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. 2025:2968:485-508.
doi: 10.1007/978-1-0716-4750-9_29.

Single-Molecule Studies with AFM and High-Speed AFM: From Nucleosomes to Chromosomes

Daniël P Melters  1 , Keir C Neuman  2 , Yamini Dalal  3
Affiliations

Single-Molecule Studies with AFM and High-Speed AFM: From Nucleosomes to Chromosomes

Daniël P Melters et al. Methods Mol Biol. 2025.

Abstract

Atomic force microscopy (AFM) is a single-molecule imaging technique invented in 1985. Development of high-speed AFM (HS-AFM) in 2001 now allows for the direct visualization of the dynamics and kinetics of biological molecules. In this chapter, we describe methods to both reconstitute in vitro and extract in vivo chromatin for air mode AFM and HS-AFM studies. With these methods, sub-nanometer static and time-resolved topographical measurements of nucleosome and chromatin conformations and dynamics can be obtained. Furthermore, we discuss how HS-AFM data can be analyzed to obtain quantitative measures of nucleosome dynamics.

Keywords: Atomic force microscopy; Chromatin; Chromosome; Diffusion constant; High-speed AFM; Mean square displacement (MSD); Nucleosome.

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