Generation of synthetic RNA-based thermosensors.

Structured RNAs with fundamental sensory and regulatory potential have been discovered in all kingdoms of life. Bacterial RNA thermometers are located in the 5'-untranslated region of certain heat shock and virulence genes. They regulate translation by masking the Shine-Dalgarno sequence in a temperature-dependent manner. To engineer RNA-based thermosensors, we used a combination of computer-based rational design and in vivo screening. After only two rounds of selection, several RNA thermometers that are at least as efficient as natural thermometers were obtained. Structure probing experiments revealed temperature-dependent conformational changes in these translational control elements. Our study demonstrates that temperature-controlled RNA elements can be designed by a simple combined computational and experimental approach.