ABSTRACT
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
Footnotes
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than the author(s) must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from permissions{at}acm.org. BCB ’19, September 07-10, 2019, Niagara Falls, ON © 2019 Copyright held by the owner/author(s). Publication rights licensed to ACM. ACM ISBN 978-1-4503-9999-9/18/06…$15.00 https://doi.org/10.1145/1122445.1122456