Farajpour, N. | Search bioRxiv

bioRxiv2022

Exploring Capacitance and Non-Linear Electrokinetics in Nanopores Yields Insight into Single Molecule Recordings

The pervasive model for a solvated, ion-filled nanopore is often a resistor in parallel with a capacitor. However, for conical nanopore geometries, we propose the inclusion of a Warburg-like element which is necessary to explain otherwise anomalous observations such as negative capacitance and lowpass filtering of translocation events (i.e., a phenomenon we term Warburg filtering). The negative capacitance observed here is characterized as having long equilibration times and memory (i.e., mem-capacitance) at negative voltages. Next, we used the transient occlusion of the pore using {lambda}-DNA and 10-kbp DNA to test whether events are being attenuated by purely ionic phenomena even when there is sufficient amplifier bandwidth. The inclusion of the Warburg-like element is mechanistically linked to concentration polarization and the activation energy to generate and maintain localized concentration gradients. We conclude the study with a new interpretation of molecular translocations which is not simply based on the pulse-like resistance changes but rather a complex and non-linear storage of ions that changes during molecular transit.

biophysics↗

bioRxiv2020

The Origin of Conductive-Pulse Sensing Inside a Nanopore and the Role of Electro-Hydrodynamics

Nanopore sensing is nearly synonymous with resistive pulse sensing due to the characteristic reduction of ionic flux during molecular occupancy of a pore, particularly at high salt concentrations. However, conductive pulses are widely reported at low salt conditions wherein electroosmotic flow can be quite significant. Aside from transporting molecules like DNA, we investigated whether electroosmotic flow has other potential impacts on sensing attributes such current enhancements due to the analyte molecule. The overwhelming majority of literature reports counterions as the dominant mechanism of conductive events (a moleculecentric theory for conductive events). Conductive events are not well understood due to the complex interplay between (charged) nanopore walls, DNA grooves, ion mobility, and counterion clouds. Yet, the prevailing consensus of counterions being introduced into the pore by the molecule does not fit well with a growing number of experiments including the fact that proteins can generate conductive events despite having a heterogeneous surface charge. Herein, we demonstrate theory and experiments underpinning the translocation mechanism (i.e., electroosmosis or electrophoresis), pulse direction (i.e., conductive or resistive) and shape (e.g., monophasic or biphasic) through fine control of chemical, physical, and electronic parameters. Results from these studies predict strong electroosmosis plays a role in driving DNA events and generating conductive events due to polarization effects (i.e. a pore-centric theory). We believe these findings will stimulate a useful discussion on the nature of conductive events and their impact on molecular sensing in nanoscale pores.

biophysics↗