EtBr staining of RNA

John Nelson jnelson at
Thu Aug 17 16:02:06 EST 1995

In article <40vpcf$5rn at>, mb935645 at (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
>Dave Clarke (D.L.Clarke at 
	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

Good Luck,

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

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