Abstract: An assessment method of the interaction between cytochrome c (Cyt c) selected as a representative basic protein and three lengths of single strain deoxyribonucleic acid (ssDNA) pools was presented based on capillary electrophoresis. The investigation of ionic strength effect on the interaction was made. The interactions between Cyt c and the ssDNA pools with 20 nt, 40 nt and 60 nt random sequences were compared by capillary zone electrophoresis (CZE) based on an uncoated fused capillary and a coated capillary. Using the uncoated fused capillary, the interaction difference could not be observed due to the strong adsorption of Cyt c on the inner surface of the capillary. However, under negative potential with the assistance of pressure driving, the peak area change of free ssDNA indicated the interaction difference of the three pools with Cyt c using the coated capillary, and the results showed that the ssDNA pool with 20 nt random sequence exhibited the strongest interaction. In addition, NaCl concentration had great effect on the interaction of Cyt c with ssDNA60, and 0.02 mol/L NaCl solution was favored. For the selection of basic target proteins, the adjustment of salt concentration would inhibit the non-specific electrostatic interaction, improve the selection efficiency of a selection round. The favorable salt concentration could be optimized with an uncoated fused capillary by comparing the peak area change of the complex and free ssDNA pool.

Key words: aptamer, basic protein, cytochrome c, ssDNA pool, capillary electrophoresis （CE）