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

Dongsheng Lei, Alexander E. Marras, Jianfang Liu, Chao-Min Huang, Lifeng Zhou, Carlos E. Castro, Hai-Jun Su () and Gang Ren ()
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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

Nature Communications, 2018, vol. 9, issue 1, 1-8

Abstract: 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.

Date: 2018
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DOI: 10.1038/s41467-018-03018-0

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