Drinking straw electrophoresis!
Feb. 7th, 2009 02:42 am![[personal profile]](https://www.dreamwidth.org/img/silk/identity/user.png){kind=small}
maradyddGel 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
![[identity profile]](https://www.dreamwidth.org/img/silk/identity/openid.png){kind=small}
(no subject)
Date: 2009-02-07 05:09 am (UTC)(no subject)
Date: 2009-02-07 05:24 am (UTC)(no subject)
Date: 2009-02-07 05:47 am (UTC)You mean she hasn't yet? What on EARTH do you call her current state in that case??
(no subject)
Date: 2009-02-07 06:37 am (UTC)(no subject)
Date: 2009-02-07 06:39 am (UTC)WOW
Date: 2009-02-07 06:46 am (UTC)Of course i will need to check the protocol and try it by myself, but maybe with this i will have a degree before time.
THANK YOU, THANK YOU, THANK YOU.
TRULY YOURS (WHENEVER YOU WANT)
QUETZAL HERNANDEZ
Re: WOW
Date: 2009-02-07 06:51 am (UTC)So glad to be of help. :)
crazy straws...
Date: 2009-02-07 07:03 am (UTC)Have you seen this? http://www.pacificbiosciences.com/index.php?q=observation-window
Re: crazy straws...
Date: 2009-02-07 07:33 am (UTC)(no subject)
Date: 2009-02-07 12:21 pm (UTC)(no subject)
Date: 2009-02-07 12:26 pm (UTC)imaging
Date: 2009-02-07 01:58 pm (UTC)For DNA: Are the straws UV transparent? Can you get straws that are?
For proteins: There is no easy way to get the whole strip of gel out of the straw is there? It would be hard to further stain the protein. Maybe if you placed the straw horizontally in a tray and filled the tray so that only half of the straw was filled with gel horizontally. That way you could just chuck the straw in coomasie and stain your protein or cut the straw lengthwise and transfer the protein on to nitrocellulose or PVDF.
Re: imaging
Date: 2009-02-07 02:06 pm (UTC)That's a great idea! Definitely worth a shot when we try this for PAGE. (I haven't worked with polyacrylamide yet, but the idea totally makes sense.) We could try it out now with agarose and DNA, too, using methylene blue.
On the UV transparency issue: not sure, but that doesn't strike me as a showstopper, as there are gel stains you can add to the warm agarose that work just as well with blue light as they do with UV.
(no subject)
Date: 2009-02-07 03:09 pm (UTC)Oh, and most plastics are UV transparent btw..
!/2 filled straw....horizontal..cutting..
Date: 2009-02-07 03:36 pm (UTC)straw cutting...
Date: 2009-02-07 03:39 pm (UTC)(no subject)
Date: 2009-02-07 06:31 pm (UTC)(no subject)
Date: 2009-02-07 07:26 pm (UTC)Straws v.s. Flat 2D gells
Date: 2009-02-07 08:11 pm (UTC)(no subject)
Date: 2009-02-07 09:36 pm (UTC)Re: Straws v.s. Flat 2D gells
Date: 2009-02-07 10:37 pm (UTC)Slightly off-topic but...
Date: 2009-02-08 02:22 am (UTC)You're kidding me - you mean I'm not the ONLY one who can't help but mentally insert a "Doo dah, doo dah" after any 7-syllable utterance with the right cadence?...
Re: imaging
Date: 2009-02-08 04:42 am (UTC)Drinking straw electrophoresis - Removal Method
Date: 2009-02-08 05:33 am (UTC)I just stumbled here from Boing Boing and have no experience with your DNA gel. So I don't know what would happen to the quality of your gel sample if it were to be frozen. However, if freezing the sample without damaging it is possible, you might try this for extracting the cores:
First, freeze the gel-straw. Then, hold it gently in your hand so that your body heat slightly warms the plastic straw, but leaves the gel inside still frozen. This should create a slippery film between the wall of the straw and the gel. Finally, using a sterile plunger (pipette?) of the appropriate size, push the gel out of the straw and into your chosen container.
I hope this helps you guys,
Brian
Drinking straw electrophoresis!
Date: 2009-02-08 07:43 am (UTC)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.