Rapid Prototyping of Wireframe Scaffolded DNA Origami using ATHENA

Jun, Hyungmin; Wang, Xiao; Wp, Bricker; Jackson, Steve; Bathe, Mark

doi:10.1101/2020.02.09.940320

Cited by 14 publications

(10 citation statements)

References 31 publications

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“…Recently, two new software have been reported that enhance the capabilities of DNA origami design by combining features from the 1G and 2G software. ATHENA 51 integrates features of other existing 2G software, specifically that of DAEDALUS, PERDIX, TALOS and METIS. Adenita 52 is an open source platform that combines almost all of the 1G and 2G design software capabilities.…”

Section: Experimentationmentioning

confidence: 99%

DNA origami

Dey

Chen

Gothelf

et al. 2021

Nat Rev Methods Primers

527

386

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Biological materials are self-assembled with near-atomic precision in living cells, whereas synthetic 3D structures generally lack such precision and controllability. Recently, DNA nanotechnology, especially DNA origami technology, has been useful in the bottom-up fabrication of well-defined nanostructures ranging from tens of nanometres to sub-micrometres. In this Primer, we summarize the methodologies of DNA origami technology, including origami design, synthesis, functionalization and characterization. We highlight applications of origami structures in nanofabrication, nanophotonics and nanoelectronics, catalysis, computation, molecular machines, bioimaging, drug delivery and biophysics. We identify challenges for the field, including size limits, stability issues and the scale of production, and discuss their possible solutions. We further provide an outlook on next-generation DNA origami techniques that will allow in vivo synthesis and multiscale manufacturing.

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Section: Experimentationmentioning

confidence: 99%

DNA origami

Dey

Chen

Gothelf

et al. 2021

Nat Rev Methods Primers

527

386

View full text Add to dashboard Cite

show abstract

“…All of the described solutions have recently been incorporated into one platform, called ATHENA [ 48 ]. It provides the user with an intuitive GUI, which drastically increases the easy usability of each of the previous algorithms, so that any wireframe DNA origami in two- or three dimensions using either 2 HB or 6 HB edges can be created.…”

Section: Scaffolded Dna Origamimentioning

confidence: 99%

The Art of Designing DNA Nanostructures with CAD Software

et al. 2021

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Since the arrival of DNA nanotechnology nearly 40 years ago, the field has progressed from its beginnings of envisioning rather simple DNA structures having a branched, multi-strand architecture into creating beautifully complex structures comprising hundreds or even thousands of unique strands, with the possibility to exactly control the positions down to the molecular level. While the earliest construction methodologies, such as simple Holliday junctions or tiles, could reasonably be designed on pen and paper in a short amount of time, the advent of complex techniques, such as DNA origami or DNA bricks, require software to reduce the time required and propensity for human error within the design process. Where available, readily accessible design software catalyzes our ability to bring techniques to researchers in diverse fields and it has helped to speed the penetration of methods, such as DNA origami, into a wide range of applications from biomedicine to photonics. Here, we review the historical and current state of CAD software to enable a variety of methods that are fundamental to using structural DNA technology. Beginning with the first tools for predicting sequence-based secondary structure of nucleotides, we trace the development and significance of different software packages to the current state-of-the-art, with a particular focus on programs that are open source.

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“…Published by Springer Nature Ltd., 2019. (g) reproduced with permission from [84]. Copyright by the authors of [84], 2020.…”

Section: Automatic Top-down Fabrication With Daedalus Perdix Talosmentioning

confidence: 99%

“…All these distinct algorithms are embedded in a software package ATHENA [84,85] that has an intuitive graphical interface, thus allowing the user to design any kind of 2D or 3D wireframe structure with 2HB or 6HB edges (Figure 4g). The scaffold routing and staple sequences are defined automatically for the target shape, and importantly, external editing of sequences using most commonly employed caDNAno software [14,15] is enabled in the workflow.…”

Section: Automatic Top-down Fabrication With Daedalus Perdix Talosmentioning

confidence: 99%

“…The transformation of any desirable shape visualized on the computer screen into billions of real objects in a test tube is straightforward and fast, owing to the sophisticated CAD software for each distinct DNA design paradigm. As described above, all the algorithms for automated top-down design methods developed by Bathe et al are now integrated into one graphical software ATHENA [84,85]. In addition, the modeling and visualization software Adenita by Barišić and co-workers provides a way to combine lattice-based design to wireframe constructions, thus also allowing hybrid structure designs [16].…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

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Increasing Complexity in Wireframe DNA Nanostructures

et al. 2020

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Structural DNA nanotechnology has recently gained significant momentum, as diverse design tools for producing custom DNA shapes have become more and more accessible to numerous laboratories worldwide. Most commonly, researchers are employing a scaffolded DNA origami technique by “sculpting” a desired shape from a given lattice composed of packed adjacent DNA helices. Albeit relatively straightforward to implement, this approach contains its own apparent restrictions. First, the designs are limited to certain lattice types. Second, the long scaffold strand that runs through the entire structure has to be manually routed. Third, the technique does not support trouble-free fabrication of hollow single-layer structures that may have more favorable features and properties compared to objects with closely packed helices, especially in biological research such as drug delivery. In this focused review, we discuss the recent development of wireframe DNA nanostructures—methods relying on meshing and rendering DNA—that may overcome these obstacles. In addition, we describe each available technique and the possible shapes that can be generated. Overall, the remarkable evolution in wireframe DNA structure design methods has not only induced an increase in their complexity and thus expanded the prevalent shape space, but also already reached a state at which the whole design process of a chosen shape can be carried out automatically. We believe that by combining cost-effective biotechnological mass production of DNA strands with top-down processes that decrease human input in the design procedure to minimum, this progress will lead us to a new era of DNA nanotechnology with potential applications coming increasingly into view.

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Rapid Prototyping of Wireframe Scaffolded DNA Origami using ATHENA

Cited by 14 publications

References 31 publications

DNA origami

DNA origami

The Art of Designing DNA Nanostructures with CAD Software

Increasing Complexity in Wireframe DNA Nanostructures

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