Challenges and opportunities for structural DNA nanotechnology

Pinheiro, André Vidal; Han, Dongran; Shih, William M.; Yan, Hao

doi:10.1038/nnano.2011.187

Cited by 1,185 publications

(930 citation statements)

References 158 publications

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“…[10b, 13] Moreover, in combination with photolithography [8] and DNA origami lattice formation [14] methods, the process can be scale up to create micrometer scale patterns. The ability to program a pattern into a DNA origami frame and covalently transfer single DNA molecules further expands the 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 Submitted to 3 potential applications of DNA programmed materials, [15] while improving on the ability to recycle prescribed pattern and functionality, overcoming the bottlenecks associated with existent DNA-based methodologies for nanoscale patterning. [8,10] Design and Assembly of DNA Origami Stamp.…”

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DNA‐Origami‐Driven Lithography for Patterning on Gold Surfaces with Sub‐10 nm Resolution

et al. 2017

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The programmability [1] and self-assembly properties of DNA provides means of precise organization of matter at the nanoscale. [2] DNA origami allows the folding of DNA into twodimensional [3] and three-dimensional [4] structures, and has been used to organize biomolecules, [2b, e, 5] nanophotonic [2a, c, f, 6] and electronic [7] components with a resolution of 6 nm / pixel. [8] Two-dimensional DNA origami has been also used as a platform to organize other chemical [9] species that can then be placed on technologically relevant substrates. [2c, 10] Nevertheless, these approaches have only used the DNA nanostructure to hold the chemical species on the surface and, to the best of our knowledge, have never been utilized to immobilize nucleic acids patterns on surfaces with sub-10 nm resolution providing an enable 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 Submitted to 2 platform for potential applications such as multiplexed biochemical assays. [11] to the creation of metasurfaces [12] with potentially reconfigurable features. Revised ManuscriptHerein we report on the use of a two-dimensional DNA origami as a template to covalently attach DNA with a pre-programmed pattern on a surface (see Scheme 1). The method utilizes the incorporation of modified staple strands in programmed positions of the DNA origami (DNA origami stamp), acting as DNA ink. Once the DNA origami is immobilized on the surface, the modified staples can react with the surface creating a defined DNA pattern (Stamping step). The pattern can then be exposed upon denaturation of the DNA origami stamp (Unmasking step), allowing the non-bound staples to be rinsed off of the surface. As a proof-of-principle of this methodology, we have created a linear pattern of thiolmodified DNA ink on gold surfaces. The formation of the linear pattern was revealed by the successful formation of bead-on-a-string-like structures (here named "chains" for simplicity) composed of gold nanoparticles conjugated with thiol-oligonucleotides (OGNP) that are hybridized to the DNA ink pattern (Development step). The linear pattern provided a direct evidence of the stamping process and was chosen as a simple geometry that can be statistically analysed in our experimental setup. Montecarlo Simulations have been used for better understanding of our statistical results and to determine key elements governing the process that can be used for future optimization of pattern information transfer with DNA origami stamp methodology. Furthermore, we have studied the development of more complex patterns using Montecarlo Simulations.We demonstrate that our approach can be employed to form DNA patterns with sub-10 nm resolution to flat gold surfaces, an unsolved goal to date. This methodology can thus be extended to other surfaces utilizing different covalent strategies. [10b, 13] M...

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DNA‐Origami‐Driven Lithography for Patterning on Gold Surfaces with Sub‐10 nm Resolution

et al. 2017

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“…[1][2][3] For example, many novel nanostructures were created based on DNA programmable assembly. [4][5][6] Interfacing DNA with inorganic nanomaterials is a key step of bottom-up fabrication to produce functional hybrids and devices.…”

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Tandem Phosphorothioate Modifications for DNA Adsorption Strength and Polarity Control on Gold Nanoparticles

Zhou

Wang

Ding

et al. 2014

ACS Appl. Mater. Interfaces

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Unmodified DNA was recently used to functionalize gold nanoparticles via DNA base adsorption. Compared to thiolated DNA, however, the application of unmodified DNA is limited by the lack of sequence generality, adsorption polarity control and poor adsorption stability. We report that these problems can be solved using phosphorothioate (PS) DNA. PS DNA binds to gold mainly via the sulfur atom and is thus less sequence dependent. The adsorption affinity is ranked to be thiol > PS > adenine > thymine. Tandem PS improves adsorption strength, allows tunable DNA density, and the resulting conjugates are functional at a low cost.

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“…The potential of DNA nanostructures in the fields of energy transfer and photonics is beginning to be uncovered [19]. For example, some nanostructures are able to immobilize components found within energy transfer systems while facilitating electron flow, much like the photosynthetic machinery of plants and other organisms is able to accomplish [19,20].…”

Section: Applications Of Dna Origamimentioning

confidence: 99%

“…For example, some nanostructures are able to immobilize components found within energy transfer systems while facilitating electron flow, much like the photosynthetic machinery of plants and other organisms is able to accomplish [19,20]. Creating DNA pegboards enabled positioning of light-harvesting complexes in close proximity with charge transfer units [19]. DNA molecular pegboards are structures that allows for the precise placement of molecules at predetermined locations [21].…”

Section: Applications Of Dna Origamimentioning

confidence: 99%

Beyond the smiley face: applications of structural DNA nanotechnology

Arora

Silva

2018

Nano Reviews & Experiments

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Since the development of DNA origami by Paul Rothemund in 2006, the field of structural DNA nanotechnology has undergone tremendous growth. Through DNA origami and related approaches, self-assembly of specified DNA sequences allows for the ‘bottom-up’ construction of diverse nanostructures. By utilizing different sets of small ‘staple’ DNA strands to direct the folding of a long scaffold strand in diverse ways, DNA origami has particularly been incorporated into a variety of prototypical applications beyond the two-dimensional (2D) smiley face. In this review, the basis of DNA nanotechnology, methods of self-assembly, and Rothemund’s DNA origami breakthrough are discussed first. Next, some of the most promising applications of structural DNA nanotechnology since 2006 are summarized. These include utilizing DNA origami as a tool for creating 3D nanostructures (including DNA bricks), as well as structural (ligand capsid binding, viral capsid binding, DNA NanoOctahedron, DNA mold, photonic devices, energy transfer units), and dynamic (DNA box-with-lid, DNA nano-robot, DNA barges, amphipathic DNA structures, DNA nanocircuits) applications of DNA origami.

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Challenges and opportunities for structural DNA nanotechnology

Cited by 1,185 publications

References 158 publications

DNA‐Origami‐Driven Lithography for Patterning on Gold Surfaces with Sub‐10 nm Resolution

DNA‐Origami‐Driven Lithography for Patterning on Gold Surfaces with Sub‐10 nm Resolution

Tandem Phosphorothioate Modifications for DNA Adsorption Strength and Polarity Control on Gold Nanoparticles

Beyond the smiley face: applications of structural DNA nanotechnology

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