DNA is a negatively charged molecule because of its phosphate groups (see
Figure 7.1). In an electric field, DNA migrates to the positive electrode
(anode). Since the double-stranded DNA molecules have a net charge to
mass ratio approximately the same, under constant-voltage conditions, the
migration rate of the DNA molecules through a support medium depends
largely on their sizes and conformations. Smaller DNA molecules will travel
faster as compared to the larger ones. For DNA molecules of the same size,
the order of migration velocity in the increasing order of various forms of
DNA is: supercoiled DNA > linear double stranded DNA > open circular
DNA. Electrophoresis can also be used to evaluate the quality of high
molecular weight DNA. Presence of a thick band near mouth of the wells will
indicate that DNA is of high molecular weight whereas sheared DNA will
appear as a smear throughout the gel lane indicating poor quality of the
preparation. RNA contamination is indicated by smear near the bottom of the
gel.