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Rhombic-Shaped Nanostructures and Mechanical Properties of 2D DNA Origami Constructed with Different Crossover/Nick Designs

Rhombic-Shaped Nanostructures and Mechanical Properties of 2D DNA Origami Constructed with Different Crossover/Nick Designs
Toshiyuki Tsuchiya, Zhipeng Ma, Hirofumi Yamada, Seongsu Park, Yunfei Huang, Yoshikazu Hirai, Osamu Tabata, Kentaro Kawai, Do-Nyun Kim
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. Direct visualization of 2D DNA origami structures constructed with different crossover/nick designs is performed in aqueous solution using frequency-modulation atomic force microscopy (FM-AFM), showing rhombic-shaped nanostructures owing to the crossover rotations as a result of interhelical electrostatic repulsion. The structural robustness of fabricated DNA origami structures and the effect of crossover/nick are comparatively investigated by damaging them using force-controlled AFM.

Publisher URL: http://onlinelibrary.wiley.com/resolve/doi

DOI: 10.1002/smll.201702028

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