  RNA thermometers are mRNA strands with a temperature dependent secondary
structure: depending on the spatial conformation, the mRNA strand can get
translated (on-state) or can be inaccessible for ribosomes binding (off-state).
These have been found in a number of microorganisms (mainly pathogens), where
they are used to adaptively regulate the gene expression, in response to
changes in the environmental temperature. Besides naturally occurring RNA
thermometers, synthetic RNA thermometers have been recently designed by
modifying their natural counterparts (Hofacker et al., 2003). The newly
designed RNA thermometers are simpler, and exhibit a sharper switching between
off- and on-states. However, the proposed trial-and-error design procedure has
not been algorithmically formalized, and the switching temperature is rigidly
determined by the natural RNA thermometer used as template for the design.
  We developed a general algorithmic procedure (consensus distribution) for the
design of RNA thermo-switches with a tunable switching temperature that can be
decided in advance by the designer. A software tool with a user friendly GUI
has been written to automate the design of RNA thermo-switches with a desired
threshold temperature. Starting from a natural template, a new RNA thermometer
has been designed by our method for a new desired threshold temperature of 32C.
The designed RNA thermo-switch has been experimentally validated by using it to
control the expression of lucifarase. A 9.2 fold increase of luminescence has
been observed between 30C and 37C, whereas between 20C and 30C the luminescence
increase is less than 3-fold.
  This work represents a first step towards the design of flexible and tunable
RNA thermometers that can be used for a precise control of gene expression
without the need of external chemicals and possibly for temperature
measurements at a nano-scale resolution.
