EtBr staining of RNA
Petri T. Kursula
pkursula at zombie.oulu.fi
Fri Aug 18 06:18:57 EST 1995
> 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...
More information about the Methods