2018Lei DNABennet

Citation

3D Structural Dynamics of DNA Origami Mechanisms and Machines Using Individual-Particle Electron Tomography, Dongsheng Lei, Alex Marras, Jianfang Liu, Chaomin Huang, Lifeng Zhou, Carlos Castro, Hai-Jun Su, Gang Ren, Nature Communications, (2018), 9:592, DOI: 10.1038/s41467-018-03018-0

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.

Keywords

Cryo-ET, single molecule structure, individual-particle cryo-electron tomography, IPET, DNA origami Bennett linkages, structural flexibility

Paper links

https://www.nature.com/articles/s41467-018-03018-0

Related video

https://www.youtube.com/watch?v=2Cjaxv9-btU