Agarose gel migration artifacts of PCR products.

[Mark Schweder]

In article <9212100007.AA26748 at phobos.med.pitt.edu>, bsh at MED.PITT.EDU (Basavaraju Shankarappa) writes:
> 
> Hi Netfolks:
> 	We have been trying to resolve the amplified product on a
> agarose gel.  Usually we have no problem.  But in one case we tried
> primers that contained lot of degeneracies.  When we run this product
> on an agarose gel, there is a kind of smearing effect in the lanes.
> This smear is clearly not caused by the presence of products of varied
> sizes.  The lane looks like the DNA appears to have aggregated and
> travels as a streak along the two edges of the lane.  We can also 
> faintly see the band at the appropriate positions.
> 	We tried running the amplified product after diluting it and 
> also added SDS.  But it does not seem to go away.  Has anybody else
> seen this happen or has worked out a solution.  If I get a reply
> that solves the problem, I will post on the net.
> 	Thanks 
> Raj Shankarappa
> Univ of Pittsburgh
> bsh at med.pitt.edu

 Try using a 3% gel that is composed of 50% normal agarose (SeaKem) and 50% low 
melting point agarose (NuSieve). It will increase resolution tremendously, but 
probably won't get rid of a long smear.
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