Origin of Superstructural Organization in DNA

Intrinsic and induced superstructures of DNAs are investigated using a theoretical model of the sequence dependent curvature based on the integration of the slight deviations of the 16 different dinucleotides steps from the canonical B DNA structure as evaluated by conformational energy calculations. The influence of the thermal fluctuations on the electrophoretic manifestations of the curvature are critically discussed assuming a simple kinetic model of the electrophoretic mobility in a tight polyacrilamide gel. The proposed model reproduces the gel electrophoretic retardation of synthetic as well as biologically relevant DNA tracts in very good agreement with the experimental results. The induced superstructures due to circularization or to nucleosome formation are obtained from the intrinsic superstructures by minimizing the distortion energy evaluated by adopting a simple harmonic model and an original analitical mathematical method. In particular, virtual positioning (rotational and translational) of nucleosomes along DNAs is predicted by localizing the minima of the distortion energy function in fairly good agreement with experimental data.