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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?
Werner Arber, Daniel Nathans and Hamilton O. Smith were awarded the 1978 Nobel Prize in Medicine for the discovery of "restriction enzymes and their application to problems of molecular genetics".
http://nobelprize.org/medicine/laureates/1978/index.html
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. adam
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). AdamRetchless 13:21, 6 Jul 2004 (UTC)
I like the examples linking bacteria with RE's --adds something tangible to the spooky game of pair base preoocupations .- more art too might add to understanding the physical constraints of cellular activity, or don't boundaries matter that much anymore ?
Although this is not a problem with this article, I think this is the best place for this comment. The pages for each restriction enzyme are structured differently and it is difficult to find the information about them. Planet and star pages, for instance, have charts giving information about them. I think that would be nice if a similar system could be implemented for restriction endonucleases. If not, similar sections and information should at least be provided. I would do this myself, but do not have the time (sorry...).
Thank you in advance. —Preceding unsigned comment added by 76.89.247.164 ( talk) 03:11, 15 March 2008 (UTC)
"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" Correct me if I'm wrong, but although true of Type I enzymes, this statement is not true of Type III enzymes. Type II enzymes cut at a relatively short, specific distance outside of an asymmetrical recognition sequence, and require two recognition sites in opposing orientation to cut. Type I and some Type II enzymes also require two recognition sites to cut, but these need not normally be in opposing orientations.
Also, is it worth mentioning Kobayashi's theory that Type II (but not Type I or III) enzymes are primarily, genomic parasites, rather than a mechanism for blocking parasites such as viruses?-- 203.166.255.148 14:10, 24 November 2005 (UTC)
Endonuclease should be merged into this article. Brazucs ( TALK | CONTRIBS) 17:43, 14 April 2006 (UTC)
They are different technical subjects. We shoudl refrain from giving into the temptaion to merge all similar articles as this will only result in readers needign to sift frther through an article to find the specific information they are after, thus reducing overall readability adn effeciveness. In addition it tends to create enormous articles that are both unwieldy and over generalized. User:AnthonyBachler
"Endonuclease" covers other enzymes, such as DNase and RNase, which are certainly diferent from restriction enzymes - although a subtopic, I would think they deserve an exclusive article, and indeed the title 'restriction endonuclease' seems more appropriate. (Rafael) 25.april.2006
I also think this article and Endonuclease should be kept separate. There is no reason to burden the reader with extracting what he wants from extraneous information. I will remove the merge tags. - R. S. Shaw 19:31, 23 May 2006 (UTC)
Interesting discussion. But, isn't it too much lagging behind the page's renovation? First, re the merging topic above: Have you forgotten what the original topic was? Even though Brazucs may be a bit confused, I believe he is suggesting to merge restriction enzyme with restriction endonuclease. I second the move. Shaw should give up shifting the topic of discussion. Tell me, how many restriction endonucleases are not restriction enzymes? Isopropyl understands the principal of discussion: respect the history and adhere to the subject of discussion. The fact that they are merged today is a relief.
Now, the page still contains many confusing statements and misconceptions. Many imprecise wording shows how up-to-date the editorialship is on this topic. The situation is particularly bad for non-molecular biologists who try to pick up some meaningful general idea. I am going to put my two cents in the mix. -- Achian ( talk) 01:40, 22 June 2008 (UTC)
The examples are all wrong, the 'recognition sequences' are muddled up. If the author does not correct these in the next 72 hours then I shall. —The preceding unsigned comment was added by 81.107.151.178 ( talk • contribs) 21:32, 4 May 2006 (UTC)
A suggestion was made to merge sticky end/blunt end into DNA ligase. Another possibility mentioned is to merge it here. The issue is being discussed at Talk:DNA ligase. // habj 13:31, 8 October 2006 (UTC)
Would anyone have any objections to me making and adding more images besides the examples. I'm thinking an image each would look pretty good, they would be the same size and format as the two images already on the page. I'm going to start working on this, if anyone has any objections after I add them to the page, post here and if its serious please feel free to revert to article and let me know here or on my talk. Thanks, Urdna 23:16, 30 May 2007 (UTC)
Has anyone heard of a way to code two different functional organisms from one genome basically the organism makes restriction enzymes that cause a 5'---->3' to be a 5'-[restriction enzyme site]-3' genome that produces two different 5'-->3' (ligate) 5'-->3' genomes; wikipedia notes that the flu codes a restriction enzyme thus that could go with a customized bacterial restriction enzyme site to produce a bacteria makes flu virus unless the virus made restriction enzyme is present at sufficient quantities to block (remove) the prefer to make virus rather than bacteria program
kind of like Bacterial duogenome is 5' [full bacterial genome][restriction site] [virus genome that codes restriction enzyme] [restriction site] ][restriction site][virus genome that codes restriction enzyme][restriction site] ][restriction site]
when the bacteria replicates if theres no virus (absence of restriction enzyme) the bacteria codes bacteria plus some virus, if there is a medium amount of virus bacteria plus much more viruses are going to be made, if theres a huge amount of virus only the bacteria will be made as the stochastically rare first restriction enzyme site gets activated
I'm making a way to combine a longevity peptide like AEDG with a recurring virus like herpes duogenome with a flu to create an organism that makes people live longer which spreads rapidly
It could also be Yeast or bacterial genome that codes the beneficial recurring zerpes longevity virus
Biologicalworld.com has spammed wikipedia like no tomorrow. He is a site of only a few pages and a LOT of adsense. Not much information is given except for "protocols" which are not referenced, and cannot be trusted from a site of that quality.
check: Links from Wikipedia
The following have been cleaned up:
and many more Sciencetalks ( talk) —Preceding comment was added at 03:01, 4 January 2008 (UTC)
Does anyone else think that a new page should be made that lists restriction enzymes and their recognition sequences. From what I understand there are many more than listed on this page too. Smartse ( talk) 14:09, 12 March 2009 (UTC)
The IUPAC changed the convention on writing restriction enzymes names in 2003:
I have corrected this on the restriction enzyme pages that I could find. Shastrix ( talk) 19:32, 24 April 2009 (UTC)
The current glossary seems too large and rather distracting from the lead, which is presumably what we intend the reader to be focused on when they first enter the article. Also, some of the terms and definitions could probably be pared down. I have a draft of what I think would be a better glossary here; any feedback would be appreciated. Emw2012 ( talk) 15:42, 17 September 2009 (UTC)
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The caption says "Two catalytic magnesium ions (one from each monomer)", but the image is from PDB: 1QPS, which actually has manganese and not magnesium: https://www.rcsb.org/structure/1QPS . Not being an expert in restriction enzymes, I am hesitant to modify the text directly given that the biologically relevant ion appears to be magnesium.
Restriction enzyme is a former featured article candidate. Please view the links under Article milestones below to see why the nomination failed. For older candidates, please check the archive. | ||||||||||
|
This
level-5 vital article is rated C-class on Wikipedia's
content assessment scale. It is of interest to the following WikiProjects: | ||||||||||||||
|
This article was the
MCB Collaboration of the Month for the month of May–August 2008. For more details, see the
MCB Collaboration of the Month history. |
This article is or was the subject of a Wiki Education Foundation-supported course assignment. Further details are available on the course page. Student editor(s): Joyspark, Sherapg. Peer reviewers: Joyspark.
Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT ( talk) 08:05, 17 January 2022 (UTC)
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?
Werner Arber, Daniel Nathans and Hamilton O. Smith were awarded the 1978 Nobel Prize in Medicine for the discovery of "restriction enzymes and their application to problems of molecular genetics".
http://nobelprize.org/medicine/laureates/1978/index.html
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. adam
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). AdamRetchless 13:21, 6 Jul 2004 (UTC)
I like the examples linking bacteria with RE's --adds something tangible to the spooky game of pair base preoocupations .- more art too might add to understanding the physical constraints of cellular activity, or don't boundaries matter that much anymore ?
Although this is not a problem with this article, I think this is the best place for this comment. The pages for each restriction enzyme are structured differently and it is difficult to find the information about them. Planet and star pages, for instance, have charts giving information about them. I think that would be nice if a similar system could be implemented for restriction endonucleases. If not, similar sections and information should at least be provided. I would do this myself, but do not have the time (sorry...).
Thank you in advance. —Preceding unsigned comment added by 76.89.247.164 ( talk) 03:11, 15 March 2008 (UTC)
"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" Correct me if I'm wrong, but although true of Type I enzymes, this statement is not true of Type III enzymes. Type II enzymes cut at a relatively short, specific distance outside of an asymmetrical recognition sequence, and require two recognition sites in opposing orientation to cut. Type I and some Type II enzymes also require two recognition sites to cut, but these need not normally be in opposing orientations.
Also, is it worth mentioning Kobayashi's theory that Type II (but not Type I or III) enzymes are primarily, genomic parasites, rather than a mechanism for blocking parasites such as viruses?-- 203.166.255.148 14:10, 24 November 2005 (UTC)
Endonuclease should be merged into this article. Brazucs ( TALK | CONTRIBS) 17:43, 14 April 2006 (UTC)
They are different technical subjects. We shoudl refrain from giving into the temptaion to merge all similar articles as this will only result in readers needign to sift frther through an article to find the specific information they are after, thus reducing overall readability adn effeciveness. In addition it tends to create enormous articles that are both unwieldy and over generalized. User:AnthonyBachler
"Endonuclease" covers other enzymes, such as DNase and RNase, which are certainly diferent from restriction enzymes - although a subtopic, I would think they deserve an exclusive article, and indeed the title 'restriction endonuclease' seems more appropriate. (Rafael) 25.april.2006
I also think this article and Endonuclease should be kept separate. There is no reason to burden the reader with extracting what he wants from extraneous information. I will remove the merge tags. - R. S. Shaw 19:31, 23 May 2006 (UTC)
Interesting discussion. But, isn't it too much lagging behind the page's renovation? First, re the merging topic above: Have you forgotten what the original topic was? Even though Brazucs may be a bit confused, I believe he is suggesting to merge restriction enzyme with restriction endonuclease. I second the move. Shaw should give up shifting the topic of discussion. Tell me, how many restriction endonucleases are not restriction enzymes? Isopropyl understands the principal of discussion: respect the history and adhere to the subject of discussion. The fact that they are merged today is a relief.
Now, the page still contains many confusing statements and misconceptions. Many imprecise wording shows how up-to-date the editorialship is on this topic. The situation is particularly bad for non-molecular biologists who try to pick up some meaningful general idea. I am going to put my two cents in the mix. -- Achian ( talk) 01:40, 22 June 2008 (UTC)
The examples are all wrong, the 'recognition sequences' are muddled up. If the author does not correct these in the next 72 hours then I shall. —The preceding unsigned comment was added by 81.107.151.178 ( talk • contribs) 21:32, 4 May 2006 (UTC)
A suggestion was made to merge sticky end/blunt end into DNA ligase. Another possibility mentioned is to merge it here. The issue is being discussed at Talk:DNA ligase. // habj 13:31, 8 October 2006 (UTC)
Would anyone have any objections to me making and adding more images besides the examples. I'm thinking an image each would look pretty good, they would be the same size and format as the two images already on the page. I'm going to start working on this, if anyone has any objections after I add them to the page, post here and if its serious please feel free to revert to article and let me know here or on my talk. Thanks, Urdna 23:16, 30 May 2007 (UTC)
Has anyone heard of a way to code two different functional organisms from one genome basically the organism makes restriction enzymes that cause a 5'---->3' to be a 5'-[restriction enzyme site]-3' genome that produces two different 5'-->3' (ligate) 5'-->3' genomes; wikipedia notes that the flu codes a restriction enzyme thus that could go with a customized bacterial restriction enzyme site to produce a bacteria makes flu virus unless the virus made restriction enzyme is present at sufficient quantities to block (remove) the prefer to make virus rather than bacteria program
kind of like Bacterial duogenome is 5' [full bacterial genome][restriction site] [virus genome that codes restriction enzyme] [restriction site] ][restriction site][virus genome that codes restriction enzyme][restriction site] ][restriction site]
when the bacteria replicates if theres no virus (absence of restriction enzyme) the bacteria codes bacteria plus some virus, if there is a medium amount of virus bacteria plus much more viruses are going to be made, if theres a huge amount of virus only the bacteria will be made as the stochastically rare first restriction enzyme site gets activated
I'm making a way to combine a longevity peptide like AEDG with a recurring virus like herpes duogenome with a flu to create an organism that makes people live longer which spreads rapidly
It could also be Yeast or bacterial genome that codes the beneficial recurring zerpes longevity virus
Biologicalworld.com has spammed wikipedia like no tomorrow. He is a site of only a few pages and a LOT of adsense. Not much information is given except for "protocols" which are not referenced, and cannot be trusted from a site of that quality.
check: Links from Wikipedia
The following have been cleaned up:
and many more Sciencetalks ( talk) —Preceding comment was added at 03:01, 4 January 2008 (UTC)
Does anyone else think that a new page should be made that lists restriction enzymes and their recognition sequences. From what I understand there are many more than listed on this page too. Smartse ( talk) 14:09, 12 March 2009 (UTC)
The IUPAC changed the convention on writing restriction enzymes names in 2003:
I have corrected this on the restriction enzyme pages that I could find. Shastrix ( talk) 19:32, 24 April 2009 (UTC)
The current glossary seems too large and rather distracting from the lead, which is presumably what we intend the reader to be focused on when they first enter the article. Also, some of the terms and definitions could probably be pared down. I have a draft of what I think would be a better glossary here; any feedback would be appreciated. Emw2012 ( talk) 15:42, 17 September 2009 (UTC)
Hello fellow Wikipedians,
I have just modified 2 external links on Restriction enzyme. Please take a moment to review my edit. If you have any questions, or need the bot to ignore the links, or the page altogether, please visit this simple FaQ for additional information. I made the following changes:
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Cheers.— InternetArchiveBot ( Report bug) 17:29, 26 July 2017 (UTC)
The caption says "Two catalytic magnesium ions (one from each monomer)", but the image is from PDB: 1QPS, which actually has manganese and not magnesium: https://www.rcsb.org/structure/1QPS . Not being an expert in restriction enzymes, I am hesitant to modify the text directly given that the biologically relevant ion appears to be magnesium.