PT  - JOURNAL ARTICLE
AU  - Hua-Ting Yao
AU  - Mireille Regnier
AU  - Cedric Chauve
AU  - Yann Ponty
TI  - Exponentially few RNA structures are designable
AID  - 10.1101/652313
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 652313
4099  - http://biorxiv.org/content/early/2019/06/02/652313.short
4100  - http://biorxiv.org/content/early/2019/06/02/652313.full
AB  - The problem of RNA design attempts to construct RNA sequences that performs a predefined biological function, identified by several additional constraints. One of the foremost objective of RNA design is that the designed RNA sequence should adopt a predefined target secondary structure preferentially to any alternative structure, according to a given metrics and folding model. It was observed in several works that some secondary structures are undesignable, i.e. no RNA sequence can fold into the target structure while satisfying some criterion measuring how preferential this folding is compared to alternative conformations.In this paper, we show that the proportion of designable secondary structures decreases exponentially with the size of the target secondary structure, for various popular combinations of energy models and design objectives. This exponential decay is, at least in part, due to the existence of undesignable motifs, which can be generically constructed, and jointly analyzed to yield asymptotic upper-bounds on the number of designable structures.ACM Reference Format Hua-Ting Yao, Cedric Chauve, Mireille Regnier, and Yann Ponty. 2019. Exponentially few RNA structures are designable. In The 10th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB). ACM, New York, NY, USA, 11 pages. https://doi.org/10.1145/1122445.1122456