Automated design of 3D DNA origami with non-rasterized 2D curvature

Fu, Daniel; Narayanan, Raghu Pradeep; Prasad, Abhay; Zhang, Fei; Williams, Dewight; Schreck, John S.; Yan, Hao; Reif, John H.

doi:10.1126/sciadv.ade4455

Cited by 12 publications

(6 citation statements)

References 67 publications

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“…Following these examples, polymer chains obtained through precision synthesis could also form ordered network structures by interlinking. If the system exhibits a specific conformation, such as a protein or nucleic acid that shows a function in vivo, an ordered network structure may be formed through self-assembly, similar to MOFs , and the fine particle aggregates. , However, forming an ordered uniform network structure through self-assembly has been considered difficult due to the dynamic conformational changes of artificial polymer chains caused by thermal motion.…”

Section: Introductionmentioning

confidence: 99%

Synthesizing Ordered Network Structures Using Linear Polymers: A Study on Optimal Synthetic Conditions

Ohshima,

Kwon,

Wang

et al. 2024

Macromolecules

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We have successfully synthesized linear bifunctional PNIPA polymers with uniform molecular weight using living radical polymerization. Our objective was to construct a polymer network with a consistent and an ordered structure. To achieve this, we prepared a solution with a concentration higher than the overlap concentration (C*) of the linear PNIPA polymers with uniform molecular weight. Next, we introduced a cross-linking agent to bond the polymer ends together. Under our experimental conditions using this linear PNIPA polymer, we prepared polymer networks at different concentrations: 1.2C*, 1.5C*, and 2.0C*. Notably, the polymer network formed at 1.2C*, which is slightly higher than the overlap concentration, exhibited a significantly more ordered structure compared to those prepared at 1.5C* or 2.0C*. This observation was substantiated by the analysis of the polymer network degradation products through SEC measurements and the SAXS results of the polymer network. In the case of PNIPA star-shaped polymers, it has been found that a uniform network structure can be obtained by preparing the polymer network at a concentration of about 2.0C*, which is much higher than C*. The difference in excluded volume between linear polymers and star polymers appears to play a pivotal role in favoring the formation of a more ordered network structure when the concentration reaches the overlap concentration threshold. In summary, our study showcases the successful synthesis of linear bifunctional PNIPA polymers with uniform molecular weight through living radical polymerization. Moreover, we demonstrate that by carefully controlling the concentration during polymer network synthesis, it is possible to achieve a relatively ordered structure, especially when the concentration slightly exceeds the overlap concentration threshold. The insights gained from our findings contribute to a better understanding of polymer network formation and have implications for the design and fabrication of advanced materials.

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Section: Introductionmentioning

confidence: 99%

Synthesizing Ordered Network Structures Using Linear Polymers: A Study on Optimal Synthetic Conditions

Ohshima,

Kwon,

Wang

et al. 2024

Macromolecules

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“…MagicDNA’s combination of graphical interfaces for 3D design manipulation and design parameter input, automated routing algorithms, and coupling to simulation to facilitate iterative design enables realization of complex multicomponent assemblies with user control over local mechanical and dynamic properties. In addition, the recently developed tool DNAxiS leverages simulation to design shapes with curvature but is currently limited to structures with revolved symmetry, either axisymmetric or periodic circular symmetry ( 35 ). However, even with these advanced design tools, achieving true free-form geometric designs is still challenging and often requires many iterations to tune the desired geometry.…”

Section: Introductionmentioning

confidence: 99%

Versatile computer-aided design of free-form DNA nanostructures and assemblies

et al. 2023

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Recent advances in structural DNA nanotechnology have been facilitated by design tools that continue to push the limits of structural complexity while simplifying an often-tedious design process. We recently introduced the software MagicDNA, which enables design of complex 3D DNA assemblies with many components; however, the design of structures with free-form features like vertices or curvature still required iterative design guided by simulation feedback and user intuition. Here, we present an updated design tool, MagicDNA 2.0, that automates the design of free-form 3D geometries, leveraging design models informed by coarse-grained molecular dynamics simulations. Our GUI-based, stepwise design approach integrates a high level of automation with versatile control over assembly and subcomponent design parameters. We experimentally validated this approach by fabricating a range of DNA origami assemblies with complex free-form geometries, including a 3D Nozzle, G-clef, and Hilbert and Trifolium curves, confirming excellent agreement between design input, simulation, and structure formation.

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“…MagicDNA's combination of graphical interfaces for 3D design manipulation and design parameter input, automated routing algorithms, and coupling to simulation to facilitate iterative design enables realization of complex multi-component assemblies with user control over local mechanical and dynamic properties. Additionally, the newly developed tool DNAxiS leverages simulation to design shapes with curvature, however currently limited to structures with revolved symmetry, either axisymmetric or periodic circular symmetry (35). However, even with these advanced design tools, achieving true freeform geometric designs is still challenging and often requires many iterations to tune the desired geometry.…”

Section: Introductionmentioning

confidence: 99%

Versatile Computer Aided Design of Freeform DNA Nanostructures and Assemblies

Pfeifer

Huang

Poirier

et al. 2023

Preprint

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Recent advances in structural DNA nanotechnology have been facilitated by design tools that continue to push the limits of structural complexity while simplifying an often-tedious design process. We recently introduced the software MagicDNA, which enables design of complex 3D DNA assemblies with many components; however, the design of structures with freeform features like vertices or curvature still required iterative design guided by simulation feedback and user intuition. Here, we present an updated design tool, MagicDNA 2.0, that automates the design of freeform 3D geometries, leveraging design models informed by coarse-grained molecular dynamics simulations. Our GUI-based, stepwise design approach integrates a high level of automation with versatile control over assembly and sub-component design parameters. We experimentally validated this approach by fabricating a range of DNA origami assemblies with complex freeform geometries, including a 3D Nozzle, G-clef, and Hilbert and Trifolium curves, confirming excellent agreement between design input, simulation, and structure formation.

show abstract

Automated design of 3D DNA origami with non-rasterized 2D curvature

Cited by 12 publications

References 67 publications

Synthesizing Ordered Network Structures Using Linear Polymers: A Study on Optimal Synthetic Conditions

Synthesizing Ordered Network Structures Using Linear Polymers: A Study on Optimal Synthetic Conditions

Versatile computer-aided design of free-form DNA nanostructures and assemblies

Versatile Computer Aided Design of Freeform DNA Nanostructures and Assemblies

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