The permeability of liquid crystal templated ZnS mesoporous hollow spheres is programmed and investigated with molecular probes. Pore size programming was achieved by swelling of the hydrophobic regions of the lyotropic liquid crystal used to template the mesoporous shell. Small angle X-ray scattering and transmission electron microscopy confirm that the mesopore diameter can be tuned between 2.5 and 4.1 nm. Predictions of the mesopore permeability of ssDNA from Flory scaling theory inspire the selection of fluorescently tagged ssDNA probes. Short ssDNA strands were found to easily penetrate the mesoporous shell, while large strands were excluded. Intermediate length ssDNA strands were able to penetrate shells with 4.1 nm mesopores, while being sterically excluded from 2.5 nm mesopores.