Abstract
DNA origami can be applied as a "ruler" for nanoscale calibration or super-resolution fluorescence microscopy with an ideal structure for defining fluorophore arrangement, allowing the distance between fluorophores to be precisely controlled at the nanometer scale. DNA origami can also be used as a nanotag with arbitrary programmable shapes for topological identification. In this study, we formed a hexagonal origami structure embedded with three different fluorescent dyes on the surface. The distance between each fluorescent block was ~120 nm, which is below the diffraction limit of light, allowing for its application as a nano-ruler for super-resolution fluorescence microscopy. The outside edge of the hexagonal structure was redesigned to form three different substructures as topological labels. Atomic and scanning force microscopy demonstrated the consistent nanoscale distance between morphological and fluorescent labels. Therefore, this fluorophore-embedded hexagonal origami platform can be used as a dual nanoruler for optical and topological calibration.
Highlights
DNA origami has various applications, including DNA computing, nanoarchitecture, and drug design. [1,2,3,4,5,6,7,8,9] Single-DNA origami is formed by a long circular scaffold strand with the help of hundreds of staple strands, [10] each of which is known in advance and has a unique position in the final assembled structure
Background:DNA origami can be applied as a “ruler” for nanoscale calibration or super-resolution fluorescence microscopy with an ideal structure for defining fluorophore arrangement, allowing the distance between fluorophores to be precisely controlled at the nanometer scale
Conclusion:We assembled the hexagonal origami platform and confirmed the fluorescent and topological labels, this fluorophore-embedded hexagonal origami platform can be used as a dual nano-ruler for both optical and topological calibration
Summary
DNA origami has various applications, including DNA computing, nanoarchitecture, and drug design. [1,2,3,4,5,6,7,8,9] Single-DNA origami is formed by a long circular scaffold strand with the help of hundreds of staple strands, [10] each of which is known in advance and has a unique position in the final assembled structure. DNA origami provides an excellent platform for super-resolution fluorescent microscopy owing to advantages of optical calibration, which allows for precise docking of the fluorophores at predesigned positions. [16] Further, fluorophore-embedded origami structures were demonstrated to serve as an ideal calibration ruler for a variety of super-resolution microscopy applications, including stimulated emission depletion microscopy (STED), direct stochastic optical reconstruction microscopy, or confocal microscopy. As a single origami structure is in the nanometer size scale, several origamis need to be assembled into a larger shape to enable fluorescent microscopy at different scales, including the microscale, for various purposes. DNA origami can be applied as a “ruler” for nanoscale calibration or super-resolution fluorescence microscopy with an ideal structure for defining fluorophore arrangement, allowing the distance between fluorophores to be precisely controlled at the nanometer scale. Conclusion:We assembled the hexagonal origami platform and confirmed the fluorescent and topological labels, this fluorophore-embedded hexagonal origami platform can be used as a dual nano-ruler for both optical and topological calibration
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