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Unexpected Binding Motifs for Subnucleosomal Particles Revealed by Atomic Force Microscopy

Dessy N. Nikova ^* , Lisa H. Pope ^* ¶, Martin L. Bennink ^* , Kirsten A. van Leijenhorst-Groener ^*, Kees van der Werf ^* and Jan Greve ^*

^* Biophysical Techniques, Department of Science and Technology, and MESA+ Research Institute, University of Twente, Enschede, The Netherlands; University of Muenster, Institute of Physiology, Muenster, Germany; and ^¶ University of Illinois at Chicago, Department of Physics, Chicago, Illinois USA

Correspondence: Address reprint requests to D. N. Nikova, University of Muenster, Institute of Physiology, 27b Robert Koch St., 48149 Muenster, Germany. Tel.: 49-251-8355336; Fax: 49-251-8355331; E-mail: nikovad{at}uni-muenster.de.

The structure of individual nucleosomes organized within reconstituted 208-12 arrays at different levels of compaction was examined by tapping mode atomic force microscopy in air and liquid. Reconstitution at lower histone octamer to DNA weight ratios showed an extended beads-on-a-string morphology with less than the expected maximum of 12 nucleosome core particles per array, each particle located in the most favored positioning site. A correlation of the contour lengths of these arrays with the number of observed particles revealed two distinct populations of particles, one with 50 nm of bound DNA and a second population with 25 nm. The measured nucleosome center-to-center distances indicate that this 25 nm is not necessarily symmetrically bound about the dyad axis, but can also correspond to DNA bound from either the entry or exit point of the particle to a location at or close to the dyad axis. An assessment of particle heights suggests that particles wrapping 25 nm of DNA are most likely to be subnucleosomal particles, which lack either one or both H2A-H2B dimers. At a higher reconstitution ratio, folded compact arrays fully populated with 12 nucleosome core particles, were observed. Liquid measurements demonstrated dynamic movements of DNA loops protruding from these folded arrays.

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