Algorithmic design of cotranscriptionally folding 2D RNA origami structures

Abdulmelik Mohammed, Pekka Orponen, Sachith Pai

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2 Citations (Scopus)
228 Downloads (Pure)


We address a biochemical folding obstacle of “polymerase trapping” that arises in the remarkable RNA origami tile design framework of Geary, Rothemund and Andersen (Science 2014). We present a combinatorial formulation of this obstacle, together with an optimisation procedure that yields designs minimising the risk of encountering the corresponding topological trap in the tile folding phase. The procedure has been embedded in an automated software pipeline, and we provide examples of designs produced by the software, including an optimised version of the RNA smiley-face tile proposed by Geary and Andersen (DNA 2014).
Original languageEnglish
Title of host publicationUnconventional Computation and Natural Computation
Subtitle of host publication17th International Conference, UCNC 2018, Fontainebleau, France, June 25-29, 2018, Proceedings
EditorsSusan Stepney, Sergey Verlan
ISBN (Electronic)978-3-319-92435-9
ISBN (Print)978-3-319-92434-2
Publication statusPublished - 31 May 2018
MoE publication typeA4 Conference publication
EventInternational Conference on Unconventional Computation and Natural Computation - Fontainebleau, Paris, France
Duration: 25 Jun 201829 Jun 2018
Conference number: 17

Publication series

NameLecture Notes in Computer Science
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


ConferenceInternational Conference on Unconventional Computation and Natural Computation
Abbreviated titleUCNC


  • RNA origami
  • RNA tiles
  • RNA nanotechnology
  • Rational design
  • Cotranscriptional folding
  • Grid graphs
  • Spanning trees
  • rna


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