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Drinking straw electrophoresis!

purple hair
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!

Tito's keiki gels!


ETA: Tito wrote a protocol, doo dah, doo dah

Comments

( 102 comments — Leave a comment )
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m4dh4tt3r
Feb. 7th, 2009 03:26 am (UTC)
That is hewn from raw awesome!
maradydd
Feb. 7th, 2009 03:32 am (UTC)
Better yet? Elapsed time from initial idea to reduction-to-practice, approximately three days.

Here Comes Everybody, indeed!
(no subject) - m4dh4tt3r - Feb. 7th, 2009 03:38 am (UTC) - Expand
(no subject) - maradydd - Feb. 7th, 2009 03:39 am (UTC) - Expand
(no subject) - m4dh4tt3r - Feb. 7th, 2009 03:46 am (UTC) - Expand
michiexile
Feb. 7th, 2009 03:30 am (UTC)
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.
maradydd
Feb. 7th, 2009 03:34 am (UTC)
Hah, that's a great idea! Especially since straws come like a thousand to a box. You'd never run out.
(no subject) - michiexile - Feb. 7th, 2009 03:36 am (UTC) - Expand
(no subject) - maradydd - Feb. 7th, 2009 03:41 am (UTC) - Expand
(no subject) - maradydd - Feb. 7th, 2009 03:49 am (UTC) - Expand
(no subject) - feyandstrange - Feb. 7th, 2009 04:30 am (UTC) - Expand
(no subject) - maradydd - Feb. 7th, 2009 04:57 am (UTC) - Expand
morbid_curious
Feb. 7th, 2009 03:31 am (UTC)
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
Feb. 7th, 2009 03:33 am (UTC)
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.
anaisdjuna
Feb. 7th, 2009 04:00 am (UTC)

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
Feb. 7th, 2009 04:06 am (UTC)
Thank you! I look forward to hearing what she thinks, especially if she has any ideas on how to improve it. :)
mycroftxxx
Feb. 7th, 2009 04:23 am (UTC)
Oh, that is nice work. That's elegant on the level of the eggbeater-centrifuge.
maradydd
Feb. 7th, 2009 04:39 am (UTC)
"The street finds its own uses for things -- uses the manufacturers never imagined." - William Gibson
Great quote - (Anonymous) - Feb. 8th, 2009 08:49 pm (UTC) - Expand
Re: Great quote - maradydd - Feb. 8th, 2009 08:56 pm (UTC) - Expand
feyandstrange
Feb. 7th, 2009 04:26 am (UTC)
Oh, this rocks! Great for field laboratories, budget-poor applications, kids in classrooms, and so on. Yay crowdsourcing science.
maradydd
Feb. 7th, 2009 04:28 am (UTC)
Best mailing list EVAR, srsly.
mellowtigger
Feb. 7th, 2009 04:55 am (UTC)
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
Feb. 7th, 2009 05:00 am (UTC)
Sweet! I just friended you so that I can follow your exploration of your genome. :)
barbarienne
Feb. 7th, 2009 05:05 am (UTC)
"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. :-)

Edited at 2009-02-07 05:07 am (UTC)
maradydd
Feb. 7th, 2009 05:09 am (UTC)
Hey, there's a reason why my Gmail username is 'clonearmy'. ;)
straw design - (Anonymous) - May. 19th, 2009 05:43 pm (UTC) - Expand
(no subject) - michiexile - Feb. 7th, 2009 05:47 am (UTC) - Expand
mutiny
Feb. 7th, 2009 06:37 am (UTC)
Can I use this to find out exactly who the father of somebody's baby is?
maradydd
Feb. 7th, 2009 06:39 am (UTC)
Next step is sequencing, chromosome identification and stuff like that. We're working on it!
nicaprio.blogspot.com
Feb. 7th, 2009 06:46 am (UTC)
WOW
Freaking bloody amazing, my name is Quetzal a molecular biologist to be in my last days in the university here in mexico city, and i have been crying because without being able to enter to my school lab, i been due with my final project that is the identification and isolation of a protein, but this, THIS, is just amazing, i will have plenty of material and time in home to rush some items in my work. Lady, this work is a bless.

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

maradydd
Feb. 7th, 2009 06:51 am (UTC)
Re: WOW
Oh, awesome! Please get in touch with Tito ASAP (his blog's at titojankowski.com), he can answer any questions you have about the protocol he worked up -- and if your work in turn can help us improve this for everyone, then that will be really fantastic!

So glad to be of help. :)
Re: WOW - (Anonymous) - Feb. 28th, 2010 04:10 pm (UTC) - Expand
(Anonymous)
Feb. 7th, 2009 07:03 am (UTC)
crazy straws...
Again, completely brilliant.

Have you seen this? http://www.pacificbiosciences.com/index.php?q=observation-window
maradydd
Feb. 7th, 2009 07:33 am (UTC)
Re: crazy straws...
Damn, and just one molecule of Taq in each well! I want to know how they made these. Thanks for the link!
Re: crazy straws... - soon_lee - Feb. 8th, 2009 09:03 am (UTC) - Expand
Re: crazy straws... - maradydd - Feb. 8th, 2009 08:36 pm (UTC) - Expand
(Anonymous)
Feb. 7th, 2009 12:21 pm (UTC)
Thank you for sharing this idea. What can we use as a buffer that might be as inexpensive?
maradydd
Feb. 7th, 2009 12:26 pm (UTC)
Tris-borate-EDTA is great if you can get it (it's not restricted or anything, just a little expensive), but if not, plain old salt water works just fine. A pinch of salt per cup of water is plenty.
Buffers are necessary! - (Anonymous) - Feb. 9th, 2009 08:37 pm (UTC) - Expand
(Anonymous)
Feb. 7th, 2009 01:58 pm (UTC)
imaging
So the real problem I envision is post gel imaging.

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.
maradydd
Feb. 7th, 2009 02:06 pm (UTC)
Re: imaging
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'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.

Edited at 2009-02-07 02:08 pm (UTC)
Re: imaging - madeofmeat - Feb. 8th, 2009 04:42 am (UTC) - Expand
Re: imaging - maradydd - Feb. 8th, 2009 08:36 pm (UTC) - Expand
siliconshaman
Feb. 7th, 2009 03:09 pm (UTC)
Occurs to me that if you picked up a secondhand computer, or just the pSU, you'd have a regulated 5vdc or 12vdc power supply which you could use together with a modified audio amplifier [or the dc voltage step up circuit from an inkjet printer] to step up the voltage and act as a cheap lab supply for this. You could probably get all the parts you'd need on freecycle.

Oh, and most plastics are UV transparent btw..
maradydd
Feb. 9th, 2009 01:24 am (UTC)
I use the 5V and 12V rails from PSUs as quick-and-dirty power supplies all the time, though hadn't thought about the voltage step up circuit. By what ratio do they typically raise the voltage? Junked printers are easy to find.
(no subject) - siliconshaman - Feb. 9th, 2009 01:46 am (UTC) - Expand
(no subject) - maradydd - Feb. 9th, 2009 01:51 am (UTC) - Expand
(Anonymous)
Feb. 7th, 2009 03:36 pm (UTC)
!/2 filled straw....horizontal..cutting..
...once you want to cut the straw don,t use scissors or a blade...use a tool from your notions dept. (seeing) called a seam ripper ...Perfect for slicing open straws longitudinally...that's all,PEACE ,bye Dr Mark
maradydd
Feb. 8th, 2009 08:38 pm (UTC)
Re: !/2 filled straw....horizontal..cutting..
*facepalm* You're absolutely right! I haven't done any serious sewing in forever, but I still have a couple of those in my box o' tricks. Thanks for the suggestion!

Crowdsourced science really is the best thing ever.
(Anonymous)
Feb. 7th, 2009 03:39 pm (UTC)
straw cutting...
That's seWing not seeing....Dr.MARK
tdj
Feb. 7th, 2009 06:31 pm (UTC)
Passing along to the DeCal class that works with high schoolers! Thanks.
maradydd
Feb. 8th, 2009 08:38 pm (UTC)
No, thank you! If they tell you how well it worked, I look forward to hearing about it. :)
renwick
Feb. 7th, 2009 07:26 pm (UTC)
Now I just need to figure out how to make my own restriction enzymes...
soon_lee
Feb. 8th, 2009 09:13 am (UTC)
My boss remembers a time before commercially available restriction enzymes when they had to isolate their own. And it wasn't *that* long ago.

Of course, some source organisms will be less hazardous to grow than others: EcoRI vs. HindIII for example.
(no subject) - maradydd - Feb. 8th, 2009 08:39 pm (UTC) - Expand
(no subject) - renwick - Feb. 8th, 2009 09:08 pm (UTC) - Expand
(no subject) - maradydd - Feb. 8th, 2009 10:42 pm (UTC) - Expand
dirkx.webweaving.org
Feb. 7th, 2009 08:11 pm (UTC)
Straws v.s. Flat 2D gells
If memory serves me correctly; was not the whole point historically for going from straws to flat 2D spaces that these worked better: more reliable to compare (dV/dA ratio lower; and hence ^2 error margin); ability to use low (agar) concentrations and comparable or better separation - whilst less surface/jump boundary corruption in the eV field. Or have I missed something and is this not a step back?
mrtee
Feb. 7th, 2009 10:37 pm (UTC)
Re: Straws v.s. Flat 2D gells
You are correct. Leading edge effect of current flow at the gel boundery.
(Anonymous)
Feb. 7th, 2009 09:36 pm (UTC)
MWM needed
drdubious
Feb. 8th, 2009 02:22 am (UTC)
Slightly off-topic but...
"ETA: Tito wrote a protocol, doo dah, doo dah"

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?...

maradydd
Feb. 8th, 2009 08:40 pm (UTC)
Re: Slightly off-topic but...
Nope, you're definitely not the only one. It pops up whether I want it to or not. *grin*
(Anonymous)
Feb. 8th, 2009 05:33 am (UTC)
Drinking straw electrophoresis - Removal Method
Hi
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
maradydd
Feb. 8th, 2009 08:41 pm (UTC)
Re: Drinking straw electrophoresis - Removal Method
I don't know off the top of my head, but given that both plasmids and linear DNA are often stored at -4C, I reckon it wouldn't hurt the bands at all. Thanks!
Re: Drinking straw electrophoresis - Removal Method - (Anonymous) - Feb. 9th, 2009 05:27 am (UTC) - Expand
(Anonymous)
Feb. 8th, 2009 07:43 am (UTC)
Drinking straw electrophoresis!
I have stumbled here from slashdot. I have been doing electrophoresis (agarose and PAGE) for over 20 years now. Some comments about the discussion on this page:

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.
maradydd
Feb. 8th, 2009 08:54 pm (UTC)
Re: Drinking straw electrophoresis!
Wow, can you point me to that $200 power supply? I have a (broken, needs a hard-to-find transistor replaced) Bio-Rad power supply lying around which lists at $6K -- though it has a whole lot of fancy features like the ability to do timed runs, the ability to do two different runs simultaneously, and so on and so forth.

Re your #2, what do you think about my comment to nativeprincess below?

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.

Edited at 2009-02-08 08:55 pm (UTC)
Re: Drinking straw electrophoresis! - (Anonymous) - Feb. 9th, 2009 05:24 am (UTC) - Expand
Re: Drinking straw electrophoresis! - (Anonymous) - Feb. 9th, 2009 05:19 am (UTC) - Expand
Re: Drinking straw electrophoresis! - (Anonymous) - Feb. 9th, 2009 05:37 am (UTC) - Expand
nativeprincess
Feb. 8th, 2009 06:18 pm (UTC)
Straw electrophoresis....best thing ever.
Down side seems to be that you can't run it next to a ladder for comparison. You could do that in a separate straw but that's not going to be under identical conditions. More than likely its close enough, but have you thought of ways to get around this issue and still use the straw concept?
maradydd
Feb. 8th, 2009 08:51 pm (UTC)
Well, here's the thing. When we do electrophoresis in a rectangular gel with multiple wells, the gel behaves (electrically) as a single, fairly high-valued resistor. This allows us to be confident that each well is being exposed to the same amount of current (which is basically "motive force", in electrical terms) and that the molecules travel at the same rate.

Now, when I was building radios and antennas, we sometimes had to worry about impedance matching (which is fundamentally resistance-matching) in cables. Two lengths of cable (or any other material that has the same resistance per unit length) that are of identical length will have identical impedance. So I'm pretty sure that two gel-filled straws of identical length will also have identical resistance.

Putting two gel-filled straws of identical length in the same bath and running current through it is equivalent to putting two resistors in parallel, and by Ohm's law we know that when we put N identical resistors in parallel, each resistor draws the same amount of current. (The math has a lot of fractions in it and isn't easy to demonstrate in HTML, but it's easy to find if you google "resistors in parallel".) Thus, my hypothesis is that if one uses straws of identical length, and put the DNA into each straw at the same point, the DNA will migrate down the gel at the same rate.

We plan to test this in the near future by running, say, five keiki gels all containing identical molecular weight marker samples at the same time. If they produce the same ladders, then (modulo repeating this a number of times to make damn certain it wasn't an anomaly, of course, and repeating it with different types of DNA ladder) I think we can be pretty confident that we will be able to run a sample of interest in one straw and a DNA ladder in another straw, provided that both straws are of the same length and samples are loaded at the same point in the gel.

I haven't put a whole lot of thought yet into how we'll get around this if my hypothesis proves false, but one thing at a time. :)

Edited at 2009-02-09 01:09 am (UTC)
(no subject) - kragen - Feb. 9th, 2009 04:45 pm (UTC) - Expand
(Anonymous)
Feb. 9th, 2009 02:35 am (UTC)
Agar vs. agarose
Not one to nitpick (oh, hell, yes I am...) but I think the kind of polymer you can get at the grocery is agar, rather than agarose. :)
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