Drinking straw electrophoresis!

[maradydd]

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

Comments

[m4dh4tt3r.livejournal.com]

That is hewn from raw awesome!

[michiexile]

This should lend itself to easy mass production: take a largish tub, mix water and agar-agar in it and dump a couple of whole-sale packages of drinking straws in the tub.

Lift each straw back out, pinching the ends, and put it to cool and set.

And in a few hours, you've a years supply of phoresis tubes.

[drcuriosity]

That's a wonderful bit of science. It also looks like it'd be great for a school-based science extension project, so doubles as a tool for getting kids interested in scientific inquiry too :-)

[maradydd.livejournal.com]

Better yet? Elapsed time from initial idea to reduction-to-practice, approximately three days.

Here Comes Everybody (http://www.amazon.com/Here-Comes-Everybody-Organizing-Organizations/dp/1594201536), indeed!

[maradydd.livejournal.com]

That's definitely part of the idea! Do feel free to share with teachers, parents, principals, whoever. Tito will be posting a step-by-step protocol on OpenWetWare soon; I'll update the post with a link when it's ready.

[maradydd.livejournal.com]

Hah, that's a great idea! Especially since straws come like a thousand to a box. You'd never run out.

[michiexile]

Also, it uses a tech level accessible to the poorest corners of the 3rd world. Surely there are reasons to perform electrophoresis in the field?

[m4dh4tt3r.livejournal.com]

That's pretty impressive. I've just started to look at diybio stuff. It's very interesting. Innovation doesn't require gigantic budgets, and this is a great example. Thanks for sharing this. :-)

[maradydd.livejournal.com]

Do join the mailing list! People kick out ideas all the time, it's a great place to share and enjoy.

[maradydd.livejournal.com]

Oh hells yeah. The other name for electrophoresis is "DNA fingerprinting". It has health and forensics applications everywhere.

[m4dh4tt3r.livejournal.com]

Done!

[maradydd.livejournal.com]

N.B.: you will also need to add an appropriate stain in order for the DNA bands to be visible. I like GR Safe, but it's only easy to get if you live in the first world. Tito's going to be testing with isolated DNA pretty soon, and he'll be using methylene blue, a common and safe dye that's very cheap and easy to acquire.

[anaisdjuna.livejournal.com]

Interesting. I'll have to pass this along to my homegirl who is a molecular biologist not connected to a lab at the mo'.

I enjoy your writing style. It's very bright and shiny and flows well.

[maradydd.livejournal.com]

Thank you! I look forward to hearing what she thinks, especially if she has any ideas on how to improve it. :)

[mycroftxxx.livejournal.com]

Oh, that is nice work. That's elegant on the level of the eggbeater-centrifuge.

[feyandstrange.livejournal.com]

Oh, this rocks! Great for field laboratories, budget-poor applications, kids in classrooms, and so on. Yay crowdsourcing science.

[maradydd.livejournal.com]

Best mailing list EVAR, srsly.

[feyandstrange.livejournal.com]

I would be tempted to hunt up those old straw-holders that diners used to have - the kind that look like a sugar dispenser? or possibly just some tall, flat-bottomed round containers. Heck, plastic 2-liters with tops cut off might work, and they're disposable. Fill those with straws on their ends. Mix your bulk agar, then pour over the tops of these until the straws are completely full and just a little liquid over the top. Let the whole mess set, with the top covered if need be, then pull straws out - eliminates the need to pinch the suckers.

[maradydd.livejournal.com]

"The street finds its own uses for things -- uses the manufacturers never imagined." - William Gibson

[mellowtigger]

DOH! And after I shelled out $400 I don't have in order to get some testing done for me by 23andme.com.

http://mellowtigger.livejournal.com/75005.html

[maradydd.livejournal.com]

I guess you'd want to have as many straws in there as possible, to minimize the amount of agar clumping them together -- but yeah, this sounds very workable!

[maradydd.livejournal.com]

Sweet! I just friended you so that I can follow your exploration of your genome. :)

[enochsmiles.livejournal.com]

The straw holder things I think you're talking about might be a little awkward, given the internal base (pushing that through a viscous fluid would be hard, I'd think, though the base is probably removable).

The advantage over the other suggestions you had would be the convenient sanitary selection of a single straw (i.e., their purpose in the first place!) but I think the flat-bottomed round containers (maybe the kind people put flour and sugar, etc., in?) would be perfect -- you'd just have to be careful when pulling out one of your gelstraws.

[enochsmiles.livejournal.com]

Bringing modern microbiology techniques to the third world is one of the derivative goals of the DIYBIO list / movement, and we've got a number of high school/university teachers from South America on the list, actively working to put into practice the hacks we're doing to play with this stuff at home.

"Making science more accessible" is a key goal here.

[barbarienne.livejournal.com]

"In a bizarre collision of a Monty Python sketch, a bit from Douglas Adams, and those crazy people who are terrified of biohacking, Meredith was encouraged to continue stovetop genetic experimentation in the country of Belgium."

No, seriously, you're like a walking concatenation of geek references. Soon you will either (a) form some sort of geek black hole, or (b) reach geek critical mass and chain out.

You're so entertaining. :-)