Real-time study of a DNA strand displacement reaction using dual polarization interferometry

A DNA strand displacement reaction on a solid-liquid interface was investigated using dual polarization interferometry. This effective analytical technique allows the real-time, simultaneous determination of the thickness, density, and mass of a biological layer. The displacement process was examined, and the changes in thickness, density, and mass were determined. Injection of the displacement DNA resulted in an increase in density and a decrease in mass and thickness, which indicated that a portion of the target DNA was displaced from the double-stranded DNA (dsDNA). The effects of the displacement DNA concentration and toehold length on the displacement efficiency were also examined. Increasing the displacement DNA concentration and the toehold length increased the changes in mass and the displacement efficiency. At the concentration of 0.2 μM, the toeholds with 4, 5, 6, and 7 bases had displacement percentages of 24.54%, 25.99%, 30.16%, and 70.41%, respectively. At displacement DNA concentrations exceeding that of the dsDNA, the displacement percentage was not concentration-dependent. Above a certain concentration, the percentage remained stable with increasing concentration. Comparison using different toehold sequences showed that the displacement efficiency increases with increasing bonding force between the base pairs.