Figure 2.

Bending of short (20–30 bp) linker DNA imposes large energy penalties for 1-start fibers and compromises stacking in 2-start fibers. The average conformation of the DNA of three adjacent nucleosomes, including their linker DNA, was calculated for the 0-start, 1-start and 2-start structures. The tension in the individual base pairs in the linker DNA is represented by the red color, which shows the bending energy compared to the starting, minimal energy structure. When no stacking interactions were simulated, the linker DNA was on average straight. In this conformation, nucleosome breathing was observed at the outer contact points of each nucleosome, resulting in red base pairs that reflect an increased standard deviation of their coordinates as compared to the start conformation. The bending of the linker DNA in a 1-start structure required strong deformation of the linker DNA, indicated by large energy penalties. NRL 167 fibers showed approximately straight linker DNA in a 2-start structure. Increasing the linker length imposed deviations from optimal stacking, which was maximal for NRL 172. Increasing the linker length to NRL 177 recovered proper stacking.