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Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography

Author

Listed:
  • Dongsheng Lei

    (Lawrence Berkeley National Laboratory)

  • Alexander E. Marras

    (The Ohio State University)

  • Jianfang Liu

    (Lawrence Berkeley National Laboratory)

  • Chao-Min Huang

    (The Ohio State University)

  • Lifeng Zhou

    (The Ohio State University)

  • Carlos E. Castro

    (The Ohio State University)

  • Hai-Jun Su

    (The Ohio State University)

  • Gang Ren

    (Lawrence Berkeley National Laboratory)

Abstract

Scaffolded DNA origami has proven to be a powerful and efficient technique to fabricate functional nanomachines by programming the folding of a single-stranded DNA template strand into three-dimensional (3D) nanostructures, designed to be precisely motion-controlled. Although two-dimensional (2D) imaging of DNA nanomachines using transmission electron microscopy and atomic force microscopy suggested these nanomachines are dynamic in 3D, geometric analysis based on 2D imaging was insufficient to uncover the exact motion in 3D. Here we use the individual-particle electron tomography method and reconstruct 129 density maps from 129 individual DNA origami Bennett linkage mechanisms at ~ 6–14 nm resolution. The statistical analyses of these conformations lead to understanding the 3D structural dynamics of Bennett linkage mechanisms. Moreover, our effort provides experimental verification of a theoretical kinematics model of DNA origami, which can be used as feedback to improve the design and control of motion via optimized DNA sequences and routing.

Suggested Citation

  • Dongsheng Lei & Alexander E. Marras & Jianfang Liu & Chao-Min Huang & Lifeng Zhou & Carlos E. Castro & Hai-Jun Su & Gang Ren, 2018. "Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography," Nature Communications, Nature, vol. 9(1), pages 1-8, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-03018-0
    DOI: 10.1038/s41467-018-03018-0
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    Cited by:

    1. Zhiyuan Ding & Si Gao & Weina Fang & Chen Huang & Liqi Zhou & Xudong Pei & Xiaoguo Liu & Xiaoqing Pan & Chunhai Fan & Angus I. Kirkland & Peng Wang, 2022. "Three-dimensional electron ptychography of organic–inorganic hybrid nanostructures," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    2. Jianfang Liu & Ewan K. S. McRae & Meng Zhang & Cody Geary & Ebbe Sloth Andersen & Gang Ren, 2024. "Non-averaged single-molecule tertiary structures reveal RNA self-folding through individual-particle cryo-electron tomography," Nature Communications, Nature, vol. 15(1), pages 1-18, December.

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