Our research group has recetly bought CBS Scientific Adjustable Sequencing Kit (SG-400-20) and we are facing troubles with our electrophoretic separations because we are unable to obtain sharp bands on our gels.

I have attached two images of denaturating PAGE of our primer extension experiments performed under same conditions with two different electrophoretic systems. Denaturating PAGE gels (12,5% with urea) (Rotiphorese Sequencing Gel concentrate (Roth) and 1x TBE buffer) were pre-heated to 50 deg. Celsius before loading and then run at 42 mA for 1 hour. Separations of the same samples were performed using CBS Scientific Adjustable Sequencing Kit and BioRad Sequi-Gen GT System. Both systems use 0.4 mm spacers and 40x20 cm glass plates. With the BioRad system sharp bands were obtained while with the CBS Sientific systems the bands are smeared. Could you please provide me with your recommendations that could lead to sharp bands with the CBS Scientific system? It seems that usually the shorter the DNA is the more sharp is the band. What could be the reason for it?

Thank you in advance.