haeting RNA before electrophoresis - (Aug/26/2014 )

Hi

I am going to isolate RNA from mammalian cells and I plan to run it on 1% non denaturing agarose gel. I have read protocols which recomand to heat RNA sample followed by chilling it on ice. Some of my lab mate have advised me to just run the sample without heating, but I am not sure if it will affect my work. I also have some trouble understanding how does etbr help visualizing the single stranded RNA with no secondary structure?

thanks in advance

It depends on what you are trying to see - if you just want some sort of measure of the integrity of the DNA, then you don't really need to denature it (which is what the heating step is for), as the 18S and 32S bands should still be visible and you don't really need to worry about secondary structure. Note that ssRNA doesn't stain with EtBr as brightly as dsRNA or dsDNA, due to how it intercalates with the molecules.
 

If you were doing a Northern blot on the other hand, you would want to run a denaturing gel and denature the RNA before loading.