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A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems

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DNA Nanotechnology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1811))

Abstract

The DNA origami method exploits the self-assembly property of nucleic acids to build diverse nanoscale systems. The all-atom molecular dynamics (MD) method has emerged as a powerful computational tool for atomic-resolution characterization of the in situ structure and physical properties of DNA origami objects. This chapter provides step-by-step instructions for building atomic-scale models of DNA origami systems, using the MD method to simulate the models, and performing basic analyses of the resulting MD trajectories.

The original version of this chapter was revised. The correction to this chapter is available at https://doi.org/10.1007/978-1-4939-8582-1_23

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Change history

  • 06 November 2018

    Correction to: Chapter 15 in: Giampaolo Zuccheri (ed.), DNA Nanotechnology: Methods and Protocols, Methods in Molecular Biology, vol. 1811, https://doi.org/10.1007/978-1-4939-8582-1_15

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Acknowledgement

Funding for the creation of this tutorial was provided by the NSF via Grant Award Number DMR-1507985.

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Authors and Affiliations

  1. Department of Physics, University of Illinois, Urbana−Champaign, Urbana, IL, USA

    Jejoong Yoo, Chen-Yu Li, Scott Michael Slone, Christopher Maffeo & Aleksei Aksimentiev

Authors
  1. Jejoong Yoo
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  2. Chen-Yu Li
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  3. Scott Michael Slone
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  4. Christopher Maffeo
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  5. Aleksei Aksimentiev
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Corresponding author

Correspondence to Aleksei Aksimentiev .

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Editors and Affiliations

  1. Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy

    Giampaolo Zuccheri

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Yoo, J., Li, CY., Slone, S.M., Maffeo, C., Aksimentiev, A. (2018). A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems. In: Zuccheri, G. (eds) DNA Nanotechnology. Methods in Molecular Biology, vol 1811. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8582-1_15

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  • DOI: https://doi.org/10.1007/978-1-4939-8582-1_15

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8581-4

  • Online ISBN: 978-1-4939-8582-1

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