Algorithmic design of cotranscriptionally folding 2D RNA origami structures

Abdulmelik Mohammed; Pekka Orponen; Sachith Pai

doi:10.1007/978-3-319-92435-9_12

Algorithmic design of cotranscriptionally folding 2D RNA origami structures

Abdulmelik Mohammed, Pekka Orponen, Sachith Pai

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Scientific › peer-review

2 Citations (Scopus)

228 Downloads (Pure)

Abstract

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 language	English
Title of host publication	Unconventional Computation and Natural Computation
Subtitle of host publication	17th International Conference, UCNC 2018, Fontainebleau, France, June 25-29, 2018, Proceedings
Editors	Susan Stepney, Sergey Verlan
Publisher	Springer
Pages	159-172
ISBN (Electronic)	978-3-319-92435-9
ISBN (Print)	978-3-319-92434-2
DOIs	https://doi.org/10.1007/978-3-319-92435-9_12
Publication status	Published - 31 May 2018
MoE publication type	A4 Conference publication
Event	International Conference on Unconventional Computation and Natural Computation - Fontainebleau, Paris, France Duration: 25 Jun 2018 → 29 Jun 2018 Conference number: 17

Publication series

Name	Lecture Notes in Computer Science
Publisher	Springer
Volume	10867
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	International Conference on Unconventional Computation and Natural Computation
Abbreviated title	UCNC
Country/Territory	France
City	Paris
Period	25/06/2018 → 29/06/2018

Keywords

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

Access to Document

10.1007/978-3-319-92435-9_12

ucnc_2018Accepted author manuscript, 424 KB

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ALBION: Algorithmic Designs for Biomolecular Nanostructures (ALBION)
Orponen, P., Elonen, A., Lohikko, A., Saman Booy, M., Mohammed, A., Vo, T., Gautam, V. & Korpela, D.
01/09/2017 → 31/08/2021
Project: Academy of Finland: Other research funding

Science-IT
Mikko Hakala (Manager)
School of Science
Facility/equipment: Facility

Cite this

Mohammed, A., Orponen, P., & Pai, S. (2018). Algorithmic design of cotranscriptionally folding 2D RNA origami structures. In S. Stepney, & S. Verlan (Eds.), Unconventional Computation and Natural Computation: 17th International Conference, UCNC 2018, Fontainebleau, France, June 25-29, 2018, Proceedings (pp. 159-172). (Lecture Notes in Computer Science; Vol. 10867). Springer. https://doi.org/10.1007/978-3-319-92435-9_12

Mohammed, Abdulmelik ; Orponen, Pekka ; Pai, Sachith. / Algorithmic design of cotranscriptionally folding 2D RNA origami structures. Unconventional Computation and Natural Computation: 17th International Conference, UCNC 2018, Fontainebleau, France, June 25-29, 2018, Proceedings. editor / Susan Stepney ; Sergey Verlan. Springer, 2018. pp. 159-172 (Lecture Notes in Computer Science).

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Mohammed, A, Orponen, P & Pai, S 2018, Algorithmic design of cotranscriptionally folding 2D RNA origami structures. in S Stepney & S Verlan (eds), Unconventional Computation and Natural Computation: 17th International Conference, UCNC 2018, Fontainebleau, France, June 25-29, 2018, Proceedings. Lecture Notes in Computer Science, vol. 10867, Springer, pp. 159-172, International Conference on Unconventional Computation and Natural Computation, Paris, France, 25/06/2018. https://doi.org/10.1007/978-3-319-92435-9_12

Algorithmic design of cotranscriptionally folding 2D RNA origami structures. / Mohammed, Abdulmelik; Orponen, Pekka; Pai, Sachith.
Unconventional Computation and Natural Computation: 17th International Conference, UCNC 2018, Fontainebleau, France, June 25-29, 2018, Proceedings. ed. / Susan Stepney; Sergey Verlan. Springer, 2018. p. 159-172 (Lecture Notes in Computer Science; Vol. 10867).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Scientific › peer-review

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AB - 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).

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Mohammed A, Orponen P, Pai S. Algorithmic design of cotranscriptionally folding 2D RNA origami structures. In Stepney S, Verlan S, editors, Unconventional Computation and Natural Computation: 17th International Conference, UCNC 2018, Fontainebleau, France, June 25-29, 2018, Proceedings. Springer. 2018. p. 159-172. (Lecture Notes in Computer Science). doi: 10.1007/978-3-319-92435-9_12

Algorithmic design of cotranscriptionally folding 2D RNA origami structures

Abstract

Publication series

Conference

Keywords

Access to Document

OpenUrl availability

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Projects

ALBION: Algorithmic Designs for Biomolecular Nanostructures (ALBION)

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Science-IT

Cite this