PROs and CONs of visualization of DNA in agarose gel by EtBr

Rustle Laidman rustle at
Thu Mar 30 02:57:49 EST 2000

Hi Jongrak,

The advantage to adding the EtBr to the gel before pouring is that of
time.  It takes approx 30 - 60 min to stain an agarose gel after
electrophoresis and there's the messy EtBr shaking on the rotomixer
which might splash around.  Staining the gel on the other hand gives a
gel that's ready for visualization as soon as the electrophoresis is
done!  Very time saving.  The disadvantage to putting the EtBr in the
gel rather than afterward is that there may be EtBr residue left in the
gel box if you're running something to be hybridised another time.
Since EtBr is broken down by UV light, you could irradiate it with a UV
light, or as we do in my lab, just have some gel boxes that are
designated ok for EtBr and some that are designated "clean".  There is
also a third way to add EtBr for visualization and that is to add it
directly to your sample and run on a regular agarose gel.  We do this
for Northerns in order to visualize our RNA in the control lane.  One
thing to note is that EtBr runs in the opposite direction from nucleic
acids so if you add to the gel or the sample you will see some EtBr
artifacts in the gel, it might be brighter in half of the gel.  I have
not experienced any difficulty in visualizing gels because of this and
since EtBr intercollates with nucleic acids, it doesn't seem to come out
of the sample once it's intercollated even though it runs off the gel.

Janel Wheeler
Vellanoweth Lab
Cal State University, Los Angeles

Jongrak Kittiworakarn wrote:

> Hi All
> One of a common technique that is found in most mol bio lab
> is visualsation of DNA by EtBr.  I found that some lab prefers
> adding EtBr into the melting agarose, while some prefers
> stainning the DNA (in the agarose gel) after the electrophoresis.
> I would like to ask for your comment on the pros and cons of
> both methods.
> Thanks
> jongrak kittiworakarn
> Bat 152  CEA/Saclay
> 91191 Gif-sur-Yvette Cedex, FRANCE
> e-mail  jongrak at
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