diy agar => agarose?

[J. S. John]

Did anyone figure out how to purify store bought agar into agarose only? What I learned in the lab is that there is an inverse proportionality between DNA size and percentage of gel. This means that that low concentartions work better for smaller DNA sizes and vice versa.

So agar is not so great in molecular bio and agarose is expensive (ebay:50g for $25). Any ideas?

[Cliff]

50g for 25 dollars is not so expensive really. Did you consider
reusing your gels? depending on what you are doing can either run the
old sample right off the gel or re-melt and re-pour the gel. Also
considering that a normal 1% gel takes around .4 g of agarose (for a
40ml gel) you could get over 100 gels for 25 dollars and perhaps over
200 gels for 25 dollars if you re-use them (thats like 12 cents a
gel!).

[Nathan McCorkle]

I wonder if you could make a big gel, then run concentrated agar solution through it to purify... dunno how you would stain/track the smallest particles, and also how to keep concentrate from hardening... you might be able to run the concentrate through a warm polyacrylimide gel, I don't think heat alone will depolymerise (I have read that you can use H2O2 + perchloric acid + heat to depolymerise tho)

[Eugen Leitl]

Not worth your money to spend a lot of time and brain cycles on it.

A lab is expensive. Can't stand the heat, get out of the kitchen.

If you don't want to buy it, contact your local university or R&D
shop. You might obtain equipment or surplus stuff cheaply to free.

--
Eugen* Leitl <a href="http://leitl.org">leitl</a> http://leitl.org
______________________________________________________________
ICBM: 48.07100, 11.36820 http://www.ativel.com http://postbiota.org
8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE

[Bryan Bishop]

On Wed, Jul 8, 2009 at 4:49 PM, Eugen Leitl <eu...@leitl.org> wrote:
> A lab is expensive. Can't stand the heat, get out of the kitchen.

A lab is expensive because typically people with lots of money run
those labs. Cheap labs are cheap.

- Bryan
http://heybryan.org/
1 512 203 0507

[Stacy]

>or re-melt and re-pour the gel.  

If you've used ethidium bromide to stain your gel, you really don't
want to remelt it unless you have a fume hood (and please don't use
the vent on your kitchen stove for this).
If you're trying to save money, just use the smallest gel you can to
get the job done. It's not one of the more expensive supplies, and
fussing around with cleaning out the ethidium safely will just cost
more than it's worth. Also, the salts won't quite be the same as your
buffer after the first use, and the gel won't run right. Trust me on
this one.

A word about disposing of ethidium gels: when they dry out, they take
up very little space. Keep a bucket in the garage and dump them in
there and leave the lid a little loose. You can run gels for years
and the bucket won't fill up.

And I'm sure you all know, but for the casual reader: you want to wear
gloves for handling ethidium bromide, gels that contain it, and keep
one flask dedicated to making gels and don't use it for anything
else. Also let the agarose cool down a bit before you add it,
otherwise nasty vapors will be in your house. It's one of the yuckier
molbio chemicals.

[Tito Jankowski]

Here's a vote for SYBRsafe, rather than ethidium bromide. Much cheaper when you take into account the costs of ethidium bromide disposal/harm to the environment.

http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Nucleic-Acid-Purification-and-Analysis/Nucleic-Acid-Gel-Electrophoresis/nucleic_acid_gel_electrophoresis/Nucleic-Acid-Stains/SybrSafe-A-better-DNA-gel-stain.html

Tito

[Eugen Leitl]

On Wed, Jul 08, 2009 at 05:06:18PM -0500, Bryan Bishop wrote:
>
> On Wed, Jul 8, 2009 at 4:49 PM, Eugen Leitl <eu...@leitl.org> wrote:
> > A lab is expensive. Can't stand the heat, get out of the kitchen.
>
> A lab is expensive because typically people with lots of money run

Nope. It's a market demand thing. Taq is expensive because you can't
buy it at your grocer. Few people have it in their home fridge.

> those labs. Cheap labs are cheap.

Can you show me examples of cheap labs?

My cheap lab needs a couple liters of 99.9% deuterium oxide. Can you
get me some on fire sale?

[ridgway]

http://groups.google.com/group/diybio/browse_thread/thread/3d7e7d6424e0d2a6/bbab3ffcb5b7913e
has some agar purification recipes. When I was doing the HV food dye
electrophoresis with food agar, I found that even one change of water
reduced the conductivity ~10x, so I tried reusing as much as possible.
The reformed gels started getting pretty fragile, though, not entirely
sure why.

[Nathan McCorkle]

I definitely vote for one of the "safe" DNA stains, SYBR, GR, maybe
others... better to handle, better to dispose, better to illuminate
(at least ethidium only intercalates in the DNA, UV breaks and
dimerizes it)

http://www.labsupplymall.com/nucleic-acid-stains-84/gr-safe-nucleic-acid-stain-290.html

Enzymes are going to get cheaper, and per reaction they really aren't
that expensive as it is. Won't be long before someone in the DIY
community will culture and purify enzymes, and sell them at a
discounted rate.

--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

[Bryan Bishop]

On Thu, Jul 9, 2009 at 12:18 AM, Nathan McCorkle wrote:
> Enzymes are going to get cheaper, and per reaction they really aren't
> that expensive as it is. Won't be long before someone in the DIY
> community will culture and purify enzymes, and sell them at a
> discounted rate.

I've been meaning to get around to listing out some esoteric methods
of purifying enzymes, besides HPLC or besides affinity chromatography
(or perhaps I should say, in addition to). Could someone bug me to get
around to doing this soon? :-)

[Nathan McCorkle]

Dangit Bryan, get cookin!