Mechanics and Electrostatics on Supercoiled DNA
David Argudo (University of Pennsylvania), Prashant Purohit (University of Pennsylvania)
Soft Materials and Structures
Mon 4:20 - 5:40
Barus-Holley 158
We develop an elastic-isotropic rod model for twisted DNA in the supercoiled regime. We account for DNA elasticity, entropic effects due to thermal fluctuations and electrostatic interactions in the presence of monovalent and multivalent ions. We apply our model to single molecule experiments on a DNA molecule attached to a substrate at one end, while subjected to a tension and twisted by a given number of turns at the other end. The free energy of the DNA molecule is minimized subject to the imposed end rotations. Experiments suggest that in the presence monovalent ions, as the applied number of turns increases, supercoiled structures are formed. We compute key features of the rotation-extension curves for different ionic concentrations of monovalent salts. Our model yields excellent fits to mechanical data from a large number of experiments. Furthermore, the condensation of free DNA into toroidal structures in the presence of multivalent ions is well known. Recent single molecule experiments have shown that condensation into toroids occurs even when the DNA molecule is subjected to tensile forces. Here we show that the combined tension and torsion of DNA in the presence of condensing agents dramatically modifies this picture by introducing supercoiled DNA as a competing structure in addition to toroids. We combine a fluctuating elastic rod model of DNA with phenomenological models for DNA interactions in the presence of condensing agents to compute the minimum energy configuration . We show that for each tension there is a critical number of end rotations above which the supercoiled solution is preferred and below which toroids are the preferred state. Our results closely match recent extension-rotation experiments on DNA in the presence of condensing agents. Motivated by this we construct a phase diagram for the preferred DNA states as a function of tension and end rotations and identify a region where new experiments are needed to determine the preferred state.