Mapping mRNA Localization and Internal Structure in Lipid Nanoparticles through Solid-State Dynamic Nuclear Polarization NMR and Proton Spin-Diffusion Modeling.

Lipid nanoparticles (LNPs) are the cornerstone of RNA-based vaccine delivery, yet their internal structure, particularly in the presence of large, single-stranded messenger RNA (mRNA), remains poorly understood. Here, we apply relayed dynamic nuclear polarization (DNP)-enhanced solid-state NMR to directly detect encapsulated mRNA and map the spatial distribution of lipid and nucleic acid components within intact LNPs formulated with clinically relevant excipients. By refining cryoprotectant removal and polarizing matrix composition, we report the solid-state NMR observation of the mRNA cargo within functional LNPs, with clear C1'-H1' correlation confirming resonance assignment. Quantitative analysis of polarization enhancements and build-up kinetics reveals a concentric architecture: PEG-lipids reside at the surface, helper lipids (DOPE, cholesterol) in intermediate layers, and mRNA within the core. These experimental trends are reinforced by numerical simulations that model the polarization transport by spin diffusion across a library of eight structural models. A multi-layered core-shell configuration, placing mRNA at the center surrounded by stratified lipid shells, best fits the full set of NMR observables. Together, these results confirm relayed-DNP MAS NMR as a powerful method for probing nanometer-scale spatial organization in LNPs and provide a quantitative structural framework to guide the rational design of RNA delivery systems.