Notes on gel electrophoresis
Plasmid DNA that has not been cut with a restriction endonuclease will migrate in 3 forms: supercoiled closed circular DNA, single-strand nicked open circle DNA, and sheared linear DNA. http://www.sfu.ca/biology/courses/bisc431/lab3.htm
Supercoiled plasmid DNA will migrate faster than linear forms.
The effect of loading dye may cause mismatch between sample DNA bands and the DNA ladder bands.