Publication Date
10-25-2022
Document Type
Article
Publication Title
ACS Nano
Volume
16
Issue
10
DOI
10.1021/acsnano.2c06035
First Page
16608
Last Page
16616
Abstract
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.
Funding Number
1800443/1764366
Funding Sponsor
National Science Foundation
Keywords
cryo-EM, kissing loops, polyhedra, RNA origami, self-assembly, wireframe
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
Department
Biomedical Engineering
Recommended Citation
Antti Elonen, Ashwin Karthick Natarajan, Ibuki Kawamata, Lukas Oesinghaus, Abdulmelik Mohammed, Jani Seitsonen, Yuki Suzuki, Friedrich C. Simmel, Anton Kuzyk, and Pekka Orponen. "Algorithmic Design of 3D Wireframe RNA Polyhedra" ACS Nano (2022): 16608-16616. https://doi.org/10.1021/acsnano.2c06035
