Acidic TBE buffer - is it even effective? (Aug/30/2006 )
I'm trying to run an agarose gel for cationic quantum dots (1% gel). I tried with the typical pH of ~8.3-8.4 in 0.5x TBE buffer but it only seemed to work for anionic particles. I believe the pH is too high for the cationic dots to run and want to try it in a more acidic buffer of pH ~7.0. The problem is when i add more boric acid to the buffer, it remains stable at pH 8.0 for a long time... I've added quite a lot of boric acid already (about 100mM Boric acid to ~65mM of Tris/Borate) and it seems like if I add it till pH 7, the buffer wouldn't really work too well.
Is there some other buffer I can use for running / making the agarose gels if I want it at pH 7.0?
Thanks. I'm pretty clueless about this.
I would use TAE, as boric acid may interact with polycations. Most cationic groups, such as lys or arg side chain has pK 9.5-10 or ~12. You are ok with this pH.