High-resolution analysis of the dynamic interaction network that enables optoribogenetics

• Applicants: Dr. Manuel Etzkorn; Professor Dr. Günter Mayer
• Subject Area: Biochemistry ; Biological and Biomimetic Chemistry ; Biophysics
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 571945635

Complex formation of the photoreceptor protein NmPAL and its related aptamers can be used to reversibly control biological functions by light. This process is known as optoribogenetics and is based on chimeric RNAs consisting of the aforesaid aptamers that are linked to regulatory RNA molecules, e.g. siRNAs, guide RNAs, or ribozymes, via so-called 'communication modules'. Light-dependent binding of NmPAL with these chimeric RNAs, trigger conformational changes in the regulatory domains that ultimately enable the control of gene expression. This regulatory function involves a dynamic network of molecular interactions, including NmPAL-RNA interactions, contacts between the RNA modules, and possible modulations by metal ions or other cellular factors. The aim of the project is 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 and on the unique conformational activation of the NmPAL/aptamer system will be combined with studies on the kinetics, thermodynamics and function of the conformational activation of selected NmPAL/aptamer pairs. These characteristics of the aptamer-NmPAL interaction will be studied in vitro and under cellular conditions, as the latter have been shown to influence the function of chimeric RNAs. The project is not limited to a single prototypical NmPAL system but aims to explore ist modular architecture. In particular, we are interested in different (i) aptamer motifs with cell type-specific activities, (ii) specifically designed or selected communication modules that convey the binding status of the aptamer and control the efficiency of the system, and (iii) regulatory domains enabling specific gene-modulating activities. In addition to gaining a better understanding of the individual modules, their complex formation, dynamics, and modes of action, we plan to use the knowledge gained to systematically optimize the optoribogenetic capabilities.

• DFG Programme: Research Grants