Figure 6.

Nanoscale modeling of the stem (A) H1-protection color-coded nucleosomes with straight linkers (left) and two geometrical stem models. For both of them, protected sites (white spots on the linker) do not face each other. These models do not account for the observed protection pattern. (B) To determine the most likely stem structure compatible with the observed protection pattern, we minimized the DNA nanoscale elastic energy under the constraint that the most protected sites face each other. The initial configuration of the relaxation is illustrated here, with straight linkers. 4 springs (black cylinders) enforce contact between the protected sites. Only C5′ atoms were depicted, color-coded according to the experimental protection pattern (gray when no signal). The green sphere represents the dyad. Views from the NCP superhelical axis and perpendicular. (C) Stem structure obtained as a result of the relaxation [already shown in (23)]. Views in direction of the superhelical axis and 30 apart (dark gray histones, light blue histone tail with arbitrary conformation). The DNA is colored in blue within possible extension of the truncated H1 tail.