Slanted Bands on Agarose Gels

Thomas A. Brown tbrown at nervm.nerdc.ufl.edu
Thu Jun 2 12:06:27 EST 1994


In article <1994Jun1.144723.28647 at news.unige.ch>, mike at divsun.unige.ch
(Mike Morris) wrote:

> In article 206 at usenet.ucs.indiana.edu, wfischer at bio.indiana.edu (Will Fischer) writes:
> *Christopher W Botka (cwbotka at MERCURY.SFSU.EDU) wrote:
> *: Has anyone experienced bands(DNA) that run slanted on an agarose gel? -
> *: i.e. the bottom of the EtBr stained frag. of DNA seems to be migrating
> *: faster than the top. 
> *
> *  Seems the culprit is different buffer conc. between gel and
> *running buffer, generally due to volume loss while dissolving the agarose.
> *
> *
> 	I have always believed that it was due to a TEMPERATURE gradient in the gel, not buffer concentration. I avoid it by running gels more slowly, or 
> in the cold room.
> 
> *******************************************************************
> Michael Morris PhD            
> Division of Medical Genetics       tel (Switzerland) (22) 702.56.94
> CMU, University of Geneva          fax (Switzerland) (22) 702.57.06
> Geneva, Switzerland                email mike at medsun.unige.ch  

We've found that it is often due to differential EtBr concentration.  If
EtBr is left out of the gel but included in the tank buffer you can get
slanting of bands if the equilibration time is too short (EtBr reduces
mobility of linear DNA by about 15%).  Our solution was to include EtBr in
the gel as well as the tank buffer, or leave it out altogether and
post-stain.              

-- 
Thomas A. Brown, Ph.D.             tel (904) 392-4370
Dept. of Oral Biology, Box 100424  fax (904) 392-3070 
University of Florida
Gainesville, Fl 32610



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