Unravelling the Biophysical Properties of Chromatin Proteins and DNA Using Acoustic Force Spectroscopy

Szu-Ning Lin; Liang Qin; Kees-Karel H Taris; Gijs J L Wuite; Remus T Dame

doi:10.1007/978-1-0716-3930-6_24

Unravelling the Biophysical Properties of Chromatin Proteins and DNA Using Acoustic Force Spectroscopy

Methods Mol Biol. 2024:2819:519-534. doi: 10.1007/978-1-0716-3930-6_24.

Authors

Szu-Ning Lin^{1

2}, Liang Qin¹, Kees-Karel H Taris², Gijs J L Wuite², Remus T Dame^{3

4

5}

Affiliations

¹ Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
² Department of Physics and Astronomy, VU University Amsterdam, Amsterdam, The Netherlands.
³ Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands. [email protected].
⁴ Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands. [email protected].
⁵ Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands. [email protected].

PMID: 39028522
DOI: 10.1007/978-1-0716-3930-6_24

Abstract

Acoustic force spectroscopy (AFS) is a single-molecule micromanipulation technique that uses sound waves to exert force on surface-tethered DNA molecules in a microfluidic chamber. As large numbers of individual protein-DNA complexes are tracked in parallel, AFS provides insight into the individual properties of such complexes as well as their population averages. In this chapter, we describe in detail how to perform AFS experiments specifically on bare DNA, protein-DNA complexes, and how to extract their (effective) persistence length and contour length from force-extension relations.

Keywords: Bacterial chromatin protein; DNA-binding protein; Protein–DNA interaction; Single-molecule manipulation; Acoustic force spectroscopy.

MeSH terms

Acoustics
Chromatin* / chemistry
Chromatin* / metabolism
DNA* / chemistry
DNA-Binding Proteins / chemistry
DNA-Binding Proteins / metabolism
Microscopy, Atomic Force / methods
Single Molecule Imaging / methods
Spectrum Analysis / methods

Substances

DNA
Chromatin
DNA-Binding Proteins