title: AFM studies in diverse ionic environments of nucleosomes reconstituted on the 601 positioning sequence.
abstract: Atomic force microscopy (AFM) was used to study mononucleosomes reconstituted from a DNA duplex of 353 bp containing the strong 601 octamer positioning sequence, together with recombinant human core histone octamers. Three parameters were measured: 1) the length of DNA wrapped around the core histones; 2) the number of superhelical turns, calculated from the total angle through which the DNA is bent, and 3) the volume of the DNA-histone core. This approach allowed us to define in detail the structural diversity of nucleosomes caused by disassembly of the octasome to form subnucleosomal structures containing hexasomes, tetrasomes and disomes. At low ionic strength (TE buffer) and in the presence of physiological concentrations of monovalent cations, the majority of the particles were subnucleosomal, but physiological concentrations of bivalent cations resulted in about half of the nucleosomes being canonical octasomes in which the exiting DNA duplexes cross orthogonally. The dominance of this last species explains why bivalent but not monovalent cations can induce the initial step towards compaction and convergence of neighboring nucleosomes in nucleosomal arrays to form the chromatin fiber in the absence of linker histone. The observed nucleosome structural diversity may reflect the functional plasticity of nucleosomes under physiological conditions.
authors.affiliation: Institute of Cytology, RAS, Tikhoretski Ave. 4, Saint-Petersburg, RF, 194064, Russia. Electronic address: i.nazarov@incras.ru.
authors.forename: Igor
authors.initials: I
authors.lastname: Nazarov
authors.affiliation: Institute of Cytology, RAS, Tikhoretski Ave. 4, Saint-Petersburg, RF, 194064, Russia.
authors.forename: Iana
authors.initials: I
authors.lastname: Chekliarova
authors.affiliation: Institute of Physics, Nanotechnology and Telecommunications, NRU Peter the Great St.Petersburg Polytechnic University, Polytechnicheskaya 29, Saint-Petersburg, RF, 195251, Russia; Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, NRC "Kurchatov Institute", Orlova Roscha, Gatchina, 188300, Russia.
authors.forename: Georgy
authors.initials: G
authors.lastname: Rychkov
authors.affiliation: Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, NRC "Kurchatov Institute", Orlova Roscha, Gatchina, 188300, Russia; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.
authors.forename: Andrey V
authors.initials: AV
authors.lastname: Ilatovskiy
authors.affiliation: Biophysics Laboratories, St. Michael's Building, University of Portsmouth, Portsmouth, PO1 2DT, UK.
authors.forename: Colyn
authors.initials: C
authors.lastname: Crane-Robinson
authors.affiliation: Institute of Cytology, RAS, Tikhoretski Ave. 4, Saint-Petersburg, RF, 194064, Russia.
authors.forename: Alexey
authors.initials: A
authors.lastname: Tomilin
mesh_terms: D002843:Chromatin / Q000378:metabolism; D006801:Humans; D018625:Microscopy, Atomic Force; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000378:metabolism*
chemical_list: D002843:Chromatin; D009707:Nucleosomes
keywords: 30 nm fibre; AFM; Nucleosomes; Superhelical turns