What makes gels smile?

brett brett at BORCIM.WUSTL.EDU
Sat Dec 7 13:02:02 EST 1996


>Anyone have any ideas on how to prevent gels from smileling?  In 
>particular I'm talking about Urea/acrylamide gels, the kind typically 
>used for sequenceing.  I've heard all kinds of folk lore on this but 
>I'm interested in if anyone has a sure fire way to keep the smile from 
>happening.  
>
>I've tried running fast or slow, long or short prerunning times, long 
>or short polymerization times, but I haven't seen a real correlation 
>between all these.  
>
>Any suggestions would be helpfull.
>
>Thanks,
>Matt thomas
>Thomas at molbio.uoregon.edu

You tried slow?!? Smiling comes from uneven heat distribution within the gel,
the heat being focused in the center of the gel. This lowers the resistance in
the center, and boosts the current. As the nucleic acids (and dyes) migrate
with this current, they move faster in the center of the gel. The only solution
is to redistribute the heat, and there are two ways to do that. First, attach
a heat sink to your plates, such as an aluminum plate (obviously so that it
is not conducting (you'd be suprised someone wouldn't think of this!)). The
other thing to do would be to simply run slower. However, for denaturing gels
this may not be desirable, and you'll have to find a balance between smiling and
resolution. I usually run large heat-sinked sequencing gels at 65W, which
gives me about 55oC gels, with no smiling.


Brett Lindenbach
    
Program in Immunology                              
Washington University - St Louis                  
brett at borcim.wustl.edu                             




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