Talk:Restriction enzyme

message: 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)
thread_title: Types

message: 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)
replies: text: 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)
thread_title: Examples

message: "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)
thread_title:  Type III enzymes 

message: 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)
thread_title:  Major Problem 

message: 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)
thread_title:  Merge [[sticky end/blunt end]]? 

message: 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)
replies: text: 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)
thread_title:  More images 

message: 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)
thread_title:  One genome codes two organisms with restriction enzymes 

message: 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)
thread_title:  Spamming Wikipedia 

message: 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)
replies: text: 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)

text: 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)
replies: text:  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)

text:  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)

text:  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)
thread_title:  List of restriction enzymes? 

message: 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)
replies: text: 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)
replies: text:  Released the draft, all terms now showing by default. Emw2012 (talk) 13:56, 18 September 2009 (UTC)
thread_title: Restriction enzyme glossary

message: 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:
*Added archive https://web.archive.org/web/20080531095339/http://www.rcsb.org/pdb/static.do?p=education_discussion%2Fmolecule_of_the_month%2Fpdb8_1.html to http://www.rcsb.org/pdb/static.do?p=education_discussion%2Fmolecule_of_the_month%2Fpdb8_1.html
*Corrected formatting/usage for http://rebase.neb.com/
When you have finished reviewing my changes, you may follow the instructions on the template below to fix any issues with the URLs.
Cheers.—InternetArchiveBot (Report bug) 17:29, 26 July 2017 (UTC)
thread_title:  External links modified 

message: 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)
thread_title:  Type II image may be labeled incorrectly