Using atomic force microscopy to study chromatin structure and nucleosome remodeling

D. Lohr, R. Bash, H. Wang, J. Yodh, Stuart Lindsay

Research output: Contribution to journalArticle

48 Citations (Scopus)

Abstract

Atomic force microscopy (AFM) is a technique that can directly image single molecules in solution and it therefore provides a powerful tool for obtaining unique insights into the basic properties of biological materials and the functional processes in which they are involved. We have used AFM to analyze basic features of nucleosomes in arrays, such as DNA-histone binding strength, cooperativity in template occupation, nucleosome stabilities, nucleosome locations and the effects of acetylation, to compare these features in different types of arrays and to track the response of array nucleosomes to the action of the human Swi-Snf ATP-dependent nucleosome remodeling complex. These experiments required several specific adaptations of basic AFM methods, such as repetitive imaging of the same fields of molecules in liquid, the ability to change the environmental conditions of the sample being imaged and detection of specific types of molecules within compositionally complex samples. Here, we describe the techniques that allowed such analyses to be carried out.

Original languageEnglish (US)
Pages (from-to)333-341
Number of pages9
JournalMethods
Volume41
Issue number3
DOIs
StatePublished - Mar 2007

Fingerprint

Nucleosomes
Atomic Force Microscopy
Chromatin
Atomic force microscopy
Molecules
Acetylation
Occupations
Histones
Biological materials
Adenosine Triphosphate
Imaging techniques
DNA
Liquids
Experiments

Keywords

  • AFM
  • Chromatin
  • Nucleosomal arrays
  • Nucleosome
  • Remodeling
  • SPM
  • Swi-Snf

ASJC Scopus subject areas

  • Molecular Biology

Cite this

Using atomic force microscopy to study chromatin structure and nucleosome remodeling. / Lohr, D.; Bash, R.; Wang, H.; Yodh, J.; Lindsay, Stuart.

In: Methods, Vol. 41, No. 3, 03.2007, p. 333-341.

Research output: Contribution to journalArticle

Lohr, D. ; Bash, R. ; Wang, H. ; Yodh, J. ; Lindsay, Stuart. / Using atomic force microscopy to study chromatin structure and nucleosome remodeling. In: Methods. 2007 ; Vol. 41, No. 3. pp. 333-341.
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