Literature DB >> 25827873

Chromatin imaging with time-lapse atomic force microscopy.

Yuri L Lyubchenko1, Luda S Shlyakhtenko.   

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.

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Year:  2015        PMID： 25827873      PMCID： PMC4930652          DOI： 10.1007/978-1-4939-2474-5_3

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  23 in total

Review 1.  Epigenetic consequences of nucleosome dynamics.

Authors:  Kami Ahmad; Steven Henikoff
Journal:  Cell       Date:  2002-11-01       Impact factor: 41.582

2.  Rapid spontaneous accessibility of nucleosomal DNA.

Authors:  Gu Li; Marcia Levitus; Carlos Bustamante; Jonathan Widom
Journal:  Nat Struct Mol Biol       Date:  2004-12-05       Impact factor: 15.369

Review 3.  Nucleosome and chromatin fiber dynamics.

Authors:  Karolin Luger; Jeffrey C Hansen
Journal:  Curr Opin Struct Biol       Date:  2005-04       Impact factor: 6.809

4.  Dynamics of nucleosomes assessed with time-lapse high-speed atomic force microscopy.

Authors:  Atsushi Miyagi; Toshio Ando; Yuri L Lyubchenko
Journal:  Biochemistry       Date:  2011-08-23       Impact factor: 3.162

5.  Crystal structure of the nucleosome core particle at 2.8 A resolution.

Authors:  K Luger; A W Mäder; R K Richmond; D F Sargent; T J Richmond
Journal:  Nature       Date:  1997-09-18       Impact factor: 49.962

6.  Visualization of mobility by atomic force microscopy.

Authors:  Toshio Ando; Noriyuki Kodera
Journal:  Methods Mol Biol       Date:  2012

Review 7.  Imaging of nucleic acids with atomic force microscopy.

Authors:  Yuri L Lyubchenko; Luda S Shlyakhtenko; Toshio Ando
Journal:  Methods       Date:  2011-02-16       Impact factor: 3.608

8.  Dynamics of nucleosomes revealed by time-lapse atomic force microscopy.

Authors:  Luda S Shlyakhtenko; Alexander Y Lushnikov; Yuri L Lyubchenko
Journal:  Biochemistry       Date:  2009-08-25       Impact factor: 3.162

9.  AFM for analysis of structure and dynamics of DNA and protein-DNA complexes.

Authors:  Yuri L Lyubchenko; Luda S Shlyakhtenko
Journal:  Methods       Date:  2008-10-07       Impact factor: 3.608

10.  The role of histone H4 biotinylation in the structure of nucleosomes.

Authors:  Nina A Filenko; Carol Kolar; John T West; S Abbie Smith; Yousef I Hassan; Gloria E O Borgstahl; Janos Zempleni; Yuri L Lyubchenko
Journal:  PLoS One       Date:  2011-01-27       Impact factor: 3.240
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  2 in total

1.  Direct AFM Visualization of the Nanoscale Dynamics of Biomolecular Complexes.

Authors:  Yuri L Lyubchenko
Journal:  J Phys D Appl Phys       Date:  2018-08-20       Impact factor: 3.207

2.  In Vitro Chromatin Assembly: Strategies and Quality Control.

Authors:  U Muthurajan; F Mattiroli; S Bergeron; K Zhou; Y Gu; S Chakravarthy; P Dyer; T Irving; K Luger
Journal:  Methods Enzymol       Date:  2016-02-19       Impact factor: 1.600
  2 in total

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