[2] The experimental procedure first requires a sample of purified plasmid DNA for each digest to be run.
A second possible source of error is that the gel was not dense enough and therefore was unable to resolve fragments close in size.
The large genomic DNA is subject to tangling and staying denatured when the pH is lowered during the neutralization.
The circular supercoiled plasmids' strands will stay relatively closely aligned and will renature correctly.
Therefore, the genomic DNA will form an insoluble aggregate and the supercoiled plasmids will be left in solution.