Algorithmic Design of 3D Wireframe RNA Polyhedra
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 s...
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| Published in: | ACS nano Vol. 16; no. 10; pp. 16608 - 16616 |
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| Main Authors: | , , , , , , , , , |
| Format: | Journal Article |
| Language: | English |
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American Chemical Society
25-10-2022
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| 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. |
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| AbstractList | 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. 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 molecular dynamics simulator for easy simulation and visualization. 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. |
| Author | Oesinghaus, Lukas Kawamata, Ibuki Seitsonen, Jani Elonen, Antti Simmel, Friedrich C. Natarajan, Ashwin Karthick Suzuki, Yuki Mohammed, Abdulmelik Kuzyk, Anton Orponen, Pekka |
| AuthorAffiliation | Ochanomizu University Division of Chemistry for Materials, Graduate School of Engineering Frontier Research Institute for Interdisciplinary Sciences Department of Applied Physics and Nanomicroscopy Center Department of Neuroscience and Biomedical Engineering Natural Science Division, Faculty of Core Research Physics Department E14 Department of Biomedical Engineering Department of Computer Science Tohoku University Department of Robotics, Graduate School of Engineering Mie University |
| AuthorAffiliation_xml | – name: Department of Neuroscience and Biomedical Engineering – name: Department of Computer Science – name: Frontier Research Institute for Interdisciplinary Sciences – name: Physics Department E14 – name: Tohoku University – name: Natural Science Division, Faculty of Core Research – name: Department of Applied Physics and Nanomicroscopy Center – name: Ochanomizu University – name: Division of Chemistry for Materials, Graduate School of Engineering – name: Mie University – name: Department of Biomedical Engineering – name: Department of Robotics, Graduate School of Engineering |
| Author_xml | – sequence: 1 givenname: Antti surname: Elonen fullname: Elonen, Antti organization: Department of Computer Science – sequence: 2 givenname: Ashwin Karthick orcidid: 0000-0001-7897-708X surname: Natarajan fullname: Natarajan, Ashwin Karthick organization: Department of Neuroscience and Biomedical Engineering – sequence: 3 givenname: Ibuki orcidid: 0000-0002-1955-8827 surname: Kawamata fullname: Kawamata, Ibuki organization: Ochanomizu University – sequence: 4 givenname: Lukas surname: Oesinghaus fullname: Oesinghaus, Lukas organization: Physics Department E14 – sequence: 5 givenname: Abdulmelik orcidid: 0000-0002-5931-5854 surname: Mohammed fullname: Mohammed, Abdulmelik organization: Department of Biomedical Engineering – sequence: 6 givenname: Jani surname: Seitsonen fullname: Seitsonen, Jani organization: Department of Applied Physics and Nanomicroscopy Center – sequence: 7 givenname: Yuki orcidid: 0000-0003-1848-0105 surname: Suzuki fullname: Suzuki, Yuki organization: Mie University – sequence: 8 givenname: Friedrich C. orcidid: 0000-0003-3829-3446 surname: Simmel fullname: Simmel, Friedrich C. organization: Physics Department E14 – sequence: 9 givenname: Anton orcidid: 0000-0001-8060-6122 surname: Kuzyk fullname: Kuzyk, Anton organization: Department of Neuroscience and Biomedical Engineering – sequence: 10 givenname: Pekka orcidid: 0000-0002-0417-2104 surname: Orponen fullname: Orponen, Pekka email: pekka.orponen@aalto.fi organization: Department of Computer Science |
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| Keywords | self-assembly RNA origami kissing loops wireframe polyhedra cryo-EM |
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| Snippet | 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... 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... |
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| SubjectTerms | DNA - chemistry Nanostructures - chemistry Nanotechnology Nucleic Acid Conformation RNA |
| Title | Algorithmic Design of 3D Wireframe RNA Polyhedra |
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