Working the kinks out of nucleosomal DNA

Condensation of DNA in the nucleosome takes advantage of its double-helical architecture. The DNA deforms at sites where the base pairs face the histone octamer. The largest so-called kink-and-slide deformations occur in the vicinity of arginines that penetrate the minor groove. Nucleosome structures formed from the 601 positioning sequence differ subtly from those incorporating an AT-rich human α-satellite DNA. Restraints imposed by the histone arginines on the displacement of base pairs can modulate the sequence-dependent deformability of DNA and potentially contribute to the unique features of the different nucleosomes. Steric barriers mimicking constraints found in the nucleosome induce the simulated large-scale rearrangement of canonical B DNA to kink-and-slide states. The pathway to these states shows nonharmonic behavior consistent with bending profiles inferred from AFM measurements.

► Advances in experimental and theoretical analyses of the mechanisms of DNA folding in nucleosome are reviewed. ► The sequence-dependent kink-and-slide deformations of DNA found in nucleosome core-particle structures hint of a structural basis for the positioning of nucleosomes on DNA. ► The 601 positioning sequence exhibits conformational responses more drastic than the α-satellite DNA incorporated in most nucleosome structures, including signs of DNA ‘melting’. ► Incorporation of constraints that mimic the binding of the histone arginines in the minor groove facilitates kink-and-slide deformations in atomic calculations.