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 language | English (US) |
|---|---|
| Pages (from-to) | 333-341 |
| Number of pages | 9 |
| Journal | Methods |
| Volume | 41 |
| Issue number | 3 |
| DOIs | |
| State | Published - Mar 2007 |
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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 journal › Article
}
TY - JOUR
T1 - Using atomic force microscopy to study chromatin structure and nucleosome remodeling
AU - Lohr, D.
AU - Bash, R.
AU - Wang, H.
AU - Yodh, J.
AU - Lindsay, Stuart
PY - 2007/3
Y1 - 2007/3
N2 - 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.
AB - 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.
KW - AFM
KW - Chromatin
KW - Nucleosomal arrays
KW - Nucleosome
KW - Remodeling
KW - SPM
KW - Swi-Snf
UR - http://www.scopus.com/inward/record.url?scp=33847026837&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=33847026837&partnerID=8YFLogxK
U2 - 10.1016/j.ymeth.2006.08.016
DO - 10.1016/j.ymeth.2006.08.016
M3 - Article
VL - 41
SP - 333
EP - 341
JO - Methods
JF - Methods
SN - 1046-2023
IS - 3
ER -