The influence of DNA stiffness upon nucleosome formation

The rotational and translational positioning of nucleosomes on DNA is dependent to a significant extent on the physicochemical properties of the double helix. We have investigated the influence of the axial flexibility of the molecule on the affinity for the histone octamer by substituting selected DNA sequences with either inosine for guanosine or diaminopurine for adenine. These substitutions, respectively, remove or add a purine 2-amino group exposed in the minor groove and, respectively, decrease and increase the apparent persistence length. We observe that for all sequences tested inosine substitution, with one exception, increases the affinity for histone binding. Conversely diaminopurine substitution decreases the affinity. In the sole example where replacement of guanosine with inosine decreases the persistence length as well as the affinity for histones, the substitution concomitantly removes an intrinsic curvature of the DNA molecule. We show that, to a first approximation, the binding energy of DNA to histones at 1M NaCl is directly proportional to the persistence length. The data also indicate that a high local flexibility of DNA can favour strong rotational positioning.