Sodium Borate Buffer for Cheaper, Better Electrophoresis

[Cathal Garvey]

Hey all,
After reading two papers this morning, I'm planning to make my next gel with Sodium Borate buffer instead of TAE/TBE. I've outlined the reasons with more here, but in brief:

According to this paper: http://is.gd/7xfA0 the buffer of choice is Lithium Borate, but Sodium Borate worked really well also, outclassing TBE and TAE in resolution, lack of heat production and the upper ceiling of voltage that could be applied. Lanes and bands come out prettier and the DNA can be extracted for downstream use with fewer complications than TBE. (More details: http://is.gd/7xNjB)

Perhaps most importantly, the cost of SB buffer compared to TAE and TBE was also staggeringly low. The per-litre price of TBE versus SB after my one-minute price hunt turned out to be $1.28 against $0.04, and while I found Sodium Borate powder for sale on ebay, TBE or TAE aren't available. If you want to go ahead and try, get yourself some disodium borate decahydrate (I believe this is the predominant powdered form) and add 1.907g to 1L to make up 1x SB buffer. It should be about pH8 - 8.5

For DIYbio, this seems to be the way to go if it works as well as the papers seem to show. I'll be using it for my next gel in the lab, and I'll report on my results.
All the best,
Cathal

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[leaking pen]

OOOO. Trying to find TBE has been a PAIN. PLEASE PLEASE let us know
how it goes.

Alex

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[Nathan McCorkle]

Here we have both TAE and LB commonly available, I haven't ever run two gels with the same DNA in either media to compare, but the main difference I've found is that LB can just run faster... not sure what properties allow that, something with resistance, but I guess its higher for LB. Not sure why bands would be tighter either.

I'm interested to find some better alternatives to the gels used in capillary electrophoresis for separation of oligos differing by only 1 nucleotide for sequencing. Or maybe some sort of mechanical sorting could help, combined with better buffer to get things running faster and more accurately.

 

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[Derek]

Nice.

When I got my OpenGelBox from Pearl it contained a small sample bottle
of a sodium borate based running buffer from http://www.fasterbettermedia.com/

I haven't fully gotten rid of my Tris-based buffers but expect to move
away from them over time given my positive experience with the sodium
borate buffer.

--Derek

On Feb 2, 7:06 am, leaking pen <itsat...@gmail.com> wrote:
> OOOO.   Trying to find TBE has been a PAIN.  PLEASE PLEASE let us know
> how it goes.
>
> Alex
>

> On Tue, Feb 2, 2010 at 7:37 AM, Cathal Garvey <cathalgar...@gmail.com> wrote:
> > Hey all,
> > After reading two papers this morning, I'm planning to make my next gel with
> > Sodium Borate buffer instead of TAE/TBE. I've outlined the reasons with more
> > here, but in brief:
>

> > According to this paper:http://is.gd/7xfA0the buffer of choice is Lithium

[Aaron Hicks]

Should be easy enough to make sodium borate at home, too; boric acid ("roach pruf" or similar from Wal-Mart or whatever) plus sodium hydroxide (crystal drain cleaner from Home Depot, used to replace Red Devil lye). The usual caveats apply- sodium hydroxide is caustic and nasty and toxic. But the reaction is straightforward, along with the stoichiometry.

Commercial borax detergents like "20 Mule Team" would work. A cursory check of teh Intarwebs puts it at 99.5% purity, according to people who checked with the company.

-AJ

[Cathal Garvey]

Indeed, you make up 5mMol Sodium Hydroxide and titrate with Boric Acid to pH8.

If you can get household chems of that purity, it should be a snap. Watch out for other ingredients that might be inimical to DNA like HCl or whatever.

I'd say a quick call to the manufacturer would clear up any questions.

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[Nathan McCorkle]

On Tue, Feb 2, 2010 at 2:49 PM, Aaron Hicks <aaron...@gmail.com> wrote:

Should be easy enough to make sodium borate at home, too; boric acid ("roach pruf" or similar from Wal-Mart or whatever) plus sodium hydroxide (crystal drain cleaner from Home Depot, used to replace Red Devil lye). The usual caveats apply- sodium hydroxide is caustic and nasty and toxic. But the reaction is straightforward, along with the stoichiometry.

Drain cleaners often have aluminum in them... FYI, I wouldn't use that route.

 

Commercial borax detergents like "20 Mule Team" would work. A cursory check of teh Intarwebs puts it at 99.5% purity, according to people who checked with the company.

-AJ

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[leaking pen]

The one mentioned is supposed to be 100% caustic lye, no aluminium.
I've used it for making soap before, good stuff.

[Aaron Hicks]

On Tue, Feb 2, 2010 at 2:00 PM, leaking pen <itsa...@gmail.com> wrote:

The one mentioned is supposed to be 100% caustic lye, no aluminium.
I've used it for making soap before, good stuff.

Yeah- Red Devil got pulled off the market since it did what the label boasts (destroys organic matter with no discretion whatsoever), same as "strike anywhere" matches. I forget the name brand of the stuff that's still available, but it comes in a metal can, IIRC- sodium hydroxide with no aluminum added.

We're fortunate that gasoline doesn't burn, or we'd have to pull that off the market as well.

-AJ
 

[Ben Gadoua]

Just FYI guys, you're probably going to want to adjust the pH to about 8. As the electrophoretic process proceeds the pH will increase some, making 8 (the lower end of Na2B4O7's buffering range) an ideal target, as it gets closer to the pH where it has maximum buffering capacity (somewhere like 9.6 iirc) the pH will change less and less. You can run gels at 5-35V/cm with an SB buffer, iirc. Make sure not to overrun your gels the first few times, and use a loading dye.

Ben