RPA analysis

Brenda Leeuwenberg brendal at warc.cri.nz
Wed Jun 16 18:47:10 EST 1993

I'm using ribonuclease protection assays (RPA) to look at the specificity of 
my riboprobe (normally used for Northern blotting.  I have run into a problem
with my markers.  My products are run out on a 5% acrylamide/urea gel.  My 
markers are 32P-labelled DNA markers - because i didn't have any others.
My products should be running at 200bp, ie just above the xylene cyanol band.
Howver according to the markers the xylene cyanol is running at about 500bp.
Does anyone have any information about
the reliability of DNA markers on 
polyacrylamide gels?  Would i be better to rely on the xylene cyanol band as a
 size guide, or the markers?
any advice would be appreciated.

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