TAE gel in TBE buffer - Does it work? (Dec/19/2008 )

So, I'm pretty sure it doesn't work. I accidentally ran a gel made with TAE in a gel chamber filled with TBE buffer. The samples and ladder got all scrunched up in the gel and the dyes escaped from their proper lanes and migrated all along the width of the gel. The whole thing was uninterpretable. So, I know it doesn't work, but I want to know why. TAE is hanging out in the gel, TBE is conducting the current, sounds like it should not be a problem?? Someone please help, this is going to drive me crazy!!!

I believe it has to do with the relative concentration of charge carriers and nature of the charge carrier it self. TBE has 87mM of boric acid (-3) and TAE has 20mM of acetate (-1).

As a result TBE is better change carrier and conducts most of the electrical current in the gel electrophrosis compared to TAE. DNA moves down a potential gradient because it too is a charge carrier. But I am guessing that the difference in charge carrying ability of TBE and TAE short circuits the gel tank. Since the TBE is now carrying most the charge, the DNA with a TAE environment doesn't move as much.

I am guessing that the dye isn't affected as much as the DNA.

That would mean that TBE gels would run in TAE buffer, right?

Did anyone try that?

So why do some people choose TAE over TBE? Our lab has just merged with another and some of us prefer TBE while others prefer TAE which means we have tanks labelled with things like "TAE ONLY!!!" What are your preferences and why?

Look up the following links. Generally gel run on TBE can tolerate a higher voltage setting than TAE gels due to its higher electroconductivity. So TBE gels are faster.

So in theory, for smaller DNA bands TBE gels will give better band resolution compared TAE gel as the DNA has less time to diffuse. And by the same token TAE gels resolve larger DNA fragments better than TBE. It must be noted that difference in band resolution between TAE and TBE has been reported to be marginal by several member in the forum.

It is also believed that one should use TAE when conducting DNA ligation. However several members in the forum have stated that there is no difference. The difference between TAE and TBE gels in this respect is uncertain, unless somebody spends the time and conducts a proper experiment.

http://www.protocol-online.org/forums/inde...showtopic=18864

Note, there have been improvements in gel electrophoresis. Li-borate buffer.

http://www.protocol-online.org/forums/inde...?showtopic=9431