DNA origami is one of the most promising ways to create novel 2D and 3D structures, assemble inorganic and organic materials, and synthesize functional micro/nano systems. In particular, DNA origami structures consisting of nanotube configurations can function as mechanical components for encapsulating materials such as gold particles or drug proteins, due to their tubular structure, relatively high rigidity, high aspect ratio, and other desirable characteristics, but certain mechanical properties such as radial rigidity have yet to be fully determined experimentally. Here, we present the direct measurement of the radial modulus of a DNA nanotube structure by force-distance curve-based atomic force microscopy (AFM), in a magnesium ion solution. A Hertz model, corrected using the finite element method (FEM) to achieve greater realism, was employed to determine the DNA nanotube's actual radial modulus in two states, corresponding to the rigidity of a porous and electrostatically repulsive nanotube lattice, and the rigidity of a packed and elastic honeycomb lattice. Furthermore, the biphasic radial modulus was verified by estimation of the inter-helix electrostatic force and torsional rigidity of a 6-helix DNA nanotube, with results comparable to those reported elsewhere. The anisotropy of the DNA nanotube honeycomb lattice revealed by our radial measurements should be useful when developing new DNA structures and may enable further applications that utilize DNA origami structures as a mechanical component.

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To create a nanogap-based device for single-molecule label-free detection using surface-enhanced Raman spectroscopy (SERS), a new approach utilising DNA origami (DO) as a sacrificial nanostructure is proposed. In this approach, 15-nm diameter gold nanoparticles (AuNPs) are precisely self-assembled to form a dimer structure on opposite faces of a rectangular DO structure. The AuNPs are then fixed on a silicon chip supporting an amino-terminated monolayer and the DO is selectively removed by vacuum ultraviolet (VUV) treatment followed by ultrapure water cleaning. X-ray photoelectron spectroscopy measurements confirmed the successful removal of the DNA nanostructures and the VUV treatment had little effect on the diameter of the AuNPs. Quantitative evaluations showed that the original gap distance of about 3.8 nm was reduced to <2 nm after the DO structures were removed by the VUV treatment and ultrapure water rinse. The proposed technique can therefore be considered a simple and low-cost alternative to EB lithography approaches.

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DNA origami methods enable the fabrication of various nanostructures and nanodevices, but their effective use depends on an understanding of their structural and mechanical properties and the effects of basic structural features. Frequency‐modulation atomic force microscopy is introduced to directly characterize, in aqueous solution, the crossover regions of sets of 2D DNA origami based on different crossover/nick designs. Rhombic‐shaped nanostructures formed under the influence of flexible crossovers placed between DNA helices are observed in DNA origami incorporating crossovers every 3, 4, or 6 DNA turns. The bending rigidity of crossovers is determined to be only one‐third of that of the DNA helix, based on interhelical electrostatic forces reported elsewhere, and the measured pitches of the 3‐turn crossover design rhombic‐shaped nanostructures undergoing negligible bending. To evaluate the robustness of their structural integrity, they are intentionally and simultaneously stressed using force‐controlled atomic force microscopy. DNA crossovers are verified to have a stabilizing effect on the structural robustness, while the nicks have an opposite effect. The structural and mechanical properties of DNA origami and the effects of crossovers and nicks revealed in this paper can provide information essential for the design of versatile DNA origami structures that exhibit specified and desirable properties.