Algorithmic Design of Cotranscriptionally Folding 2D RNA Origami Structures
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).
KeywordsRNA origami RNA tiles RNA nanotechnology Rational design Cotranscriptional folding Grid graphs Spanning trees
We thank Ebbe Andersen and Cody Geary for introducing us to the problem of polymerase trapping in RNA origami tile design, and their encouragement to proceed with the solution approach discussed in this paper.
- 4.Geary, C., Meunier, P.E., Schabanel, N., Seki, S.: Programming biomolecules than fold greedily during transcription. In: Proceedings, 41st International Conference on Mathematical Foundations of Computer Science (MFCS 2016). LIPIcs, vol. 58, pp. 43:1–43:14. Dagstuhl Publishing (2016). https://doi.org/10.4230/LIPIcs.MFCS.2016.43