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Characterization of Structural and Configurational Properties of DNA by Atomic Force Microscopy

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Genome Instability

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1672))

Abstract

We describe a method to extract quantitative information on DNA structural and configurational properties from high-resolution topographic maps recorded by atomic force microscopy (AFM). DNA molecules are deposited on mica surfaces from an aqueous solution, carefully dehydrated, and imaged in air in Tapping Mode. Upon extraction of the spatial coordinates of the DNA backbones from AFM images, several parameters characterizing DNA structure and configuration can be calculated. Here, we explain how to obtain the distribution of contour lengths, end-to-end distances, and gyration radii. This modular protocol can be also used to characterize other statistical parameters from AFM topographies.

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Acknowledgments

We thank Francesca Borghi for support in AFM analysis. A.P. thanks the Dept. of Physics of the University of Milano for financial support under the project “Piano di Sviluppo dell’Ateneo per la Ricerca 2014. Linea B: Supporto per i giovani ricercatori”. Work in M.M-F lab is supported by AIRC (n.15631) and Telethon (GGP15227).

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Authors and Affiliations

  1. Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133, Milano, Italy

    Alice Meroni, Federico Lazzaro & Marco Muzi-Falconi

  2. Dipartimento di Fisica and C.I.Ma.I.Na, Università degli Studi di Milano, via Celoria 16, 20133, Milano, Italy

    Alessandro Podestà

Authors
  1. Alice Meroni
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  2. Federico Lazzaro
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  3. Marco Muzi-Falconi
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  4. Alessandro Podestà
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Corresponding author

Correspondence to Alessandro Podestà .

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Editors and Affiliations

  1. Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Milano, Italy

    Marco Muzi-Falconi

  2. Donnelly Centre and Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada

    Grant W Brown

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Meroni, A., Lazzaro, F., Muzi-Falconi, M., Podestà, A. (2018). Characterization of Structural and Configurational Properties of DNA by Atomic Force Microscopy. In: Muzi-Falconi, M., Brown, G. (eds) Genome Instability. Methods in Molecular Biology, vol 1672. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7306-4_37

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  • DOI: https://doi.org/10.1007/978-1-4939-7306-4_37

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7305-7

  • Online ISBN: 978-1-4939-7306-4

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