DNA Topology Analysis in the Undergraduate Biochemistry Laboratory

The ability of a cell to control precisely and regulate DNA winding and topology is critical for many intracellular processes, such as replication, transcription, recombination, and repair. A set of complementary experiments is described which are useful in teaching the principles of DNA topology to undergraduate biochemistry students. In one experiment, a copper- o -phenanthroline complex is used to oxidatively cleave closed circular supercoiled DNA and generate nicked and linear forms. In the second experiment, the antitumor agent cis -diamminedichloroplatinum is used to gradually remove supercoils by unwinding the DNA helix. In a third experiment, DNA topoisomerase I is used to generate a set of topoisomers of covalently closed circular DNA. In all experiments, the results are readily analyzed by agarose gel electrophoresis. Together, these experiments greatly facilitate the students' understanding of the basic principles of DNA topology and provide an interesting backdrop for teaching agarose gel electrophoresis methodology. They also serve to introduce topics such as small molecule-DNA interactions and DNA damage and repair.