The viscometric behavior of native and relaxed closed circular PM2 DNAs at intermediate and high ethidium bromide concentrations

We have measured the specific viscosity of closed circular PM2 DNA in the presence of concentrations of ethidium bromide ranging up to 5 mg/ml. Both native viral PM2 DNA I and enzymatically prepared relaxed, closed circular PM2 DNA I₀ exhibit a complex dependence of the specific viscosity upon the extent of supercoiling. As the number of superhelical turns is increased in the positive sense from zero, the viscosity first decreases to a minimum, then passes through a secondary maximum, and eventually again increases as the dye-induced duplex unwinding proceeds. In the case of DNA I, a corresponding behavior is mirrored in the negative sense as dye is removed from the principal viscometric maximum (complete relaxation of the DNA by dye). The shape of the curve relating specific viscosity to extent to supercoiling is similar for superhelical DNAs of either handedness, a result which we interpret to mean that the influence of any regions of special secondary structure (such as denatured loops) upon the viscosity is minimal. At very high dye concentrations the specific viscosity decreases dramatically. This effect might arise either from intermolecular aggregation or from a dye-induced collapse in the DNA secondary structure.