Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability

Abstract

A statistical mechanistic approach to evaluate the sequence-dependent thermodynamic stability of nucleosomes is proposed. The model is based on the calculation of the DNA intrinsic curvature, obtained by integrating the nucleotide step deviations from the canonical B-DNA structure, and on the evaluation of the first order elastic distortion energy to reach the nucleosomal superstructure. Literature data on the free energy of nucleosome formation as obtained by competitive nucleosome reconstitution of a significant pool of different DNA sequences were compared with the theoretical results, and a satisfactorily good correlation was found. A striking result of the comparison is the emergence of two opposite roles of the DNA intrinsic curvature and flexibility in determining nucleosome stability. Finally, the obtained results suggest that the curvature-dependent DNA hydration should play a relevant role in the sequence-dependent nucleosome stability.