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Abstract: Featured ApplicationA first demonstration of a shape annealing algorithm for automatic generation of DNA origami designs based on defined objectives and constraints. AbstractStructural DNA nanotechnology involves the design and self-assembly of DNA-based nanostructures. As a field, it has progressed at an exponential rate over recent years. The demand for unique DNA origami nanostructures has driven the development of design tools, but current CAD tools for structural DNA nanotechnology are limited by requiring users to fully conceptualize a design for implementation. This article introduces a novel formal approach for routing the single-stranded scaffold DNA that defines the shape of DNA origami nanostructures. This approach for automated scaffold routing broadens the design space and generates complex multilayer DNA origami designs in an optimally driven way, based on a set of constraints and desired features. This technique computes unique designs of DNA origami assemblies by utilizing shape annealing, which is an integration of shape grammars and the simulated annealing algorithm. The results presented in this article illustrate the potential of the technique to code desired features into DNA nanostructures.Keywords: shape annealing; DNA origami; computer-aided design (CAD); automated generative design; structural DNA nanotechnology

DNA origami nanostructures have tremendous potential to serve as versatile platforms in self-assembly -based nanofabrication and in highly parallel nanoscale patterning. However, uniform deposition and reliable anchoring of DNA nanostructures often requires specific conditions, such as pre-treatment of the chosen substrate or a fine-tuned salt concentration for the deposition buffer. In addition, currently available deposition techniques are suitable merely for small scales. In this article, we exploit a spray-coating technique in order to resolve the aforementioned issues in the deposition of different 2D and 3D DNA origami nanostructures. We show that purified DNA origamis can be controllably deposited on silicon and glass substrates by the proposed method. The results are verified using either atomic force microscopy or fluorescence microscopy depending on the shape of the DNA origami. DNA origamis are successfully deposited onto untreated substrates with surface coverage of about 4 objects/mm2. Further, the DNA nanostructures maintain their shape even if the salt residues are removed from the DNA origami fabrication buffer after the folding procedure. We believe that the presented one-step spray-coating method will find use in various fields of material sciences, especially in the development of DNA biochips and in the fabrication of metamaterials and plasmonic devices through DNA metallisation.

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DNA has astonishing potential as programmable nanoscale construction material for the bottom-up-based nanofabrication1 and for a great variety of bionanotechnological applications2. To date, a plethora of design strategies for assembling DNA molecules into customized structures and templates have been introduced2. Arguably, one of the most elegant one is a scaffolded DNA origami technique, which enables a straightforward fabrication of arbitrary two- (2D)3 and three-dimensional (3D)4,5 nanoshapes, meshed structures6 as well as large assemblies with high spatial addressability7.

Recently, DNA nanoarchitectures have been utilized in various innovative applications that truly underline the feasibility of the structural DNA nanotechnology. DNA origamis can serve as molecular scale circuit boards in nanoelectronics8, scaffolds for plasmonic structures9,10 and gatekeepers for solid-state nanopores11,12. Biotechnological examples include smart molecular devices13,14 such as nanorobots15, cellular delivery vehicles16,17 and synthetic ion channels18.

Despite the fact that DNA origami itself has limited properties in optics and in electronics19,20,21,22, its use in templating is extremely promising. There exist plenty of placement and deposition methods for DNA origamis that are useful for patterning on different substrates. One straightforward way is to utilize chemically modified surfaces, which enable selective anchoring of the origamis23,24,25, whereas some substrates can be used to assist large-scale lattice formation of DNA origamis26,27,28. In addition, hierarchically ordered nanosystems can be obtained by combining DNA structures with patterned substrates, such as lithographically fabricated confined wells29,30 and other surface patterns, which are specifically designed for the alignment of DNA structures31,32. Moreover, single DNA molecules33,34,35 and complex DNA nanoarchitectures36,37,38 can be selectively guided and anchored onto substrates by means of electric fields. Nevertheless, in order to utilize such approaches one has to pay extra attention to the deposition conditions (salt concentration, pH, surface chemistry etc.). In many occasions, the required treatments and prevalent conditions set strict limitations to the conceivable applications.

In general, print-coating technologies provide high-throughput and low-cost patterning methods for solution processable materials39. Although aqueous dispersion of DNA is solution processable, these techniques have not been so far adapted in the field of structural DNA nanotechnology. However, in this article we show that the high spatial addressability of the structurally different DNA origamis can be genuinely combined with the large-scale print-coating methods. The authors have previously demonstrated the feasibility of the solution processing techniques in various other applications, such as stretchable electrodes40, piezoelectric sensors41,42, transparent touch panels43, supercapacitors44,45 and energy harvesters46,47. The same methods are now expanded to the field of DNA nanotechnology.

The agarose gel analysis was repeated 14 weeks later for the spin-filtered samples in water (Supplementary Fig. S2). It showed that the DNA origamis are stable in water over long time. However, it is probable that slight agglomeration of the objects starts to occur over time if the storage solution has a high origami concentration. Hence, all the spray-coating experiments reported in this article were performed immediately after the purification step.

Further, since the structures used in these experiments were flat, the structural details of the DNA objects could be fully resolved by AFM. For both structures the correct DNA origami shapes are well preserved as seen in Fig. 3c,d. This is a significant observation, taking into account that the salt has been removed from the deposition solution. The DT structure is highly flexible (the most flexible among these four structures, see Supplementary Fig. S3) and thus some objects tend to adopt slightly bent conformations on the substrate. In addition, some DT bundles were observed, but these small aggregates are formed already in the folding process via unspecific base stacking interactions between the objects (this can be seen as a faint multimer-tail in the DT lane in Fig. 1e).

The PDMS mask attaches well to flat substrates, such as silicon, glass or plastic, preventing the spray-coated drops from penetrating between the mask and the substrate45. In addition, the removal of the mask does not harm the obtained DNA origami pattern and the same mask can be used several times for coating. The pattern design can be arbitrarily chosen and the silicon mold for the mask can be prepared with high accuracy by exploiting conventional microfabrication methods. In addition, as shown in Fig. 4c, the patterning can be realised in a sequential fashion, enabling the controllable formation of complex patterns. These results show that the proposed method is highly applicable for a large-scale substrate patterning with DNA origami nanostructures.

As a conclusion, we have shown that structurally distinct DNA origami nanostructures can be uniformly deposited on different substrates. The proposed deposition method is versatile and has outstandingly high yield, since all the material placed in the spray-coating device will be homogeneously deposited onto the selected substrates, opposite to the common drop casting techniques. This is also a straightforward coating method, since it does not require additional washing steps or optional pre-treatments of the substrates. Furthermore, the method enables wafer-scale deposition and patterning of DNA origamis within minutes making the method highly cost-effective. This is an important detail in the field of structural DNA nanotechnology, since large-scale fabrication of complex DNA nanostructures is still relatively expensive53. Thus, the efficient large-scale deposition methods are urgently needed for conceivable applications. An estimated cost of large-scale DNA origami coating with the surface coverage obtained in this work (about 4 objects/m2) would be of the order of 1 euro per square meter, which is rather inexpensive compared to typical substrate costs.

The substrates with homogeneously covered single-layer DNA origami structures (ST and DT) were characterised using atomic force microscopy (AFM). For multilayer DNA structures (HT and HB), fluorescence microscopy was utilized. The structural characterisation of multilayer origamis was carried out using transmission electron microscopy (TEM) (Supplementary Fig. S1 and Supplementary Note 2).

Cute heart decorations, a couple little organization baskets, twisty straws that I know my kids would love (and we would throw away in a week) and craft supplies that looked so fun. I quickly reminded myself of all of the bins of unused craft supplies I had at home; two reams of this kraft paper cardstock for the Jedi Robe origami as the perfect example. It brought me back to focusing on what I have and how I can better use it.

Researchers at the University of Washington have developed robotic microfliers that can change how they move while in the air by snapping into a folding position during descent. The microfliers use a Miuri-ori origami fold when dropped from a drone to switch from tumbling and dispersing outward through the air to dropping straight to the ground. e24fc04721