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

ABSTRACT: 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.

SUBMITTER: Pfeifer WG

PROVIDER: S-EPMC10371015 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature

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

Pfeifer Wolfgang G WG Huang Chao-Min CM Poirier Michael G MG Arya Gaurav G Castro Carlos E CE

Science advances 20230726 30

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 ...[more]

PMID: 37494445

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Project description:ContextAntioxidants are known to play a beneficial role in human health. Caffeic acid has been previously recognized as efficient in this context. However, such a capability can be enhanced through structural modification. Thus, 3829 caffeic acid derivatives were computational designed to that purpose by adding functional groups (-OH, -SH, -OCH3, -COOCH3, -F, -CF3, and -N(CH3)(C2H5)) to its framework. Promising candidates were chosen considering drug-like behavior, toxicity, and synthetic accessibility. The best candidates, dCAF-2, dCAF-16, and dCAF-82, were identified by comparison with reference antioxidants. The thermochemistry and kinetics of their reaction with •OOH are provided. The global rate coefficients were estimated to be 1.76 × 109 M-1 s-1, 3.19 × 109 M-1 s-1, and 1.79 × 109 M-1 s-1 in aqueous solution for dCAF-2, dCAF-16, and dCAF-82, respectively. In lipid medium, their total rate coefficients were estimated to be 3.65 × 103 M-1 s-1, 3.73 × 103 M-1 s-1, and 8.63 × 104 M-1 s-1 for dCAF-2, dCAF-16, and dCAF-82, respectively. These values allow predicting the designed caffeic acid derivatives as excellent antioxidants in both environments. The reaction forces for the main reaction path of the dCAF-2, dCAF-16, and dCAF-82 reactions with •OOH were explored.MethodsThree protocols were used: (i) CADMA-Chem (computer-assisted design of multifunctional antioxidants, based on chemical properties) to quantify ADME (absorption, distribution, metabolism, and excretion) properties, toxicity and synthetic accessibility; (ii) eH-DAMA (electron and hydrogen donating ability map) tool, to identify the derivatives expected to behave as the best antioxidants; (iii) QM-ORSA (quantum mechanics-based test for overall free radical scavenging activity), to calculate the rate constants. Electronic structure calculations were performed with Gaussian 09, at the M05-2X/6-311 + g(d,p) level of theory. Both aqueous and lipid environments were considered using the SMD continuous solvation model. Intrinsic reaction coordinate (IRC) calculations, as implemented in Gaussian 09, were used to obtain the reaction force.

Dataset Information

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

Publications

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

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