Algorithmic design of cotranscriptionally folding 2D RNA origami structures

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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).

Details

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
Publication statusPublished - 31 May 2018
MoE publication typeA4 Article in a 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
PublisherSpringer
Volume10867
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

ConferenceInternational Conference on Unconventional Computation and Natural Computation
Abbreviated titleUCNC
CountryFrance
CityParis
Period25/06/201829/06/2018

    Research areas

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

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