Algorithmic design of cotranscriptionally folding 2D RNA origami structures

Mohammed, Abdulmelik; Orponen, Pekka; Pai, Sachith

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Algorithmic design of cotranscriptionally folding 2D RNA origami structures

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Title:	Algorithmic design of cotranscriptionally folding 2D RNA origami structures
Author(s):	Mohammed, Abdulmelik ; Orponen, Pekka ; Pai, Sachith
Date:	2018-05-31
Language:	en
Pages:	159-172
Department:	Department of Computer Science
ISBN:	978-3-319-92434-2 978-3-319-92435-9
Series:	Unconventional Computation and Natural Computation, Lecture Notes in Computer Science, Volume 10867
ISSN:	0302-9743 1611-3349
DOI-number:	10.1007/978-3-319-92435-9_12
Subject:	Computer Science Applications, 113 Computer and information sciences, Theoretical computer science
Keywords:	RNA origami, RNA tiles, RNA nanotechnology, Rational design, Cotranscriptional folding, Grid graphs, Spanning trees, rna, Computer Science Applications, 113 Computer and information sciences, Theoretical computer science
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Citation: 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 . DOI: 10.1007/978-3-319-92435-9_12
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).

Permanent link to this item: http://urn.fi/URN:NBN:fi:aalto-201812105928 Email this Export to RefWorks QR Code Print BibTex Tweet