The equilibrium partition coefficient of fluorescently labeled dextrans with molecular masses from 10 to 70 kDa and of two fluorescently labeled proteins was measured for anionic and cationic polyacrylamide gels with 5% bisacrylamide cross-linking. The gels were synthesized using 2-acrylamido-2-methylpropanesulfonic acid and (3-(methacryloylamino)propyl)trimethylammonium chloride monomers within fused silica capillaries with a square section. Partition coefficients were obtained by measuring the fluorescence intensity in the gel-filled capillaries equilibrated with dilute solutions of each probe. The partition coefficients show an exponential decay with gel concentration in agreement with the Ogston model for partitioning in fibrous gels. Comparison of the data for 10 kDa dextran with this model yields fiber radii of 0.79 and 0.99 nm for the anionic and the cationic gels, respectively, which are similar in magnitude to values reported in the literature for neutral polyacrylamide gels. Mesh sizes calculated on the basis of a single-pore-radius model vary between about 11 and about 6 nm for gels with gel concentrations between 0.1 and 0.26 g/cm(3). Predictions of the dependence of the partition coefficient on the size of the solute based on the Ogston model are, however, only approximate. Better predictions are obtained with an empirical fit based on a model that considers the flexibility of the polymer chains.