MODELING SELF-CONTACT FORCES IN THE ELASTIC THEORY OF DNA SUPERCOILING

A DNA polymer with thousands of base pairs is modeled as an elastic ro d with the capability of treating each base pair independently. Elasti c theory is used to develop a model of the double helix which incorpor ates intrinsic curvature as well as inhomogeneities in the bending, tw isting, and stretching along the length of the polymer. Inhomogeneitie s in the elastic constants can also be dealt with, thus, sequence-depe ndent structure and deformability can be taken into account. Additiona lly, external forces have been included in the formalism, and since th ese forces can contain a repulsive force, DNA self-contact can be expl icitly treated. Here the repulsive term takes the form of a modified D ebye-Huckel force where screening can be varied to account for the eff ect of added salt, The supercoiling of a naturally straight, isotropic rod in 0.1M NaCl is investigated and compared with earlier treatments of supercoiled DNA modeled by a line of point charges subject to elec trostatic interactions and an elastic potential. (C) 1997 American Ins titute of Physics.