Keiki gels: gel electrophoresis in a straw
I am running gel electrophoresis through a straw. I hope to show that this is faster and more convenient than regular gel electrophoresis. But first — does it work?
My first experiments have been a success – electrophoresis works through a straw.
To the left you can see my most recent results. These 3 straws were filled with agar gel, placed in a gel box full of buffer, and run in parallel. From the top, green, red, blue. As expected, the dyes separate into pure colors.
I’ll be adding a protocol to OpenWetWare in the next week.
Let me know what you think!
More Details:
Run 1: The band of blue dye in my first run moved only about half an inch. The full length of the straw was diagonally, to fit in the gel box.
Run 2: I ran 2 shorter straws of green dye, in parallel. These straws are about 3 inches long, the same length of a traditional gel. One of the straws separated nicely – the green dye became blue and yellow. The other gel did not separate at all. This is unexpected, but I’m glad to see that under some situations, food coloring will migrate through a straw gel. In regards to speed, I think my 9v batteries are dying. That said, a regular gel took me 2 hrs to run last week on these batteries, whereas this run was only 1 hr.
Run 3: A lot of dye leaks out of the ends of the straws.I poked little holes about half an inch from the end of the straw and put the dye in there instead. Worked a lot better, though my buffer was still colored at the end of the run.
Similar experiment with regular gel
Keiki gels setup in parallel (Run 2)
[...] conversation between Tito Jankowski and Meredith Patterson on the DIYbio list about how to bring the costs of electrophoresis (a way of [...]
Pingback by Drinking straw electrophoresis | GENOMICON — February 7, 2009 @ 12:55 am
There is a reason why we sciencey folk switched from running tube gels to slab gels in the late 1960s. Comparability, and capacity.
Comment by bob — February 7, 2009 @ 3:11 am
Good to know – comparability is definitely a concern, thanks Bob. Any ideas for standardization? Were tube gels faster for you?
Comment by admin — February 7, 2009 @ 3:21 am
FYI, a standard mol bio DNA gel is 1% agarose – comparitively, you’re running a 6.25 % agarose gel. At that density, you’ll only be able to separate tiny fragments (see 6% gels in figs 3 and 4 here http://www.med.yale.edu/genetics/ward/tavi/p15.html).
And another note on standardization. Another reason slab gels are popular is that they allow you to run a molecular weight ladder along side your sample, adding additional assurance that the DNA you desire is the correct size and allowing comparison between separate gels.
Comment by maryr — February 7, 2009 @ 11:11 am
And another note on standardization. Another reason slab gels are popular… is that you can leave outer lanes empty to avoid edge effects. With such narrow walls you may have to load extremely small samples when dealing with bigger molecules.
The slightly alkaline TBE and TAE buffers (which aren’t exactly exotic) usually used for nucleic acid electrophoresis tend to keep the DNA/RNA deprotonated (-) to allow for better resolution. An unbuffered salt solution may not resolve much in terms of DNA.
Comment by andy — February 7, 2009 @ 3:43 pm
Awesome! I don’t know, will edge effects be a problem? Isn’t that from inconsistent current across the width of the gel? I bet SDS-PAGE could work well in a skinny little coffee straw! (though, I’ve never seen a clear one of those) Or, how about the tip of a disposable glass pipette? Thanks, this is neat!
Comment by Jeff — February 8, 2009 @ 3:39 pm
I was working on something like this as “midnight” project during an undergrad co-op term, using 1 mL pipettes to cast IEF gels (see website link) in – you might want to try IEF and then you can play with 2D gels as well (the original reason I was trying it). Also, if you have trouble with the gel sliding out of a vertical straw, you can try casting a thread into it – you can pull the gel out of the tube afterwards this way too. Careful with the high voltage stuff tho…
Comment by Mark — February 8, 2009 @ 9:27 pm
So the IEF link was not as obvious as I thought – here it is: http://en.wikipedia.org/wiki/Isoelectric_focusing
PS RE your sample-escaping problem, this is where vertical tubes come in handy – in my case I drilled a bunch of holes in the bottom of a plastic box for the upper chamber (P1000 tip box lid), wedged some small-diameter rubber tubing in the holes, wedged the pipettes with gel in into the tubing, and then suspended it over the lower chamber so the bottom ends of the gels hung free into the buffer. Another advantage of this layout is that the current is only flowing through the gel, not through the whole cross section of the buffer box, so the total load on your power supply and resistive heating are minimized – IIRC (it was >10 years ago), this is why I did it that way. I used a conventional bio lab voltage source for it though, can’t remember the settings but >>9V for sure – might have even been a thousand.
PPS RE Run #2 – from your image I am going to guess that if you had linear electrodes across the full width of the gel box at both ends, both straws would have worked. I think maybe the use of “point” electrodes is giving you a funny-shaped field that may also be reducing the quality of the separations in the straws that do work (although the nice gel image on the left may argue against this, so maybe I’m wrong).
Comment by Mark — February 8, 2009 @ 9:45 pm
Excellent – thanks for the comments, everyone.
Mark, my next run will use linear electrodes – I’ll post about how it goes!
Tito
Comment by admin — February 15, 2009 @ 4:57 pm