Evaluation of the interactions between oligonucleotides and small molecules by partial filling-nonequilibrium affinity capillary electrophoresis.

Recently, high-throughput analysis with minimal reagent consumption has been desired to assess interactions between drug candidates and disease-related oligonucleotides. To realize an ideal assay for drug screening, a rapid assay based on affinity capillary electrophoresis was generated to reduce the consumption of samples/reagents by a partial-filling technique under nonequilibrium conditions. In the proposed method, the first sample, oligonucleotide as a ligand, and second sample zones were injected into a capillary with spacers of background solution between the samples and oligonucleotide zones. After applying voltages, only the second sample zone passed through the partially filled oligonucleotide zone, resulting in variations in the peak parameters owing to this interaction. The electropherograms obtained were analyzed using equilibrium, reaction kinetics, and moment theories. In the interaction analyses between small molecules and DNA aptamers, only the small molecules binding to the aptamer showed significant changes in their peak heights and shapes. The estimated kinetic parameters were in good agreement with the reported values, indicating the applicability of the proposed method for drug screening. When interactions between drug candidates and disease-related RNAs were analyzed, one of the candidates showed remarkable variation in the peak parameters upon the addition of potassium ions. Consequently, the proposed method could be one of the ideal assays for drug screening.