title: Analyses of nuclear proteins and nucleic acid structures using atomic force microscopy.
abstract: Since the inception of atomic force microscopy (AFM) in 1986, the value of this technology for exploring the structure and biophysical properties of a variety of biological samples has been increasingly recognized. AFM provides the opportunity to both image samples at nanometer resolution and also measure the forces on the surface of the sample. Here, we describe a variety of methods for studying nuclear samples including single nucleic acid molecules, higher-order chromatin structures, the nucleolus, and the nucleus. Protocols to prepare nucleic acids, nucleic acid-protein complexes, reconstituted chromatin, the cell nucleus, and the nucleolus are included, as well as protocols describing how to prepare the AFM substrate and the AFM tip. Finally, we describe how to perform conventional imaging, high-speed imaging, recognition imaging, force spectroscopy, and nanoindentation experiments.
authors.affiliation: Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan.
authors.forename: Jamie L
authors.initials: JL
authors.lastname: Gilmore
authors.forename: Aiko
authors.initials: A
authors.lastname: Yoshida
authors.forename: Hirohide
authors.initials: H
authors.lastname: Takahashi
authors.forename: Katashi
authors.initials: K
authors.lastname: Deguchi
authors.forename: Toshiro
authors.initials: T
authors.lastname: Kobori
authors.forename: Emilie
authors.initials: E
authors.lastname: Louvet
authors.forename: Masahiro
authors.initials: M
authors.lastname: Kumeta
authors.forename: Shige H
authors.initials: SH
authors.lastname: Yoshimura
authors.forename: Kunio
authors.initials: K
authors.lastname: Takeyasu
mesh_terms: D004247:DNA / Q000648:ultrastructure; D006367:HeLa Cells; D006801:Humans; D007091:Image Processing, Computer-Assisted; D018625:Microscopy, Atomic Force / Q000295:instrumentation / Q000379:methods*; D009687:Nuclear Proteins / Q000648:ultrastructure*; D009696:Nucleic Acids / Q000648:ultrastructure*; D012313:RNA / Q000648:ultrastructure
chemical_list: D009687:Nuclear Proteins; D009696:Nucleic Acids; D012313:RNA; D004247:DNA