Double-stranded acquire DNA structures topological properties if organized into a topological domain, which is a closed region in which the two strands are linked. The known types of elementary topological domains are closed circular duplex DNA (cdDNA), in which the two strands are separately covalently continuous; and protein-sealed closed DNA loops (Fig. 1) (1). The vast majority of experimental and theoretical work on DNA topological domains has been done with purified closed circular DNA. An elementary topological domain, in which the DNA is topologically monomeric, is one in which the axis of the DNA is not itself linked to that of any other DNA. DNAs of this type are widespread in nature, including bacterial plasmids and episomes, the virion and replicative forms of both eukaryotic and prokaryotic viruses, mitochondrial DHNA, and many others (2). The nomenclature used to describe these molecules derives in part from protein chemistry and is imprecise when applied to closed circular DNA. Among the terms commonly used are superhelical DNA and supercoiledDNA. These are not meant to indicate different structural types, but are used as synonyms to indicate that the DNA in question is more compact than either its relaxed closed circular or nicked circular counterpart. They are used interchangeably with the more generic closed circular DNA or, alternatively, closed duplex DNA (cdDNA).
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