Year: 2023
Type: article
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.
Source: Science Advances
Institutions: The Ohio State University, Duke University
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $4,500
Awards: EFRI CEE: DNA origami tools to engineer chromatin structure and function in live cells, G4737709065, DMREF/Collaborative Research: DNA-based Sensing, Communicating, and Phase-Separating Materials, Atomic Force Microscope, DMREF/Collaborative Research: DNA-based Sensing, Communicating, and Phase-Separating Materials, XSEDE: eXtreme Science and Engineering Discovery Environment
OpenAlex ID: W4385284421