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 & Gang Ren
Nature Communications volume 9, Article number: 592 (2018)
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Cryoelectron tomography DNA and RNA Molecular machines and motors Organizing materials with DNA
Received: 13 July 2017 Accepted: 11 January 2018
Published online: 09 February 2018
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.
Acknowledgements
We thank Drs. Shawn Zheng, Michael Braunfeld, and David Agard at University of California, San Francisco, for their great supporting in cryo-EM data acquisition, K2 images alignment, and editing in the manuscript. This material is based upon work supported by the National Science Foundation under Grant DMR-1344290. Work at the Molecular Foundry was supported by the Office of Science, Office of Basic Energy Sciences of the U.S. Department of Energy under Contract Number DE-AC02-05CH11231. G.R. is supported by the National Heart, Lung, and Blood Institute of the National Institutes of Health (number R01HL115153) and the National Institute of General Medical Sciences of the National Institutes of Health (number R01GM104427). C.E.C., C.H., A.M., H.-J.S., and L.Z. acknowledge the support of National Science Foundation (grant number CMMI-1536862).
Author information
Affiliations
The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
Dongsheng Lei, Jianfang Liu & Gang Ren
Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
Alexander E. Marras, Chao-Min Huang, Lifeng Zhou, Carlos E. Castro & Hai-Jun Su
Contributions
This project was initiated and designed by C.E.C., H.-J.S., and G.R. A.E.M. prepared the DNA origami sample. D.L. and J.L. prepared the TEM samples. D.L., J.L., and G.R. acquired the data. D.L. and G.R. processed the data and solved the IPET 3D structures. D.L. docked and analyzed the models. D.L., A.E.M., J.L., C.-M.H., L.Z., C.E.C., H.-J.S., and G.R. interpreted and manipulated the structures. D.L. drafted the initial manuscript, which was revised by G.R., A.E.M., J.L., C.-M.H., L.Z., C.E.C., and H.-J.S.
Competing interests
The authors declare no competing financial interests.
Corresponding authors
Correspondence to Hai-Jun Su or Gang Ren.
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