Geometry

Although most plasmids possess a circular geometry, there are now many exam­ples in a variety of bacteria of plasmids that are linear (15,16). As linear plasmids require specialized mechanisms to replicate their ends, which circular plasmids and chromosomes do not, linear plasmids tend to exist in bacteria that also have linear chromosomes (17).

Circular plasmids can have more than one topology determined by the opposing actions of DNA gyrases and topoisomerases (18). Plasmid DNA is mostly maintained in a covalently closed circular, supercoiled form (analogous to the behavior of an elas­tic band that is held fixed at one position while it is twisted at the 180° position). However, if a nick is introduced into one of the strands of the DNA double helix, supercoiling is relieved and the plasmid adopts an open circular form that migrates more slowly in an agarose gel than the covalently closed circular form. If nicks are introduced at opposite positions on both DNA strands, the plasmid is linearized. In addi­tion, the activity of DNA homologous recombination enzymes can convert plasmid monomers to dimers and higher-order species that, because of their larger size, will migrate more slowly during agarose gel electrophoresis than the monomeric forms.