Electrophoresis is an extremely useful procedure when applied to analysis of
nucleic acids as it can resolve molecules of different sizes with relative
ease and accuracy. Large molecules migrate more slowly than small molecules in
agarose gels. However, the fact that nucleic acids of the same length may
exist in a variety of conformations can often complicate the interpretation of
electrophoretic separations. For instance, when a single species of a
bacterial plasmid is isolated from cells, the individual plasmids may exist in
three forms (depending on the genotype of their host and conditions of
isolation): superhelical/supercoiled (form I), nicked/open circle (form
\(\mathrm{II}\) ), and linear (form III). Form I is compact and very tightly
coiled, with both DNA strands continuous. Form II exists as a loose circle
because one of the two DNA strands has been broken, thus releasing the
supercoil. All three have the same mass, but each will migrate at a different
rate through a gel. Based on your understanding of gel composition and DNA
migration, predict the relative rates of migration of the various DNA
structures mentioned above.
