EtBr staining of RNA

[John Nelson]

In article <40vpcf$5rn at hippo.shef.ac.uk>, mb935645 at silver.shef.ac.uk (D L Clarke) says:
>
>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.
>
>Any suggestions would be gratefully accepted
>
>Thanks
>
>Dave Clarke (D.L.Clarke at sheffield.ac.uk) 
>
Clarke,
	Is single stranded impossible to visualise with EtBr?  Answer NO.
	I routinely use EtBr to stain RNA gels.  I use a 50 ug/ml solution
for 10 min. in whatever buffer the gel (1%-2.5%) was run in; my case MOPS.
Works fine if you incubate for 5 min. but for my purposes I stain for 10,
destain for 5-10 for the best resulting picture.  Now for your Northern 
that would be a problem, but 5 min should be long enough to see something.
	There are other alternatives out now besides EtBr, such as SYBR
Green.

Good Luck,

John Nelson
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jnelson at bioch.tamu.edu
Dr. E. D. Harris Laboratory
Department Of Biochemistry & Biophysics
Texas A&M University
College Station, TX, U. S. A.