Advanced design of structural RNAs using RNARedPrint

Yann Ponty (1) , Stefan Hammer (2, 3) , Hua-Ting Yao (1, 4) , Sebastian Will (1, 5)

1 AMIBIO - Algorithms and Models for Integrative BIOlogy
2 University of Vienna [Vienna]
3 Leipzig University / Universität Leipzig
4 McGill University = Université McGill [Montréal, Canada]
5 X-DEP-INFO - Département d'informatique de l'École polytechnique

RNA design addresses the need to build novel RNAs, e.g. for biotechnological applications in synthetic biology, equipped with desired functional properties. This chapter describes how to use the software RNARedPrint for the de novo rational design of RNA sequences adopting one or several desired secondary structures. Depending on the application , these structures could represent alternate configurations or kinetic pathways. The software makes such design convenient and sufficiently fast for practical routine, where it even overcomes notorious problems in the application of RNA design, e.g. it maintains realistic GC content.

Mots clés: RNA design; Kinetic landscapes; Riboswitches

Domaines: Bio-informatique [q-bio.QM]

Yann Ponty, Stefan Hammer, Hua-Ting Yao, Sebastian Will. Advanced design of structural RNAs using RNARedPrint. Ernesto Picardi. RNA Bioinformatics, 2284, pp.1--15, 2021, Methods in Molecular Biology, 978-1-0716-1306-1. ⟨10.1007/978-1-0716-1307-8_1⟩. ⟨hal-02990264⟩