Algorithmic design of 3D wireframe RNA polyhedra

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. Towards 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 bipyramid and a prism. The design software is openly available, and also provides an export of the targeted 3D structure into the oxRNA molecular dynamics simulator for easy simulation and visualization.

Algorithmic Design of 3D Wireframe RNA Polyhedra

“…We have developed a software tool, S panning T ree E ngineered RNA design ( Sterna ), that automates the secondary-structure design process described above . This tool has been implemented as a Python add-on module to the open-source Blender 3D graphic design software suite .…”

“…We have developed a software tool, S panning T ree E ngineered RNA design ( Sterna ), that automates the secondary-structure design process described above. 32 This tool has been implemented as a Python add-on module to the open-source Blender 3D graphic design software suite. 33 To initiate a design task, the user creates a model of the desired polyhedron using the tools in the Blender suite or imports an existing model from an external library.…”

“… 36 , 37 (For further information, see Supporting Information Note S1 and the software tutorial on the Sterna website.) 32 …”

“…We have presented a general high-level and fully automated design scheme for rendering 3D wireframe polyhedra as native conformations of single-stranded RNA molecules. An open-source distribution of the design software is available on the Sterna website . The method has been demonstrated by designing, synthesizing, and characterizing three small-to-moderate sized structures: a tetrahedron (435 bases), a triangular bipyramid (643 bases), and a triangular prism (781 bases).…”

“…K.KawamataI.OesinghausL.MohammedA.SeitsonenJ.SuzukiY.SimmelF. C.KuzykA.OrponenP. Elonen, A. Natarajan, A. K. Kawamata, I. Oesinghaus, L. Mohammed, A. Seitsonen, J. Suzuki, Y. Simmel, F. C. Kuzyk, A. Orponen, P. 2022 …”