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A Plasmonic Nanorod That Walks on DNA Origami

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A Plasmonic Nanorod That Walks on DNA Origami

Chao Zhou et al. Nat Commun.

Abstract

In nano-optics, a formidable challenge remains in precise transport of a single optical nano-object along a programmed and routed path toward a predefined destination. Molecular motors in living cells that can walk directionally along microtubules have been the inspiration for realizing artificial molecular walkers. Here we demonstrate an active plasmonic system, in which a plasmonic nanorod can execute directional, progressive and reverse nanoscale walking on two or three-dimensional DNA origami. Such a walker comprises an anisotropic gold nanorod as its 'body' and discrete DNA strands as its 'feet'. Specifically, our walker carries optical information and can in situ optically report its own walking directions and consecutive steps at nanometer accuracy, through dynamic coupling to a plasmonic stator immobilized along its walking track. Our concept will enable a variety of smart nanophotonic platforms for studying dynamic light-matter interaction, which requires controlled motion at the nanoscale well below the optical diffraction limit.

Figures

Figure 1
Figure 1. Schematic of the plasmonic walker.
Two gold nanorods (AuNRs) are assembled perpendicularly to one another on a double-layer DNA origami template, forming a left-handed configuration at station I. The yellow AuNR on the top surface represents the ‘walker' and the red AuNR on the bottom surface represents the ‘stator'. The walking track comprises six rows of footholds (A–F) extended from the origami surface to define five walking stations (I–V). The distance between the neighbouring stations is 7 nm, which also corresponds to the step size. In each row, there are five binding sites with identical footholds. Only the footholds in the front line are coloured to highlight the different strand segments. The walker AuNR is fully functionalized with foot strands. To enable robust binding, the walker steps on two rows of neighbouring footholds at each station. The red beam indicates the incident circularly polarized light.
Figure 2
Figure 2. Walking mechanism, measured and simulated CD spectra at each station.
(a) Walking mechanism. Initially, the walker resides at station I. On addition of blocking strand a and removal strand formula image, two toehold-mediated strand-displacement reactions occur simultaneously. Blocking strand a triggers the dissociation of the walker's feet from footholds A. Row A is then site-blocked. Meanwhile, removal strand formula image releases blocking strand c from footholds C. Row C is therefore site activated to bind the feet of the walker. Subsequently, the walker carries out one step forward, reaching station II. For simplicity, only the front line of the associated strands is shown. (b) Measured CD spectra at different stations. (c) Simulated CD spectra at different stations. The right-handed preference at station III was not included in the calculation.
Figure 3
Figure 3. TEM images of the DNA origami templates and the plasmonic walker structures.
(a) TEM image of the double-layer DNA origami (58 × 42 × 7 nm) after negative staining, Scale bar, 50 nm. (b) Exemplary TEM image of the plasmonic walker structures at station I. In the individual structures, two AuNRs (35 × 10 nm) are assembled on one origami template. The plasmonic structures display certain deformation due to the drying process on the TEM grids. Scale bar, 200 nm. (c) Enlarged views of the plasmonic walker structures from different perspectives. Scale bars, 20 nm.
Figure 4
Figure 4. Directional and progressive walking of the plasmonic walker detected by in situ CD spectroscopy.
The CD intensity was monitored at a fixed wavelength of 685 nm, while the walker performs stepwise walking, following a route I–II–III–IV–V–IV–III–IV.
Figure 5
Figure 5. Stepwise walking on 3D DNA origami.
(a) Schematic of the plasmonic walker on a 3D triangular prism DNA origami platform. The walking track comprises seven rows of footholds (A–G) extended from the origami surface to define six walking stations (I–VI). The walking process starts at station I, where the walker and the stator form a right-handed configuration. The distances between the neighbouring stations are slightly different owing to the irregular side surfaces of the 3D origami. The successive step sizes are ∼7, 7, 12, 12 and 11 nm. (b) Measured CD spectra and corresponding TEM images of the plasmonic walker structures at different stations. The frame size of each TEM image is 80 nm. The plasmonic structures display certain deformation due to the drying process on the TEM grids.

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