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

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

doi:10.1038/s41467-018-03018-0

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

Journal Article · Fri Feb 09 00:00:00 EST 2018 · Nature Communications

DOI:https://doi.org/10.1038/s41467-018-03018-0· OSTI ID:1433119

Lei, Dongsheng ^[1];

^[2]; Liu, Jianfang ^[1]; Huang, Chao-Min ^[2]; Zhou, Lifeng ^[2];

^[2]; Su, Hai-Jun ^[2]; Ren, Gang ^[1]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). The Molecular Foundry
The Ohio State Univ., Columbus, OH (United States). Dept. of Mechanical and Aerospace Engineering

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. In this paper, 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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); Univ. of California, San Francisco, CA (United States); National Science Foundation (NSF); National Institutes of Health (NIH)

Grant/Contract Number:: AC02-05CH11231; DMR-1344290; R01HL115153; R01GM104427; CMMI-1536862

OSTI ID:: 1433119

Journal Information:: Nature Communications, Vol. 9, Issue 1; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 41 works

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Single-molecule 3D imaging of human plasma intermediate-density lipoproteins reveals a polyhedral structure Lei, Dongsheng; Yu, Yadong; Kuang, Yu-Lin Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, Vol. 1864, Issue 3 https://doi.org/10.1016/j.bbalip.2018.12.004	journal	March 2019
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