Any ideas on edible electrophoresis buffers?

[Patrik D'haeseleer]

So I got the idea of trying some jello shot electrophoresis for Science Hack Day this year. We won the judge's prize last year with a drinkable DNA extraction protocol, and this is my very transparent attempt at bribing the judges with booze (and a little science) again this year...

Turns out you can get some really nice results with food colors on a gel. And of course regular agarose or agar gel is edible. Problem is that damn Tris-borate EDTA buffer... First thing I thought of was to just replace the buffer with table salt, but that would likely just give you a lot of electrolysis, and Chlorine!

So... any idea what kinds of salts might be worth trying? Needs to be edible (of course), produce a well conducting solution, and not prone to producing toxic compounds by electrolysis.

I'm not looking for anything laboratory quality, mind you. Just looking for something that will allow me to electrophorese some bands of food coloring into a slab of agar, while still staying edible...

[Cathal Garvey]

Table salt is probably OK: you'd get chlorine gas, yes, but that's all
they add to tap water and it boils off pretty quickly. Besides, if
you're talking about eating the gel, the chlorine will get produced at
one of the terminals; it shouldn't make it to the gel in any worrying
quantity.

As for dyes, I encountered a paywalled paper suggesting that the primary
dye in turmeric (the name of which I have forgotten) worked as an
acceptable co-stain with an artificial counterion, but the counterion
wasn't edible. However, some quick hacking might find a suitably edible
counterion.

Of course, methylene blue is edible; there are some minor concerns about
carcinogenicity, but I get the impression that it's very minor; possibly
less significant than eating burnt toast. So if you stain and destain
properly, the Methylene Blue will be minimal and you'll get visible
bands if you use enough DNA.

Agarose itself is perfectly edible of course, and you don't need EDTA,
nor do you really need much buffering if it's just for culinary delight.
So, just enough salt to permit conduction, otherwise perhaps just water,
DNA and food-grade bromophenol blue/glycerol loading dye.

You may want to destain with something flavoursome to imbue a taste
other than bland salty gel. So, after running DNA, destain in salt-free
water first, then salt-free solution containing plenty of sweetener and
flavouring?

On 01/11/12 07:53, Patrik D'haeseleer wrote:
> So I got the idea of trying some jello shot electrophoresis for Science

> Hack Day <http://sf.sciencehackday.com/> this year. We won the judge's
> prize last year with a drinkable DNA extraction<http://www.instructables.com/id/DNAquiri-the-delicious-DNA-extraction/>protocol, and this is my very transparent attempt at bribing the judges

> with booze (and a little science) again this year...
>

> Turns out you can get some really nice results with food colors on a gel<http://peer.tamu.edu/curriculum_modules/cell_Biology/Module_4/Electrophoresis%20on%20Agarose%20Gel%20-%20Student.ppt>.

> And of course regular agarose or agar gel is edible. Problem is that damn
> Tris-borate EDTA buffer... First thing I thought of was to just replace the
> buffer with table salt, but that would likely just give you a lot of
> electrolysis, and Chlorine!
>
> So... any idea what kinds of salts might be worth trying? Needs to be
> edible (of course), produce a well conducting solution, and not prone to
> producing toxic compounds by electrolysis.
>
> I'm not looking for anything laboratory quality, mind you. Just looking for
> something that will allow me to electrophorese some bands of food coloring
> into a slab of agar, while still staying edible...
>

--
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PGP Public Key: http://bit.ly/CathalGKey

[Simon Quellen Field]

A little lemon juice and sodium bicarbonate should both make it more conductive and act as a pH buffer once the foaming has stopped.

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[Patrik D'haeseleer]

I'm not even planning to run any DNA - probably just food dyes by themselves, since that seems to work fairly well.

Good to hear the reassurances on using table salt. I may aim for something like a dirty martini jello shot, where the salty tang wouldn't really detract from the experience - heck, olive juice is probably worth trying as a buffer by itself! But frankly alcohol and taste are optional for our first try. I'd be happy with an edible gel with some visible band. Having it actually taste and look great and carry enough alcohol to sway the judges would be a bonus ;-)

Any guesses on how well gelatin works as an electrophoresis gel, how much alcohol you might be able to dissolve in an agarose gel, or how alcohol and sugar in the gel might affect electrophoresis?

Patrik

[Cathal Garvey]

I'd say agarose and alcohol work well together, although it might affect
migration of certain dyes etc?

Gelatin can be used for a gel but expect poorer bands I'd say. Collagen
is a protein with inhomogenous side-chain structure, whereas even impure
agar is largely only two polysaccharides; far less complicated, more
compact gel structure. Ideally, agarose will give you good gels and
should be edible.

I don't think sugar will affect electrophoresis, and it's not charged,
so it'd probably remain as-is. Enough sugar will reliably make your gel
buffer more viscuous though, so perhaps it'll make migration slower.
Also, enough sugar might somehow interact with gel formation due to
pi-bonding (is benzene-stacking pi-bonding? Can't recall..), would be
interested to hear if you see any serious qualitative differences
between sucrose gels and normal gels.

Olive juice? Is that well buffered?

Also Simon, as you seem to know more: what sort of buffering
range/capacity do you get out of citric acid/bicarbonate like lemon and
sodium bicarb? I've long been looking into a domestic crude replacement
for tris, are there any carbonate-based buffer combinations that you can
knock up easily in this range (~8 -> ~11)?

[Nathan McCorkle]

I started a list of potential DIY buffer molecules, but it's pretty
bad as of now. The bottom of the list has some relatively common
aminos that could probably be found at a nutritional supplement store,
but I don't seem to have populated the pKas for them.

Anyway here's the link, I made it editable by anyone with the link. We
should try to get this list fixed up in the next month or so, and put
it on a wiki FAQ or something.
Potential DIY Biotech Buffer Molecules
https://docs.google.com/spreadsheet/ccc?key=0AkTsdtdxo56DdGpFSEZXZVdHOVBfVjZ6ZDU3b0FsdEE

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[Ravasz]

Hi,

My two cents would be using PBS as buffer. You can both add it to the gel and use it as a running buffer. It has the salt (NaCl) and the buffering capacity (phosphate) you need, plus its edible. As Cathal suggested, be very careful with the chlorine gas produced during the electrophoresis. Chlorine is extremely reactive, and greatly damages the lungs upon inhalation.

Alternatively you could try phosphoric acid and phosphate as a buffer system, plus low amounts of table salt for conductivity.

Hope this helps,
Mat

[Cathal Garvey]

Hehe, I was suggesting not worrying at all about the chlorine.. Unless
it smells more, uh, chlorinous, than a swimming pool, of course. I guess
just do it in a ventilated room and leave the gel sit for a little while
before considering eating it, to let the gas evaporate?

Alternatively, heat the gel a little afterwards; chlorine boils out of
solution at around 60C, I think. Still well below agarose's melting
temperature.

On 02/11/12 12:22, Ravasz wrote:
> Hi,
>
> My two cents would be using PBS as buffer. You can both add it to the gel
> and use it as a running buffer. It has the salt (NaCl) and the buffering
> capacity (phosphate) you need, plus its edible. As Cathal suggested, be
> very careful with the chlorine gas produced during the electrophoresis.
> Chlorine is extremely reactive, and greatly damages the lungs upon
> inhalation.
>
> Alternatively you could try phosphoric acid and phosphate as a buffer
> system, plus low amounts of table salt for conductivity.
>
> Hope this helps,
> Mat
>
>
> On Thursday, 1 November 2012 08:53:56 UTC+1, Patrik D'haeseleer wrote:
>>
>> So I got the idea of trying some jello shot electrophoresis for Science

>> Hack Day <http://sf.sciencehackday.com/> this year. We won the judge's
>> prize last year with a drinkable DNA extraction<http://www.instructables.com/id/DNAquiri-the-delicious-DNA-extraction/>protocol, and this is my very transparent attempt at bribing the judges

>> with booze (and a little science) again this year...
>>

>> Turns out you can get some really nice results with food colors on a gel<http://peer.tamu.edu/curriculum_modules/cell_Biology/Module_4/Electrophoresis%20on%20Agarose%20Gel%20-%20Student.ppt>.

>> And of course regular agarose or agar gel is edible. Problem is that damn
>> Tris-borate EDTA buffer... First thing I thought of was to just replace the
>> buffer with table salt, but that would likely just give you a lot of
>> electrolysis, and Chlorine!
>>
>> So... any idea what kinds of salts might be worth trying? Needs to be
>> edible (of course), produce a well conducting solution, and not prone to
>> producing toxic compounds by electrolysis.
>>
>> I'm not looking for anything laboratory quality, mind you. Just looking
>> for something that will allow me to electrophorese some bands of food
>> coloring into a slab of agar, while still staying edible...
>

[Patrik D'haeseleer]

Well, you were all right on not worrying about chlorine development from salt in the buffer. It was barely noticeable, even when I tasted the buffer during running - benefits of using 100% food safe equipment and ingredients! :-D We actually wound up using KCl because that's what we had on hand (Picked up as "salt substitute" at the grocery store for experimentation), plus some lime juice for citrate ions. The buffer while running tasted like a very weak margherita, diluted with slightly chlorinated water. I've definitely tasted more heavily chlorinated tap water - and swallowed far more bleach in swimming pools.

You can see some of our pics from the weekend on our Flickr group here:

http://www.flickr.com/groups/jelloshotelectrophoresis/

[Patrik D'haeseleer]

We wound up wasting a lot of time on the first day trying to get electrophoresis to work on gelatin gels. We actually did get a tiny bit of migration of the food dyes with a very solid gel (think "ballistics gel" rather than jello!). But at lower gelatin concentrations that should have given better migration into the gel, and would have been far more palatable, the gels kept melting as soon as we applied current.

Joseph Elsbernd (@CodonAUG) wound up bring much of his home lab to Science Hack Day, so we did much of the initial experimentation on that, while we worked to build a gel electrophoresis apparatus from scratch:



And how's this for a gel comb hack. Yes, I know there are far easier ways to make a gel comb, but this was more fun, and created lovely slated wells:



Patrik

[Patrik D'haeseleer]

Here's Joseph loading food dye in our Agar-agar gel:



We did use the big stack of 9V batteries on some of the gels, but we wound up using the power supply on this one for simplicity. Note our ice bath top left (made from the water jug we had cut up to make the gel platform), and the foot of Joseph's PVC pipe pipetter stand:



And here's the final results with our food dyes. Lovely bands, if I say so myself. Perhaps not research grade, but definitely food grade:



Since we were running short on time, we didn't get a chance to optimize our recipe for alcohol content and taste, so after showing off the gel to the judges, we wound up cutting it up and serving it in shot glasses with some flavored vodka - which definitely made the kinda grainy agar gel go down more easily.

We got a medal for "most reproducible" hack, which I guess means we'll probably wind up turning this into an instructable at some point. Many thanks to my science co-conspirators Joseph, Sarah, Yasa and Rolf for pulling this off in under 24 hours!

Patrik

[Sebastian S. Cocioba]

Would a clear soda like sprite have enough salt ions to work? Would be cool if it worked. Im guessing the KCL used in your buffer was a multimolar solution? Either way, awesome hack. The stack of silverware as a comb was brilliant! :)

Sebastian S Cocioba

CEO & Founder

New York Botanics, LLC

Sent via Mobile E-Mail 

On Nov 5, 2012, at 7:26 PM, "Patrik D'haeseleer" <pat...@gmail.com> wrote:

We wound up wasting a lot of time on the first day trying to get electrophoresis to work on gelatin gels. We actually did get a tiny bit of migration of the food dyes with a very solid gel (think "ballistics gel" rather than jello!). But at lower gelatin concentrations that should have given better migration into the gel, and would have been far more palatable, the gels kept melting as soon as we applied current.

Joseph Elsbernd (@CodonAUG) wound up bring much of his home lab to Science Hack Day, so we did much of the initial experimentation on that, while we worked to build a gel electrophoresis apparatus from scratch:

<image.jpeg>

And how's this for a gel comb hack. Yes, I know there are far easier ways to make a gel comb, but this was more fun, and created lovely slated wells:

<image.jpeg>

Patrik

[Patrik D'haeseleer]

On Monday, November 5, 2012 4:49:40 PM UTC-8, Sebastian wrote:

Would a clear soda like sprite have enough salt ions to work? Would be cool if it worked. Im guessing the KCL used in your buffer was a multimolar solution?

Sprite would probably work.Our solution was only very slightly salty to the taste, and I know most sodas include salts as taste enhancers. No idea what the carbonation will do though.

Also, we didn't really care about buffering capacity of our "buffer", since we weren't woking with proteins or DNA where pH control really matters.

Joseph wrote down all our recipes/protocols, so I'll wait for him to post those somewhere.

Patrik



 

[Cathal Garvey]

Nice work guys! I did love the knives-as-comb hack. :)

What did you use for electrodes, though? Wouldn't do any harm once in a
while but if it were a regular party-piece, I'd invest in graphite
electrodes (artist's graphite pencils should do?). After
copper-containing electrodes used just once (at the DIYbio summit in
Manchester), I got to see just how much ionic metal gets dumped in the
buffer! Bright blue, frothy buffer!

On 06/11/12 00:57, Patrik D'haeseleer wrote:
> On Monday, November 5, 2012 4:49:40 PM UTC-8, Sebastian wrote:
>>
>> Would a clear soda like sprite have enough salt ions to work? Would be
>> cool if it worked. Im guessing the KCL used in your buffer was a multimolar
>> solution?
>>
>
> Sprite would probably work.Our solution was only very slightly salty to the
> taste, and I know most sodas include salts as taste enhancers. No idea what
> the carbonation will do though.
>
> Also, we didn't really care about buffering capacity of our "buffer", since
> we weren't woking with proteins or DNA where pH control really matters.
>
> Joseph wrote down all our recipes/protocols, so I'll wait for him to post
> those somewhere.
>
> Patrik
>
>
>
>
>
>> Either way, awesome hack. The stack of silverware as a comb was brilliant!
>> :)
>>
>> Sebastian S Cocioba
>> CEO & Founder
>> New York Botanics, LLC
>>
>> Sent via Mobile E-Mail
>>

>> On Nov 5, 2012, at 7:26 PM, "Patrik D'haeseleer" <pat...@gmail.com<javascript:>>

>> wrote:
>>
>> We wound up wasting a lot of time on the first day trying to get
>> electrophoresis to work on gelatin gels. We actually did get a tiny bit of
>> migration of the food dyes with a very solid gel (think "ballistics gel"
>> rather than jello!). But at lower gelatin concentrations that should have
>> given better migration into the gel, and would have been far more
>> palatable, the gels kept melting as soon as we applied current.
>>
>> Joseph Elsbernd (@CodonAUG) wound up bring much of his home lab to Science
>> Hack Day, so we did much of the initial experimentation on that, while we
>> worked to build a gel electrophoresis apparatus from scratch:
>>
>> <image.jpeg>
>>
>> And how's this for a gel comb hack. Yes, I know there are far easier ways
>> to make a gel comb, but this was more fun, and created lovely slated wells:
>>
>> <image.jpeg>
>>
>> Patrik
>>
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>

[Patrik D'haeseleer]

We used stainless steel wire as electrodes, which seemed to work fine - at least for the weekend. We didn't see any noticeable corrosion after a few hours of running. You do have to make sure you really get stainless steel, not galvanized! The hardware store had 4-5 types of galvanized steel wire, but only one spool of stainless steel.

Graphite electrodes is a good idea. Of course, you still need to connect the graphite electrode to a wire somewhere, and you may need to protect that connection point if it's immersed in the liquid.

Patrik

[John Griessen]

On 11/09/2012 08:28 AM, John Griessen wrote:
> Getting long graphite to use as electrodes should be easy, but fragile.

What if you used thick graphite so it could be handled with less breakage?
Then it could simply lay in gel box slots and not go through the dish-washer action
when you need to clean your gel box, but be cleaned separately, perhaps
along with the other contact rod of graphite I proposed to avoid metal in the
electrolyte medium.

[Sebastian S. Cocioba]

Heavy duty D batteries have a rigid graphite rod in the middle which is fairly easy to remove. Ive used the as electrolysis electrodes for a hydrogen generator a while back.

Sebastian S Cocioba
CEO & Founder
New York Botanics, LLC

Sent via Mobile E-Mail

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[John Griessen]

On 11/09/2012 08:48 AM, Sebastian S. Cocioba wrote:
> Heavy duty D batteries have a rigid graphite rod in the middle which is fairly easy to remove.

Yes, those are an easy starting point for small gel cartridge size boxes, and small is beautiful.

[John Griessen]

On 11/09/2012 02:00 AM, Patrik D'haeseleer wrote:
> Graphite electrodes is a good idea. Of course, you still need to connect the graphite electrode to a wire somewhere, and you may
> need to protect that connection point if it's immersed in the liquid.

Getting long graphite to use as electrodes should be easy, but fragile.

The point of connection to metal can be offset from the lanes some and any
corrosion products would not get in your electrophoresis lanes.
Graphite strips or rods, (pencil leads), could just push fit into bent wire clips
of stainless steel. The whole gel box should be dishwasher safe, so it's not a trivial design.

One long rod could be below gel level in a tray, and another rod push down to contact it
from out of the gel, and have spring force when the gel box lid closes to make good contact.
With a gel box shape design that protects the graphite pieces from impacts,
yet lets dishwasher action clean well, you'd then have no metal in the medium.