Bridged DNA Circles: A New Model System To Study DNA Topology

We demonstrate the assembly of two bridged circular DNA molecules. The circles are specially engineered plasmid DNAs a few thousands base pairs in length connected by the synthetic double-stranded linker. The construct represents a very convenient system for studying DNA topology and its enzymatic transformations, since at thermodynamic equilibrium the circles have comparable probability to adopt two different topological states and the exchange between the states is an intramolecular reaction. We obtained the equilibrium distribution of these states, in which the circles form the simplest link or remain unlinked, by opening and closing the long sticky ends made in one of the bridged circles. Separation of the linked and unlinked circles by gel electrophoresis allowed us to determine the fraction of linked circles. The obtained value is in very good agreement with the results of computer simulation