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Capillary electrophoresis is a well-documented separation technique offering rapid, automated analyses with low-sample volume requirements and broad applicability to biological and inorganic analytes. Here it serves as a platform to investigate the binding affinity between small molecules and bovine serum albumin. It is also used to characterize the surface properties of surface-modified polystyrene particles, including the zeta potential and surface conductance. In both instances, the electrophoretic mobility of the analytes is prioritized through passivation of the surface silanols of the fused silica capillary, which suppresses electroosmotic flow. For the affinity studies, suppression of electroosmotic flow allows for the separation of multiple ligands based on differences in their electrophoretic mobility. The ligands then interact sequentially with the target in-capillary. The result is a versatile screening assay which can potentially be used to investigate competitive binding or combinatorial analyses involving multiple targets and ligands. In particle surface characterization studies, suppression of electroosmotic flow reduces a significant source of variability allowing for more accurate and precise measurements. These measurements serve as a basis for predicting the behavior of the particles when analyzed with a miniaturized dielectrophoresis chip containing patterned quadrupole electrodes. This allows for a rapid optimization of the conditions required to separate particles with different surface functionalities via dielectrophoresis. Changes in surface conductance resulting from the introduction of biotinylated ligands to streptavidin-modified particles are also investigated.