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.
Highlights
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 motioncontrolled
Castro and colleagues[2] used transmission electron microscopy (TEM) to image DNA origami mechanisms (DOM) deposited on a surface and obtained geometric parameters, including lengths and angles
The 2D imaging of fabricated DOMs using TEM suggested those mechanisms are dynamic in 3D structure[2]
Summary
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 motioncontrolled. Castro and colleagues[2] used transmission electron microscopy (TEM) to image DOM deposited on a surface and obtained geometric parameters, including lengths and angles As these measurements were performed only on twodimensional (2D) projections, they are inadequate for complete validation of 3D structures. Single-particle 3D reconstruction methods using TEM can achieve atomic resolution, it requires image averaging over many homogeneous structures. This is unsuitable for dynamic mechanisms that adopt many different conformations. By comparing the conformations revealed from each 3D reconstruction, this approach enables us to understand how the underlying design is related to the structural mobility and motion of DNA origamibased machines
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