Talk:Gel electrophoresis

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Comment
Umm, this is mostly about molecules, not about electrophoresis... -- Marj Tiefert (26 March 2002)


 * as it should be - gel electrophoresis is used almost exclusively to seperte and characterize molecules; the theory is not of much intrinsic interest. — Preceding unsigned comment added by 24.60.137.141 (talk) 2:59, 31 September 2006 (UTC)

BS; theory is of huge interest, see the paper by Viovy in Rev of Modern Physics (I think 2000 or so)Cinnamon colbert (talk) 02:30, 5 April 2011 (UTC)

Gel electrophoresis =/ electrophoresis
This section should be deleted as the electrophoresis article makes all this moot USP cites Gel, Disk, Zone among others. Also, USP Capillary Electrophoresis, as well as Capillary Zone electrophoresis. Perhaps electrophoresis should not redirect here.

Eh, I'm an idiot, although I do still think Gel electrophoresis is still too specific for electrophoresis to redirect here.Ix 01:47, 31 May 2004 (UTC)

Its not very accurate either. Normally electrophoresis of marcomolecules separates based on size and shape, rather than charge, or at least that's the way it is used. You can also separate based upon the isoelectric point. I think it would be worthwhile redoing the article. This probably should be one place that electrophoresis is linked, but surely not the only one. srlasky 22:43, 2004 Oct 24 (UTC) Both are wrong. Electrophoresis and Gel electrophoresis seperate on a combination of NET charge and frictional resistance. The net charge of a molecule depends on the surrounding medium; the frictional resistance is mostly a function of shape - how hard it is for the molecule to flow through the gel. basically velocity = electrical force X net charge - friction. (in some cases, the two scale with size, this is why there is no size dependent seperation of dna without a gel).aditya aditya, thanks for bringing some minimal level of sophistication to this article; those of you who understand, say biased reptation, can talk knowlegeably hereCinnamon colbert (talk) 02:30, 5 April 2011 (UTC)

Electrophoresis redirect?
This section candidate for deletion now that electrophoresis article available Think electrophoresis should be seperate article. Electrophoresis refers to the movement of charge particles in a medium induced by an electric potential, and gel electrophoresis is merely the most commom application, strongly recommend that electrophoresis not redirect to this article. Does not adequately explain concepts such as the role of the zeta potential, sediment potentials, streaming potential, electrophoretic mobility etc, nor does it explain related phenomena such as electroosmosis and other electrokinetic actions. Also does not allow for proper understanding of equations modelling electrophoretic movement for example Smoluchowski equation and O'Brien and White's model.

Strongly believe electrophoresis should be a more general article linking to this page and other applications such as electrophoretic deposition.


 * Someone made electrophoresis a separate article recently, FYI. Nathan J. Yoder 22:52, 15 October 2005 (UTC)

A couple of suggestions
I think the first pragraph should give a hint of the modus operandi of the method, ie say that the separation occurs because of different velocity. I also think it would be more explanatory to say that one of the factors that determine the speed is the charge of the molecule, rather than say that it is the isoelectric point. The isoelectric point is just one of the factors that determine the charge that determines the velocity. The other factor is the pH of the medium in which it moves. The pH is normally determined by the buffer that is added. matrix is a word that is often used for the gel or medium in which the molecules move. But matrix is a word that has many meanings in different contexts. gel should be appropriate, or possibly medium. --Etxrge 13:15, 6 January 2006 (UTC)

"...applying an electric current, the molecules will move through the matrix at different rates, towards the anode if negatively charged or towards the cathode if positively charged (note that gel electrophoresis operates as an electrolytic cell; the anode is positive and the cathode is negative)."

Can this be elaborated on? I thought that electrons always ran from cathode to anode. But it seems like the terminology is reversed for electrophoresis.

Does the negatively charged DNA migrate in the same direction as the electrons?

Anode and Cathode are confusing terms. What is important is that the anode is positively charged [A good source]. The wiki article on cathode can help clear up some of the confusion. anode and cathode are a continual source of confusion; this memonic may help: anions (neg ions) run toward the anode...since DNA is negative, it runs to the cathode, although, ifyou had a pH 1 or so buffer, DNA would run to the cathode (I know depurination starts to kick in around pH 5 or so...)Cinnamon colbert (talk) 02:33, 5 April 2011 (UTC)

Spamming External Links
A lot of people spamming the wikipedia. www.westernblotting.org for example has spammed the following pages:


 * en.wikipedia.org/wiki/Gel_electrophoresis
 * en.wikipedia.org/wiki/Cell_membrane
 * en.wikipedia.org/wiki/Coomassie
 * en.wikipedia.org/wiki/Bradford_protein_assay
 * en.wikipedia.org/wiki/Blot_(biology)
 * en.wikipedia.org/wiki/Fluid_mosaic_model
 * en.wikipedia.org/wiki/Polyacrylamide_gel_electrophoresis
 * en.wikipedia.org/wiki/Slot_blot
 * en.wikipedia.org/wiki/Cell-surface

And many others I got tired of pasting. For a site of a few pages large, there is very little information from this site for users especially a made for adsense site.

Factors
I think we should mention which particle factors influence migration, like electrical charge, shape, and size. 128.230.44.239 (talk) 02:39, 7 March 2008 (UTC)

Scope
The article scope is too limited. It is not _only_ limited to applications of DNA, RNA and protein molecules, eitehr in theory or practice. See e.g. LUDMILLA SHIRSHOVA and RAGNAR ÖSTERBERG; “Electrophoresis of podzol soil humic acids”;  Environment International ;  July–August 1998;  24 (5–6): pp. 625–628. . —DIV (128.250.80.15 (talk) 07:08, 23 October 2008 (UTC))


 * WP:SOFIXIT -- MarcoTolo (talk) 18:35, 23 October 2008 (UTC)
 * agree - there have been several papers recentlhy on sepration of nanoparticles by agarose gels Cinnamon colbert (talk) 04:02, 18 January 2011 (UTC)

Merge with article on Agarose Gel Electrophoresis?
Another article exists on Agarose gel electrophoresis. The content overlaps considerably with this entry. I'm putting out there the suggestion to merge the two articles. 68.194.106.90 (talk) 20:07, 10 August 2010 (UTC)


 * no; the agarose gel electrophoresis article is crappy, full of errors and typos; this article ain't so great, but its at least a startCinnamon colbert (talk) 02:30, 5 April 2011 (UTC)

I was just thinking about a merge myself. While agarose gel electrophoresis could possibly have its own article, most of the content that is actually there pertains to gel electrophoresis in general, and that material should be moved here. The same goes for Denaturing gel electrophoresis, Native gel electrophoresis, and Native PAGE. These five articles should all be merged together. Antony–22 (talk⁄contribs) 00:15, 26 October 2011 (UTC)


 * Yeah all those related pages should be merged into this article with individual sections for them. But the Agarose gel electrophoresis article should be merged into this one, not the other way around, as there are other types of gels used in gel electrophoresis, which don't only use gels made from agarose. The electrophoresis article can be the general info and overview, and can link to this one, which can provide more detailed information on gel electrophoresis. - M0rphzone (talk) 06:40, 26 October 2011 (UTC)

Okay, I've merged the five articles. You can see from the merged article how little material there was in any of these articles that talked about the specific topics they were supposed to. Antony–22 (talk⁄contribs) 17:35, 28 October 2011 (UTC)

Further remarks on article improvement

 * Continued from WT:MCB

I have a couple of comments on the recent changes. The first is that the discussion of TAE and TBE buffers is relevant to both agarose and polyacrylamide, and the article should reflect that. Also, I agree that much of the material in the Visualization section can be moved to the applications subarticles and a shorter summary written here. Be careful not to make the mistake of assuming that nucleic acids are only run in agarose gels; shorter oligonucleotides are better resolved in polyacrylamide gels. Antony–22 (talk⁄contribs) 01:20, 12 June 2013 (UTC)

I think the whole Buffers section needs some cleanup. There are patches of sentences that make it hard to read and understand. — Preceding unsigned comment added by 94.230.83.69 (talk) 21:57, 8 December 2013 (UTC)

Unmerging Agarose Gel Electrophoresis?
I see that there was a discussion on merging of the agarose gel electrophoresis which I think came to the wrong conclusion. If an article is crappy, full of errors and typos, then the article should be corrected and improved, but not merged. An important technique should have its own page, whether there are overlap in information with another important technique is not a valid reason for merging. Agarose gel electrophoresis is an important, regularly used technique in molecular biology, and its use and technique is quite distinct from polyacrylamide gel electrophoresis (PAGE, now usually only used for protein and small DNA fragment). While there should be a general page on gel electrophoresis (as distinct from electrophoresis), there should also be further individual pages on agarose gel electrophoresis and PAGE (this will include the variants on the same technique - native, gradient, etc.). At the moment there is too much in one page to give all the details that might be worth putting in for each individual technique. Hzh (talk) 02:37, 22 June 2013 (UTC)
 * We have discussed this recently (see link in the comment above by Antony) and conclusion was that we should expand this article and then we'll see if it is worth unmerging. I guess it's about time to do it as there is definitely enough information for agarose gel electrophoresis article. We could polish both articles after splitting. --Faskal (talk) 07:58, 22 June 2013 (UTC)
 * I think the issue isn't about whether there is enough information to unmerge it (there is unquestionably enough), but that it is a separate technique that should not have been merged with PAGE. People wanting to know about agarose gel electrophoresis would have to pick out little bits of information scattered all over this article on why you want to use the technique, how to cast a gel, run the gel, stain and visualize the gel. This page is therefore too clunky to use, especially when there are missing information.  There wasn't that much overlap in information anyway, so while it is useful to have a general article on gel electrophoresis, agarose should have a separate article on its own. It is a distinct subject by itself.  You also now the odd situation of having a page on SDD-AGE but none on agarose gel electrophoresis. Hzh (talk) 11:09, 22 June 2013 (UTC)
 * PAGE and agarose gel electrophoresis are nearly identical procedures; the only difference is the material used for the gel matrix and the size of the analytes that each works best for. Other than these they work on the same physical principles and are stained, visualized, and analyzed in the same ways.  The reason the article were merged was not because either article was poorly written; it's because the topics overlap so much that it's hard to see what can be written about agarose electrophoresis that does not also apply to polyacrylamide electrophoresis.
 * There are currently only three paragraphs in this article that are specifically about agarose gels. If this subsection is expanded with enough material specifically about agarose electrophoresis, then a split would be warranted.  However, I think that the more appropriate divide is between procedures for electrophoresis of proteins (which nearly always uses PAGE) and of nucleic acids (which uses both types of gel).  These are actually stained and analyzed in different ways, which is why there are separate articles on those topics. Antony–22 (talk⁄contribs) 23:31, 22 June 2013 (UTC)
 * It is a distinct and important topic by itself, one that many would be interested, which is why it should have its own page. The overlap or lack of content is irrelevant, you can have a three paragraph article, and you can always extend it. The problem now is that you can't extend it because it doesn't have its own page, so you are in fact using a circular argument.  At the moment the article is clunky to use and it is a good enough reason not to merge per Merging.  The vast majority of people doing agarose gel electrophoresis don't use PAGE for DNA, so whether there is some overlap with PAGE is completely irrelevant to them.  Wikipedia is about being useful, at the moment it is not useful for its users. The fact that there are individual pages on SDD-AGE and pulsed field gel electrophoresis showed how odd the situation is.  The whole thing no longer makes sense. The structure should be -
 * Gel electrophoresis
 * Agarose gel electrophoresis
 * SDD-AGE
 * Pulse field gel electrophoresis


 * That is, SDD-AGE and Pulse field gel electrophoresis should not exist without an agarose gel electrophoresis page, they would have been merged into it. There is an argument for pulse field gel electrophoresis as a separate page because it uses a special technique, but there is none for SDD-AGE without a page for agarose gel electrophoresis first (it is a minor variation and would have been part of the content for agarose gel electrophoresis, but please don't use it as an argument to merge that article, I am merely using it to illustrate the illogicality of the present situation).  I would stress that it is a good thing to have a general page on gel electrophoresis, one that can give an overview on the subject, the different methods available, and give a discussion on when why different methods are chosen.  Agarose gel electrophoresis however is important subject by itself that should not be merged into another.  Hzh (talk) 04:04, 23 June 2013 (UTC)


 * BTW, I'm considering adding something about EEO of agarose gel, also maybe on the migration of DNA bands vs concentration of gel. If someone can make a figure by running DNA markers in 0.5%, 1%, and 2% gel, that would be great.  This would be on the page for agarose gel electrophoresis since adding it here would made it too much of a jumble of facts. This page I think can stay as it is without modification, but a separate page on agarose gel electrophoresis would be more useful for content specific to it. Hzh (talk) 12:21, 23 June 2013 (UTC)

I see what you mean about having all these short finely-defined articles on different methods. But I think the following hierarchy would be just as meaningful as yours: You see the problem: there are many ways we can divide up this topic. As I said, I think that the protein/nucleic acid divide is the most useful one to have as our top-level division, because they use quite different methodologies and are analyzed in somewhat different ways. My feeling is that someone working with DNA would probably be interested in both agarose and polyacrylamide methods, while they would be unlikely to care about protein methods. So it would make less sense to put the agarose methods for the two analytes in the same article rather than keeping the DNA parts together.
 * Gel electrophoresis
 * Gel electrophoresis of proteins
 * SDD-AGE
 * Gel electrophoresis of nucleic acids
 * Pulse field gel electrophoresis

What specifically would you intend to be the content of agarose gel electrophoresis article? Would you mainly be merging in other articles, or would you be mainly writing new material? Antony–22 (talk⁄contribs) 18:03, 23 June 2013 (UTC)


 * Of course someone working with DNA may be interested in both agarose and polyacrylamide method, that isn't the point. My point is that someone interested in agarose gel electrophoresis would be interested in that subject, and this page is too clunky for use for that purpose.  I'm also not sure why you should be concerned about an article being short, short articles abound in wikipedia, it is not an issue.  In any case any article on agarose gel electrophoresis would not be short, the page on SDS-PAGE isn't short, people have a lot of time expanding it, and there is no reason why agarose gel electrophoresis couldn't also be expanded.  I would be interested in your rationale for not merging SDS-PAGE article here because it covers exactly the same scope as this page. It's puzzling to me because I have no idea why an article on agarose gel electrophoresis got merged but not SDS-PAGE.  It makes absolutely no sense. To me both agarose gel electrophoresis and SDS-PAGE are both important techniques, which is why they should have both their own article.


 * I would likely to be starting from the original article on agarose gel electrophoresis, adding some content and deleting some. Someone with the time to make some figures can also use the SDS-PAGE article as an example on how it can be expanded. Hzh (talk) 19:31, 23 June 2013 (UTC)


 * I didn't really have a logical reason for not merging the SDS-PAGE article. Mostly, it's written in a practical how-to style that's somewhat discouraged on Wikipedia, but it is fairly well written and quite long, so I didn't want to deal with figuring out how to break it up.
 * After thinking about it, I suppose there's room for separate agarose and polyacrylamide articles that focus on methodology, while other articles focus on physical principles and analysis. I've already moved all the material from the old article to the appropriate place, and as you can see there were only three paragraphs worth that were specifically about agarose electrophoresis; everything else was redundant with polyacrylamide electrophoresis.  So I'd recommend starting essentially from scratch, and avoiding topics that are common between all types of gel electrophoresis.  It looks like the SDS-PAGE article can be easily recast to talk about PAGE in general, since the methodologies are identical except for the inclusion of SDS itself. Antony–22 (talk⁄contribs) 05:51, 24 June 2013 (UTC)


 * I think there should be separate articles agarose gel electrophoresis and SDS-PAGE. First thing that student of molecular biology usually sees is agarose gel stained by EtBr. For general public and popularization of science "gel electroporesis" is usually the agarose gel electrophoresis. While there has to be an article that describes different variants of this method, the most common variant should have its own article.


 * I would not suggest to "merge" articles but to simply cut&paste 1/3 of the content of this article to a new one. I've said it multiple times - this article is about agarose gel electrophoresis and SDS-PAGE, not about gel electrophoresis in general. Just look at the "buffers" section - it's description of the most common buffers for agarose gel electrophoresis system. What should be there is, say... why it is necessary to use buffers, something about conductivity, when use one buffer system and when discontinuous one... Currently it is such a mess that deletion of some content (... or unmerging...) would actually improve the article.


 * How can you know there couldn't be good article about agarose gel electrophoresis when there is no article about it at all? --Faskal (talk) 16:05, 24 June 2013 (UTC)


 * I think this article can stay largely as it is, it just needs some additional information to make it a general introduction to gel electrophoresis (for example, a few more sentences about 2D-electrophoresis, pulse-field gel electrophoresis, and others), and trimming parts of it. For the buffers section, it would be better to give a general description of what the buffer does, and why they are chosen for the different systems, then some common examples.  Even the buffer section on SDS-PAGE article needs improving, for example there is no mention of commonly-used Tris-tricine buffer system.  The theoretical side can be expanded here (sieving and reptation), and an article on agarose gel electrophoresis can then refer back to this article on the theory behind gel electrophoresis so that it doesn't need to concentrate on it, but can mention others specific to agarose gel like the EEO (unless I'm mistaken, I don't think EEO is important for PAGE). This way different articles can be useful for different things. Hzh (talk) 18:11, 24 June 2013 (UTC)
 * Suggestions for agarose gel electrophoresis/agarose: analysis of DNA topology, Comet assay, history (PMID:16511967), low-melting agarose&DNA isolation, TAE/TBE/TPE, immobilization of microorganisms, chondrocyte/agarose, analysis of proteins/mucopolysaccharides/..., and other topics. I'll be without internet for two weeks so please save something for me. --Faskal (talk) 16:17, 25 June 2013 (UTC)
 * I don't think I can write too much on it, but I'll just give some of the basics and you can be expanded it later. I'll probably start in a few days' time, unless someone else wants to give it ago before that.  Hzh (talk) 20:15, 25 June 2013 (UTC)

On a separate issue, I'm wondering is if gel electrophoresis of nucleic acids should be changed to electrophoresis of nucleic acids? I don't know much about capillary electrophoresis, but I gather that it may use gel as well as other polymers as sieving matrix, so perhaps using a broader term can give a broader view of electrophoresis of nucleic acids. Hzh (talk) 21:59, 25 June 2013 (UTC)


 * I like Hzh's plan: a methodology-focused article similar in scope to SDS-PAGE would be appropriate. I'm happy to make the relatively minor changes to turn the SDS-PAGE articl into one about PAGE in general.  I think capillary electrophoresis is different enough from gel electrophoresis in its physical principles and analysis that it would be awkward to put both in the same article.  Antony–22 (talk⁄contribs) 02:16, 26 June 2013 (UTC)

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