EtBr staining of RNA

[Petri T. Kursula]

> I have ran a 2% w/v  formamide gel for a Northern blot.
> However, when I stained the markers in 1ug/ml EtBr I could see
> nothing after a 5min incubation. I know I could have degraded
> my RNA but I would expect to see some sort of smear even
> if it has degraded.  Is single stranded impossible to visualise
> with EtBr?  Should I incubate for longer or change from
> DEPC water to TAE or TBE during the incubation.
> 
I think you should get rid of the formamide before staining. At least 
when I've used a formaldehyde gel, the formaldehyde that keeps RNA 
single-stranded must be washed out of the gel. This can be done with 
DEPC-treated water e.g. 3 times 10 minutes or something.
When the denaturing agent is no longer present you can visualise the RNA with 
EtBr. I remember using a longer time to stain the gel anyway...

Pete