Algorithmic Design of 3D Wireframe RNA Polyhedra

• Published in: ACS nano Vol. 16; no. 10; pp. 16608 - 16616
• Main Authors: Elonen, Antti, Natarajan, Ashwin Karthick, Kawamata, Ibuki, Oesinghaus, Lukas, Mohammed, Abdulmelik, Seitsonen, Jani, Suzuki, Yuki, Simmel, Friedrich C., Kuzyk, Anton, Orponen, Pekka
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 25-10-2022
• Subjects: DNA - chemistry; Nanostructures - chemistry; Nanotechnology; Nucleic Acid Conformation; RNA; self-assembly; RNA origami; kissing loops; wireframe; polyhedra; cryo-EM
• ISSN: 1936-0851; 1936-086X
• DOI: 10.1021/acsnano.2c06035

We address the problem of de novo design and synthesis of nucleic acid nanostructures, a challenge that has been considered in the area of DNA nanotechnology since the 1980s and more recently in the area of RNA nanotechnology. Toward this goal, we introduce a general algorithmic design process and software pipeline for rendering 3D wireframe polyhedral nanostructures in single-stranded RNA. To initiate the pipeline, the user creates a model of the desired polyhedron using standard 3D graphic design software. As its output, the pipeline produces an RNA nucleotide sequence whose corresponding RNA primary structure can be transcribed from a DNA template and folded in the laboratory. As case examples, we design and characterize experimentally three 3D RNA nanostructures: a tetrahedron, a triangular bipyramid, and a triangular prism. The design software is openly available and also provides an export of the targeted 3D structure into the oxDNA molecular dynamics simulator for easy simulation and visualization.