Re: [DIYbio] Any ideas on edible electrophoresis buffers?

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

On Thu, Nov 1, 2012 at 2:39 PM, Cathal Garvey <cathalgarvey@gmail.com> wrote:
> 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)?
>
> On 01/11/12 18:00, Patrik D'haeseleer wrote:
>> 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
>>
>> On Thursday, November 1, 2012 4:57:08 AM UTC-7, Cathal wrote:
>>>
>>> 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...
>>>>
>>>
>>> --
>>> www.indiebiotech.com
>>> twitter.com/onetruecathal
>>> joindiaspora.com/u/cathalgarvey
>>> PGP Public Key: http://bit.ly/CathalGKey
>>>
>>
>
> --
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> twitter.com/onetruecathal
> joindiaspora.com/u/cathalgarvey
> PGP Public Key: http://bit.ly/CathalGKey
>
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--
-Nathan

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