The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA.
Nat Commun. 2018 Feb 9;9(1):592. doi: 10.1038/s41467-018-03018-0.
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.
支架 DNA 折纸已被证明是一种强大而有效的技术，通过将单链 DNA 模板链编程折叠成三维 (3D) 纳米结构来制造功能纳米机器，旨在精确地进行运动控制。尽管使用透射电子显微镜和原子力显微镜对 DNA 纳米机器进行二维 (2D) 成像表明这些纳米机器在 3D 中是动态的，但基于 2D 成像的几何分析不足以揭示 3D 中的精确运动。在这里，我们使用单个粒子电子断层扫描方法，从 129 个单个 DNA 折纸 Bennett 连接机制中重建了 129 个密度图，分辨率约为 6-14nm。对这些构象的统计分析导致了对 Bennett 连接机制的 3D 结构动力学的理解。此外，我们的努力为 DNA 折纸的理论运动学模型提供了实验验证，该模型可用于通过优化 DNA 序列和布线来反馈改进运动的设计和控制。
