Restriction enzyme
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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 bases. The chemical bonds that the enzymes cleave can be reformed by other enzymes known as ligases, so that restriction fragments carved from different chromosomes or genes can be spliced 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.
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Sites of cleavage
Rather than cutting DNA indiscriminately, a restiction enzyme cuts only double-helical segments that contain a particular nucleotide 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 "blunt 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-pairing 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.
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Restriction_enzyme.jpg
Illustration of typical restriction enzyme cleavage.
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Sma1.jpg
Illustration of Sma1 restriction enzyme cleavage.
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 palindromic; 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
- Restriction enzymes: protein data bank molecule of the month (http://nist.rcsb.org/pdb/molecules/pdb8_1.html)
- REBASE - The Restriction Enzyme Database (http://rebase.neb.com)de:Restriktionsenzym
fr:Enzyme de restriction ja:制限酵素 nl:Restrictie-enzym pl:Enzym_restrykcyjny