RNA gels - staining and denaturing

Daniel Kim dkim at nmsu.edu
Sat Jul 15 13:49:05 EST 1995

Re:  RNA gels and ethidium bromide:

I have found glyoxal/DMSO gels also to work well.  The ethidium bromide 
may not stain RNA as well as DNA, because of the single stranded 
structure. Appropriate hydrophobic regions (base stacks) may not appear 
as often in RNA because of this, so there may not be as much 
fluorescence.  How much RNA are you running on a lane?

An alternative would be to stain with Acridine Orange, which can 
distinguish between ds and ss nucleic acids, giving different 
fluorescence for each.

Daniel Kim

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