title: Principles for Predicting RNA Secondary Structure Design Difficulty.
abstract: Designing RNAs that form specific secondary structures is enabling better understanding and control of living systems through RNA-guided silencing, genome editing and protein organization. Little is known, however, about which RNA secondary structures might be tractable for downstream sequence design, increasing the time and expense of design efforts due to inefficient secondary structure choices. Here, we present insights into specific structural features that increase the difficulty of finding sequences that fold into a target RNA secondary structure, summarizing the design efforts of tens of thousands of human participants and three automated algorithms (RNAInverse, INFO-RNA and RNA-SSD) in the Eterna massive open laboratory. Subsequent tests through three independent RNA design algorithms (NUPACK, DSS-Opt and MODENA) confirmed the hypothesized importance of several features in determining design difficulty, including sequence length, mean stem length, symmetry and specific difficult-to-design motifs such as zigzags. Based on these results, we have compiled an Eterna100 benchmark of 100 secondary structure design challenges that span a large range in design difficulty to help test future efforts. Our in silico results suggest new routes for improving computational RNA design methods and for extending these insights to assess "designability" of single RNA structures, as well as of switches for in vitro and in vivo applications.
authors.affiliation: Eterna Massive Open Laboratory.
authors.forename: Jeff
authors.initials: J
authors.lastname: Anderson-Lee
authors.affiliation: Eterna Massive Open Laboratory.
authors.forename: Eli
authors.initials: E
authors.lastname: Fisker
authors.affiliation: Eterna Massive Open Laboratory; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.
authors.forename: Vineet
authors.initials: V
authors.lastname: Kosaraju
authors.affiliation: Eterna Massive Open Laboratory; Program in Biomedical Informatics, Stanford University, Stanford, CA 94305, USA.
authors.forename: Michelle
authors.initials: M
authors.lastname: Wu
authors.affiliation: Eterna Massive Open Laboratory; Department of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
authors.forename: Justin
authors.initials: J
authors.lastname: Kong
authors.affiliation: Eterna Massive Open Laboratory; Department of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
authors.forename: Jeehyung
authors.initials: J
authors.lastname: Lee
authors.affiliation: Eterna Massive Open Laboratory; Department of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
authors.forename: Minjae
authors.initials: M
authors.lastname: Lee
authors.affiliation: Eterna Massive Open Laboratory.
authors.forename: Mathew
authors.initials: M
authors.lastname: Zada
authors.affiliation: Eterna Massive Open Laboratory; Department of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Robotics Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
authors.forename: Adrien
authors.initials: A
authors.lastname: Treuille
authors.affiliation: Eterna Massive Open Laboratory; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA; Department of Physics, Stanford University, Stanford, CA 94305, USA. Electronic address: rhiju@stanford.edu.
authors.forename: Rhiju
authors.initials: R
authors.lastname: Das
authors.affiliation: Eterna Massive Open Laboratory.
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D006801:Humans; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012313:RNA
keywords: RNA design; RNA secondary structure; benchmark; citizen science; inverse folding