Design of a Toolbox of RNA Thermometers

Abstract

Biomolecular temperature sensors can be used for efficient control of large-volume bioreactors, for spatiotemporal imaging and control of gene expression, and to engineer robustness to temperature in biomolecular circuit design. While RNA-based sensors, called 'thermometers', have been investigated in both natural and synthetic contexts, an important challenge is to design diverse responses to temperature, differing in sensitivities and thresholds. We address this issue by constructing a library of RNA thermometers, based on thermodynamic computations, and experimentally measuring their activities in cell-free biomolecular 'breadboards'. Using free energies of the minimum free energy structures as well as melt profile computations, we estimated thata diverse set of temperature responses were possible. We experimentally found a wide range of responses to temperature in the temperature range 29 ◦C–37 ◦C, with fold-changes varying over 3-fold around the starting thermometer. The sensitivities of these responses ranged over 10-fold around the starting thermometer. We correlated these measurements with computational expectations, finding that while there was no strong correlation for the individual thermometers, overall trends of diversity, fold-changes, and sensitivities were similar. These results present a toolbox of RNA-based circuit elements with diverse temperature responses.

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