6 - Circular DNA

Summary

In 1963 Dulbecco and Vogt, and Weil and Vinograd, discovered that dsDNA of the polyoma virus exists in a closed circular form (Dulbecco & Vogt 1963, Weil & Vinograd 1963). It turned out that this form is typical of bacterial DNA and of cytoplasmic DNA in animals. The distinctive feature of closed circular molecules is that its topological state cannot be altered by any conformational rearrangement that does not involve breaking DNA strands. This topological constraint is the basis for the fascinating properties of circular DNA molecules. The physical properties of circular DNA molecules is a subject of the current chapter.

Linking number of complementary strands and DNA supercoiling

Two forms of circular DNA molecules are extracted from the cell; they were designated as form I and form II (Weil & Vinograd 1963). The more compact form I was found to turn into form II after a single-stranded break was introduced into one chain of the double helix. Subsequent studies performed by Vinograd and co-workers linked the compactness of form I, in which both DNA strands are intact, to supercoiling. Form I is called the closed circular form. In this form each of the two strands that make up the DNA molecule are closed in on themselves. A diagram of closed circular DNA is presented in Fig. 6.1. The two strands of the double helix in closed circular DNA are topologically linked. In topological terms, the links between two strands of the double helix belong to a particular class, called the torus class (see Section 6.7). The quantitative description of such links is called the linking number, Lk, which may be determined in the following way (Fig. 6.2). One of the strands defines the edge of an imaginary surface (any such surface gives the same result). Lk is the algebraic (i.e. sign-dependent) number of intersections of the surface by the other strand.