text: The conformation of the DNA molecule can significantly affect the movement of the DNA, for example, supercoiled DNA usually moves faster than relaxed DNA because it is tightly coiled and hence more compact.  In a normal plasmid DNA preparation, multiple forms of DNA may be present, and gel from the electrophoresis of the plasmids would normally show a main band which would be the negatively supercoiled form, while other forms of DNA may appear as minor fainter bands.  These minor bands may be nicked DNA (open circular form) and the relaxed closed circular form which normally run slower than supercoiled DNA, and the single-stranded form (which can sometimes appear depending on the preparation methods) may move ahead of the supercoiled DNA.  The rate at which the various forms move however can change using different electrophoresis conditions, for example linear DNA may run faster or slower than supercoiled DNA depending on conditions, and the mobility of larger circular DNA may be more strongly affected than linear DNA by the pore size of the gel.  Unless supercoiled DNA markers are used, the size of a circular DNA like plasmid therefore may be more accurately gauged after it has been linearized by restriction digest.
  DNA damage due to increased cross-linking will also reduce electrophoretic DNA migration in a dose-dependent way.