EtBr in agarose gels vs. EtBr staining later

John Tudor jtudor at
Wed Mar 1 08:48:16 EST 1995

I don't think that low bp bands at the bottom will be unstained.  Only 
free EtBr migrates in the opposite direction.  When EtBr complexes with
DNA, it migrates with the DNA (or RNA).  Although I don't routinely add
EtBr to the gel, as DNA moves through the gel, it will pick up EtBr and 
they will move together (as someone else mentioned, this will affect
the migration rate).
By the way, since EtBr migrates, it will end up in the running buffer.
For those of you who incorporate EtBr in the gel, how do you dispose
of your running buffer?

kalch (kalch at wrote:
: In article <D4GKBu.8Ar at>, rmoldwin at wrote:

: > 
: > If I recall correctly, when I tried it, the EtBr migrated in the opposite 
: > direction as the DNA.  Also, when you add EtBr to the gel, you can see
: that the 
: > bottom of the gel is always darker than the top.  I think this is because the 
: > EtBr migrates upward.  The implication is that low bp bands at the bottom of 
: > the gel may not show up under UV light.  Am I right about this

: ------------------------------------
: yes there is always the problem that you will have to re-stain anyway but
: for general purposes its easier to have the EtBr in the gel.
:    Another trick is to add a little to the bottom buffer chamber on a long
: run to ensure the bottom bands do show up

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