RNAiFold2T: Constraint Programming design of thermo-IRES switches.
RNA thermometers (RNATs) are cis-regulatory elements that change secondary structure upon temperature shift. Often involved in the regulation of heat shock, cold shock and virulence genes, RNATs constitute an interesting potential resource in synthetic biology, where engineered RNATs could prove to be useful tools in biosensors and conditional gene regulation.



Solving the 2-temperature inverse folding problem is critical for RNAT engineering. Here we introduce RNAiFold2T, the first Constraint Programming (CP) and Large Neighborhood Search (LNS) algorithms to solve this problem. Benchmarking tests of RNAiFold2T against existent programs (adaptive walk and genetic algorithm) inverse folding show that our software generates two orders of magnitude more solutions, thus allowing ample exploration of the space of solutions. Subsequently, solutions can be prioritized by computing various measures, including probability of target structure in the ensemble, melting temperature, etc. Using this strategy, we rationally designed two thermosensor internal ribosome entry site (thermo-IRES) elements, whose normalized cap-independent translation efficiency is approximately 50% greater at 42 °C than 30 °C, when tested in reticulocyte lysates. Translation efficiency is lower than that of the wild-type IRES element, which on the other hand is fully resistant to temperature shift-up. This appears to be the first purely computational design of functional RNA thermoswitches, and certainly the first purely computational design of functional thermo-IRES elements.



RNAiFold2T is publicly available as part of the new release RNAiFold3.0 at https://github.com/clotelab/RNAiFold and http://bioinformatics.bc.edu/clotelab/RNAiFold, which latter has a web server as well. The software is written in C ++ and uses OR-Tools CP search engine.



clote@bc.edu



Supplementary data are available at Bioinformatics online.
Biology Department, Boston College, Chestnut Hill, MA 02467, USA.
Juan Antonio
JA
Garcia-Martin
Department of Experimental and Health Sciences, Research Programme on Biomedical Informatics (GRIB), Universitat Pompeu Fabra. Dr. Aiguader 88, Barcelona, Spain.
Ivan
I
Dotu
Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid, 28049 Madrid, Spain.
Javier
J
Fernandez-Chamorro
Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid, 28049 Madrid, Spain.
Gloria
G
Lozano
Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid, 28049 Madrid, Spain.
Jorge
J
Ramajo
Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid, 28049 Madrid, Spain.
Encarnacion
E
Martinez-Salas
Biology Department, Boston College, Chestnut Hill, MA 02467, USA.
Peter
P
Clote
D000465:Algorithms; D001483:Base Sequence; D000067556:Internal Ribosome Entry Sites; D009690:Nucleic Acid Conformation; D012313:RNA; D059370:RNA Folding; D012984:Software
D000067556:Internal Ribosome Entry Sites; D012313:RNA