EtBr in gel vs. staining later

M. William Lensch LENSCH at CHOP.EDU
Thu Feb 23 14:46:40 EST 1995

In article <9502221219.aa22434 at>, betts at ORION.ETSU.EDU
> It seems to me there are two options for visualizing DNA in agarose gels:
> run a gel with EtBr in the gel or staining the gel after the run.  What are
> the relative merits of the two methods?
> Thanks,
> Gordon Betts
> Biology Dept.
> East Texas State University
> Commerce, TX 75429-3011
> 903/886-5369

My personal opinion is as follows: Staining in gel during the run is a
matter of simplicity. One does not need to wait for staining after the run
to see their product. Also, it allows a more controlled situation if the
gel needs to be run further. Some have argued that the EtBr impairs the
migration of DNA in the gel, with which I agree. If you stain a gel after
the run, and then put it back into the tank to run more (in buffer that
contains no EtBr), the nucleic acids may run differently between lanes and
their homogeneous migration will be impaired as EtBr diffuses out of the
sample (in a non-unifrom manner) over the run. This may result in smearing
or bands appearing as sizes other than they actually are. So, if you want
to stain after the run, don't rely on the ability to re-run the gel a
little more and have it be ok (even though it might). On the other hand,
gels run best (if you want to put EtBr in the gel) when the running buffer
as well as the gel contain EtBr for the reasons mentioned above
(homogeneous running). But, this creates a situation where a lot of
equipment is being contaminated with EtBr instead of one staning basin. So,
I prefer to run w/o EtBr, stain later, and try not to create a situation
where I may have to run the gel a little more.-Willy

> ============================================================================
> ======
> Life is like a bowl of stew, you need to stir things up once in a while so 
> the scum doesn't rise to the top.
>       Author unknown
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