Torsional fluctuations in columnar DNA assemblies

Abstract

In columnar assemblies of helical bio-molecules the azimuthal degrees of freedom, i.e. rotations about the long axes of molecules, may be important in determining the structure of the assemblies especially when the interaction energy between neighbouring molecules explicitly depends on their relative azimuthal orientations. For DNA this leads to a rich variety of mesophases for columnar assemblies, each categorized by a specific azimuthal ordering. In a preceding paper [A. Wynveen, D. J. Lee, and A. A. Kornyshev, Eur. Phys. J. E, 16, 303 (2005)] a statistical mechanical theory was developed for the assemblies of torsionally rigid molecues in order to determine how thermal fluctuations influence the structure of these mesophases. Here we extend this theory by including torsional fluctuations of the molecules, where a DNA molecule may twist about its long axis at the cost of torsional elastic energy. Comparing this with the previous study, we find that inclusion of torsional fluctuations further increases the density at which the transition between the hexagonal structure and the predicted rhombic phase occurs and reduces the level of distortion in the rhombic phase. As X-ray diffraction may probe the 2-D lattice structure of such assemblies and provide information concerning the underlying interaction between molecules, we have also calculated correlation functions for the azimuthal ordering which are manifest in an x-ray scattering intensity profiles.