Restriction endonucleases: Difference between revisions

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Restriction endonucleases recognise specific base pairs within [[DNA|DNA]] sequences where they exhibit [[Enzyme|enzymatic activity]] through the cleaving of DNA into smaller fragments. They are found in [[Bacteria|bacteria]] and it is thought that their original biological role was to protect the DNA of the [[Bacteria|bacteria]] within which they were contained from being infected by viral DNA by cleaving it before it could cause damage.&nbsp;Different restriction endonucleases are specific to different sequences (they can recognise sequence anywhere from 4-8 base pairs in length) and this results in a variety of fragment lengths being produced depending upon which restriction [[Enzyme|enzyme]] is used. Restriction endonucleases cleave both strands of double stranded DNA by cutting a nucleotide between a 3'-OH group and a phosphate (the [[Phosphodiester bond|phosphodiester bond]] found in DNA) and always produce fragments with a 5' phosphate and a 3'-OH. Some restriction endonucleases cut at the symmetry centre of the sequence they are specific for and produce what is know as a [[Blunt ends|'blunt end]]', ie. it has no overhang of single stranded DNA. Others produce what we call '[[‘sticky’ ends|sticky or cohesive ends]]' in which a single stranded overhang is produced. These cohesive strands are what give restriction endonucleases their role in producing [[Recombinant DNA Technology|recombinant DNA]] as any two peices of DNA (including those from different [[Genome|genomes]]) that have been cut with the same restriction endonuclease will have the same 'sticky ends' and therefore be complementary to each other, enabling complementary base pair binging under the right conditions <ref>Alberts B, Johnson A, Lewis J, Raff M, Roberts K and Walter P. (2008) Molecular Biology of the Cell, Fifth Edition, New York, Garland Science.</ref>.  
Restriction endonucleases recognise specific base pairs within [[DNA|DNA]] sequences where they exhibit [[Enzyme|enzymatic activity]] through the cleaving of DNA into smaller fragments. They are found in [[Bacteria|bacteria]] and it is thought that their original biological role was to protect the DNA of the [[Bacteria|bacteria]] within which they were contained from being infected by viral DNA by cleaving it before it could cause damage.&nbsp;Different restriction endonucleases are specific to different sequences (they can recognise sequence anywhere from 4-8 base pairs in length) and this results in a variety of fragment lengths being produced depending upon which restriction [[Enzyme|enzyme]] is used. Restriction endonucleases cleave both strands of double stranded DNA by cutting a nucleotide between a 3'-OH group and a phosphate (the [[Phosphodiester bond|phosphodiester bond]] found in DNA) and always produce fragments with a 5' phosphate and a 3'-OH. Some restriction endonucleases cut at the symmetry centre of the sequence they are specific for and produce what is know as a [[Blunt ends|'blunt end]]', ie. it has no overhang of single stranded DNA. Others produce what we call '[[‘sticky’ ends|sticky or cohesive ends]]' in which a single stranded overhang is produced. These cohesive strands are what give restriction endonucleases their role in producing [[Recombinant DNA Technology|recombinant DNA]] as any two peices of DNA (including those from different [[Genome|genomes]]) that have been cut with the same restriction endonuclease will have the same 'sticky ends' and therefore be complementary to each other, enabling complementary base pair binging under the right conditions <ref>Alberts B, Johnson A, Lewis J, Raff M, Roberts K and Walter P. (2008) Molecular Biology of the Cell, Fifth Edition, New York, Garland Science.</ref>.<br>


Also see&nbsp;[[Restriction enzyme|Restriction enzyme]]
There are four major types of restriction endonucleases: Type I,II,III and IV which are summarisedc below:


=== Reference  ===
*Type I restriction endonulceases, which are also known as ATP-dependent [[DNAase|DNases]]<ref>http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&amp;amp;amp;amp;amp;ec=3.1.21.3</ref>, cut double stranded DNA at random points far off from the restriction site, the site of cleavge can be as far as 1000bp from the restriction site. Cleavge is always coupled to ATP hydorlysis and these enzymes are seen as being multifunctional proteins as they can aid in restriction and methylation of substrates<ref>http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&amp;amp;amp;amp;amp;ec=3.1.21.3</ref>.
*Type II restriction endonucleases are the most commonly used for DNA anaylsis as mentioned above. They are a very diverse with most being either [[Dimer|homodimeric]] or [[Tetrameric|tetrameric]] which (unlike type I) cleave the DNA at the restriction sites. In addition, they require [[Magnesium|Mg<sup>2+</sup>]] ions to carry out restriction<ref>Pingoud A,Fuxreiter M,Pingoud V, Wende W.Type II restriction endonucleases:structure and mechanism.Cellular and molecular life sciences.2005.63;685</ref>.
*Type III restriction endonucleases are found in most bacteria, especially in pathogenic strands<ref>Rao D N, Dryden D T, Bheemanaik S. Type III restriction-medication enzymes: a historical perspective. Nucleic acids research.2014;42:45-55</ref> . These cleave DNA which is present a short disatnce away from the restriction site. Like type I they require [[ATP|ATP]] but this is not hydrolysed during the reaction<ref>http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&amp;amp;amp;amp;amp;ec=3.1.21.5</ref>.
*Type IV restriction endonucleases recognise methylate DNA<ref>http://www.ebi.ac.uk/interpro/entry/IPR011336</ref>. They are not commonly used for DNA analysis.<br>


<references /><br>
Also see [[Restriction enzyme|Restriction enzyme]]
 
=== References  ===
 
<references />

Latest revision as of 01:00, 6 December 2017

Restriction endonucleases recognise specific base pairs within DNA sequences where they exhibit enzymatic activity through the cleaving of DNA into smaller fragments. They are found in bacteria and it is thought that their original biological role was to protect the DNA of the bacteria within which they were contained from being infected by viral DNA by cleaving it before it could cause damage. Different restriction endonucleases are specific to different sequences (they can recognise sequence anywhere from 4-8 base pairs in length) and this results in a variety of fragment lengths being produced depending upon which restriction enzyme is used. Restriction endonucleases cleave both strands of double stranded DNA by cutting a nucleotide between a 3'-OH group and a phosphate (the phosphodiester bond found in DNA) and always produce fragments with a 5' phosphate and a 3'-OH. Some restriction endonucleases cut at the symmetry centre of the sequence they are specific for and produce what is know as a 'blunt end', ie. it has no overhang of single stranded DNA. Others produce what we call 'sticky or cohesive ends' in which a single stranded overhang is produced. These cohesive strands are what give restriction endonucleases their role in producing recombinant DNA as any two peices of DNA (including those from different genomes) that have been cut with the same restriction endonuclease will have the same 'sticky ends' and therefore be complementary to each other, enabling complementary base pair binging under the right conditions [1].

There are four major types of restriction endonucleases: Type I,II,III and IV which are summarisedc below:

  • Type I restriction endonulceases, which are also known as ATP-dependent DNases[2], cut double stranded DNA at random points far off from the restriction site, the site of cleavge can be as far as 1000bp from the restriction site. Cleavge is always coupled to ATP hydorlysis and these enzymes are seen as being multifunctional proteins as they can aid in restriction and methylation of substrates[3].
  • Type II restriction endonucleases are the most commonly used for DNA anaylsis as mentioned above. They are a very diverse with most being either homodimeric or tetrameric which (unlike type I) cleave the DNA at the restriction sites. In addition, they require Mg2+ ions to carry out restriction[4].
  • Type III restriction endonucleases are found in most bacteria, especially in pathogenic strands[5] . These cleave DNA which is present a short disatnce away from the restriction site. Like type I they require ATP but this is not hydrolysed during the reaction[6].
  • Type IV restriction endonucleases recognise methylate DNA[7]. They are not commonly used for DNA analysis.

Also see Restriction enzyme

References

  1. ↑ Alberts B, Johnson A, Lewis J, Raff M, Roberts K and Walter P. (2008) Molecular Biology of the Cell, Fifth Edition, New York, Garland Science.
  2. ↑ http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&amp;amp;amp;amp;ec=3.1.21.3
  3. ↑ http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&amp;amp;amp;amp;ec=3.1.21.3
  4. ↑ Pingoud A,Fuxreiter M,Pingoud V, Wende W.Type II restriction endonucleases:structure and mechanism.Cellular and molecular life sciences.2005.63;685
  5. ↑ Rao D N, Dryden D T, Bheemanaik S. Type III restriction-medication enzymes: a historical perspective. Nucleic acids research.2014;42:45-55
  6. ↑ http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&amp;amp;amp;amp;ec=3.1.21.5
  7. ↑ http://www.ebi.ac.uk/interpro/entry/IPR011336
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