Crowdsourced science: HOWTO do agarose gel electrophoresis using nothing but a drinking straw, a 9V battery and a pair of alligator clips

Discuss

40 Responses to “Crowdsourced science: HOWTO do agarose gel electrophoresis using nothing but a drinking straw, a 9V battery and a pair of alligator clips”

  1. Bugs says:

    BBBOY “And no, you can’t run the ladder with the sample.”
    Why not? I’ve never tried this so I’m not going to contradict you, but what’s your reasoning here? If the expected size of your DNA fragment is different from all of your ladder fragments, surely you can just look for the extra band in the lane?

    I’m intrigued now, I might give this a try later in the week…

    @Maryr
    “And while a thermocycler (that fancy hot plate) is going to be expensive, it should be somewhere in the $3-5K range, new.”
    I had the impression that a lot of that price is the licence fee to Roche.* It can’t be that hard to make a good-enough machine for a home setup.

    For non-biologists: a thermal cycler is, as said above, basically a controllable hotplate. You stick a tube in it, then run a programme like this one:

    Heat to 95 degrees c (hold there for 2 min)
    __Do 30 times:
    _____Heat to 95 (30 sec)
    _____Cool to 61 (30 sec)
    _____Heat to 70 (30 sec)
    __End do
    Heat to 70 (10 min)
    [optional: cool to 4deg until the scientist comes along to move the tube into the fridge]

    I’m not much of a techie, but I’d bet the folks at Make or Instructables could knock one up for a couple of £hundred, probably less. I’m picturing a system where each tube is wrapped in a heating coil. There’s a spare tube with a temperature probe mounted inside, and a fan. All of this is hooked up to a tiny computer (arduino?). I wouldn’t want to diagnose patients with it, but for amplifying most DNA fragments — where the occasional failure doesn’t matter — it’d probably be ok.

    *Here’s a good one for the anti-copyright/patent people. Roche own the IP rights (a patent, I assume?) for the Polymerase Chain Reaction (PCR), a reaction used to very efficiently make many more copies of a given length of DNA. Without it molecular biology is effectively impossible. Every time we buy a thermal cycler (machine designed to run the reaction) or the necessary enzyme, a chunk of the price is actually a licence fee to Roche, paying for the right to use “their” technique.

  2. Bugs says:

    Interesting New Scientist article about amateur biology: Rise of the Garage Genome Hackers.

    (sorry to double post, but this is cool).

  3. Viadd says:

    #17 Maryr,

    What is so difficult about garage PCR? Building a thermocycler seems like a simple job for an electronics hobbyist, unless there are some specific issues that don’t get discussed often. (Do you need better than 0.1 C accuracy in temperature or specific heating/cooling rates? Do you need perfect isothermality over a broad area if you aren’t trying to do 96 samples at a time?)

    If all it takes is moving test tubes between three water baths for three hours, then you can do it with LEGO Mindstorms. (I would do it with electrical heating/cooling and a microcontroller rather than the LEGO and water baths, but that’s because of my specific skillset and mechanical ineptitude.)

  4. Marisa says:

    I don’t get why you’d want to be able to do this in the ‘garage’. The reason this is so useful is because it lets you do so many other analysis. Are there garages with all the equipment for further analysis but this?

  5. zuzu says:

    There aren’t enough words to describe how awesome Meredith L. Patterson is.

    Previously:
    * DIY biohackers in the news
    * CodeCon 2005: SciTools

  6. GuidoDavid says:

    AFAIK the patent for PCR expired not long ago.
    And yes, Thermal Cyclers are way too expensive, that is one of the main causes of PCR not being more available, but some new technologies will change that rather soon.

  7. Takuan says:

    sure there are! awesome awesomeawseome,awesome awseome awesomeAWESOMEawesomeawe-some! So awesome I forgive her for making me look pathetic.

  8. mlp says:

    @Marisa: One step at a time. :) First we had DNA extraction in a shot glass, now electrophoresis in a drinking straw. This opens the door to other low-cost techniques — sequencing, Southern blots, PCR, you name it — it’s a homebrew tool for building even more homebrew tools.

  9. mikefinch says:

    So – First you need to separate the DNA from the cells – doable but not a simple process. Then you need to build yourself a 70$ at home “molecular separator” – then you must determine wtf to do with the stuff.

    I applaud the ingenuity and creativity espoused by making laboratory equipment – however, as DIY projects go, this one seems like building a keyboard for a computer you dont have.

    If more than ten people on earth have practical garage based applications for this “separator” i will eat my hat.

    But hey – its your blog right? Although – if generally useless stuff is going to be your game you know what would be really cool to learn how to do? MAKE PANCAKES IN A ZERO G VACUUM ENVIRONMENT!!!!

  10. zuzu says:

    agarose gel electrophoresis is simply the name of the freakin’ protocol. each word means something specific — why are you guys against learning new terminology?

    Just wait until they get to the acronyms and initialisms, such as SDS-PAGE, ELISA, and HPLC.

  11. BBBoy says:

    Bugs – You run into the same problem with comparison. A standard DNA ladder has a lot of bands. And when you get into the smaller size regions especially, the bands get very close together. So unless you already know your sample is pretty pure and of a size that will be easily discernible from the standard ladder rungs, it’s not a good idea. If your sample is not pure, you’ll get more than one band, which compounds the problem. I’ve just never seen anyone do it and I’m guessing that’s the reason why.

  12. Anonymous says:

    In Theory this is all nice and cute,

    but in actual execution, the amount of steps required to actually get meaningful results is just not worth the effort.

    Visualization of results requires a UV lamp, and visualization chemicals, which are relatively easy to come by, but the less you spend, the more dangerous they are likely to be. if you really need this stuff done, you can send it to labs to be done for you, at relatively cheap prices.

    protein gels dont work well in agarose, and need to be run in Polyacrylamide gels, which are made from toxic acrylamide, and immunoblots require antibodies, which are 300 bucks a pop.

    CVS sells DNA comparison kits (paternity tests) for 300 dollars, where they will analyze the 2 sets of dna, and send you as much data as you request about that dna.

    don’t get me wrong, i think the idea is awsome, i just think it wont get much farther for the price range most DIY scientists like.

  13. Bugs says:

    One of the big secrets of molecular biology is that a lot of it isn’t actually all that difficult to do. Some of the reagents and equipment can be expensive but, as this shows, can often be worked around by making them yourself. A setup for doing some basic genetic modification – modifying plasmids and getting them expressed in bacterial cells* – could easily be set up in someone’s garage. Much less expensive than all the CNC milling or laser cutting machines they’re always talking about on Make.

    I suppose you could call it a drinking-straw molecule separator in the headline, but agarose gel electrophoresis has a clear and specific meaning that any biologist would recognise. After all, it’s a gel made of agarose (as opposed to e.g. acrylamide) that’s used for electrophoresis. The folks in that thread obviously know what they’re talking about, so it makes sense that they’d use the proper term.

    *For non-biologists: a plasmid is a circular piece of DNA that encodes one or more genes (typically antibiotic resistance + whatever protein you’re interested in expressing) and its own “origin of replication”. They’re separate from a cell’s genome, but can still use the cell’s machinery to express the encoded gene(s) and get themselves copied when the cell divides. Bacteria tend to swap plasmids a lot (“horizontal gene transfer”), which is how e.g. antibiotic resistance can spread so rapidly through a dispirate population of bacteria: it’s spreading between peers, not just from parent -> child.

  14. Dangerpants says:

    I wonder how useful drinking straw electrophoresis could be without access to cell dye?

    @MLP: here’s a crazy thought: all you really need for PCR (aside from like, a whole bunch of spare DNA scraps) is an accurate and timer-controlled heating element.

    I interned in a bio research lab a few summers ago and one of the first things the told me was “this is the PCR setup. It’s basically a hotplate with test-tube slots that costs more than both of your parents’ cars combined.”

  15. zuzu says:

    don’t get me wrong, i think the idea is awsome, i just think it wont get much farther for the price range most DIY scientists like.

    Agreed, yet, do you remember the prices for parts used by those in the Homebrew Computer Club? They were similarly “prosumer” aka “expensive hobby”, but laid the foundation for ever greater degrees of “democratizing innovation“.

    c.f. Planning the Software Industrial Revolution by Brad Cox.

    Meanwhile, well-heeled biotech research and commercialization are using the equivalent of IBM mainframes — big, expensive, and proprietary. More versatile and less expensive alternatives created in cooperation with the DIY community will provide network effect benefits — lowering the cost of research and consequently products such as biologics.

    c.f. The history of amateur radio and decommissioned commercial / business radios becoming affordable on the used market and repurposed for amateur use.

  16. Anonymous says:

    Hi everyone,

    I put together a more detailed writeup of the experiment on OpenWetWare:

    http://openwetware.org/wiki/DIYbio:Notebook/Keiki_Gels

    Let me know if you try it out!

    Tito

  17. mlp says:

    @Dangerpants: Two words, “methylene blue.” Available at any pet store that sells fish supplies. Or, for folks with a few bucks to spare, SYBR Safe or GR Safe. (Ethidium bromide’s nasty stuff anyway.)

    And yeah, I want to get my hands on a Peltier device and introduce it to my Arduino.

  18. neurolux says:

    Cool idea, but what good is DNA electrophoresis without restriction enzymes?

  19. Kieran O'Neill says:

    #10: mikefinch: Back in my Biochem department, they used to do demos at science shows where they carried out a complete mini-prep DNA extraction using only household chemicals (alcohol, washing detergent). DNA extraction really is pretty straightforward.

    And yeah, what Bugs said about the name. It is necessarily complex terminology. (Of course, in casual conversation, most biologists would just talk about “a gel”.)

    Also what Bugs said about doing home (plasmid) cloning experiments. It’s do-able, and some people may want to play with this. (Though I’m wondering if there’s a non-carcinogenic/teratogenic dye for DNA. Ethidium bromide is not something which I think most people can get easy access to, for good reasons.)

    For the uninformed: What you would use an agarose gel for usually would be crude detection of strands of DNA of different lengths. (e.g. to check whether your modified plasmid really did get taken up by the bacteria you tried to clone it into). However, in order to see the DNA in the gel, you need to stain it. Ethydium bromide is a common stain, which glows under UV when bound to DNA. However, it is highly carcinogenic.

    Lastly, IIRC, the reason you use agarose and not agar (which is a mixture of agarose and some other polymers) is that the other polymers tend to be charged, which somewhat screws up DNA separation (which is itself charge-based). OTOH, I doubt that gel-grade agarose is enormously expensive.

  20. BBBoy says:

    I feel compelled to express my dismay with this supposedly DIY agarose gel electrophoresis setup. The whole point of conducting a scientific experiment is to make it reproducible, accurate, and precise. Perhaps the most obviously problem is that you have no ladder (a standard). There’s no way you’ll know what size your bands of DNA are. Run two at the same time? I don’t think so, because the two “gels” are different. You would never run a sample on one gel and compare it to a ladder run on another even with the most precise of setups. Furthermore, the grocery-store grade “agar” you used won’t solidify as nicely as the industrial-grade powder real scientists buy, leading to places of higher and lower density. And no, you can’t run the ladder with the sample. In regards to plasmids, you can’t just buy a plasmid. You have to construct one. That requires precise agarose gels in the first place so you can identify and isolate the pieces of DNA you’d like to insert into your construct. Basically, I don’t think this really counts as a DIY agarose gel electrophoresis. It’s more like, “use an electric current to separate molecules with my mom’s Agar-Agar as medium and the straw I took from the juice box as a casing.”

  21. Anonymous says:

    “First we had DNA extraction in a shot glass, now electrophoresis in a drinking straw. This opens the door to other low-cost techniques — sequencing, Southern blots, PCR, you name it — it’s a homebrew tool for building even more homebrew tools.”

    This is appallingly ignorant. Really, it’s embarrassing. I’m embarrassed for you. So far, you’ve taken simple, elementary molecular biology techniques and made them difficult, dirty, and imprecise. And you think you’re going to jump right into sequencing?

    It’s really idiotic that boingboing is breathlessly reporting everything she does, even though she doesn’t have any results at all.

  22. AirPillo says:

    I’ve done agarose gel electrophoresis and I wasn’t under the impression that it was all that difficult or in need of much simplification.

    All you bloody well need is a container, agarose, and a DC power source. It’s hardly that much more complicated than this when demonstrated in a biology lab.

  23. maryr says:

    A few notes:

    This is going to sound needlessly condescending, but… separating a dye mix to its individual dyes is not all that impressive. I can do that in my garage as well – it’s called a coffee filter. And that’s easier to extract your sample from – assuming you have access to a centrifuge. How do the DIY folk do all this without a centrifuge? Is there some sort of blender rig?

    That said, you can buy a lot of equipment for mol bio for not too much money on eBay. I work for a biotech and that’s what we do.

    #9: Homebrew gel electrophoresis is a looong way from inexpensive garage PCR. Whlie PCR can be done without a thermocycler, I don’t see a lot of people spending their free time moving tubes between three water baths for 3 hours.

    #12: You mean DNA dye – cell dye is easy. Things that stick to DNA will be expensive or toxic – as noted in #13 and 14. And while a thermocycler (that fancy hot plate) is going to be expensive, it should be somewhere in the $3-5K range, new. I think. Google keeps trying to sell me one for $999, but I can’t believe that one would be any good.

    #14: Gel grade agarose isn’t terrible in the realm of mol bio costs, but it is pricier than you’d think. A quick internet check indicates about between $0.80-2.00 per gram, depending on how much you buy (more is less).

    #15: Yeah, you pretty much nailed what I was going to say. A gel without a ladder is next to useless. Heh, the article says “electrophoresis using large rectangular gels has some drawbacks. It’s a bit messy, and in order to recover the particular band of DNA you want, you have to slice it out of the gel with a razor blade or something similar”. Oh no, not a razor blade! That’s dangerous equipment! Can you imagine the mess you’d make with scissors and a straw? Ugh…

  24. misshallelujah says:

    How about the visualization? In my experience, gel electrophoresis is the easiest part of any experiment. The visualization part… not so much. Particularly since it usually involves the use of techniques that tend to mess up your DNA otherwise (carcinogenic dyes + UV light)…

  25. WA says:

    I wrote something here agreeing with those who noted that this isn’t really useful as anything but a gimmick, due to its lack of repeatability and inherent limitation to a single lane. However, I then read the protocol there…

    which convinced me that this is even more of an exercise in pointlessness than I had expected. It essentially requires almost everything that one would need for a traditional agarose gel, except for the comb and something to form the gel (plastic/tape/almost anything). Certainly, these gels are smaller, but I’ve run traditional rectangular agarose gels that are smaller still. And as an added bonus, those gels are actually cheaper to run than these, since they don’t require a straw, and can run multiple lanes in less agarose than a single straw gel! Of course, to get accurate results, you’ll need to use electrodes that actually work evenly, and aren’t just floating in the buffer, but that’s yet another problem with this protocol.

    It would be interesting to see someone try an acrylamide gel with this, but considering how many people doing this seem extremely inexperienced, I’d be quite concerned for their safety.

    As for thermocyclers, they are overpriced, yes. Decent modern used thermocyclers can be purchased for less than $2k, however, and older ones can be acquired for free, if one is willing to deal with their problems. Depending on the techniques one is using, a cheap constructed system might be possible. However, one must keep in mind how much one’s own time is worth in such things, especially since unreliable equipment can be a horrible problem.

    In my opinion, the best way to build up a bio lab is to look at equipment being auctioned off or given away, instead of trying to improvise things like these. The equipment is usually better, more powerful, and cheaper.

  26. GuidoDavid says:

    Misshallelujah:

    You can use Methylene Blue for visualization, is a bit less sensitive than Ehtydium Bromide, but it works.

  27. stuckinkiel says:

    @13,33,36,37 and anyone else who is interested in visualization: It is possible to visualize DNA bands with a UV lamp alone, using a simple trick. I used to do this by placing my gels on a piece of UV reflective paper (filter paper for Southern blots, if you want to know). Shining a UV light on the gel will generate a shadow under the DNA band. Of course, to use this method there has to be enough DNA to cast a shadow, which might be a drawback if you are looking for small amounts.

    Also, for separating enzymes I used to use gels made of corn starch instead of polyacrylamide. For those who may not know, acrylamide is a very toxic until it is congealed into it’s gel form.

  28. GuidoDavid says:

    Takuan:
    Yes, I am on that mailing list. It is fun and gives me hopes, plus I am working in another project that would support the community. You can contact me for details.

    PCR and other techniques will be improved and updated for and by the DIY crowd. There are some start ups dealing with this. They are building the basic blocks of this as I write these lines, think of this age for biology pretty much as the age in which the computers started being something else than mainframes. Eventually the PC arrived and hackers had a full set of tools easier to use than the clumsy languages from yore or the assembler.

  29. mdh says:

    BBBoy – what you say is true, however your tone is off as that is exactly what they purport it to be.

    And it ain’t bad at all for 3 days effort.

  30. AAltair says:

    “HOWTO do agarose gel electrophoresis using nothing but a drinking straw, a 9V battery and a pair of alligator clips” …. and some Agar gel…

  31. Takuan says:

    Guido David? you reading this?

  32. Fee says:

    I was prepared to accept that I didn’t have a clue what agarose gel electrophoresis is, without visiting the original story to find out.

    The fact that they have adopted another jargon term “keiki gels” as the “quick” name for this DIY replacement for agarose gel electrophoresis is rather distressing: it just adds to the number of things someone outside the club has to look up. While keiki may be a well-known term for small in your neck of the woods, it certainly isn’t in mine. Hang on a moment, “small gel” doesn’t seem to tell you what it is any more efficiently or descriptively than agarose gel electropheresis!

    Wouldn’t it have been possible to use a descriptive quick name like “drinking straw molecule separator”, which actually explains what it does in the name?

  33. Takuan says:

    does the American government throw people into prison for exporting used bio lab gear? Any more anyway?

  34. Anonymous says:

    oddly enough, the first I heard that anything came out of this was through boingboing. here is the original idea if anyone is interested:
    http://groups.google.com/group/diybio/browse_thread/thread/4bb35278daf9fd17/03a955483651a05c?#03a955483651a05c

    aaltair, you can get agar-agar (which is just a less purified form of agarose) at most asian grocery stores.

    I prefer “drinking straw molecule separator” as well.

    -fenn

  35. Daemon says:

    Next unfounded bio-terror panic caused by uni kid doing homework or artist in 3… 2… 1…

  36. Anonymous says:

    oh, geez.

    agarose gel electrophoresis is simply the name of the freakin’ protocol. each word means something specific — why are you guys against learning new terminology?

    “drinking straw molecule separator” doesn’t tell me hardly anything. it’s like saying “i’m having plated flour sugar tubes for breakfast!”

  37. Ian70 says:

    That, some blue dye and some chemical detergent and you could have your own home paternity test kit.

    Ossom!

  38. David Carroll says:

    Fee@#3

    So I am at the water cooler and I mention to my boss that I read an article on a “drinking straw molecule separator”… or I casually mention that I read up on “agarose gel electrophoresis using keiki gels” last night..

    Which one do you think will get me closer to moving into a corner office? ;{)

    But seriously: I am all for “plain language” text in contracts, government forms and journalism, but sometimes I like to use big, obscure, fun to pronounce words. I suspect Cory does too.

  39. Fee says:

    Depends on your aim. If you want people to understand what you are talking about and respond to what you are saying, plain words work better.

    I don’t think you ever benefit by using big words, unless it is clear that your audience understand them and they are the most apposite for the contingency. If people understand them, you have gained no kudos, they are on your level already. If they don’t understand them, they may well resent you rather than admiring your vocabulary or scientific knowledge.

    I’d argue you have as much to lose as to gain by showing off to the boss. Many avoid promoting anyone who may be cleverer than they are and thus threaten their position.

  40. fenn says:

    oddly enough(?) the first I heard that anything had come out of this was through boingboing. if anyone is interested, the original idea which was a bit more complicated, is here:
    http://groups.google.com/group/diybio/browse_thread/thread/4bb35278daf9fd17/03a955483651a05c?#03a955483651a05c

    aaltair, most asian grocery stores sell agar-agar, which is just an unpurified form of agarose.

    i’m all for “drinking straw molecule separator”

Leave a Reply