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Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution

Author

Listed:
  • Massimo Kube

    (Technische Universität München)

  • Fabian Kohler

    (Technische Universität München)

  • Elija Feigl

    (Technische Universität München)

  • Baki Nagel-Yüksel

    (Technische Universität München)

  • Elena M. Willner

    (Technische Universität München)

  • Jonas J. Funke

    (Technische Universität München)

  • Thomas Gerling

    (Technische Universität München)

  • Pierre Stömmer

    (Technische Universität München)

  • Maximilian N. Honemann

    (Technische Universität München)

  • Thomas G. Martin

    (MRC Laboratory of Molecular Biology)

  • Sjors H. W. Scheres

    (MRC Laboratory of Molecular Biology)

  • Hendrik Dietz

    (Technische Universität München)

Abstract

The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is folded by many short DNA oligonucleotides, can be employed to make objects comprising hundreds of unique DNA strands and thousands of base pairs, thus in principle providing many degrees of freedom for modelling complex objects of defined 3D shapes and sizes. Here, we address the problem of accurate structural validation of DNA objects in solution with cryo-EM based methodologies. By taking into account structural fluctuations, we can determine structures with improved detail compared to previous work. To interpret the experimental cryo-EM maps, we present molecular-dynamics-based methods for building pseudo-atomic models in a semi-automated fashion. Among other features, our data allows discerning details such as helical grooves, single-strand versus double-strand crossovers, backbone phosphate positions, and single-strand breaks. Obtaining this higher level of detail is a step forward that now allows designers to inspect and refine their designs with base-pair level interventions.

Suggested Citation

  • Massimo Kube & Fabian Kohler & Elija Feigl & Baki Nagel-Yüksel & Elena M. Willner & Jonas J. Funke & Thomas Gerling & Pierre Stömmer & Maximilian N. Honemann & Thomas G. Martin & Sjors H. W. Scheres &, 2020. "Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
  • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-20020-7
    DOI: 10.1038/s41467-020-20020-7
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    Cited by:

    1. Molly F. Parsons & Matthew F. Allan & Shanshan Li & Tyson R. Shepherd & Sakul Ratanalert & Kaiming Zhang & Krista M. Pullen & Wah Chiu & Silvi Rouskin & Mark Bathe, 2023. "3D RNA-scaffolded wireframe origami," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Jae Young Lee & Heeyuen Koh & Do-Nyun Kim, 2023. "A computational model for structural dynamics and reconfiguration of DNA assemblies," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    3. Katya Ahmad & Abid Javed & Conor Lanphere & Peter V. Coveney & Elena V. Orlova & Stefan Howorka, 2023. "Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

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