Mohammed, Abdulmelik; Orponen, Pekka; Pai, Sachith Algorithmic design of cotranscriptionally folding 2D RNA origami structures. (English) Zbl 1508.68105 Stepney, Susan (ed.) et al., Unconventional computation and natural computation. 17th international conference, UCNC 2018, Fontainebleau, France, June 25–29, 2018. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 10867, 159-172 (2018). Summary: We address a biochemical folding obstacle of “polymerase trapping” that arises in the remarkable RNA origami tile design framework of C. Geary et al. [“A single-stranded architecture for cotranscriptional folding of RNA nanostructures”, Science 345, No. 6198, 799–804 (2014; doi:10.1126/science.1253920)]. 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 C. W. Geary and E. S. Andersen [Lect. Notes Comput. Sci. 8727, 1–19 (2014; Zbl 1509.92011)].For the entire collection see [Zbl 1390.68028]. Cited in 1 Document MSC: 68Q07 Biologically inspired models of computation (DNA computing, membrane computing, etc.) 51M15 Geometric constructions in real or complex geometry 92C40 Biochemistry, molecular biology Keywords:RNA origami; RNA tiles; RNA nanotechnology; rational design; cotranscriptional folding; grid graphs; spanning trees Citations:Zbl 1509.92011 PDFBibTeX XMLCite \textit{A. Mohammed} et al., Lect. Notes Comput. Sci. 10867, 159--172 (2018; Zbl 1508.68105) Full Text: DOI Link