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

On Sun, Jun 24, 2012 at 3:53 PM, Cathal Garvey <cathalgarvey@gmail.com> wrote:
> 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.

Tris is a pain to get in what sense? The tris /wiki page says/ its
used because its cheap... (and since everything on the internet is
correct...) :P

>
>
> 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
>> M.S. Civil & Environmental Engineering 2012
>> George R. Brown School of Engineering | Rice University
>> E: rpo1@rice.edu<mailto:rpo1@rice.edu>| P: 847.641.1285
>>
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>
>
>
>
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--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

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