Exploiting circular DNA

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Abstract
In many ways circular DNA is unique among biological macromolecules. Its properties are unusual and interesting because they are affected greatly by the topology of the molecule. The properties of circular DNA are not only an object of study, but provide an important tool for the investigation of the double helix and its interactions with ligands and proteins. The specific features of circular DNA were used to determine the bending and torsional rigidities of the double helix (1–7), its effective diameter (8–9), helical repeat of DNA in solution (10–12), and the unwinding of the double helix by bound ligands (see references in reviews in refs. 13 and 14). All of these applications are based on the measurement of the linking number difference of closed circular DNA, which can be accomplished with remarkable accuracy and with very simple equipment. Therefore it seems hardly possible to find a new application for these well-understood properties. However, the paper by Zeman et al. (15) published in this issue of the Proceedings proved the contrary. They have developed a new method to study DNA-ligand complexes. Using circular DNA to measure the degree of unwinding of the double helix caused by ligand binding was one of the first applications of the specific properties of circular DNA. The approach is conceptually simple. Consider a nicked circular DNA of N base pairs that is bound to molecules of a ligand so that the ratio of bound ligands to base pairs is equal to ν. If φ is the angle of unwinding of the double helix by one bound ligand, the change of the equilibrium twist of the DNA, ΔTw, is given by the equation 1 It is easy to measure ΔTw by using the topological properties of circular DNA. …

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