RNA-Lipid Interactions Control Structure and Dynamics of Lipid Nanoparticles

Ionizable lipids, such as DLin-MC3-DMA (MC3), play a central role in nucleic acid encapsulation and intracellular delivery, yet the molecular mechanisms governing LNP structure and function remain incompletely understood. The internal organization of LNP cores is highly sensitive to pH and has been described by inverse hexagonal, cubic, and lamellar phases that influence delivery performance.

Here, we investigate the pH-dependent structure and dynamics of MC3-containing LNPs using two-dimensional infrared (2D IR) spectroscopy and molecular dynamics (MD) simulations. Both experiments and simulations reveal pronounced pH-dependent changes in the local environment surrounding the lipid ester linkage. At pH 4, strong electrostatic interactions between RNA and protonated MC3 produce broader spectral features consistent with increased interfacial heterogeneity and hydration.