Nucleic Acids Research Advance Access published online on August 17, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm560
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Choreography for nucleosomes: the conformational freedom of the nucleosomal filament and its limitations
Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
*To whom correspondence should be addressed. Tel: +45 35327768; Fax: +45 35327732; Email: engelhardt{at}imbg.ku.dk
Received May 3, 2007. Revised July 7, 2007. Accepted July 9, 2007.
Eukaryotic DNA is organized into nucleosomes by coiling around core particles of histones, forming a nucleosomal filament. The significance for the conformation of the filament of the DNA entry/exit angle (
) at the nucleosome, the angle of rotation (ß) of nucleosomes around their interconnecting DNA (linker DNA) and the length of the linker DNA, has been studied by means of wire models with straight linkers. It is shown that variations in and ß endow the filament with an outstanding conformational freedom when is increased beyond 60–90°, owing to the ability of the filament to change between forward right-handed and backward left-handed coiling. A wealth of different helical and looped conformations are formed in response to repeated ß sequences, and helical conformations are shown to be able to contract to a high density and to associate pairwise into different types of double fibers. Filaments with random ß sequences are characterized by relatively stable loop clusters connected by segments of higher flexibility. Displacement of core particles along the DNA in such fibers, combined with limited twisting of the linkers, can generate the ß sequence necessary for compaction into a regular helix, thus providing a model for heterochromatinization.