TAE or TBE, which is best? Well, of course, it depends on what you want to do. Here are the pros and cons of both:
- TBE (Tris-borate-EDTA) is a better conductive medium than TAE (Tris-acetate EDTA) so is less prone to overheating so use TBE for long runs
- Borate is an enzyme inhibitor so TBE is not a good buffer to use if you will be isolating the DNA for downstream enzymatic steps. For example, borate carry-over could affect your ligations, so use TAE instead.
- Acetate gives improved separation of large DNA fragments
- On the other hand, borate resolves <2kb fragments better, so use TBE for smaller fragments
- And finally, TBE is reputed to give nicer bands than TAE (although I’m not sure why – does anyone know?)
But you might be better of using neither of these buffers. Despite the fact that they have been firmly established as the most popular buffers for DNA electrophoresis since their emergence in the early 1970s, TBE and TBE are not really optimised for the job and have a lot of disadvantages.
Borate and acetete are simply carry-overs from earlier work on protein electrophoresis buffers upon which the technology of DNA electrophoresis was built. And while the reasons that Tris was chosen as the primary cation by early pioneers of DNA electrophoresis are not clear, the draw-backs certainly are. As well as being expensive, Tris-based buffers are not ideal for DNA electrophoresis because, even under optimal conditions, they are prone to a temperature-current feedback loop that causes the solution, and therefore your gel, to overheat. And finally, EDTA is a relic from RNA electrophoresis, which has been unecessarily retained in DNA electrophoresis buffers.
In an earlier article here on Bitesize Bio, Bala described new and improved DNA electrophoresis buffers developed by scientists at John’s Hopkins University. These are optimised for the job and are faster, cheaper and less prone to overheating than TAE and TBE.
For more information on this, check out this article, which details the history of DNA electrophoresis buffers and the development of the new buffers. The authors of this paper (and the inventors of the new buffers) have started a company called Faster, Better Media to manufacture and distribute the buffers.
So what do you normally use; TBE, TAE, or something else?
TAE or TBE, which is best? Neither TAE nor TBE! There is nothing better than Borax!! The bands are sharp and the gels can be run at high voltages. And in addition, at least so far, I did not notice that it does interfere with any column purification kits.
I’ve also started using borax and it’s really outstanding compared to TBE and TAE. But does anyone know if the borate in borax also is a potential inhibitor for downstream enzymatic steps?
Does anyone have any suggestions on what to use for genomic DNA Southern Blot gels? I have been using TBE (as standard protocols say this (mainly due to the heat/depletion issues with TAE and overnight runs)).
Lindsey,
I used to do Southern blots in an “industrial” setting. We used TAE buffer and ran the gels slowly to avoid any overheating issues. As long as you don’t run too long or try to re-use the buffer, you should be fine with TAE. I’ve also used the Borate buffer that the original post here mentions for several years and it has worked great for agarose gel separations of DNA and even RNA (as long as the gels are “fresh” for RNA)and has the advantage of being much cheaper and simpler to prepare. But when I tried to do Southern blots out of agarose gels made in Borate buffer, it was a total disaster…the DNA would not transfer–it seemed to be immobilized. So I switched back to TAE for the Southerns and all worked well.
HI NICK,
WHAT HAPPENS IF WE USE CONCENTRATED PHENOL FOR RNA ISOLATION?
WHAT HAPPENS IF WE STORE PRECIPITATED RNA AT ROOM TEMPERATURE?IS IT NECESSARY THAT WE SHOULD STORE IT AT LOW TEMPERATURE
sir,
i’m gonna purify my restricted vector and pcr products by native PAGE followed by electrodialysis… TAE or TBE, which is more suitable for a native PAGE?
I ran with Borax once (for a test) and i observed that the gel separated much more of the lower bands (the gel was a 1% agarose which we commonly use for standard applications). Can one explain or observed similar fact?