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I just stumbled upon an article promoting 10 mM sodium borate as an alternative to the well-known TAE and TBE buffers for agarose gel electrophoresis of DNA (Brody & Kern, 2004). They claim that sodium borate outperforms TBE and TAE at high-voltage conditions due to the significantly lower heat development.

I'm currently using TBE buffer and gels with 7M urea for my denaturing PAA gels, and I'm wondering if there are similar alternative conditions for those denaturing PAA gels of nucleic acids?

I couldn't find anything on using sodium borate for denaturing PAA gels, so I'm wondering if it should work the same as for the agarose gels or if it just isn't a good buffer for that kind of gel.

Brody, J. R. & Kern, S. E. Sodium boric acid: a Tris-free, cooler conductive medium for DNA electrophoresis. BioTechniques 36, 214–216 (2004).

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  • $\begingroup$ Not related to your question but what voltage are you running your gels? It seems as if your having all sorts of issues with over-heating. $\endgroup$
    – bobthejoe
    Mar 29, 2012 at 17:37
  • $\begingroup$ 250V (results in ~30-35mA), I'm having no significant overheating problems, but if I could just run the gels faster at higher voltages it might be useful. $\endgroup$
    – Mad Scientist
    Mar 29, 2012 at 17:55
  • $\begingroup$ @bobthejoe PAGE and PAA gel electrophoresis are the same thing, if you mean a discontinuous gel like SDS-PAGE for proteins that doesn't exist for nucleic acids as far as I know. $\endgroup$
    – Mad Scientist
    Mar 30, 2012 at 8:39
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    $\begingroup$ For what it's worth, I use TAE with agarose and never exceed 90 V (~20 mA). Resolution is always better at lower temperature conditions, in this case, meaning lower voltages. $\endgroup$
    – user560
    Mar 30, 2012 at 12:00
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    $\begingroup$ This is a good question. I'll look around for a reference later, but I'm fairly certain that as long as the current has not exceeded a certain threshold (such that the gel and buffer heat up to the point of causing the gel to contract or distort) resolution is function of migration distance. $\endgroup$
    – user560
    Mar 31, 2012 at 13:30

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You can try SB (sodium boric acid), LA (lithum acetate) or LB (lithium boric acid) buffers. Thex generate must less heat then TAE or TBE buffers and can be run on much higher voltages and are much cheaper than TAE or TBE. Also they do not interfere with standard applications such as band excision and they last longer.

For more info try this sites:

http://www.fasterbettermedia.com/products.html http://ddgehelp.blogspot.com/2008/01/alternative-electrophoresis-buffer-to.html

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