#REDIRECT Restriction enzyme
A restriction enzyme (or restriction endonuclease) is an enzyme that cuts double-stranded DNA. The enzyme makes two incisions, one through each of the phosphate backbones of the double helix without damaging the nucleotide. The chemical bonds that the enzymes cleave can be reformed by other enzymes known as DNA ligase, so that restriction fragments carved from different chromosomes or genes can be splicing (genetics) together, provided their ends are complementary (more below). Many of the procedures of molecular biology and genetic engineering rely on restriction enzymes. The term ''restriction'' comes from the fact that these enzymes were discovered in E. coli strains that appeared to be restricting the infection by certain bacteriophages. Restriction enzymes therefore are believed to be a mechanism evolved by bacteria to resist viral attack and to help in the removal of viral sequences. ==Sites of cleavage== Rather than cutting DNA indiscriminately, a restiction enzyme cuts only double-helical segments that contain a particular DNA sequence, and it makes its incisions only within that sequence--known as a "recognition sequence"--always in the same way. Some enzymes make strand incisions immediately opposite one another, producing "Sticky end" DNA fragments. Most enzymes make slightly staggered incisions, resulting in "sticky ends", out of which one strand protrudes. There are three known evolutionary lineages of restriction enzyme, which each cleave DNA by a different mechanism. ==Fragment complementarity and splicing== Because recognition sequences and cleavage sites differ between restriction enzymes, the length and the exact sequence of a sticky-end "overhang", as well as whether it is the 5' end or the 3' end strand that overhangs, depends on which enzyme produced it. base pair between overhangs with complementary sequences enables two fragments to be joined or "spliced" by a DNA ligase. A sticky-end fragment can be ligated not only to the fragment from which it was originally cleaved, but also to any other fragment with a compatible sticky end. If a restriction enzyme has a non-degenerate pallindromic cleavage site, all ends that it produces are compatible. Ends produced by different enzymes may also be compatible. Knowledge of cleavage sites allows molecular biologists to anticipate which fragments can be joined in which ways, and to choose enzymes appropriately. ==Restriction enzymes as tools== :''See the main article on restriction digests.'' Recognition sequences typically are only four to twelve nucleotides long. Because there are only so many ways to arrange the four nucleotides--A,C,G and T--into a four or eight or twelve nucleotide sequence, recognition sequences tend to "crop up" by chance in any long sequence. Furthermore, restriction enzymes specific to hundreds of distinct sequences have been identified and synthesized for sale to laboratories. As a result, potential "restriction sites" appear in almost any gene or chromosome. Meanwhile, the sequences of some artificial plasmids include a "linker" that contains dozens of restriction enzyme recognition sequences within a very short segment of DNA. So no matter the context in which a gene naturally appears, there is probably a pair of restriction enzymes that can snip it out, and which will produce ends that enable the gene to be spliced into a plasmid (i.e. which will enable what molecular biologists call "cloning" of the gene). ==Many Recognition sequences are palindromic== While recognition sequences vary widely, many of them are palindrome; that is, the sequence on one strand reads the same in the opposite direction on the complementary strand. The meaning of "palindromic" in this context is different from what one might expect from its linguistic usage: GTAATG is not a palindromic DNA sequence, but GTATAC is. ==Types of restriction enzymes== Restriction enzymes are classified biochemically into three types, designated Type I, Type II and Type III. In type I and III systems, both the methylase and restriction activities are carried out by a single large enzyme complex. Although these enzymes recognize specific DNA sequences, the sites of actual cleavage are at variable distances from these recognition sites, and can be hundreds of bases away. In type II systems, the restriction enzyme is independent of its methylase, and cleavage occurs at very specific sites that are within or close to the recognition sequence. The vast majority of known restriction enzymes are of type II, and it is these that find the most use as laboratory tools. == Naming == Restriction enzymes are named based on the bacteria in which they are isolated in the following manner: {| | ''E'' || ''Escherichia'' || (genus) |- | ''co'' || ''coli'' || (species) |- | R || RY13 || (strain) |- | I || First identified || Order ID'd in bacterium |} == Examples == Enzyme Source Recognition Sequence Cut EcoRI Escherichia coli 5'GAATTC 5'---G AATTC---3' 3'CTTAAG 3'---CTTAA G---5' BamHI Bacillus amyloliquefaciens 5'GGATCC 5'---G GATCC---3' 3'CCTAGG 3'---CCTAG G---5' HindIII Haemophilus influenzae 5'AAGCTT 5'---A AGCTT---3' 3'TTCGAA 3'---TTCGA A---5' MstII Microcoleus species 5'CCTNAGG 3'GGANTCC TaqI Thermus aquaticus 5'TCGA 5'---T CGA---3' 3'AGCT 3'---AGC T---5' NotI Nocardia otitidis 5'GCGGCCGC 3'CGCCGGCG HinfI Haemophilus influenzae 5'GANTC 3'CTNAG AluI* Arthrobacter luteus 5'AGCT 5'---AG CT---3' 3'TCGA 3'---TC GA---5' * = blunt ends ==External links== *[http://nist.rcsb.org/pdb/molecules/pdb8_1.html Restriction enzymes: protein data bank molecule of the month] *[http://rebase.neb.com REBASE - The Restriction Enzyme Database] Molecular biology EC 3.1 Enzymes
Under the heading "Types of restriction enzymes," the last sentence reads: "The vast majority of known restriction enzymes are of type II, and it is these that find the most use as laboratory tools." Though not explicitly illogical because the writer has not asserted any causation between the two clauses, it is implied that since the vast majority are type II, scientists have found the most uses for them. In truth, however, I think it's the fact that many applications of REs require cutting at specific nucleotide sequences that has driven many biotech. companies to search actively for more type II REs in nature. Therefore, it is an effect of their usefulness that there is a preponderance of type II REs in the literature. Just quibbling... I also agree with the later suggestion that REs be identified more precisely as "restriction endonucleases." I doubt that there are any "restriction exonucleases," that might only cut at certain sequences found at the 5' or 3' end of DNA, but "endonuclease" is more descriptive, more precise, and I believe more commonly used in the literature, though perhaps not colloquially. ---- who found restriction enzymes? ---- I think the proper name for these enzymes is "restriction endonuclease." It is more descriptive, and it is the term used by the suppliers of these enzymes. I think that "restriction enzyme" is a shorthand that we use just because "endonuclease" is a bulky word. I guess that when we figure out who first discovered them, we'll know what their official name is. user:AdamRetchless :I wrote that final sentence in "Types of restriction enzymes". I didn't mean to imply causation, and I agree that no such causation exists (I'm not sure about the causation in the opposite direction though; I suspect that there really are more type II systems out there than the other two types). Feel free to make it clearer. :As far as the name, "restriction enzyme" is perhaps a bit informal, but common even in publications. Pubmed searches for "restriction enzyme" and "restriction endonuclease" turn up roughly the same number of matches ("restriction enzyme" actually has a slight edge). In informal communications "restriction enzyme" is much more common. If we want to be sticklers, or merely precise, we could go all the way and say "restriction endodeoxyribonuclease". User:Josh Cherry 23:16, 18 Aug 2004 (UTC) ==Examples== Are we planning to make a catalog of examples? There are MANY restriciton endonucleases, and many of hte examples presented in the article are not special. Unless we are seeking a comprehensive reference, the examples list should be much shorter and only include an example of a 3' overhang, a 5' overhang, and a blunt cut. We might also want to include examples of the different types of restriction endonucleases (based on the physical relationship of recognition sequence and cut site). Finally, we should focus on the most famous or well studied ones (such as EcoRI). User:AdamRetchless 13:21, 6 Jul 2004 (UTC)
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Words begining with Restriction_enzyme:
Restriction_Enzyme
Restriction_enzyme
Restriction_enzyme
Restriction_enzymes
Restriction Enzyme
#REDIRECT Restriction enzyme
Restriction enzyme
A restriction enzyme (or restriction endonuclease) is an enzyme that cuts double-stranded DNA. The enzyme makes two incisions, one through each of the phosphate backbones of the double helix without damaging the nucleotide. The chemical bonds that the enzymes cleave can be reformed by other enzymes known as DNA ligase, so that restriction fragments carved from different chromosomes or genes can be splicing (genetics) together, provided their ends are complementary (more below). Many of the procedures of molecular biology and genetic engineering rely on restriction enzymes. The term ''restriction'' comes from the fact that these enzymes were discovered in E. coli strains that appeared to be restricting the infection by certain bacteriophages. Restriction enzymes therefore are believed to be a mechanism evolved by bacteria to resist viral attack and to help in the removal of viral sequences. ==Sites of cleavage== Rather than cutting DNA indiscriminately, a restiction enzyme cuts only double-helical segments that contain a particular DNA sequence, and it makes its incisions only within that sequence--known as a "recognition sequence"--always in the same way. Some enzymes make strand incisions immediately opposite one another, producing "Sticky end" DNA fragments. Most enzymes make slightly staggered incisions, resulting in "sticky ends", out of which one strand protrudes. There are three known evolutionary lineages of restriction enzyme, which each cleave DNA by a different mechanism. ==Fragment complementarity and splicing== Because recognition sequences and cleavage sites differ between restriction enzymes, the length and the exact sequence of a sticky-end "overhang", as well as whether it is the 5' end or the 3' end strand that overhangs, depends on which enzyme produced it. base pair between overhangs with complementary sequences enables two fragments to be joined or "spliced" by a DNA ligase. A sticky-end fragment can be ligated not only to the fragment from which it was originally cleaved, but also to any other fragment with a compatible sticky end. If a restriction enzyme has a non-degenerate pallindromic cleavage site, all ends that it produces are compatible. Ends produced by different enzymes may also be compatible. Knowledge of cleavage sites allows molecular biologists to anticipate which fragments can be joined in which ways, and to choose enzymes appropriately. ==Restriction enzymes as tools== :''See the main article on restriction digests.'' Recognition sequences typically are only four to twelve nucleotides long. Because there are only so many ways to arrange the four nucleotides--A,C,G and T--into a four or eight or twelve nucleotide sequence, recognition sequences tend to "crop up" by chance in any long sequence. Furthermore, restriction enzymes specific to hundreds of distinct sequences have been identified and synthesized for sale to laboratories. As a result, potential "restriction sites" appear in almost any gene or chromosome. Meanwhile, the sequences of some artificial plasmids include a "linker" that contains dozens of restriction enzyme recognition sequences within a very short segment of DNA. So no matter the context in which a gene naturally appears, there is probably a pair of restriction enzymes that can snip it out, and which will produce ends that enable the gene to be spliced into a plasmid (i.e. which will enable what molecular biologists call "cloning" of the gene). ==Many Recognition sequences are palindromic== While recognition sequences vary widely, many of them are palindrome; that is, the sequence on one strand reads the same in the opposite direction on the complementary strand. The meaning of "palindromic" in this context is different from what one might expect from its linguistic usage: GTAATG is not a palindromic DNA sequence, but GTATAC is. ==Types of restriction enzymes== Restriction enzymes are classified biochemically into three types, designated Type I, Type II and Type III. In type I and III systems, both the methylase and restriction activities are carried out by a single large enzyme complex. Although these enzymes recognize specific DNA sequences, the sites of actual cleavage are at variable distances from these recognition sites, and can be hundreds of bases away. In type II systems, the restriction enzyme is independent of its methylase, and cleavage occurs at very specific sites that are within or close to the recognition sequence. The vast majority of known restriction enzymes are of type II, and it is these that find the most use as laboratory tools. == Naming == Restriction enzymes are named based on the bacteria in which they are isolated in the following manner: {| | ''E'' || ''Escherichia'' || (genus) |- | ''co'' || ''coli'' || (species) |- | R || RY13 || (strain) |- | I || First identified || Order ID'd in bacterium |} == Examples == Enzyme Source Recognition Sequence Cut EcoRI Escherichia coli 5'GAATTC 5'---G AATTC---3' 3'CTTAAG 3'---CTTAA G---5' BamHI Bacillus amyloliquefaciens 5'GGATCC 5'---G GATCC---3' 3'CCTAGG 3'---CCTAG G---5' HindIII Haemophilus influenzae 5'AAGCTT 5'---A AGCTT---3' 3'TTCGAA 3'---TTCGA A---5' MstII Microcoleus species 5'CCTNAGG 3'GGANTCC TaqI Thermus aquaticus 5'TCGA 5'---T CGA---3' 3'AGCT 3'---AGC T---5' NotI Nocardia otitidis 5'GCGGCCGC 3'CGCCGGCG HinfI Haemophilus influenzae 5'GANTC 3'CTNAG AluI* Arthrobacter luteus 5'AGCT 5'---AG CT---3' 3'TCGA 3'---TC GA---5' * = blunt ends ==External links== *[http://nist.rcsb.org/pdb/molecules/pdb8_1.html Restriction enzymes: protein data bank molecule of the month] *[http://rebase.neb.com REBASE - The Restriction Enzyme Database] Molecular biology EC 3.1 Enzymes
Restriction enzyme
Under the heading "Types of restriction enzymes," the last sentence reads: "The vast majority of known restriction enzymes are of type II, and it is these that find the most use as laboratory tools." Though not explicitly illogical because the writer has not asserted any causation between the two clauses, it is implied that since the vast majority are type II, scientists have found the most uses for them. In truth, however, I think it's the fact that many applications of REs require cutting at specific nucleotide sequences that has driven many biotech. companies to search actively for more type II REs in nature. Therefore, it is an effect of their usefulness that there is a preponderance of type II REs in the literature. Just quibbling... I also agree with the later suggestion that REs be identified more precisely as "restriction endonucleases." I doubt that there are any "restriction exonucleases," that might only cut at certain sequences found at the 5' or 3' end of DNA, but "endonuclease" is more descriptive, more precise, and I believe more commonly used in the literature, though perhaps not colloquially. ---- who found restriction enzymes? ---- I think the proper name for these enzymes is "restriction endonuclease." It is more descriptive, and it is the term used by the suppliers of these enzymes. I think that "restriction enzyme" is a shorthand that we use just because "endonuclease" is a bulky word. I guess that when we figure out who first discovered them, we'll know what their official name is. user:AdamRetchless :I wrote that final sentence in "Types of restriction enzymes". I didn't mean to imply causation, and I agree that no such causation exists (I'm not sure about the causation in the opposite direction though; I suspect that there really are more type II systems out there than the other two types). Feel free to make it clearer. :As far as the name, "restriction enzyme" is perhaps a bit informal, but common even in publications. Pubmed searches for "restriction enzyme" and "restriction endonuclease" turn up roughly the same number of matches ("restriction enzyme" actually has a slight edge). In informal communications "restriction enzyme" is much more common. If we want to be sticklers, or merely precise, we could go all the way and say "restriction endodeoxyribonuclease". User:Josh Cherry 23:16, 18 Aug 2004 (UTC) ==Examples== Are we planning to make a catalog of examples? There are MANY restriciton endonucleases, and many of hte examples presented in the article are not special. Unless we are seeking a comprehensive reference, the examples list should be much shorter and only include an example of a 3' overhang, a 5' overhang, and a blunt cut. We might also want to include examples of the different types of restriction endonucleases (based on the physical relationship of recognition sequence and cut site). Finally, we should focus on the most famous or well studied ones (such as EcoRI). User:AdamRetchless 13:21, 6 Jul 2004 (UTC)
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Restriction_Enzyme
Restriction_enzyme
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Restriction_enzymes
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