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Detecting DNA Loops Using Tethered Particle Motion

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Single Molecule Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2694))

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Abstract

The range of motion of a micron-sized bead tethered by a single polymer provides a dynamic readout of the effective length of the polymer. The excursions of the bead may reflect the intrinsic flexibility and/or topology of the polymer as well as changes due to the action activity of ligands that bind the polymer. This is a simple yet powerful experimental approach to investigate such interactions between DNA and proteins as demonstrated by experiments with the lac repressor. This protein forms a stable, tetrameric oligomer with two binding sites and can produce a loop of DNA between recognition sites separated along the length of a DNA molecule.

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Acknowledgments

Kathleen Matthews generously provided the lac repressor used in this work. We are grateful to former Finzi Lab members for their contributions to the development of these TPM protocols. This work was supported by the NIH, Grant: R01GM084070 and R35GM149296 .

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Authors and Affiliations

  1. Department of Physics, Emory University, Atlanta, GA, USA

    Jin Qian, Dylan Collette, Laura Finzi & David Dunlap

Authors
  1. Jin Qian
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  2. Dylan Collette
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  3. Laura Finzi
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  4. David Dunlap
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Corresponding author

Correspondence to David Dunlap .

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Editors and Affiliations

  1. LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands

    Iddo Heller

  2. LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands

    David Dulin

  3. LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands

    Erwin J.G. Peterman

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Qian, J., Collette, D., Finzi, L., Dunlap, D. (2024). Detecting DNA Loops Using Tethered Particle Motion. In: Heller, I., Dulin, D., Peterman, E.J. (eds) Single Molecule Analysis . Methods in Molecular Biology, vol 2694. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3377-9_21

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  • DOI: https://doi.org/10.1007/978-1-0716-3377-9_21

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3376-2

  • Online ISBN: 978-1-0716-3377-9

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