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Secondary Structure Design for Cotranscriptional 3D RNA Origami Wireframes

Authors Pekka Orponen , Shinnosuke Seki , Antti Elonen

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Subject Classification

ACM Subject Classification
  • Theory of computation → Theory and algorithms for application domains
Keywords
  • RNA origami
  • wireframe nanostructures
  • cotranscriptional folding
  • secondary structure
  • kissing loops
  • algorithms
  • self-assembly

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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.

Cite As Get BibTex

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) https://doi.org/10.4230/LIPIcs.DNA.31.6

Author Details

Pekka Orponen
  • Department of Computer Science, Aalto University, Finland
Shinnosuke Seki
  • Department of Computer and Network Engineering, University of Electro-Communications, Tokyo, Japan
Antti Elonen
  • Department of Computer Science, Aalto University, Finland

Funding

This work was initiated during a visit by P.O. to the University of Electro-Communications, supported by grant "Design Tools for DNA Nanotechnology" from the Finnish Cultural Foundation, and significantly advanced during a visit by S.S. to Aalto University, supported by a Visiting Researcher grant from the Aalto Science Institute.

Acknowledgements

We thank Mr. Robin Runne for essential contributions to the implementation of our DFS tree enumeration method.

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