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

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. 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.

Authors:
 [1]; ORCiD logo [2];  [1];  [2];  [2]; ORCiD logo [2];  [2];  [1]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). The Molecular Foundry
  2. The Ohio State Univ., Columbus, OH (United States). Dept. of Mechanical and Aerospace Engineering
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); Univ. of California, San Francisco, CA (United States); National Science Foundation (NSF); National Institutes of Health (NIH)
OSTI Identifier:
1433119
Grant/Contract Number:  
AC02-05CH11231; DMR-1344290; R01HL115153; R01GM104427; CMMI-1536862
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 77 NANOSCIENCE AND NANOTECHNOLOGY; Cryoelectron tomography; DNA and RNA; Molecular machines and motors; Organizing materials with DNA

Citation Formats

Lei, Dongsheng, Marras, Alexander E., Liu, Jianfang, Huang, Chao-Min, Zhou, Lifeng, Castro, Carlos E., Su, Hai-Jun, and Ren, Gang. Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography. United States: N. p., 2018. Web. doi:10.1038/s41467-018-03018-0.
Lei, Dongsheng, Marras, Alexander E., Liu, Jianfang, Huang, Chao-Min, Zhou, Lifeng, Castro, Carlos E., Su, Hai-Jun, & Ren, Gang. Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography. United States. doi:10.1038/s41467-018-03018-0.
Lei, Dongsheng, Marras, Alexander E., Liu, Jianfang, Huang, Chao-Min, Zhou, Lifeng, Castro, Carlos E., Su, Hai-Jun, and Ren, Gang. Fri . "Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography". United States. doi:10.1038/s41467-018-03018-0. https://www.osti.gov/servlets/purl/1433119.
@article{osti_1433119,
title = {Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography},
author = {Lei, Dongsheng and Marras, Alexander E. and Liu, Jianfang and Huang, Chao-Min and Zhou, Lifeng and Castro, Carlos E. and Su, Hai-Jun and Ren, Gang},
abstractNote = {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.},
doi = {10.1038/s41467-018-03018-0},
journal = {Nature Communications},
number = 1,
volume = 9,
place = {United States},
year = {2018},
month = {2}
}

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