Hydrodynamic properties of nucleosomal fibers and chromatin higher-order structure

We studied the comparative hydrodynamic properties of chromatins differing in transcriptional activity and in linker DNA length. Chromatins were prepared from the nuclei of pigeon brain cortical neurones, rat thymus and sea urchin sperm. The sizes of linker DNA are 20, 50 and 100 base pairs (b.p.), respectively. Oligonucleosomes of different chain length were isolated from micrococcal nuclease-digested nuclei and studied by the method of sedimentation velocity. Rheological behavior of nucleosome oligomers depends on the number of nucleosomes in the chain and on the ionic strength in the range between 5 and 85 mM was analyzed on the basis of a cylinder model using different hydrodynamic theories. It is shown that hydrodynamic properties of oligonucleosomes from all types of investigated chromatins at low ionic strength can be well described by the model of a three-dimensional zig-zag chain with a diameter of about 20 nm, the DNA packing ratio growing with the increase of linker DNA length. Increasing ionic strength induces condensation of the zig-zag-shaped chain of nucleosomes into a two-start double superhelix with densely packed nucleosomes. Linkers are arranged inside the superhelix, which is bent or folded into a loop, depending on its size.