Analyzing DNA Nanotechnology: A Call to Arms For The Analytical Chemistry Community

Mathur, Divita; Medintz, Igor L.

doi:10.1021/acs.analchem.6b04033

Cited by 78 publications

(94 citation statements)

References 139 publications

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“…Currently, few studies have focused on developing DNA nanostructure characterization techniques that meet the demands of commercial manufacturing. [22][23][24][25] Super-resolution fluorescence microscopy has proven to be a powerful tool for biological imaging, and in the case of DNA-based nanostructures, the technique known as DNA-PAINT enables non-destructive, multiplexed optical imaging with resolution down to ~5 nm. …”

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confidence: 99%

Metrology of DNA arrays by super-resolution microscopy

et al. 2017

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Recent results in the assembly of DNA into structures and arrays with nanoscale features and patterns have opened the possibility of using DNA for sub-10 nm lithographic patterning of semiconductor devices. Super-resolution microscopy is being actively developed for DNA-based imaging and is compatible with inline optical metrology techniques for high volume manufacturing. Here, we combine DNA tile assembly with state-dependent super-resolution microscopy to introduce crystal-PAINT as a novel approach for metrology of DNA arrays. Using this approach, we demonstrate optical imaging and characterization of DNA arrays revealing grain boundaries and the temperature dependence of array quality.For finite arrays, analysis of crystal-PAINT images provides further quantitative information of array properties. This metrology approach enables defect detection and classification and facilitates statistical analysis of self-assembled DNA nanostructures. IntroductionAs the costs and challenges of semiconductor device scaling increase, 1 new materials and technologies that enable precise patterning and placement of nanostructures are sought to supplement or replace current photolithography techniques. 2 For example, nanoscale patterning through directed self-assembly of block-copolymer (BCP) structures has been acknowledged as a viable and inexpensive lithographic mask via the International Technology Roadmap for Semiconductor manufacturing. 3,4 While progress has been made in the precise control of BCP self-assembly, defect densities and directed self-assembly of complex patterns remain challenges for manufacturing. 5 As an alternative technology, the potential for programmable, long-range order through self-assembly makes DNA an attractive material for bottom-up fabrication of nanoscale patterns, 6 as well as for templated-assembly of electronic and photonic devices with nanometer precision. 7-10Within the last two decades, DNA-based techniques such as origami, 6 tiles, 9 and bricks 11 have demonstrated precise control over the size, shape, arrangement, and assembly of DNA nanostructures and nanocomponents. While much work is still needed to approach commercial viability, lithographically confined DNA origami and large crystalline arrays of DNA origami show potential as self-assembled lithographic masks 12 and templates for precise nanoparticle assemblies. 13-18As a result of these advances, the Semiconductor Research Corporation recently listed DNAcontrolled sub-10 nm manufacturing as a technical area for its future roadmap. 19Beyond the ability to pattern at the nanoscale, metrology of patterned structures is a crucial capability in semiconductor device manufacturing that poses increasing challenges (e.g., cost, throughput, accuracy) as the device dimensions decrease. 20,21 For example, locating dislocations within a nanoscale BCP pattern requires tedious inspection of highresolution scanning electron micrographs. Likewise, common high-resolution imaging techniques used for characterization of DNA nanostructures, such as...

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Metrology of DNA arrays by super-resolution microscopy

et al. 2017

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“…(2) The current purification approaches are limited by chromatography, gel electrophoresis, and centrifugation techniques . As the purity of assembled FNAs governs their downstream application, purification means with higher separation efficiency is highly desirable . Therefore, single‐step rapid isolation of FNAs need to be developed.…”

Section: Discussionmentioning

confidence: 99%

“…[87] As the purity of assembled FNAs governs their downstream application, purification means with higher separation efficiency is highly desirable. [88] Therefore, single-step rapid isolation of FNAs need to be developed.…”

Section: Discussionmentioning

confidence: 99%

Rational Design of Framework Nucleic Acids for Bioanalytical Applications

Liu

et al. 2019

ChemPlusChem

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With the advent of DNA nanotechnology, nucleic acids have been used building blocks for constructing various DNA nanostructures. As classical and simple DNA nanostructures, framework nucleic acids (FNAs) have attracted enormous attention in the field of biosensing. The sequence‐specific self‐assembly properties and high programmability of nucleic acids allow FNAs to be incorporated in advanced probe design. In addition, FNAs enable the engineering of surfaces for biosensing (e. g., probe orientation, probe spacing), thereby improving the accessibility of target molecules to the probes arranged on heterogeneous surfaces. Moreover, FNAs offer a universal and promising platform for sensing cellular molecules because of their prominent biocompatibility and cellular permeability. Herein recent advances in FNA‐based biosensors are summarized, including electrochemical detection, optical detection, and intracellular sensing. It is hoped that this review will provide guidelines for the design and construction of FNA scaffold‐based biosensors.

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“…Moreover, this will be exacerbated as DNA assemblies increase in size . Unfortunately, the analytical capabilities and metrologies available to probe DNA structures of such magnitude do not have the requisite capabilities or sensitivity to answer such challenging questions 61a,208. Perhaps, formation efficiencies that are “good enough” to provide a structure demonstrating enough of a requisite property will be sufficient for an application and not be precluded by the need to create and isolate only perfectly formed assemblies.…”

Section: Challenges and Outlookmentioning

confidence: 99%

Utilizing the Organizational Power of DNA Scaffolds for New Nanophotonic Applications

Bui

Dı́az

Fontana

et al. 2019

Advanced Optical Materials

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Rapid development of DNA technology has provided a feasible route to creating nanoscale materials. DNA acts as a self‐assembled nanoscaffold capable of assuming any three‐dimensional shape. The ability to integrate dyes and new optical materials such as quantum dots and plasmonic nanoparticles precisely onto these architectures provides new ways to exploit their near‐ and far‐field interactions. A fundamental understanding of these optical processes will help drive development of next‐generation photonic nanomaterials. This review is focused on latest progress in DNA‐based photonic materials and highlights DNA scaffolds for rapidly assembling and prototyping nanoscale optical devices. Three areas are discussed including intrinsically active DNA structures displaying chiral properties, DNA scaffolds hosting plasmonic nanomaterials, and fluorophore‐labeled DNAs that engage in Förster resonance energy transfer and give rise to complex molecular photonic wires. An explanation of what is desired from these optical processes when harnessed sets the tone for what DNA scaffolds are providing toward each focus. Examples from the literature illustrate current progress along with a discussion of challenges to overcome for further improvements. Opportunities to integrate diverse classes of optically active molecules including light‐generating enzymes, fluorescent proteins, nanoclusters, and metal–chelates in new structural combinations on DNA scaffolds are also highlighted.

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Analyzing DNA Nanotechnology: A Call to Arms For The Analytical Chemistry Community

Cited by 78 publications

References 139 publications

Metrology of DNA arrays by super-resolution microscopy

Metrology of DNA arrays by super-resolution microscopy

Rational Design of Framework Nucleic Acids for Bioanalytical Applications

Utilizing the Organizational Power of DNA Scaffolds for New Nanophotonic Applications

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