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Biophys. J. BioFAST: First Published September 17, 2004. doi:10.1529/biophysj.104.048983
© 2004 by the Biophysical Society.

A more recent version of this article appeared on December 1, 2004.
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SPECTROSCOPY, IMAGING, OTHER TECHNIQUES

Unexpected binding motifs for subnucleosomal particles revealed by Atomic Force Microscopy

Dessy N Nikova 1*, Lisa H Pope 2, Kirsten A van Leijenhorst-Groener 3, Kees O van der Werf 3, Jan Greve 3 and Martin L. Bennink 3

1 University of Muenster
2 University of Illinois at Chicago
3 University of Twente

* To whom correspondence should be addressed. E-mail: nikovad{at}uni-muenster.de.

Submitted on July 5, 2004
Revised on July 28, 2004
Accepted on 29 July 2004


  Abstract
The structure of individual nucleosomes organised 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 favoured 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 centre-to-centre 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.

Key Words: Atomic Force Microscopy, AFM, nucleosome core particle




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Copyright © 2004 by the Biophysical Society.