Measuring Practical Reversibility of Surface-Bound DNA for Mechanistic Insight into Folding-Based Sensors

In this paper, we characterize the mass-transport-limited response of surface-tethered redox moieties via flexible DNA linkers using measured voltammetric peak current and peak potential splitting. We demonstrate that peak splitting can be used to differentiate between reversible, quasi-reversible, and irreversible electrochemical regimes of the tethered redox molecule. Interestingly, the transition from one regime to another is dependent on the length and structure of the DNA probe. For example, as the probe length increases the transition from reversible to quasi-reversible occurs at lower scan rates. Additionally, we directly compare the dependence of the peak splitting and peak current as a function of scan rate for ssDNA, dsDNA, and other structured nucleic acids such as stem-loop and pseudoknot probes. Lastly, we find that by interrogating our surfaces with cyclic voltammetry we can observe quantitative differences in the peak splitting once the aptamer is in a bound state and correlate this to the extent of conformational change the sequence undergoes. The observations reported herein are consistent with the postulation that signaling in this class of sensor architectures is dictated by changes in nucleic acid structure and flexibility, which controls the mass transfer rate of the redox probe to the surface of the electrode.