DNA origami structures as calibration standards for nanometrology

Korpelainen, Virpi; Linko, Veikko; Seppä, Jeremias; Lassila, Antti; Kostiainen, Mauri A.

doi:10.1088/1361-6501/28/3/034001

Cited by 12 publications

(18 citation statements)

References 31 publications

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“…A large and nearly uniform step area provides enough individual measuring points for averaging. In a study where these single cross-shaped tiles were characterized on mica using metrological atomic force microscopy, 20 the average dimensions of such structures were found to match well with the designed ones. However, the variation in the dimensions was 3–10% (including the measurement error and substrate-induced deformation of dry origami), which is too high for a proper metrological calibration standard.…”

Section: Nanometrology With Dna Nanostructuresmentioning

confidence: 89%

“…(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. 20 Four flat areas with dimensions of 30 nm × 30 nm × 2 nm in each tile provide enough measuring points for averaging and reliable calibration.…”

Section: Figurementioning

confidence: 99%

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Nanometrology and super-resolution imaging with DNA

et al. 2017

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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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Section: Nanometrology With Dna Nanostructuresmentioning

confidence: 89%

Section: Figurementioning

confidence: 99%

Nanometrology and super-resolution imaging with DNA

et al. 2017

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“…For example, a crossshaped origami was utilized to construct finite arrays, and different fluorescent dyes were deposited onto the substrate. [24] In addition, polyhedra self-assembled three-dimensional origami structures were formed using DNA origami tripods with fluorophores attached onto each vertex, and the 1-60 MD super DNA gridiron was characterized using three-dimensional DNA-paint. [25] All of these previously developed structures were designed as fluorescent nanotags for calibration.…”

Section: Introductionmentioning

confidence: 99%

Optical and Topological Characterization of Hexagonal DNA Origami Nanotags

Zhang

et al. 2021

IEEE Trans.on Nanobioscience

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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. DNA origami can also be used as a nanotag with arbitrary programmable shapes. Results: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 consistency of the nanoscale distance between morphological and fluorescent labels. 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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“…The conventional tools like atomic force microscopy (AFM), optical or magnetic tweezers, and scanning tunneling microscopy are all intrusive methods as they involve microscale tips or beads. The molecular device-based method is nonintrusive and has found applications in calibrating AFM, 3 engineering nanocavity emission, 4 and delivering of molecules. 2 The positioning devices reported to date are all rather rigid structures made of multiple molecular components or even bigger DNA origami.…”

Section: Introductionmentioning

confidence: 99%

Polymer-Based Accurate Positioning: An Exact Worm-like-Chain Study

et al. 2018

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Precise positioning of molecular objects from one location to another is important for nanomanipulation and is also involved in molecular motors. Here, we study single-polymer-based positioning on the basis of the exact solution to the realistic three-dimensional worm-like-chain (WLC) model. The results suggest the possibility of a surprisingly accurate flyfishing-like positioning in which tilting one end of a flexible short polymer enables positioning of the other diffusing end to a distant location within an error of ∼1 nm. This offers a new mechanism for designing molecular positioning devices. The flyfishing effect (and reverse process) likely plays a role in biological molecular motors and may be used to improve speed of artificial counterparts. To facilitate these applications, a new force–extension formula is obtained from the exact WLC solution. This formula has an improved accuracy over the widely used Marko–Siggia formula for stretched polymers and is valid for compressed polymers too. The new formula is useful in analysis of single-molecule stretching experiments and in estimating intramolecular forces of molecular motors, especially those involving both stretched and compressed polymer components.

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DNA origami structures as calibration standards for nanometrology

Cited by 12 publications

References 31 publications

Nanometrology and super-resolution imaging with DNA

Nanometrology and super-resolution imaging with DNA

Optical and Topological Characterization of Hexagonal DNA Origami Nanotags

Polymer-Based Accurate Positioning: An Exact Worm-like-Chain Study

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