Torsional fluctuations in columnar DNA assemblies

• Published in: Journal of physics. Condensed matter Vol. 18; no. 3; pp. 787 - 823
• Main Authors: Lee, D J, Wynveen, A
• Format: Journal Article
• Language: English
• Published: Bristol IOP Publishing 25.01.2006; Institute of Physics
• Subjects: Analytical, structural and metabolic biochemistry; Biological and medical sciences; DNA, RNA; Fundamental and applied biological sciences. Psychology; General aspects; General aspects, investigation methods; Molecular biophysics; Nucleic acids; Theory and modeling; computer simulation; Fluctuations; Strain energy; Theoretical study; Density; X ray diffraction; Free energy; Columnar structure; Hexagonal lattices; Phase transformation; Macromolecule; DNA; Statistical model; Ordering; Correlation function; X ray scattering; Mesophase; Interaction energy; Organic compounds
• ISSN: 0953-8984; 1361-648X
• DOI: 10.1088/0953-8984/18/3/004

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 (Wynveen et al 2005 Eur. Phys. J. E 16 303) a statistical mechanical theory was developed for the assemblies of torsionally rigid molecules 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 2D 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 x-ray scattering intensity profiles.