Motivation

Existing RNA thermometers are designed to switch at around 37°C and do not exhibit significant conformational changes between 25°C and 30°C. As most plants cannot be expected to grow at 37°C, it was necessary to design thermometers that experienced conformational changes between 25°C and 30°C. We chose to design thermometers by finding optimal candidates using a genetic algorithm and RNA folding software, as the complexity of RNA folding thermodynamics otherwise makes it difficult to manually mutate existing thermometers to meet our performance criteria or devise them de novo. As the figures below show, A. thaliana grows best between 18–23°C and P. putida is typically grown in lab at 30°C. Along with the need for heterologous gene expression only at higher, stress-inducing temperatures to mediate a stress-mitigating response, we reasoned the need to design RNA thermometers that are optimized to melt at 30°C.