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Secondary Structure Design for Cotranscriptional 3D RNA Origami Wireframes

Authors: Pekka Orponen, Shinnosuke Seki, and Antti Elonen

Published in: LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025)

Abstract

We address the task of secondary structure design for de novo 3D RNA origami wireframe structures in a way that takes into account the specifics of a cotranscriptional folding setting. We consider two issues: firstly, avoiding the topological obstacle of "polymerase trapping", where some helical domain cannot be hybridised due to a closed kissing-loop pair blocking the winding of the strand relative to the polymerase-DNA-template complex; and secondly, minimising the number of distinct kissing-loop designs needed, by reusing KL pairs that have already been hybridised in the folding process. For the first task, we present an efficient strand-routing method that guarantees the absence of polymerase traps for any 3D wireframe model, and for the second task, we provide a graph-theoretic formulation of the minimisation problem, show that it is NP-complete in the general case, and outline a branch-and-bound type enumerative approach to solving it. Key concepts in both cases are depth-first search in graphs and the ensuing DFS spanning trees. Both algorithms have been implemented in the DNAforge design tool (https://dnaforge.org) and we present some examples of the results.

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Pekka Orponen, Shinnosuke Seki, and Antti Elonen. Secondary Structure Design for Cotranscriptional 3D RNA Origami Wireframes. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 6:1-6:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{orponen_et_al:LIPIcs.DNA.31.6,
  author =	{Orponen, Pekka and Seki, Shinnosuke and Elonen, Antti},
  title =	{{Secondary Structure Design for Cotranscriptional 3D RNA Origami Wireframes}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{6:1--6:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.6},
  URN =		{urn:nbn:de:0030-drops-238558},
  doi =		{10.4230/LIPIcs.DNA.31.6},
  annote =	{Keywords: RNA origami, wireframe nanostructures, cotranscriptional folding, secondary structure, kissing loops, algorithms, self-assembly}
}

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DOI: 10.4230/artifacts.22515

DNAforge

Authors: Antti Elonen and Leon Wimbes

Abstract

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Antti Elonen, Leon Wimbes. DNAforge (Software). Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@misc{dagstuhl-artifact-22515,
   title = {{DNAforge}}, 
   author = {Elonen, Antti and Wimbes, Leon},
   note = {Software, version 1.0.0., swhId: \href{https://archive.softwareheritage.org/swh:1:dir:37818d83c81946377fb47e15688adb686c29d84d;origin=https://github.com/dnaforge/dnaforge;visit=swh:1:snp:06299be61c159fd747fd7f0424eddb486239ade9;anchor=swh:1:rev:d7d8d660f73cfeb3092b12da8c037fa7dafa6836}{\texttt{swh:1:dir:37818d83c81946377fb47e15688adb686c29d84d}} (visited on 2024-11-28)},
   url = {https://github.com/dnaforge/dnaforge},
   doi = {10.4230/artifacts.22515},
}

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DOI: 10.4230/LIPIcs.DNA.30.4

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

Authors: Antti Elonen and Pekka Orponen

Published in: LIPIcs, Volume 314, 30th International Conference on DNA Computing and Molecular Programming (DNA 30) (2024)

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).

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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)

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@InProceedings{elonen_et_al:LIPIcs.DNA.30.4,
  author =	{Elonen, Antti and Orponen, Pekka},
  title =	{{Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops}},
  booktitle =	{30th International Conference on DNA Computing and Molecular Programming (DNA 30)},
  pages =	{4:1--4:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-344-7},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{314},
  editor =	{Seki, Shinnosuke and Stewart, Jaimie Marie},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.30.4},
  URN =		{urn:nbn:de:0030-drops-209325},
  doi =		{10.4230/LIPIcs.DNA.30.4},
  annote =	{Keywords: RNA origami, wireframe nanostructures, polyhedra, kissing loops, topological graph embeddings, self-assembly}
}

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Documents authored by Elonen, Antti

Secondary Structure Design for Cotranscriptional 3D RNA Origami Wireframes

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DNAforge

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

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