B1 - High-resolution analysis of the dynamic interaction network that enables optoribogenetics in vitro and in cellulo

The control of regulatory RNAs by light-dependent photoreceptors and chimeric functional RNAs involves a complex network of molecular interactions, including direct protein-RNA interactions modulated by light, contacts between RNA domains, and modulation by metal ions or other cellular factors. By using RNA building blocks based on short, hairpin-forming RNA aptamers that bind to the photoreceptor PAL in response to light, gene expression can be controlled at both the transcriptional and translational levels. These RNA chimeras, which are created by linking aptamers with other regulatory RNA molecules such as guide RNAs or ribozymes, enable light-mediated control of biological functions.
This project aims to gain a comprehensive understanding of the molecular structure and dynamics underlying this optoribogenetic interaction network. High-resolution NMR studies focusing on RNA-protein and RNA-RNA binding events as well as on the unique conformational activation of the PAL/aptamer system will be combined with in-depth characterization of the activity under cellular conditions. Of particular interest is the communication module that transmits information about the binding status of the aptamer to the regulatory domain and thus controls the efficiency of the system. In addition to gaining a better understanding of its mode of action, we plan to systematically optimize this central module to further improve optoribogenetic capabilities.