messy agarose bands

J.C. hbmth001 at
Tue Mar 19 14:26:38 EST 1996

Does anyone know how to make bands in agarose look sharper?  When I do 
restriction digests of lambda DNA with Hind III, Bam HI, and Eco RI using 
the respective (NE Biolab) buffers, the Eco RI digest always looks the 
sharpest.  The bands in the other digests trail blebs and streaks, 
usually at their ends, often in their middles.  

Is this problem due to the different buffer compositions for the 
different enzymes, or is it related to the stop dye concentration?  I 
don't think it's the amount of DNA on the gel because it happens with 
even 0.05 microgram samples, though the problem is worse with larger 
samples.  I suspect this is a common troubleshooting question, but I 
haven't been able to find the answer in the protocols.


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