Lafontaine lab :: Research

Riboswitches are genetic control elements that are located on the 5'-untranslated region of some messenger RNAs. These particular genetic switches exhibit two surprising properties. Firstly, the mRNA harboring the riboswitch is able to form a highly selective binding site for a target metabolite without the aid of proteins. Secondly, metabolite binding promotes an allosteric reorganization of RNA structure that leads to alterations in genetic expression.

Our research focuses on purine riboswitches that are the simplest riboswitches known so far. This group is composed of the adenine and guanine riboswitches that share a very similar tertiary structure. Strikingly, both molecules use a different metabolite (adenine or guanine) to perform two different essential biological functions. We study how these RNA molecules are using their cognate metabolites to achieve their genetic regulation without the help of proteins.

Given their essential function and their high level of evolutionary conservation, riboswitches are potentially interesting targets for antibiotic research. Morevoer, since riboswitches naturally bind small metabolites (i.e., nucleobases), it is possible to use already existing molecular databases.

We are also interested in creating artificial riboswitches having very precise functions. They could be used for the dectection of small compounds produced as precursors of diverse pathologies. When couple to fluorescent proteins (GFP and the likes), these molecular detectors could have a major impact in preventive detection of human pathologies.

Fluorescence Resonance Energy Transfer (FRET) is unique in its ability to provide accurate long-range distance information (20-80 Å) in solution under physiological conditions. In a typical FRET experiment, a nucleic acid is labeled with two different fluorophores which are covalently attached at different locations. Upon appropriate light excitation, a transfer of energy between both fluorophores is observed and this is inversely proportional to the distance between them. This is very useful to study the folding of macromolecules like RNA.

FRET can also be used to build three-dimensional models for complex RNA molecules that are otherwise difficult to acquire. A very good example of this is the VS ribozyme for which no crystal structure has yet been obtained and for which we have built a three-dimensional structure.

While steady-state measurements of FRET provide the average distance between fluorophores in solution, much more information is available from the analysis of the nanosecond emission decay of a fluorophore in time-resolved FRET (trFRET). Analysis of the decay can resolve different conformers in a heterogeneous mixture, providing information on the global structure and flexibility of each species as well as their equilibrium populations. Thus, trFRET is a tremendous technique to probe structural, energetic, and dynamic features of nucleic acids "beyond the molecular ruler".