DNA origami templated self-assembly has shown its potential in creating rationally designed nanophotonic devices in a parallel and repeatable manner. In this investigation, we employ a multiscaffold DNA origami approach to fabricate linear waveguides of 10 nm diameter gold nanoparticles. This approach provides independent control over nanoparticle separation and spatial arrangement. The waveguides were characterized using atomic force microscopy and far-field polarization spectroscopy. This work provides a path toward large-scale plasmonic circuitry.

Arrays of nanoparticles whose interactions can be characterized by hopping Hamiltonians can serve as excitation transmission lines. Here we show, that in addition suitable arrangements of nanoparticles can form beam splitters, phase shifters, and crossover splitters. With these elements, any discrete unitary transformation can be implemented on input modes via a network of nanoparticles in which all the components lie in the same plane. These nanoparticle networks can produce optical functionalities at a length scale much smaller than 1 $\mu${}m.

Nanoarchitectural control of matter is crucial for next-generation technologies. DNA origami templates are harnessed to accurately position single molecules; however, direct single molecule evidence is lacking regarding how well DNA origami can control the orientation of such molecules in three-dimensional space, as well as the factors affecting control. Here, we present two strategies for controlling the polar (θ) and in-plane azimuthal (ϕ) angular orientations of cyanine Cy5 single molecules tethered on rationally-designed DNA origami templates that are physically adsorbed (physisorbed) on glass substrates. By using dipolar imaging to evaluate Cy5′s orientation and super-resolution microscopy, the absolute spatial orientation of Cy5 is calculated relative to the DNA template. The sequence-dependent partial intercalation of Cy5 is discovered and supported theoretically using density functional theory and molecular dynamics simulations, and it is harnessed as our first strategy to achieve θ control for a full revolution with dispersion as small as ±4.5°. In our second strategy, ϕ control is achieved by mechanically stretching the Cy5 from its two tethers, being the dispersion ±10.3° for full stretching. These results can in principle be applied to any single molecule, expanding in this way the capabilities of DNA as a functional templating material for single-molecule orientation control. The experimental and modeling insights provided herein will help engineer similar self-assembling molecular systems based on polymers, such as RNA and proteins.

Crystal-PAINT super-resolution imaging enables high-throughput metrology of DNA nanostructures for quantitative analysis of arrays formed through self-assembly.

DNA nanostructures routinely self-assemble with sub-10 nm feature sizes. This capability has created industry interest in using DNA as a lithographic mask, yet with few exceptions, solution-based deposition of DNA nanostructures has remained primarily academic to date. En route to controlled adsorption of DNA patterns onto manufactured substrates, deposition and placement of DNA origami has been demonstrated on chemically functionalized silicon substrates. While compelling, chemical functionalization adds fabrication complexity that limits mask efficiency and hence industry adoption. As an alternative, we developed an ion implantation process that tailors the surface potential of silicon substrates to facilitate adsorption of DNA nanostructures without the need for chemical functionalization. Industry standard 300 mm silicon wafers were processed, and we showed controlled adsorption of DNA origami onto boron-implanted silicon patterns; selective to a surrounding silicon oxide matrix. The hydrophilic substrate achieves very high surface selectivity by exploiting pH-dependent protonation of silanol-groups on silicon dioxide (SiO₂), across a range of solution pH values and magnesium chloride (MgCl₂) buffer concentrations.