Small RNA electrophoresis: any tips?

Jerry M. JM at
Tue Oct 5 08:06:29 EST 1999


I've looked in the archives before posting this question, but I couldn't
find a satisfactory answer: what's the best way to do a nice RNA
electrophoresis to just show the size of a small (200 bp) transcript? I'm
not into doing Northerns, I just want to take a nice picture of a nice
gel. Since the gel must be denaturing, I've tried MOPS/Acetate buffer +
2.2 M formaldehyde + EtBr and the background fluorescence is a disaster no
matter what the EtBr concentration is, however I could faintly see some
bands of the marker. I've tried adding EtBr in the sample and not in the
gel: the small RNA doesn't seem to stain well enough to see something
unless there's a huge amount (>5 ug) of it, and then there's something
which couldn't really be called a band. I've tried to lower the
formaldehyde to 0.22 M: the contrast is much better but apparently it's
not denaturing enough (several upper bands appear instead of just one). I
don't know what else I could try. Methylene blue staining? Or the green
dye (sorry, can't remember the name righ now)? Would polyacrylamide-urea
gels be better? Any tip would be much appreciated.

Thanks in advance,

     Jerry M.

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