The elastic model in the mechanics of DNA deformations.

The mechanics of DNA structural fluctuations at room temperature is generally modelled with a simple one-dimensional worm-like elastic model that approximates the energy of the DNA deformations from its intrinsic sequence-dependent curvature as proportional to the square of the curvature deviations, although this approximation should be suitable for small deformations of B-DNA canonical structure. Although the high curvature of DNA in nucleosomes exclude the first order elasticity approach, the high-resolution structures of the nucleosome show that DNA essentially retains the B conformation following an almost cylindrical super-helix. However, a few significant kinks largely independent of sequence are present; in fact, the distortion energy evaluated adopting the canonical persistence length of 50 nm is in the range of base pair stacking energies. This means that unstaking of some dinucleotide steps could occur in phase along the sequence as it appears in the X-ray nucleosome structures, probably at TA sequence positions, due to the lowest stacking energy proper of this dinucleotide. The good results in predicting the thermodynamic stability of nucleosomes obtained adopting elastic models suggest the hypothesis that the DNA super-helical distortion involved in the elastic model represents an ideal fitting, almost equivalent in energy, of the actual nucleosomal structures, which is the result of local structural arrangements optimized according to the different specific histone-DNA interactions along the sequence.