: 2009Natur.459..442T. 
  51. ↑ "Precise genome modification in the crop species Zea mays using zinc-finger nucleases". Nature 459 (7245): 437–41. May 2009. doi:10.1038/nature07992. PMID 19404259. Bibcode: 2009Natur.459..437S. 
  52. ↑ "Zinc finger-based knockout punches for zebrafish genes". Zebrafish 5 (2): 121–3. 2008. doi:10.1089/zeb.2008.9988. PMID 18554175. 
  53. ↑ "Knockout rats via embryo microinjection of zinc-finger nucleases". Science 325 (5939): 433. July 2009. doi:10.1126/science.1172447. PMID 19628861. Bibcode: 2009Sci...325..433G. 
  54. ↑ "Expression, purification and characterization of cloning-grade zinc finger nuclease". Journal of Biotechnology 151 (1): 1–8. January 2011. doi:10.1016/j.jbiotec.2010.10.071. PMID 21029755. 
  55. ↑ "Targeting DNA double-strand breaks with TAL effector nucleases". Genetics 186 (2): 757–61. October 2010. doi:10.1534/genetics.110.120717. PMID 20660643. 
  56. ↑ "TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain". Nucleic Acids Research 39 (1): 359–72. January 2011. doi:10.1093/nar/gkq704. PMID 20699274. 
  57. ↑ "Development and applications of CRISPR-Cas9 for genome engineering". Cell 157 (6): 1262–78. June 2014. doi:10.1016/j.cell.2014.05.010. PMID 24906146. 
  58. ↑ "Revolutionizing Biotechnology with Artificial Restriction Enzymes". Genetic Engineering and Biotechnology News. 10 February 2017. https://www.genengnews.com/topics/omics/revolutionizing-biotechnology-with-artificial-restriction-enzymes/.  (reporting on Programmable DNA-Guided Artificial Restriction Enzymes)
  59. ↑ "PNAzymes that are artificial RNA restriction enzymes". Journal of the American Chemical Society 132 (26): 8984–90. July 2010. doi:10.1021/ja1008739. PMID 20545354. 
  60. ↑ A. Pingoud (2004). Restriction Endonucleases (Nucleic Acids and Molecular Biology). Springer. p. 3. ISBN 9783642188510. https://books.google.com/books?id=i-HwCAAAQBAJ&pg=PA3. 
  61. ↑ "Letter: A suggested nomenclature for bacterial host modification and restriction systems and their enzymes". Journal of Molecular Biology 81 (3): 419–23. December 1973. doi:10.1016/0022-2836(73)90152-6. PMID 4588280. 
  62. ↑ "A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes". Nucleic Acids Research 31 (7): 1805–12. April 2003. doi:10.1093/nar/gkg274. PMID 12654995. 
  63. ↑ Geerlof A. "Cloning using restriction enzymes". European Molecular Biology Laboratory - Hamburg. http://www.embl.de/pepcore/pepcore_services/cloning/cloning_methods/restriction_enzymes/. 
  64. ↑ Molecular cloning: a laboratory manual. Cold Spring Harbor, N.Y: Cold Spring Harbor Laboratory. 2001. ISBN 0-87969-576-5. https://archive.org/details/molecularcloning0000samb_p7p5. 
  65. ↑ "Combining allele-specific fluorescent probes and restriction assay in real-time PCR to achieve SNP scoring beyond allele ratios of 1:1000". BioTechniques 44 (2): 193–4, 196, 199. February 2008. doi:10.2144/000112719. PMID 18330346. 
  66. ↑ "SNP Cutter: a comprehensive tool for SNP PCR-RFLP assay design". Nucleic Acids Research 33 (Web Server issue): W489-92. July 2005. doi:10.1093/nar/gki358. PMID 15980518. 
  67. ↑ "Mapping". Nature. http://www.nature.com/scitable/definition/mapping-282. 
  68. ↑ Biochemistry (Fifth ed.). San Francisco: W.H. Freeman. 2002. p. 122. ISBN 0-7167-4684-0. 
  69. ↑ "Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV". The New England Journal of Medicine 370 (10): 901–10. March 2014. doi:10.1056/NEJMoa1300662. PMID 24597865. 
  70. ↑ Wayengera M (2003). "HIV and Gene Therapy: The proposed [R-M enzymatic] model for a gene therapy against HIV.". Makerere Med J. 38: 28–30. 
  71. ↑ "Frequency and site mapping of HIV-1/SIVcpz, HIV-2/SIVsmm and Other SIV gene sequence cleavage by various bacteria restriction enzymes: Precursors for a novel HIV inhibitory product". Afr J Biotechnol 6 (10): 1225–1232. 2007. 
  72. ↑ "Targeted DNA mutagenesis for the cure of chronic viral infections". Journal of Virology 86 (17): 8920–36. September 2012. doi:10.1128/JVI.00052-12. PMID 22718830. 
  73. ↑ "Newer gene editing technologies toward HIV gene therapy". Viruses 5 (11): 2748–66. November 2013. doi:10.3390/v5112748. PMID 24284874. 
  74. ↑ "Trex1 prevents cell-intrinsic initiation of autoimmunity". Cell 134 (4): 587–98. August 2008. doi:10.1016/j.cell.2008.06.032. PMID 18724932. 
  75. ↑ "ERCC1/XPF limits L1 retrotransposition". DNA Repair 7 (6): 983–9. June 2008. doi:10.1016/j.dnarep.2008.02.006. PMID 18396111. 
  76. ↑ "Restriction and modification enzymes and their recognition sequences". Nucleic Acids Research 8 (1): r63–r80. January 1980. doi:10.1093/nar/8.1.197-d. PMID 6243774. 
  77. ↑ "Restriction enzymes and their isoschizomers". Nucleic Acids Research 16 Suppl (Suppl): r271-313. 1988. doi:10.1093/nar/16.suppl.r271. PMID 2835753. 
  78. ↑ 78.0 78.1 78.2 78.3 78.4 78.5 78.6 Molecular Cell Biology (5th ed.). New York: W.H. Freeman and Company. 2004. ISBN 0-7167-4366-3. https://archive.org/details/molecularcellbio00harv. 
  79. ↑ "Stu I from Streptomyces tubercidicus". Sigma-Aldrich. http://www.sigmaaldrich.com/catalog/search/ProductDetail/SIGMA/R8013. 
  80. ↑ "A new site-specific endonuclease StuI from Streptomyces tubercidicus". Gene 11 (3–4): 219–25. November 1980. doi:10.1016/0378-1119(80)90062-1. PMID 6260571. 

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