TBE vs TAE for agarose gel electrophoresis - (Aug/06/2006 )

in our lab we use 0.5x ... no problems there, but you can run agarose gels quite fast, as the ionic strength and hence the resistance is lower. Means less heat, no melting of gel at higher power

I have to agree with scolix, I have never altered my gel extraction protocol for TBE gels.

The only thing I ever came across was when gel extracting a transgenic cassette for subsequent microinjections the protocol insisted on using TAE gels and to not use TBE but the protocol never went into the theory behind why.

Use SB, no tris, just sodium hydroxide and boric acid, so cheap and easy to make as well as good resolution and can run gels fast.

One of my lab mates is running alot of electrophoresis, in a few days, we notice that the tank is very hot, but the gel is still fine then one day smoke came out from the electrophoresis machine (not the tank) and it cannot be use anymore. We suspected it is the buffer that he made was inaccurate. Is there anyway to check it?

We use 0.5x TBE regulary and 1x TBE for long (day/night) electrophoresis, because of the believed better buffering capacity of TBE. 1x TAE is used in our lab for gel extractions because we are used to and some people claims it gives higher yield, but I never seen any proof to that.
I would personally say, that bands look a bit sharper in TBE (0.5) than in TAE.

Cambrex company has"A handbook for gel electrophoresis" in their website. According to this handbook,

TAE is used for DNA recovery and electrophoresis of large (>12 kb) DNA. TAE has low buffering capacity and recirculation may be necessary for >6 h of electrophoresis.

TBE is used for small (<1 kb) DNA and shows increased resolution of small DNA. TBE shows decreased DNA motility and has high buffering capacity, therefore recirculation is not needed for extended run times.

For electrophoresis, both buffers work for me. For DNA extraction I am using gel extraction kits and they are designed to extract and purify DNA from agarose gels in TAE and TBE buffer. I could not see a difference in the purity or amount of extracted DNA when I used any of these two buffers. Probably, for long running times or repeated use, TBE is better. Repeated use of TAE buffer results in excessive heat and failure of electrophoretic equipment.