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.
Szu-Ning Lin and Liang Qin are co-first authors.
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Acknowledgments
The authors thank Andreas Biebricher for the development of surface passivation methods, Sandrine D’Haene, Seyda Acar, and Ramon van der Valk for DNA substrate design and technical assistance, LUMICKS B.V. for assistance in developing the AFS system. This work was supported by grants from FOM (R.T.D. and G.J.L.W.), NWO-VICI (R.T.D. and G.J.L.W.), HFSP (R.T.D.) and China Scholarship Council No. 201506880001 (L.Q.).
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Lin, SN., Qin, L., Wuite, G.J.L., Dame, R.T. (2018). Unraveling the Biophysical Properties of Chromatin Proteins and DNA Using Acoustic Force Spectroscopy. In: Dame, R. (eds) Bacterial Chromatin. Methods in Molecular Biology, vol 1837. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8675-0_16
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DOI: https://doi.org/10.1007/978-1-4939-8675-0_16
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