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Cations in charge of RNA folding and function: Realistic modeling and robust predictions

Subject Area Statistical Physics, Nonlinear Dynamics, Complex Systems, Soft and Fluid Matter, Biological Physics
Biophysics
Term from 2016 to 2024
Project identifier Deutsche Forschungsgemeinschaft (DFG) - Project number 315221747
 
Final Report Year 2024

Final Report Abstract

RNA technologies revolutionize modern medicine. Due to the rapid success in the development of mRNA vaccines against COVID-19, RNA became the center of intense scientific research. In addition to mRNA, which can produce antigens or therapeutic proteins, other classes of RNA have vital and regulatory functions in cells. The aim of this Emmy Noether project was to provide molecular insights into the structure and function of such RNAs by computer simulations. Initially, our research focused on the role of cations in the folding and function of RNA. To provide a thorough understanding of ion-RNA interactions, we developed improved atomistic models and employed enhanced sampling techniques. With the improved simulation models, we were able to reproduce a broad range of important physiochemical solution properties, capture the interactions of metal ions and nucleic acids and to yield close agreement with experimentally observed nucleic acid structures. Subsequently, we investigated systems of increasing complexity ranging from double stranded nucleic acids to regulatory riboswitches and RNA quadruplexes. The simulations provided a detailed view of the distributions of ions, the influence of the ionic atmosphere on the structure and the folding pathways. Finally, the COVID-19 pandemic shifted the focus of the project toward lipid nanoparticles as smart transport systems to deliver RNA to cells. Special emphasis was placed on the development of accurate models for the ionizable lipids and their interactions with RNA. In summary, bimolecular simulations are an indispensable tool for increasingly large and complex molecular systems. This project contributed to the accurate description of ions, nucleic acids, and lipids in molecular dynamics simulations which yielded important molecular insights into nucleic acid systems.

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