Algorithmic design of 3D wireframe RNA polyhedra
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A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
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Date
2022-09-30
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Language
en
Pages
16608−16616
Series
ACS Nano, Volume 16, issue 10
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.Description
Funding Information: The research of A.E., A.M., and P.O. was supported by Academy of Finland grant 311639. A.K. and A.K.N. have been supported by Academy of Finland grant 308992. The research of I.K. was supported by Japan Society for the Promotion of Science (JSPS) Early-Career Scientists 18K18144, Fund for the Promotion of Joint International Research (B) 19KK0261, and Young Researcher Dispatch Program (School of Engineering, Tohoku University). The research of A.M. was additionally supported by NSF-DMS (grant numbers 1800443/1764366) and Nokia Foundation (2017). The research of Y.S. has been supported by JSPS Grant-in-Aid for Scientific Research (KAKENHI; grant numbers 18K19831 and 19H04201). The research of L.O. and F.C.S. was supported by European Research Council grant agreement no. 694410, project AEDNA. Publisher Copyright: © 2022 The Authors. Published by American Chemical Society.
Keywords
cryo-EM, kissing loops, polyhedra, RNA origami, self-assembly, wireframe
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Citation
Elonen, A, Natarajan, A K, Kawamata, I, Oesinghaus, L, Mohammed, A, Seitsonen, J, Suzuki, Y, Simmel, F C, Kuzyk, A & Orponen, P 2022, ' Algorithmic design of 3D wireframe RNA polyhedra ', ACS Nano, vol. 16, no. 10, pp. 16608−16616 . https://doi.org/10.1021/acsnano.2c06035