DNA sequence-dependent curvature and flexibility in stability and organization of chromatin.

Static and dynamic DNA curvature are involved in fundamental biological functions as well as in the stability of nucleosomes and their organization in the chromatin architecture. We have developed a statistical mechanics model to derive superstructural properties of DNA from the sequence-dependent curvature and flexibility. In spite of the knowledge of the nucleosome molecular structure, the role of DNA intrinsic curvature in determining nucleosome stabilization is still an open question. In this paper, we describe a general model that allows the prediction of the nucleosome stability, tested on 83 different DNA sequences, in surprising good agreement with the experimental data, carried out in ours as well as in many other laboratories. The model is based on the dual role of DNA curvature in nucleosome thermodynamic stabilization. A critical test is the evaluation of the nucleosome free energy relative to a Crithidia fasciculata kinetoplast DNA fragment, which represents the most curved DNA found so far in biological systems and, therefore, is generally believed to form a highly stable nucleosome.