2026-09-30T03:37:24Z https://drops.dagstuhl.de/oai

oai:drops-oai.dagstuhl.de:23855 2026-09-23T22:27:22Z ddc:004 open_access

Secondary Structure Design for Cotranscriptional 3D RNA Origami Wireframes Orponen, Pekka Seki, Shinnosuke Elonen, Antti RNA origami wireframe nanostructures cotranscriptional folding secondary structure kissing loops algorithms self-assembly 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. Schloss Dagstuhl – Leibniz-Zentrum für Informatik Pekka Orponen and Shinnosuke Seki and Antti Elonen 2025 Is Part Of LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025) InProceedings Text doc-type:ResearchArticle publishedVersion application/pdf doi:10.4230/LIPIcs.DNA.31.6 urn:nbn:de:0030-drops-238558 https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.6 eng https://creativecommons.org/licenses/by/4.0/legalcode