Working on this project:
Synthetic riboswitches emerge as an important tool in Chemical and Synthetic Biology. In the 2ndfunding period, we demonstrated the versatility and robustness of engineered riboswitches in regulating gene expression and developed new strategies for their application with a special focus on the control of constitutive and alternative splicing and miRNA processing. For example, an aptamer can be exploited to select between two alternative 3′ splice sites. This allows switching between two protein isoforms and thus controls the nuclear and cytosolic localization of the controlled protein. Further on, we identified a new ciprofloxacin-dependent riboswitch. A detailed structure-function analysis enabled us to show that conformational changes and different ligand binding kinetics are responsible for the switching behavior. This knowledge allowed us to optimize our selection and screening strategies for the development of synthetic riboswitches, which led to the successful identification of several new riboswitch candidates. In the 3rd funding period, we will characterize the newly identified riboswitches and apply the new selection and screening methods for the development of new riboswitches with modified ligand binding specificities and increased flexibility. We hope that this work will lead not only to the substantial expansion of the tool box of synthetic riboswitches, but also to a deep and detailed understanding of the molecular basis of this exciting RNA-based regulation.