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Automated Design of Nanoscale 3D DNA Meshes

Johnny Nguyen - Computer Science Department, SJSU;
Matthew Vu - Biomedical Engineering Department, SJSU;
Seth Gonzalez - Biomedical Engineering Department, SJSU;
Sonja Durr - Biomedical Engineering Department, SJSU;
Hao Legaspi - Biomedical Engineering Department, SJSU;
Han Nguyen - Biomedical Engineering Department, SJSU;
Dung Phan - Biomedical Engineering Department, SJSU;
Antti Elonen - Computer Science Department, Aalto University

Dr. Abdulmelik Mohammed

Technical Advisor:

Targeting general-purpose manufacturing like 3D printing, DNA origami presents a versatile method for the assembly of complex 2D and 3D DNA nanostructures. By folding a long circular strand using short synthetic DNA strands, these nanostructures offer immense potential in nanomedicine. However, a crucial challenge lies in effectively routing a scaffold strand along the edges of toroidal mesh structures. Previous automated scaffold routing schemes based on Eulerian circuits can lead to tangled scaffold states when applied on toroidal (donut and pretzel-like) surface meshes, severely limiting the scope and range of structures that can be assembled. We developed a software, RATS (Routing A-trail Scaffolds), to search for untangled scaffold routings for any surface mesh, including toroidal ones. Through additional collaboration, our research aims to physically assemble toroidal DNA nanostructures, highlighting the potential to translate toroidal designs to practical implementation. By automating the scaffold routing process, RATS enables the rapid prototyping of 3D DNA origami meshes. Through such advancements, DNA origami technology progresses closer to general purpose nanoscale “3D printing.”

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