Re: [DIYbio] Borax as a superior alternative to Tris

It would be great to use Borax for other buffers, but I gather the borate ion is inhibitory to enzymes. Tris is a pain to get hold of, so a nice replacement would be really, really cool.

On 24 June 2012 14:54, Robert O'Callahan <ropoctl@rice.edu> wrote:

I've used SB buffer to run gels. It's nice to be able to use the maximum voltage, but they don't run as well. When loading high concentrations of DNA the migration distance can do weird things, but it works well for preparatory gels when you need good separation quicker.

-Rob

On Sun, Jun 24, 2012 at 3:54 AM, Cory Tobin <cory.tobin@gmail.com> wrote:

> I read a paper a while ago showing a comparison of
> different buffers, and feel like the borax ones weren't
> as good for certain fragment sizes or something...
> what I mean is, I feel like there was some tradeoff
> between TAE and borax buffers

SB doesn't do well with high molecular weight fragments, like >8k or
so.  TAE works better in that case.

> But this could possibly made even better by reducing the
> Na in the solution.

True.  Lithium is better but it's expensive.

> Also, the above papers said that you don't really need
> EDTA either. The use of EDTA is kind of a left-over
> from RNA gels that persists in DNA gels for some reason.

This is typical of biology at universities.  Someone finds a protocol
that works and keeps using it without determining what parameters are
actually important.  There is no incentive to try running gels with
missing components because discovering that EDTA is not needed will
not get your NIH grant renewed or help you get tenure.  From any
individual's perspective it's better to just continue using protocols
that work and focus on their research, especially considering that gel
buffers are a very minor portion of any research budget.  Although,
this might not be the case for diybio.

> Does anyone here work with Borax? It is readily
> available from the supermarket and I would be
>keen to hear of anyone else's experiences

Yeah, it works well.  I've used both methods: (1) Borax only and (2)
NaOH + Boric acid.  Both work fine.  One thing to note is that you
can't make a 50X stock of SB like you can with TAE.  The max I go is
20X and even then I still get some precipitation.  It's a bit
inconvenient but not enough to make me stop using it.  Also, if you
plan on running your gel at 300V for more than 10 minutes, make sure
you have a box with large reservoirs or you'll melt the gel.


-cory

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Rob O'Callahan
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George R. Brown School of Engineering | Rice University
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