Algorithmic design of cotranscriptionally folding 2D RNA origami structures

Loading...
Thumbnail Image
Journal Title
Journal ISSN
Volume Title
Conference article in proceedings
This publication is imported from Aalto University research portal.
View publication in the Research portal
View/Open full text file from the Research portal
Date
2018-05-31
Major/Subject
Mcode
Degree programme
Language
en
Pages
159-172
Series
Unconventional Computation and Natural Computation, Lecture Notes in Computer Science, Volume 10867
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).
Description
Keywords
RNA origami, RNA tiles, RNA nanotechnology, Rational design, Cotranscriptional folding, Grid graphs, Spanning trees, rna
Other note
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 . https://doi.org/10.1007/978-3-319-92435-9_12