Figure 2.

Locations of the minor- and major-groove bending sites. (Left) The crystal structure of the 1KX5 nucleosome with 147-bp long DNA (54) shown schematically: the DNA fragment is divided into two halves, separated by the dyad (black ball and arrow). The base-pair centers in the ‘anterior’ half are represented by large balls, and the sugar-phosphate backbone is shown by a yellow ribbon. For the ‘posterior’ half of the nucleosome, the base-pair centers are connected by sticks. The fragments whose minor grooves face the histone octamer (grey cylinder) are colored in blue (minor-groove bending sites), while the fragments whose minor grooves face away from the histone are colored in red (major-groove bending sites). The minor- and major-groove sites are defined based on the Roll values of the 147-bp core DNA, shown in Figure S1. (Right) The exact location for each site in the ‘anterior’ half is given, which is symmetric to the corresponding site in the ‘posterior’ half with respect to position 74 (for the 147-bp template) or position 73.5 (for the 146-bp template). The sites with the highest Roll values (‘critical sites’) are indicated by larger letters (superhelical locations SHL −1.5, −2, −3.5, and −5.5).