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All-Atom Molecular Dynamics Simulations of Membrane-Spanning DNA Origami Nanopores

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DNA and RNA Origami

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2639))

Abstract

Building on the recent technological advances, all-atom molecular dynamics (MD) simulations have become an indispensable tool to study the molecular behavior at nanoscale. Molecular simulations have been used to characterize the structure, dynamics, and mechanical and electrical properties of DNA origami objects. In this chapter we describe a method to build all-atom model of lipid-spanning DNA origami nanopores and perform molecular dynamics simulations in explicit electrolyte solutions.

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Acknowledgments

We gratefully acknowledge support from the National Institutes of Health (P41-GM104601), National Science Foundation (DMR-1827346), and supercomputer time provided through XSEDE Allocation Grant MCA05S028 and the Blue Waters petascale supercomputer system (UIUC).

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Author notes

  1. Himanshu Joshi

    Present address: Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, India

Authors and Affiliations

  1. Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA

    Himanshu Joshi, Chen-Yu Li & Aleksei Aksimentiev

Authors
  1. Himanshu Joshi
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  2. Chen-Yu Li
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  3. Aleksei Aksimentiev
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Corresponding author

Correspondence to Aleksei Aksimentiev .

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Editors and Affiliations

  1. Aarhus university, Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus, Denmark

    Julián Valero

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Joshi, H., Li, CY., Aksimentiev, A. (2023). All-Atom Molecular Dynamics Simulations of Membrane-Spanning DNA Origami Nanopores. In: Valero, J. (eds) DNA and RNA Origami. Methods in Molecular Biology, vol 2639. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3028-0_7

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  • DOI: https://doi.org/10.1007/978-1-0716-3028-0_7

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  • Print ISBN: 978-1-0716-3027-3

  • Online ISBN: 978-1-0716-3028-0

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