Folding of the FMN dependent riboswitch

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The flavine mononucleotide (FMN) riboswitch belongs to a class of RNA molecules that sense the cellular concentration of metabolites, and in response regulate expression of genes that are fundamental to metabolism. Communication between the metabolite binding domain and the expression platform of the riboswitch is dynamic; comprehensive understanding of this process requires consideration of time-sensitive parameters. The project is divided into two parts: studying the folding kinetics of the FMN riboswitch (1) and identifying suitable FMN analoga that induce the same conformational transition (2). Folding of the riboswitch RNA will be followed by fluorescence spectroscopy using the nucleobase analgon 2-aminopurine or specific dye labels as fluorescent reporter. Furthermore, we will use a variation of novel methods to monitor the global process of RNA folding. Upon reduction of FMN, the metabolite changes its molecular geometry and is released from its binding site. We will use this strategy of ligand shape control for addressing the question whether folding of the FMN riboswitch is fully reversible. Riboswitches are attractive therapeutic targets. We will try to identify compounds that bind to the riboswitch and induce conformational switching in the same manner as FMN and study their efficacy in vitro and in vivo.