The investigation of protein-protein interactions (PPIs) and the preparation of antagonists are important for determining whether certain proteins are suitable medical targets. In the present study， we used the capillary electrophoresis-systematic evolution of ligands by exponential enrichment to generate natural and artificial nucleic acid aptamers targeting Ebola virus protein 24 (eVP24)， demonstrating that artificial aptamers， synthesised utilising a uridine analogue with an adenine residue at its C5 position， exhibited activities exceeding those of natural ones. To confirm the functionality of the as-prepared aptamers， their abilities to inhibit the PPIs of eVP24 were determined by capillary electrophoresis and bio-layer interferometry， and the obtained results unambiguously demonstrated that these aptamers interacted with the functional site of eVP24 and were thus good antagonists.