title: Chromatin imaging with time-lapse atomic force microscopy.
abstract: Time-lapse atomic force microscopy (AFM) is widely used for direct visualization of the nanoscale dynamics of various biological systems. The advent of high-speed AFM instrumentation made it possible to image the dynamics of proteins and protein-DNA complexes within millisecond time range. This chapter describes protocols for studies of structure and dynamics of nucleosomes with time-lapse AFM including the high-speed AFM instrument. The necessary specifics for the preparation of chromatin samples for imaging with AFM including the protocols for the surface preparation are provided.
authors.affiliation: Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025, Nebraska Medical Center, Omaha, NE, 68198-6025, USA, ylyubchenko@unmc.edu.
authors.forename: Yuri L
authors.initials: YL
authors.lastname: Lyubchenko
authors.forename: Luda S
authors.initials: LS
authors.lastname: Shlyakhtenko
mesh_terms: D002843:Chromatin / Q000737:chemistry / Q000235:genetics / Q000648:ultrastructure*; D042002:Chromatin Assembly and Disassembly; D006657:Histones / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D018625:Microscopy, Atomic Force / Q000379:methods; D009707:Nucleosomes / Q000235:genetics; D055503:Protein Multimerization; D059008:Time-Lapse Imaging / Q000379:methods
chemical_list: D002843:Chromatin; D006657:Histones; D009707:Nucleosomes
references.citation: Methods Mol Biol. 2012;896:57-69
references.pmid: 22821517
references.citation: Methods. 2009 Mar;47(3):206-13
references.pmid: 18835446
references.citation: Nature. 1997 Sep 18;389(6648):251-60
references.pmid: 9305837
references.citation: Nat Struct Mol Biol. 2005 Jan;12(1):46-53
references.pmid: 15580276
references.citation: Methods. 2011 Jun;54(2):274-83
references.pmid: 21310240
references.citation: PLoS One. 2011 Jan 27;6(1):e16299
references.pmid: 21298003
references.citation: Biochemistry. 2009 Aug 25;48(33):7842-8
references.pmid: 19618963
references.citation: Curr Opin Struct Biol. 2005 Apr;15(2):188-96
references.pmid: 15837178
references.citation: Biochemistry. 2011 Sep 20;50(37):7901-8
references.pmid: 21846149
references.citation: Cell. 2002 Nov 1;111(3):281-4
references.pmid: 12419239
references.citation: Methods Mol Biol. 2013;931:295-312
references.pmid: 23027008
references.citation: DNA Repair (Amst). 2005 Jul 28;4(8):855-69
references.pmid: 15925550
references.citation: Methods Enzymol. 2004;375:23-44
references.pmid: 14870657
references.citation: Nat Struct Mol Biol. 2007 Nov;14(11):989-96
references.pmid: 17984961
references.citation: EMBO J. 2006 Jul 12;25(13):3123-32
references.pmid: 16778764
references.citation: Methods Mol Biol. 2011;736:285-300
references.pmid: 21660734
references.citation: J Mol Biol. 1998 Feb 13;276(1):19-42
references.pmid: 9514715
references.citation: Mol Cell Biol. 2002 Oct;22(20):7147-57
references.pmid: 12242292
references.citation: Micron. 2011 Feb;42(2):196-206
references.pmid: 20864349
references.citation: Methods Enzymol. 2012;510:169-82
references.pmid: 22608726
references.citation: J Fluoresc. 2007 Nov;17(6):785-95
references.pmid: 17609864
references.citation: Nat Protoc. 2012 May 24;7(6):1193-206
references.pmid: 22635111
references.citation: Nat Rev Mol Cell Biol. 2006 Jun;7(6):437-47
references.pmid: 16723979