Trityl spin labels: developing labeling strategies for in cellulo and temperature-dependent pulsed dipolar EPR measurements on RNA

• Applicants: Professorin Dr. Stephanie Kath-Schorr; Professor Dr. Olav Schiemann
• Subject Area: Physical Chemistry of Molecules, Liquids and Interfaces, Biophysical Chemistry ; Biological and Biomimetic Chemistry
• Term: since 2026
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 579619180

Nucleic acid complexes are highly dynamic systems and perform a wide variety of biological functions. Over the years, many examples have shown that it is the dynamics of these complexes that drives them from their inactive energy minimum structure, as found, e.g., in crystal structures, into the active conformation, and that this dynamic is influenced by the cellular environment. Electron Paramagnetic Resonance (EPR), in particular Pulsed Dipolar EPR spectroscopy (PDS), in combination with site-directed spin labeling (SDSL), is a powerful method for providing access to the dynamics of biological systems in vitro and in cellulo either in the form of conformational ensembles or by time-resolved methods. However, inside cells, the commonly used nitroxide labels degrade very quickly, and more reduction-stable labels for nucleic acids are only used in combination with i) long, flexible linkers, which complicate the interpretation of distance distributions, and/or ii) labeling strategies that solely label the ends of nucleic acids, which limits the information on conformations and dynamics. Therefore, we aim here to develop new labeling strategies for nucleic acids with trityl labels, that are stable in cells, and to apply this methodology in combination with time-resolved EPR methods in vitro and in cellulo to answer functionally important questions for two mRNA sequences, i.e., the guanidinium-(II)-riboswitch and the ribozyme cytoplasmic polyadenylation element binding protein 3 (CPEB3).

• DFG Programme: Research Grants