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Drinking straw electrophoresis!
Gel electrophoresis is one of the most versatile, widely used tools in a microbiologist's or geneticist's toolbox. It's used for separating out DNA, RNA or protein molecules (that you presumably isolated in a previous step of your experiment) based on their molecular weight, so that you can analyze the molecules, clone them, amplify them with PCR, sequence them, lots of different things.
Electrophoresis does require some equipment to perform -- an inner tray which holds the gel, an outer tray which holds a "running buffer" solution (which keeps things cool and keeps pH stable), electrodes, and a power supply (50V-150V is pretty common). You can buy a gel box from a commercial supplier, though they're not cheap, and a fancy power supply will set you back even more; Bio-Rad has some nice ones, but they run to the thousands of dollars.
Happily, there are solutions for the biohacker on a budget. The University of Utah's genetics department has full specs for how to build your own gel box for about $25 in parts (not counting the power supply, which will run you about $50). The main components are clear acrylic and acrylic cement, which I purchased and had cut to size at TAP Plastics -- they also do mail order. My partner-in-science Tito Jankowski built one too, and did some test runs with food colouring which enabled him to separate the individual dyes which make up different colours. (The molecules in food colouring are pretty small, which is why the bands in Tito's video are a little smeary. He used agarose -- an edible, seaweed-derived polymer which you can find on the shelf in any Asian grocery store, also sold as "vegan gelatin" -- as his gel, and agarose is better suited to larger molecules like DNA. But it's definitely a proof of concept!)
Still, 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. Cleaning up the equipment is also a bit of a pain. If you're using acrylamide or polyacrylamide (common for protein electrophoresis), you need to find a safe way to get the used gel out of the gel carrier and dispose of it properly. Also, while DNA electrophoresis is run horizontally, protein electrophoresis is done vertically, so that means two different pieces of equipment.
This was a recent topic of discussion on the DIYbio mailing list. Ben Lipkowitz wondered whether it would be possible to use a narrow, rigid tube to contain the gel, rather than a big carrier. This would allow for the use of less buffer and lower voltage, since a physically smaller amount of gel is a smaller resistor.
Well, what's a narrow rigid tube that's easy for anyone to acquire? A clear drinking straw! Paper clips make for appropriately sized electrodes, and since a drinking straw is rigid, it can be used in either the horizontal or the vertical orientation. For extra bonus points, when you're ready to cut a band out of the gel, no need for mucking around with razor blades -- just take a (sterile) pair of scissors, snip snip, and you're done! Plus, disposal is extra simple, even with polyacrylamide -- just dispose of the entire straw, gel and all, properly.
Tito Jankowski tried this out, using a single 9V battery as a power supply, and after some debugging, it worked beautifully. (He also used alligator clips as electrodes, and they worked just fine.) We're calling these "keiki gels" because they're so small and cute -- and so simple, even a little kid can do them.
This is crowdsourced science at its very finest. Behold the power of collaboration!
ETA: Tito wrote a protocol, doo dah, doo dah
Electrophoresis does require some equipment to perform -- an inner tray which holds the gel, an outer tray which holds a "running buffer" solution (which keeps things cool and keeps pH stable), electrodes, and a power supply (50V-150V is pretty common). You can buy a gel box from a commercial supplier, though they're not cheap, and a fancy power supply will set you back even more; Bio-Rad has some nice ones, but they run to the thousands of dollars.
Happily, there are solutions for the biohacker on a budget. The University of Utah's genetics department has full specs for how to build your own gel box for about $25 in parts (not counting the power supply, which will run you about $50). The main components are clear acrylic and acrylic cement, which I purchased and had cut to size at TAP Plastics -- they also do mail order. My partner-in-science Tito Jankowski built one too, and did some test runs with food colouring which enabled him to separate the individual dyes which make up different colours. (The molecules in food colouring are pretty small, which is why the bands in Tito's video are a little smeary. He used agarose -- an edible, seaweed-derived polymer which you can find on the shelf in any Asian grocery store, also sold as "vegan gelatin" -- as his gel, and agarose is better suited to larger molecules like DNA. But it's definitely a proof of concept!)
Still, 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. Cleaning up the equipment is also a bit of a pain. If you're using acrylamide or polyacrylamide (common for protein electrophoresis), you need to find a safe way to get the used gel out of the gel carrier and dispose of it properly. Also, while DNA electrophoresis is run horizontally, protein electrophoresis is done vertically, so that means two different pieces of equipment.
This was a recent topic of discussion on the DIYbio mailing list. Ben Lipkowitz wondered whether it would be possible to use a narrow, rigid tube to contain the gel, rather than a big carrier. This would allow for the use of less buffer and lower voltage, since a physically smaller amount of gel is a smaller resistor.
Well, what's a narrow rigid tube that's easy for anyone to acquire? A clear drinking straw! Paper clips make for appropriately sized electrodes, and since a drinking straw is rigid, it can be used in either the horizontal or the vertical orientation. For extra bonus points, when you're ready to cut a band out of the gel, no need for mucking around with razor blades -- just take a (sterile) pair of scissors, snip snip, and you're done! Plus, disposal is extra simple, even with polyacrylamide -- just dispose of the entire straw, gel and all, properly.
Tito Jankowski tried this out, using a single 9V battery as a power supply, and after some debugging, it worked beautifully. (He also used alligator clips as electrodes, and they worked just fine.) We're calling these "keiki gels" because they're so small and cute -- and so simple, even a little kid can do them.
This is crowdsourced science at its very finest. Behold the power of collaboration!
ETA: Tito wrote a protocol, doo dah, doo dah
Drinking straw electrophoresis!
(Anonymous) 2009-02-08 07:43 am (UTC)(link)1. You can remove agarose from the straw. Agarose should be relatively concentrated (>1% for most types). Then use a syringe with a blunt needle and push water around the wall. Agarose tube will slide out. This takes some practice.
2. There are multiple reasons for slab gel, as oposed to tube. Primary ones are: a) ability to compare samples when run on parallel tracks in the slab; b) easy preparation/analysis.
3. Polyacrylamide gels are hard to make in an open atmosphere (not between 2 pieces of glass)-oxygen in the air inhibits polimerization.
4. DNA fingerprinting and gel electrophoresis are not the same. The latter is a method of separation of molecules by charge, and not in intself "fingerprinting".
5. No, one cannot substitute a $1000 piece of equipment with a $50 worth of parts. While DIY is a perfect way to get to proof of concept or to play with it, $1000 equipment costs this much because it provides precision, reliability and reproducibility not achievable with $50. BTW, commercial power supply that will do what you are describing will cost ~$200, not $1000. The gel box as described was and still is used in many labs with the exception of the wire used to provide current to the solution. In mol.bio. labs people use platinum wire.
Re: Drinking straw electrophoresis!
Re your #2, what do you think about my comment to
I did not know about #3, that's good to know. (Haven't done any wet lab protein work yet.) Do you know if they'll set up properly in, say, a CO2 atmosphere?
FWIW, the folks working on the Open Gel Box 2.0 (details available on openwetware.org) have sourced platinum wire at reasonable expense for just that reason.
Re: Drinking straw electrophoresis!
(Anonymous) 2009-02-09 05:24 am (UTC)(link)About your comment for #2: the general idea is correct. The voltage and time should be the same for all samples. In reality, other parameters should be the same too, e.g. temperature. If you run the gel "hot", often the front of the dye will not be straight, but curved with faster zone in the middle. This is due to heating up of the gel and greater heat exchange closer to the border (end) of the gel. Actually, in the case of PAGE gels, sometimes you can see DNA melting due to this.
The PAGE gel should polymerize in CO2, but why bother? Besides, regular CO2 atmosphere commonly found in tissue culture labs is actually just 5% CO2 in air. If you are going through the effort of setting up O2-free atmosphere, use nitrogen or argon. But then again, why bother?
For home use, metals other than platinum should be fine. I would imaging that silver or gold can do the trick. Expense will be much smaller, especially if one coats say copper wire with silver or gold. Silver nitrate used to be sold in pharmacies, not sure if one still can buy it.
Re: Drinking straw electrophoresis!
(Anonymous) 2009-02-09 05:19 am (UTC)(link)re1. Depending upon the diameter of the straw a wire stripper works well to cut the straw from around the gel.
re 2. I completely agree with the slab gel comments. Slab gels are much better. we tried these straw gels (our lab referred to them as "macro-capillaries") in the early 90's and although I still occasionally use them for prep work, the results always seemed to be smeary, which we guessed was due to charge distribution. Besides, you can make perfectly acceptable slab gels with microscope slides(or any other flat piece of glass - thicker is better), 1" lab tape, two bulldog clips and a piece of carved delrin or similar plastic for the comb. If memory serves correctly this was eventually published in the early maniatis molecular cloning book. Because we didn't have a lot of grant money in the early days - 1980ish, we used these mini slab gels for at least five years and got publishable results. the mini slab gels are especially good because you use very little agarose which in those days was pretty expensive (still not all that cheap).I still use them sometimes even though we have grant money. Also with a model train transformer and a multimeter you can most definitely have a cheap electrophoresis setup, just keep an eye on the current every once in a while, as that tends to shift when the buffer ph changes during the run.
re 5. I can't disagree more. Due to experience introducing high school students to molecular biology, I have made many a gel box from tupperware boxes, a little "shoogoo" which I'm guessing is a type of silicon cement (I'm too cheap to buy new tennis shoes when all I've worn out is the sole, so I usually have that lying around) and NICKEL wire - not platinum! nickel works fine. (of course platinum is optimal, but not everyone needs to drive a lexus.) also a couple alligator clips, you don't even have to use the build-it-yourself utah site which to me seems to be a whole lot of work for very little increase in function. If you can find some cheap nickel wire (or share a spool) you can build a box for under $5. Steal two bulldog clips from your office. I'm not sure why I'd need high "precision" or reproduceablilty if I have a ladder for size comparison on a slab gel or if I'm just running a prep gel which is about 99% of what people use electrophoresis for. Unless you are doing some sort of specialized electrophoresis like pulsed gel, or higher voltage for polyacrylamide gels, there is no reason to spend $1000 on electrophoresis setup when you can get the SAME results for less than $50. Try setting up 20 dna stations for high school students given a typical summer program budget. the reason you pay $1000 is because that is what fisher thinks you can pay for it. All of the expensive equipment which we pay $1000's for all started out as someone's DIY project.
Re: Drinking straw electrophoresis!
(Anonymous) 2009-02-09 05:37 am (UTC)(link)Of course, I would not setup asummer program for students using $1000 power supplies. DIY setup with a transformer to give ~ 50V and a simple bridge rectifier is sufficient. I would also add a fuse and try to run these from a GFI outlet. High-school students are too curious sometimes for their own good ( I've been in high school too some 30 yr ago).