I made a PCR product of 20ul total, ran 3ul of the product on a 2% agarose pre-cast gel. This is the first picture. There is a nice band at the correct bp size (400bp), but a fainter band is above it. So I wanted to gel purify out my correct band.
I ran the 17ul leftover on a poured 2.5% TBE gel, at 100V for 40minutes. The DNA ladder on the right lane is a 100bp ladder, so my product is 4 bands from the bottom, at 400bp. But there is a large smear running down and this gel looks nothing like that of the pre-cast gel. I am afraid I cannot purify this band because I lost some of the product due to smearing.
What does this smear mean? Did I overload the gel, did I run gel too fast? Should I use TAE instead of TBE? I always run with those conditions, so I didn’t do anything out of my norm. But I need to purify only that band seen in the precast gel, how can I make it look the same on the poured gel?