Electrostatic-undulatory theory of plectonemically supercoiled DNA

Abstract

We present an analytical calculation of the electrostatic interaction in a plectonemic supercoil within the Poisson-Boltzmann approximation. Undulations of the supercoil strands arising from thermal motion couple nonlinearly with the electrostatic interaction, giving rise to a strong enhancement of the bare interaction. In the limit of fairly tight winding, the free energy of a plectonemic supercoil may be split into an elastic contribution containing the bending and torsional energies and an electrostatic-undulatory free energy. The total free energy of the supercoil is minimized according to an iterative scheme, which utilizes the special symmetry inherent in the usual elastic free energy of the plectoneme. The superhelical radius, opening angle, and undulation amplitudes in the radius and pitch are obtained as a function of the specific linking difference and the concentration of monovalent salt. Our results compare favorably with the experimental values for these parameters of Boles et al. (1990. J. Mol. Biol. 213:931-951). In particular, we confirm the experimental observation that the writhe is a virtually constant fraction of the excess linking number over a wide range of superhelical densities. Another important prediction is the ionic strength dependence of the plectonemic parameters, which is in reasonable agreement with the results from computer simulations.