Relationships between intrinsic and induced curvature in DNAs: Theoretical prediction of nucleosome positioning.

Relationships between intrinsic and induced superstructures in DNAs are investigated using a theoretical method of sequence dependent curvature based on the integration of the slight deviations of the 16 different dinucleotide steps from the canonical B-DNA structure as evaluated by conformational energy calculations. The induced superstructures due either to circularization or to nucleosome formation are obtained from the intrinsic superstructures by localizing the minima of the distortion energy function evaluated adopting a simple harmonic model. The results in the case of circularization of a DNA fragment 169 bp are in good agreement with the experiments and offer a base of explanation to the fine features of the differential cleavage by DNAse I. The model works very satisfactorily in the prediction of the virtual positioning (rotational and translational) of nucleosomes along DNA in fairly good agreement with experimental results providing also a base for investigating their possible assembly in systems of high complexity as the minichromosomes.