RNA at Lipid/Water Interfaces: Molecular Insights from Coarse-Grained Simulations and Reflectivity Data Predictions

Abstract Interactions between RNA and lipids are fundamental for biological processes and are increasingly exploited for RNA delivery by lipid nanoparticles. However, RNA-lipid interactions remain challenging to characterize at the molecular level. Here, we address the modeling of RNA at lipid/water interfaces using coarse-grained (CG) simulations, experimental validation using scattering data and prediction of neutron (NR) and X-ray reflectivity (XRR) profiles from the simulations. Using neutral DOPC and cationic DOTAP bilayers, we show that lipid-RNA interactions depend strongly on RNA secondary structure, with single-stranded regions exhibiting higher interfacial affinity than double-stranded segments. We validate the CG lipid simulations, showing that while they reproduce experimental X-ray scattering data only qualitatively, the agreement improves markedly after backmap-ping to atomistic resolution followed by energy minimization and short all-atom molecular dynamics simulations. We further simulated distinct tRNA conformations and analyzed the influence of RNA secondary structure, concentration, solvent contrast, and lipid deuteration on NR and XRR signals identifying the conditions under which such experiments probe RNA adsorption and discriminate between different RNA conformations. Together, these results demonstrate that CG simulations combined with reflectivity data provide a powerful approach to probe RNA adsorption and structure at lipid/water interfaces and support the design and interpretation of scattering experiments. Competing Interest Statement The authors have declared no competing interest. Footnotes ↵* E-mail: ibrahim.mohd{at}tum.de; Nadine.Schwierz{at}physik.uni-augsburg.de Updated to match the final form of the peer-reviewed version https://git.rz.uni-augsburg.de/cbio-gitpub/undulation-correction-scattering