Talk:Restriction enzyme

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Types
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


 * 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". 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). 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 ?


 * I agree with AdamRetchless's point. The Example section does not seem previously planned and the idea it gives is that people simply added examples at will. Also, all the examples refer to palidromic sequences which are cut within the sequence AND in a symmetric way. Besides, this makes it nearly impossible to explain (x/y) notation. It is my intention to edit that section, as well as adding something more in the future (maybe in two to three weeks). For the time being, though, I would simply like to express my opinion. ~ Jotomicron 19:58, 7 October 2007 (UTC) —Preceding signed but undated comment was added at 19:56, 7 October 2007 (UTC)

- 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)

Type III enzymes
"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)

Merger
Endonuclease should be merged into this article. Brazucs ( TALK | CONTRIBS ) 17:43, 14 April 2006 (UTC)
 * Oh... and I also believe this page should be moved to restriction endonuclease. Brazucs ( TALK | CONTRIBS ) 17:50, 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)
 * If everyone thinks these should be separate, why have they been merged? Isopropyl 04:01, 16 October 2006 (UTC)
 * ?? Endonuclease and Restriction enzyme are still separate. -R. S. Shaw 04:28, 16 October 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)


 * Hi Achian. I have reverted your good faith edits since I think they disrupted the flow of the article.  I started to copy edit your additions:
 * The process by which the enzyme finds the nucleotide sequence is called recognition, the location of this specific nucleotide sequence is known as a recognition site, and the sequence is referred to as a recognition sequence. Since the process of a restriction enzyme cutting its target DNA at the recognition site(s) is known as restriction,citation needed the location of the restriction is known as a restriction site.
 * This copy edit for example included more appropriate internal wiki links and removed a link to restriction which was a disambiguation page which in turn linked back to this page. While including precise definitions of terminology is important, it is neither practical nor desirable to have a fully self contained set of definitions in each and every article. That is what internal wiki links are for.  As an alternative, one could include a glossary of restriction enzymes terms, analogous to Template:Transcription factor glossary.  Cheers,  Boghog2 (talk) 11:29, 22 June 2008 (UTC)
 * I went ahead and created a first draft of a Template:Restriction enzyme glossary. Would this be useful to include in the restriction enzyme article? Cheers. Boghog2 (talk) 20:02, 22 June 2008 (UTC)


 * Hi Boghog2. A glossary is definitely needed. The internal reference pages serve that kind purpose, but not as tidy and specific as a glossary. I made minor changes to your fledging glossary. There are too many loose ends to deal with. Regards. Achian (talk) 00:54, 6 July 2008 (UTC)


 * Hi Achian. I have reverted your good faith edits to the Template:Restriction enzyme glossary.  You are correct in that some of the terms such as molecular recognition have broader meanings.  However I believe it is important to keep the focus of the glossary on the subject of restriction enzymes.  Terms with broader meanings in the glossary are linked to Wikipedia articles where these subjects are already treated in a broader context.  Boghog2 (talk) 21:44, 7 July 2008 (UTC)

Major Problem
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)


 * I'm sorry you haven't yet corrected the detected errors in the examples. If you don't want to do the minor amount of editing needed, perhaps you could let others know which entries have problems. -R. S. Shaw 19:39, 23 May 2006 (UTC)

Merge sticky end/blunt end?
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)

More images
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)
 * I've been busy and on a wiki-break, but I'm back now and I should have time to do this soon. Sorry for the delay, Urdna 01:48, 24 August 2007 (UTC)

One genome codes two organisms with restriction enzymes
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


 * Good Luck! Smartse (talk) 15:28, 31 March 2009 (UTC)

Spamming Wikipedia
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:


 * en.wikipedia.org/wiki/Plasmid
 * en.wikipedia.org/wiki/Gel_electrophoresis
 * en.wikipedia.org/wiki/Green_fluorescent_protein
 * en.wikipedia.org/wiki/Homology_(biology)
 * en.wikipedia.org/wiki/HeLa
 * en.wikipedia.org/wiki/Protease
 * en.wikipedia.org/wiki/Restriction_enzyme
 * en.wikipedia.org/wiki/Petri_dish
 * en.wikipedia.org/wiki/Structural_domain
 * en.wikipedia.org/wiki/Trypsin
 * en.wikipedia.org/wiki/Oligonucleotide
 * en.wikipedia.org/wiki/Transmission_electron_microscope
 * en.wikipedia.org/wiki/Agar_plate
 * en.wikipedia.org/wiki/Calcium_phosphate
 * en.wikipedia.org/wiki/Disulfide_bond
 * en.wikipedia.org/wiki/Denaturation_(biochemistry)
 * en.wikipedia.org/wiki/DNA_ligase
 * en.wikipedia.org/wiki/Wild_type
 * en.wikipedia.org/wiki/Tissue_culture
 * en.wikipedia.org/wiki/Transmission_electron_microscopy
 * en.wikipedia.org/wiki/Reporter_gene
 * en.wikipedia.org/wiki/Northern_blot
 * en.wikipedia.org/wiki/Protein_engineering
 * en.wikipedia.org/wiki/Sticky_end/blunt_end
 * en.wikipedia.org/wiki/Taq_polymerase
 * en.wikipedia.org/wiki/Protein_domain
 * en.wikipedia.org/wiki/Coomassie
 * en.wikipedia.org/wiki/Native_state
 * en.wikipedia.org/wiki/Chinese_Hamster_Ovary_cell
 * en.wikipedia.org/wiki/Peptidase
 * en.wikipedia.org/wiki/Visking_tubing
 * en.wikipedia.org/wiki/Streptavidin
 * en.wikipedia.org/wiki/Microtiter_plate
 * en.wikipedia.org/wiki/Subcloning
 * en.wikipedia.org/wiki/Ion_exchange_chromatography
 * en.wikipedia.org/wiki/Thermal_cycler
 * en.wikipedia.org/wiki/Bovine_serum_albumin
 * en.wikipedia.org/wiki/Phosphate_buffered_saline
 * en.wikipedia.org/wiki/Glutathione_S-transferase
 * en.wikipedia.org/wiki/HEPES
 * en.wikipedia.org/wiki/Ortholog
 * en.wikipedia.org/wiki/Proteases
 * en.wikipedia.org/wiki/Salting_out
 * en.wikipedia.org/wiki/Fetal_bovine_serum
 * en.wikipedia.org/wiki/Proteolytic_enzyme
 * en.wikipedia.org/wiki/DNA_end
 * en.wikipedia.org/wiki/Supernatant
 * en.wikipedia.org/wiki/ABTS
 * en.wikipedia.org/wiki/Conserved_sequence
 * en.wikipedia.org/wiki/Peptide_mass_fingerprinting
 * en.wikipedia.org/wiki/Dithiothreitol
 * en.wikipedia.org/wiki/Uranyl_acetate

and many more Sciencetalks (talk) —Preceding comment was added at 03:01, 4 January 2008 (UTC)

List of restriction enzymes?
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)
 * I think that's a good idea, the list does give the impression that there are alot less restriction enzymes then there are. Million_Moments (talk) 11:06, 31 March 2009 (UTC)
 * I agree. The 'Examples' section has always seemed like it would be more appropriate as part of an article like the one you're suggesting. Emw2012 (talk) 14:13, 31 March 2009 (UTC)
 * Ok, I'll wait a while longer though just to make sure. Also I've noticed that there is mention of Types I, II and III in the article but no mention of which type those in the list are. Anyone got any ideas? Smartse (talk) 14:58, 31 March 2009 (UTC)
 * I just added Hga1 - it cuts 5 ntides along from the recognition site and I'm not sure about the ends produced so I left it as NN. Smartse (talk) 15:14, 31 March 2009 (UTC)
 * Finally there are loads more enzymes here if anyone is bored. Not sure if its a WP:RS though. Smartse (talk) 15:22, 31 March 2009 (UTC)

Correcting restriction enzyme writing style
The IUPAC changed the convention on writing restriction enzymes names in 2003:
 * "4. Restriction enzyme names should not include a space between the main acronym and the Roman numeral. This practice, which has been employed to avoid the inelegant look caused when characters in italic fonts are juxtaposed next to characters in a regular font, is incorrect. Now that italics will no longer be used in names there is no reason to continue this practice.".

I have corrected this on the restriction enzyme pages that I could find. Shastrix (talk) 19:32, 24 April 2009 (UTC)


 * I have removed all italicisation from the short names of the restriction enzymes in accordance with the current guidelines by NCBI and IUPAC (2003). The last sentence of Shastrix's quotation also points out that italicisation will no longer be used (although it is naturally widely used by habit by molecular biologists).
 * The NCBI Style Guide - Style Points and Conventions - Italics
 * SURVEY AND SUMMARY: A nomenclature for restriction enzymes, DNA methyltransferases, homing :endonucleases and their genes - General Rules
 * 3. "Italics will no longer be used for the first three-letter acronym of the REase or MTase name."


 * This was my first edit of Wikipedia as a registered user, so I'm sure I made some mistakes. I'm open for all criticism!
 * Kerbezena (talk) 13:07, 30 January 2018 (UTC)

Restriction enzyme glossary
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)


 * That draft looks good to me - I'd perhaps note use the [show] tabs though, I think it would be simpler just to have it all open as the current glossary is. Smartse (talk) 12:54, 18 September 2009 (UTC)


 * Released the draft, all terms now showing by default. Emw2012 (talk) 13:56, 18 September 2009 (UTC)

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Type II image may be labeled incorrectly
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.
 * Seems like the enzyme works with both magnesium or manganese, so you can change it to manganese if you want to. I have no idea why no paper was published so we know why one was used instead of the other in the crystal structure. Hzh (talk) 19:19, 29 September 2021 (UTC)