$21 gel electrophoresis box (DIY)

[CodonAUG]

I wrote a short blog post about how to build a $21 gel box. Take a
look and let me know what you think.

http://citizensciencequarterly.com/2011/10/21/cheapass-science-gel-box/

[Brian Degger]

Great stuff, planning to make one.
Cheers b

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[John Griessen]

Nice write up of all the details of what helps, what was a trade off.
I'm working on getting use of a laser cutter for acrylic, so...

Your photo labeled gel results seems to show more brightness at the edges of
the comb wells for each band of of 100bp ladder. Can you explain that?
anyone else? Could it have to do with the roughness of the comb edges
creating a rough surface with lots of surface area at the edges of wells?

John

[Samantha Clark]

This is awesome! Yeah, a laser cutter would make that comb nice and smooth.

[Brian Reichholf]

Cool! But how do you get the gel out of the gel box?

[John Griessen]

On 10/23/2011 02:55 AM, Brian Reichholf wrote:
> Cool! But how do you get the gel out of the gel box?

Dishwasher? (It melts...)

[Cathal Garvey]

Aargh no! You could really clog up a dishwasher with agarose?

Just throw it in a pot and boil it out, or microwave it 'til it melts!

[Dakota Hamill]

Great job, when I first saw it I thought the gel was the length of the box, and there were no buffer wells, but now I see that isn't the case.

When pouring the gel did you just stick the combs in sideways into the box and pour?  I know the usual boxes have that "tight seal gasket" but it looks like you got away with a pretty nice gel without having them.

Well done, that is a very affordable piece of working equipment

[Simon Quellen Field]

Agar and agarose are no worse than gelatin and gravy.

Dishwashers are designed to handle stuff like that.

Also, once it is dissolved in hot water and heavily diluted in the rinse water,

it's really hard to tell from just plain water. It isn't going to re-solidify without

breaking the Second Law of Thermodynamics.

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[Nathan McCorkle]

Sent from my mobile Android device, please excuse any typographical errors.

On Oct 22, 2011 11:15 AM, "John Griessen" <jo...@industromatic.com> wrote:
>
> On 10/21/2011 11:46 PM, CodonAUG wrote:
>>
>> I wrote a short blog post about how to build a $21 gel box.  Take a
>> look and let me know what you think.
>>
>> http://citizensciencequarterly.com/2011/10/21/cheapass-science-gel-box/
>>
> Nice write up of all the details of what helps, what was a trade off.
> I'm working on getting use of a laser cutter for acrylic, so...
>
> Your photo labeled gel results seems to show more brightness at the edges of
> the comb wells for each band of of 100bp ladder.  Can you explain that?

Its probably due to his illumination not being even... at least its what comes to mind first

> anyone else?  Could it have to do with the roughness of the comb edges
> creating a rough surface with lots of surface area at the edges of wells?
>
> John
>
>

[Cathal Garvey]

If the cycle is hot enough to fully melt it (~95c) , yes. But most modern machines default to warm rather than hot to save energy. Not only that: gelatin (lower melting point already) is a protein, easily digested by bacteria even when it does block drains. Agar/ose was originally used precisely because almost no terrestrial microbes digest it at all: blockages will require manual involvement.

If it melts, you're right: dilute it enough and there's no gel. I am concerned that many/most will instead see a sloppy gel slipping into the tubes, which would be particularly messy in a water-saving washwater-recirculating model.

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[Simon Quellen Field]

I understand your concerns, and your reluctance to do the experiment on your

own equipment. But I have done it for you.

I've used agar in cooking for years, and the dishwasher has no problems.

You don't have to melt it -- you can see this yourself by soaking some in hot

water. With lots of water, the thermodynamics of entropy are on your side.

You also might be discounting the effects of a good dishwashing detergent.

There's a lot more in those than surfactants.

Agarose resists breakdown by most of the critters we play with, which is

one reason it is used. But put a sheet of it in some garden soil and hot

water and see how much is left after a few days. There are a lot of critters

in your garden, and you'll select for those that can feed on it.

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[Cathal Garvey]

Then let's agree on caveat emptor or Your-Milage-May-Vary. I'm
ordinarily pretty happy to say "try it yourself", but when the price of
failure is hiring a plumber and the alternatives are so easy, I'm going
to go conservative on this one.

On 24/10/11 17:09, Simon Quellen Field wrote:
> I understand your concerns, and your reluctance to do the experiment on your
> own equipment. But I have done it for you.
>
> I've used agar in cooking for years, and the dishwasher has no problems.
> You don't have to melt it -- you can see this yourself by soaking some in
> hot
> water. With lots of water, the thermodynamics of entropy are on your side.
> You also might be discounting the effects of a good dishwashing detergent.
> There's a lot more in those than surfactants.
>
> Agarose resists breakdown by most of the critters we play with, which is
> one reason it is used. But put a sheet of it in some garden soil and hot
> water and see how much is left after a few days. There are a lot of critters
> in your garden, and you'll select for those that can feed on it.

--

[helicase]

Neat, it works. How are you disposing of your EtBr bath and gels?
Also, destaining 3x is overkill.

[Yuri Stephen Steinberg]

Hi, could you tell me if and how using a thinner wire would affect the results?
Would it just take longer to run the gel?

[Josiah Zayner]

Wire diameter should not really matter so much if you are using platinum wire. The wire is just there so you can create a current through the buffer.gel. Basically, most any wire, most any diameter should work. However, most of the non-platinum wires will degrade fairly rapidly. You might need to run it longer but I honestly doubt it would be noticeably longer, though I have not done those exact experiments.

I guess using thinner types of other metals could speed their degradation?

[Nathan McCorkle]

thinner wire would produce more heat for the same amperage:
http://wiki.xtronics.com/index.php/Wire-Gauge_Ampacity#Watts_of_heat_generated_in_a_wire_for_a_given_current

Here is that math converted to something pasteable... the 0.001 is the
radius of the wire in meters, and the math evaluates to wattage of
heat produced:
(((10)^2)*(1.72*10^-8)*(1)) / (pi*((0.001)^2))

Two links to that math being evaluated:
https://www.google.com/search?q=(((10)%5E2)*(1.72*10%5E-8)*(1))+%2F+(pi*((0.001)%5E2))&oq=(((10)%5E2)*(1.72*10%5E-8)*(1))+%2F+(pi*((0.001)%5E2))
http://www.wolframalpha.com/input/?i=%28%28%2810%29%5E2%29*%281.72*10%5E-8%29*%281%29%29+%2F+%28pi*%28%280.001%29%5E2%29%29

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[John Griessen]

On 05/20/2014 02:15 PM, Nathan McCorkle wrote:
> thinner wire would produce more heat for the same amperage:

But the write ups and data you posted was about current along a wire in metal.
The interface effects at the metal surface in an
electrolyte are bound to be strong. the conductivity of the solution vs. the metal is
tiny.

The smaller surface area of smaller diameter wire is going to have an effect chemically.
It may be a negligible effect -- but, I have not and am not planning to calculate it
in the next few weeks, so don't know. The main thing I am responding about is that
the wire resistance vs. the solution/total-gel-box-resistance is a tiny ratio.

Skinny wire of conductive metal is fine, OK, no problem.

[Nick R]

This is very useful to a budding microbiologist like myself, but I was wondering what you think I could use as a DIY electrophoresis HV power supply (Possibly microwave transformers with the secondary coil changed to change output voltage?). Also, would a setup like this work for a single gel, vertical electrophoresis chamber for protein electrophoreses like SDS-PAGE? Planning to make one once some funds are freed up. Thanks for the post.

[Brian Degger]

if you look online there are 12v to 80v step-up modules that is good for a 8cm minigel at 10v/cm

not current limited though

  

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[Nick R]

Thank you very much, I will look into those!