Ionic Strength and Hybridization Position near Gold Electrodes Can Significantly Improve Kinetics in DNA-Based Electrochemical Sensors

A variety of electrochemical (EC) biosensors play critical roles in disease diagnostics. More recently, DNA-based EC sensors have been established as promising for detecting a wide range of analyte classes. Since most of these sensors rely on the high specificity of DNA hybridization for analyte binding or structural control, it is crucial to understand the kinetics of hybridization at the electrode surface. In this work, we have used methylene blue-labeled DNA strands to monitor the kinetics of DNA hybridization at the electrode surface with square-wave voltammetry. By varying the position of the double-stranded DNA segment relative to the electrode surface as well as the bulk solution's ionic strength (0.125-1.00 M), we observed significant interferences with DNA hybridization closer to the surface, with more substantial interference at lower ionic strength. As a demonstration of the effect, toehold-mediated strand displacement reactions were slowed and diminished close to the surface, while strategic placement of the DNA binding site improved reaction rates and yields. This work manifests that both the salt concentration and DNA hybridization site relative to the electrode are important factors to consider when designing DNA-based EC sensors that measure hybridization directly at the electrode surface.

Automated summary

A variety of EC biosensors are critical in disease diagnostics, with DNA-based EC sensors showing promise in detecting different analyte classes. This study used methylene blue-labeled DNA strands to monitor the kinetics of DNA hybridization at the electrode surface. By varying the position of the DNA segment relative to the electrode surface and the ionic strength of the solution, interference with DNA hybridization was observed closer to the surface, with greater interference at lower ionic strength. This work highlights the importance of salt concentration and DNA hybridization site in designing DNA-based EC sensors that directly measure hybridization at the electrode surface.