Citric Acid as Green Alternative to EDTA in TE / TAE / TBE

[Cathal Garvey]

Hi again all. Last post for a while.

I've been considering an alternative to EDTA for routine labwork, because EDTA is a persistent organic pollutant. As a powerful chelating agent that just-won't-quit, it can do a lot of damage upon disposal to aquatic or terrestrial ecosystems.

For the uninitiated, EDTA is used in Molecular Biology to chelate (grab/sequester) metal ions like magnesium so they can't be used by certain proteases, DNases and RNases to destroy all those fascinating molecules we love so well. Most of these enzymes use metal ions as a critical part of their active site or to aid in folding, so EDTA effectively nullifies them.

That's why it's found in TBE, TAE and TE: buffers used commonly when working with nucleic acids. Long-term storage of DNA/RNA is more stable in Tris-EDTA because of the pH altering effect of tris and the chelation of EDTA. DNA running in TAE/TBE gels is more likely to survive because of the chelating effect of EDTA.

Thankfully there is (probably!) an alternative that poses less of a hazard to the environment: Citric Acid. The humble citric acid has been and is still used in many industrial applications to chelate metal ions (such as in pharma, where it's used to mop up free metal ions from equipment before use). It's not *as* powerful as EDTA, but it's generally regarded as a powerful chelating agent nonetheless. Because citric acid is used by virtually any organism employing the kreb's cycle of aerobic metabolism, you can be pretty sure it's unlikely to go undegraded for long in the wild.

I haven't worked with it, I've seen nobody else doing so, and I won't have a chance to experiment for a while. But it's definitely worth trying as an alternative, particularly for TAE/TBE (which get discarded much more often and in greater bulk than TE, and whose function is generally less critical).

Sorry to spam the list today! Hope this is useful/intriguing to someone.

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[Jay Woods]

On Friday, August 20, 2010 08:57:59 am Cathal Garvey wrote:
> Hi again all. Last post for a while.
> I've been considering an alternative to EDTA for routine labwork,
> because EDTA is a persistent organic pollutant. As a powerful
> chelating agent that just-won't-quit, it can do a lot of damage upon
> disposal to aquatic or terrestrial ecosystems.
>

While your at it (testing Citric Acid), it would be worthwhile also
testing Gluconic Acid. It is also used industrially as a chelating
agent.

[Cory Tobin]

Any guess as to how much citric acid would be necessary to get the
same effect as 1g of EDTA?

-Cory

[Simon Quellen Field]

You might try adding equal amounts of each to equal amounts of soapy water

with Epsom salts in it, and seeing which one foams better (the one that chelates

the magnesium will foam better).

But if it's cheap, maybe overkill is not a problem?

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[Cory Tobin]

On Fri, Aug 20, 2010 at 3:08 PM, Simon Quellen Field <sfi...@scitoys.com> wrote:
> You might try adding equal amounts of each to equal amounts of soapy water
> with Epsom salts in it, and seeing which one foams better (the one that
> chelates
> the magnesium will foam better).

Great suggestion! I'll try that out later tonight.

> But if it's cheap, maybe overkill is not a problem?

True, but in some situations the pH of the solution is important, so
minimizing the citric acid might eliminate the need to adjust it with
NaOH.

-Cory

[Nathan McCorkle]

is citric acid still a chelator when its reduced with a base?

-Cory

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

[sgt york]

On Aug 21, 12:57 am, Nathan McCorkle <nmz...@gmail.com> wrote:
> is citric acid still a chelator when its reduced with a base?
>

Citric acid only works as a chelator above pH 5. Don't quote me on
this, but I seem to recall it improving as a chelator up to a pH of
about 9 or so.

[Mackenzie Cowell]

Cathal,

Any thoughts on using citric acid to make a "greener" electrophoresis buffer?  Could and should we think about replacing Tris as well?

Mac

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[Cathal Garvey]

Well for TE, I'm thinking leave well enough alone because it is usually used for DNA stocks: not worth risking for now.

For large volumes of disposable buffer though, where chelation doesn't need to be perfect, I see a lot of merit in trying to replace the ugly stuff, particularly as EDTA adds so much sodium to the running buffer (increasing current). Having recently read some mention that tris mightn't be that harmless either I've been meaning to do some more research into why and for possible replacements.

For gels, sodium borate (borax) works great but formulated ladders may have too much salt and run too fast. I still haven't checked how ecologically damaging that stuff is, though. It kills ants so it can't be that rosy!

What you want is something that buffers fairly well and doesn't conduct electricity well. I think.

On 16 Oct 2010 02:42, "Mackenzie Cowell" <m...@diybio.org> wrote:

Cathal,

Any thoughts on using citric acid to make a "greener" electrophoresis buffer?  Could and should we think about replacing Tris as well?

Mac

On Tue, Aug 24, 2010 at 9:46 AM, sgt york <jv...@yahoo.com> wrote:
>

> On Aug 21, 12:57 am, Nathan...

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