TAE Vs TBE buffer - (Sep/11/2012 )

I reuse my SB several times before changing, probably just as frequently as I would have changed my TBE.

i am still using TBE but i don't reuse the TBE more than 3-4 times.
i will switch to SB buffer and try that as well.

I just got to situation when I need to distinguish on gel restriction fragments of very small PCR product (39 + 54 bp from uncut). As I know how problematic is TBE gel in fragments with length < 100 bp, I was thinking that trying SB buffer for this would be handy.

But problem is, it's a restriction reaction, so high salt content. These have pretty problems even in TBE gels, mostly smaller than 200 bp are just smears, because when the gel runs long enough to clean from salts, the smaller fragments are just too blurry.

I was thinking maybe desalting the samples before loading would help, but I can't use common Qiagen columns for that as their lower limit is 70 bp. Precipitation is probably a way to go, but the fragments are small and the concentration wouldn't be high either.

Try 2-3% Nusieve 3:1 agarose or Metaphor agarose for high resolution, or a Tris PAGE gel. You could desalt with drop dialysis, which is fast and easy.