Self-assembly of two-dimensional DNA origami lattices using cation-controlled surface diffusion

Woo, Sungwook; Rothemund, Paul W. K.

doi:10.1038/ncomms5889

Cited by 166 publications

(217 citation statements)

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“…[14] Future studies could lead to the integration of this methodology within multiplexed microfluidic [11] and more multipurpose read out systems, [10a] For example, the integration of modular addressability with biological processes can be utilized for the high throughput analysis of biochemical reactions and biomolecular interactions that require control over proximity and special distribution. Thereby, the DNA origami stamp method presented here brings the opportunity for a more versatile and robust functionalization and patterning of surfaces for the creation of metamaterials [12a] with applications in nanoelectronics [7] and photonics [2c] .…”

Section: Revised Manuscriptmentioning

confidence: 99%

“…This methodology can thus be extended to other surfaces utilizing different covalent strategies. [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.…”

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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

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“…Interactions between DNA units can be also directionally driven taking advantage of geometric factors, like the shape-complementarity of the binding surfaces ( Figure 1.4(d)) [71]. Finally, long-range assemblies can also be favored by confining the random Brownian motion of the constituents units to a limited space, helping them to meet and bind [72][73][74]. Both approaches, i.e.…”

Section: Dna As Building Block Of Self-assembled Nanostructuresmentioning

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Nanotechnology and the Unique Role of DNA

Schöneweiβ¹,

Jaekel²,

Saccá³

2017

DNA Nanotechnology for Bioanalysis

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“…Blunt-end stacking has been employed to provide relatively weak interactions between DNA origami tiles for surface-assisted array formation 22,27 . In the first demonstration of a two-dimensional crystal of DNA origami, tiling in solution was achieved by sticky-end hybridization 17 , as illustrated in Figure 1, which can yield stronger interactions than blunt-end stacking.…”

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Thermodynamics and Kinetics of DNA Origami Cross-Tile Array Formation

Ward¹

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The final reading approval of the thesis was granted by Elton Graugnard, Ph.D., Chair of the Supervisory Committee. The thesis was approved by the Graduate College. However, these structures are far from ideal and contain a number of defects that limit the adoption of this approach for manufacturing. In order to create large defect-free DNA arrays, further study is needed into the fundamental mechanisms governing array formation. Toward this goal, the thermodynamics and kinetics of DNA array formation were investigated using a DNA origami cross-tile that assembles into arrays through DNA hybridization. The assembly of dimers, quadramers, and unbound arrays in solution from monomers with complementary dye and quencher labeled hybridization interfaces was monitored by observing the change in fluorescence of the solution as a function of temperature and over time under varying buffer conditions and temperatures. The melting temperature of each structure was measured and generally increased with an increasing number of active sticky-ends per monomer. Values for standard thermodynamic parameters were determined for each array design. The reaction kinetics data were fit with a second order reaction model, and the effective reaction rate increased with viii increasing buffer magnesium concentrations and increasing temperatures. Finally, it was determined that large, unbounded 2D DNA origami cross-tile arrays sediment out of solution in only a few hours. The findings of this study provide insight into the mechanisms of DNA array formation and establish practical ranges for key processing parameters.

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Self-assembly of two-dimensional DNA origami lattices using cation-controlled surface diffusion

Cited by 166 publications

References 48 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

Nanotechnology and the Unique Role of DNA

Thermodynamics and Kinetics of DNA Origami Cross-Tile Array Formation

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