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.2017 Dec;42(12):951-959.
doi: 10.1557/mrs.2017.274. Epub 2017 Dec 8.

Nanometrology and super-resolution imaging with DNA

Affiliations

Nanometrology and super-resolution imaging with DNA

Elton Graugnard et al. MRS Bull.2017 Dec.

Abstract

Structural DNA nanotechnology is revolutionizing the ways researchers construct arbitrary shapes and patterns in two and three dimensions on the nanoscale. Through Watson-Crick base pairing, DNA can be programmed to form nanostructures with high predictability, addressability, and yield. The ease with which structures can be designed and created has generated great interest for using DNA for a variety of metrology applications, such as in scanning probe microscopy and super-resolution imaging. An additional advantage of the programmable nature of DNA is that mechanisms for nanoscale metrology of the structures can be integrated within the DNA objects by design. This programmable structure-property relationship provides a powerful tool for developing nanoscale materials and smart rulers.

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Figures

Figure 1.
Figure 1.
Large-scale assembly of cross-shaped DNA origami structures deposited on a suitable substrate could be used as a calibration standard in nanometrology. (a) Such origami arrays are assembled from A (blue) and B (yellow) type origami, which are (c) programmed to bind arm to arm. (b)xyz-calibration is based on the exact step heights and well-defined vertical dimensions of each single origami tile (d) as illustrated by the atomic force microscope profiles for scanning in the forward (red) and reverse (yellow) directions over an origami tile. Four flat areas with dimensions of 30 nm × 30 nm × 2 nm in each tile provide enough measuring points for averaging and reliable calibration.
Figure 2.
Figure 2.
Super-resolution microscopy, DNA origami calibration standards. (a) Principle of localization microscopy. Localization of single point emitters in a diffraction-limited area is possible with subdiffraction precision by fitting the point spread function to a 2D-Gaussian function. Adapted with permission from Reference . (b) DNA-PAINT (points accumulation in nanoscale topography) concept. Transient binding of dye-labeled oligonucleotides (colored in red) to their targets enables programmable SRES microscopy. (bottom) The fluorescence intensity versus time trace for a docking site reveals the association and dissociation times of dye-labeled oligonucleotides. Adapted with permission from Reference . (c) Diffraction-limited fluorescence image of a tunnel-like DNA origami structure from (b). Adapted with permission from 31. (d) DNA-PAINT SRES micrograph shows enhanced resolution, resolving the 16-nm distance between the two faces of the DNA origami equipped with DNA-PAINT docking strands. Adapted with permission from Reference . (e–f) DNA origami’s unique structural addressability and integrity visualized with sub-5 nm DNA-PAINT imaging of MPI and LMU logos. Adapted with permission from Reference . (g) DNA origami can act as breadboards for spatially arranging spectrally distinct dye to create nanobarcodes. Adapted with permission from Reference . (h) DNA origami as a nanoscopic ruler for SRES microscopy allows calibration and resolution checks for a variety of super-resolution techniques. Shown is a STORM (stochastic optical reconstruction microscope) image of dyes spaced ~60 nm apart on the DNA origami. Adapted with permission from Reference . (i) DNA origami can act as brightness standards for diffraction-limited microscopy with linearly increasing brightness versus number of dyes. Fluorescence images (inset top) of DNA origami with 12, 24, and 36 attached dyes, respectively, and (inset bottom) a schematic of an origami designed with 36 attached dye molecules. Adapted with permission from Reference . Scale bars = 100 nm (c–d), 10 nm (e–f), and 2 μm (i).
Figure 3.
Figure 3.
(a) Correlative atomic force microscope and super-resolution (SRES) microscope setup. Adapted with permission from Reference . (b) Atomic force microscope (AFM) image of stretched lambda-DNA. (c) SRES image obtained with Yoyo-1, an intercalating stain for double-stranded DNA, of the same region as in (b). (d) Diffraction-limited micrograph of the same region as in (b). The green arrow denotes a section of DNA visible only in AFM but not in fluorescence. The yellow arrow highlights two DNA fragments close to each other that can be resolved in the AFM and SRES image, but not in the standard diffraction-limited fluorescence image. (b–d) Adapted with permission from Reference . Scale bars = 1 μm. Note: EM, electron multiplying; CCD, charge-coupled device.
Figure 4.
Figure 4.
Programmable defect and structure metrology of DNA origami arrays. (a) (top) Schematic, (middle) super-resolution (SRES) image, and (bottom) atomic force microscope (AFM) image of DNA origami cross tiles with extended hybrid sticky-end docking sites that facilitate binding to additional cross tiles as well as state-dependent SRES imaging. The state-dependent hybrid docking sites are imaged in yellow, and conventional docking sites, included in the center of the tile, are imaged in blue. The elongated nature of the central docking sites reveals the orientations of the origami tiles. (b) At the junction of a dimer, the hybrid sticky-end docking sites are deactivated to SRES imaging, which is confirmed in the SRES image below the schematic. (c) A 2 × 2 DNA origami array results in active hybrid sticky-end docking sites at the periphery of the structure and inactive sites within the structure. (a–c) Scale bars = 50 nm. (d) (top) SRES image of the central docking sites within a polycrystalline array of ~81 origami tiles. A reconstruction of the array is shown below the image. (e) SRES image of the defect labels revealing grain boundaries between the grains of the array. (f) Combined two-color SRES image of the array. (d–f) Scale bar = 500 nm. (g) Computing radial pair-distribution functionsg(r) of the central docking sites quantifies the order present within the origami arrays. (Inset) The peak identified at 87.3 nm is the average periodicity of the origami array, which is ~13% shorter than the periodicity expected based on the origami tile width of 100 nm measured via AFM. (h) The AFM measurements are performed on origami flattened on mica, while the SRES data result from origami free to curve and twist in solution. Finite element analysis using CanDo predicts a tile curvature, and the relative change in the tile width, ΔL/L, from its full widthL to its projected widthL′ is ~12%, in agreement with the experimental results. Adapted with permission from Reference . © 2017 Royal Society of Chemistry.
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