I have done a little staining of nylon membranes using the methylene
blue protocol. The RNA stains beautifully on fresh membranes, and the
destaining step works well on the background. However after some hyb
conditions, particularly high SDS, the destaining step does not work, so
that the RNA bands do not stand out against background. Having ethidium
bromide in the RNA does not seem to be a problem.
Hope this is of help.