Algorithmic design of 3D wireframe RNA nanostructures
Prof. Pekka Orponen
Aalto University, School of Science, Department of Computer Science
In this talk I first review our work on rendering general 3D wireframe mesh models in RNA (1), building on the innovative RNA origami technique introduced by Geary, Rothemund and Andersen in 2014 (2). I then address the problem of minimising the number of potentially problematic kissing-loop connector motifs used in these designs. This task turns out to have a surprisingly efficient and elegant solution method that applies some concepts and techniques from topological graph theory (3).
[Joint work with Antti Elonen.]
(1) A. Elonen, A. K. Natarajan, I. Kawamata, L. Oesinghaus, A. Mohammed, J. Seitsonen, Y. Suzuki, F. C. Simmel, A. Kuzyk, P. Orponen, ACS Nano 2022, 16, 16608–16616. DOI: 10.1021/acsnano.2c06035
(2) C. Geary, P. W. K. Rothemund, E. S. Andersen, Science 2014, 345, 799-804. DOI: 10.1126/science.1253920
(3) Antti Elonen, Pekka Orponen, DNA 30 - 30th International Conference on DNA Computing and Molecular Programming, 2024. DOI: 10.4230/LIPIcs.DNA.30.4
