Prediction and Control in DNA Nanotechnology

DeLuca, Marcello; Sensale, Sebastian; Lin, Po-An; Arya, Gaurav

doi:10.1021/acsabm.2c01045

Cited by 9 publications

(6 citation statements)

References 281 publications

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“…The free-form design algorithms integrate seamlessly with other features in MagicDNA such as hierarchical assembly and multiscaffold designs to further broaden the design space for DNA self-assembly and provide a foundation for the realization of advanced materials, including assemblies of compliant mechanisms (47), curved polymeric DNA origami designs (48), and meta-materials (49). Moving forward, we envision enhancing the design capabilities of our software by directly including structure-property relationships into the design tools, where emerging tools like machine learning are expected to play a useful role (50).…”

Section: Expanded Design Scope With Free-form Featuresmentioning

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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Section: Expanded Design Scope With Free-form Featuresmentioning

confidence: 99%

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

et al. 2023

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“…The codes used in this study have been deposited in the public GitHub (https://github.com/marcello-deluca/dnafold-analysis and https://github.com/marcellodeluca/dnafold) without any restrictions. 64,65…”

Section: Author Contributionsmentioning

confidence: 99%

Mechanism of DNA origami folding elucidated by mesoscopic simulations

DeLuca

Poirier

et al. 2023

Preprint

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DNA nanotechnology leverages the canonical base-pairing rules and geometry of DNA to create highly precise nanoscale structures with many potential applications. While the design and fabrication of DNA nanostructures is well-established, the self-assembly process that produces these structures is still poorly understood, especially for DNA origami that involve the assembly of hundreds of strands. Many experimental and computational efforts have sought to better understand DNA origami folding, but the small length and time scales of individual binding events and the long timescale over which folding occurs have posed significant challenges. Here, we present a new mesoscopic model that uses a switchable force field to capture the mechanical behavior of single- and double-stranded DNA motifs and transition between them at a coarseness level of up to 8 nucleotides per particle, allowing access to the long assembly timescales of DNA origami up to several kilobases in size. Brownian dynamics simulations of 4-helix bundle (4HB) structures using this model reveal a hierarchical folding process involving the zipping of structural domains into a partially folded precursor structure followed by gradual crystallization into the final structure. We elucidate the role of hybridization strength, scaffold routing, and staple design in the folding order and kinetics. Simulation of larger 32HB structures reveals heterogeneous staple incorporation kinetics and frequent trapping in metastable states, as opposed to smaller, more accessible structures like the 4HB, which exhibit first-order kinetics and virtually defect-free folding. The development of this model opens an avenue to better understand and design DNA nanostructures for improved yield and folding performance.

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“…9−14 On the theoretical end, the assembly of particles with discrete interaction sites into different shapes and structures has been studied via molecular dynamics and Monte Carlo simulations. 15−18 Of these approaches, DNA-based platforms 19 have shown promise for the assembly of target finite architectures 20,21 and threedimensional (3D) superlattices 22−27 due to the ability of DNA to dictate interparticle interactions and tailoring DNA corona morphology. Work done in recent years has focused on the prescription of directional interactions or "valency" at the nanoscale, 28−33 which allows for rational assembly of the lattices.…”

Section: Introductionmentioning

confidence: 99%

“…Self-assembly, a process where the individual components organize into ordered structures with well-defined symmetries, is found throughout biology and the physical world. , In recent decades, there has been significant interest in the development of self-assembly strategies for the fabrication of materials composed of organized, functional nanoscale materials for applications in optics, , photonics, , and catalysis. , The programmable assembly of nanoparticles has been explored using a variety of self-assembly-based strategies, including manipulation of particle shapes and sizes, interparticle interactions, and charges. − On the theoretical end, the assembly of particles with discrete interaction sites into different shapes and structures has been studied via molecular dynamics and Monte Carlo simulations. − Of these approaches, DNA-based platforms have shown promise for the assembly of target finite architectures , and three-dimensional (3D) superlattices − due to the ability of DNA to dictate interparticle interactions and tailoring DNA corona morphology. Work done in recent years has focused on the prescription of directional interactions or “valency” at the nanoscale, − which allows for rational assembly of the lattices.…”

Section: Introductionmentioning

confidence: 99%

Controlling the Self-Assembly of DNA Origami Octahedra via Manipulation of Inter-Vertex Interactions

Adhikari,

Minevich,

Redeker

et al. 2023

J. Am. Chem. Soc.

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Recent studies have demonstrated novel strategies for the organization of nanomaterials into three-dimensional (3D) ordered arrays with prescribed lattice symmetries using DNA-based self-assembly strategies. In one approach, the nanomaterial is sequestered into DNA origami frames or “material voxels” and then coordinated into ordered arrays based on the voxel geometry and the corresponding directional interactions based on its valency. While the lattice symmetry is defined by the valency of the bonds, a larger-scale morphological development is affected by assembly processes and differences in energies of anisotropic bonds. To facilely model this assembly process, we investigate the self-assembly behavior of hard particles with six interacting vertices via theory and Monte Carlo simulations and exploration of corresponding experimental systems. We demonstrate that assemblies with different 3D crystalline morphologies but the same lattice symmetry can be formed depending on the relative strength of vertex-to-vertex interactions in orthogonal directions. We observed three distinct assembly morphologies for such systems: cube-like, sheet-like, and cylinder-like. A simple analytical theory inspired by well-established ideas in the areas of protein crystallization, based on calculating the second virial coefficient of patchy hard spheres, captures the simulation results and thus represents a straightforward means of modeling this self-assembly process. To complement the theory and simulations, experimental studies were performed to investigate the assembly of octahedral DNA origami frames with varying binding energies at their vertices. X-ray scattering confirms the robustness of the formed nanoscale lattices for different binding energies, while both optical and electron microscopy imaging validated the theoretical predictions on the dependence of the distinct morphologies of assembled state on the interaction strengths in the three orthogonal directions.

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Prediction and Control in DNA Nanotechnology

Cited by 9 publications

References 281 publications

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

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

Mechanism of DNA origami folding elucidated by mesoscopic simulations

Controlling the Self-Assembly of DNA Origami Octahedra via Manipulation of Inter-Vertex Interactions

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