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Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops

Authors Antti Elonen , Pekka Orponen

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LIPIcs.DNA.30.4.pdf
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Subject Classification

ACM Subject Classification
  • Theory of computation → Theory and algorithms for application domains
  • Applied computing → Computational biology
  • Applied computing → Life and medical sciences
Keywords
  • RNA origami
  • wireframe nanostructures
  • polyhedra
  • kissing loops
  • topological graph embeddings
  • self-assembly

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Abstract

We present a general design technique for rendering any 3D wireframe model, that is any connected graph linearly embedded in 3D space, as an RNA origami nanostructure with a minimum number of kissing loops. The design algorithm, which applies some ideas and methods from topological graph theory, produces renderings that contain at most one kissing-loop pair for many interesting model families, including for instance all fully triangulated wireframes and the wireframes of all Platonic solids. The design method is already implemented and available for use in the design tool DNAforge (https://dnaforge.org).

Cite As Get BibTex

Antti Elonen and Pekka Orponen. Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops. In 30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 4:1-4:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024) https://doi.org/10.4230/LIPIcs.DNA.30.4

Author Details

Antti Elonen
  • Department of Computer Science, Aalto University, Espoo, Finland
Pekka Orponen
  • Department of Computer Science, Aalto University, Espoo, Finland

Funding

Project "Algorithmic design methods and tools for DNA nanotechnology", Finnish Cultural Foundation (P.O.)

Supplementary Materials

References

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