Effective charge of RNA in a fully packaged viral particle

Electrostatic interactions govern viral genome packaging, where long nucleic acid macromolecules compact into nanometer-sized capsids via counter-ion condensation that screens the genome charge. Experimental measurements of the effective charge of viral particles remain challenging due to coupling of the electrophoretic and hydrodynamic forces. The application of the electric field induces electro-osmotic flows through displacement of mobile counterions. The flow in turn produces a hydrodynamic drag on the virion, affecting its electrophoretic mobility. Using all-atom molecular dynamics simulations, we have characterized the electrophoretic mobility and the effective charge of bacteriophage MS2 containing a 3569-nucleotide RNA genome within its icosahedral capsid. Non-equilibrium simulations under an applied electric field or external force revealed that mature MS2 virions possess an effective charge of ~2.5% its total genome charge, whereas the empty capsid is effectively charge-neutral. Additionally, the structural integrity of the virus is compromised under a 2V voltage differential, leading to capsid rupture and genome ejection. Our work thus provides a computational framework for quantifying the effects of ion condensation on electrophoretic mobility of viral particles, with implications for single-virion characterization, and guiding design and purification of drug-loaded capsids for therapeutic applications.