Application of a bipolar nanopore as a sensor: rectification as an additional device function

Abstract

We model and simulate a nanopore sensor that selectively binds analyte ions. This binding leads to the modulation of the local concentrations of the ions of the background electrolyte (KCl), and, thus, to the modulation of the ionic current flowing through the pore. The nanopore's wall carries a bipolar charge pattern with a larger positive buffer region determining the anions as the main charge carriers and the smaller negative binding region containing binding sites. This charge pattern proved to be an appropriate one as shown by a previous comparative study of varying charge patterns (Mádai et al. J. Mol. Liq., 2019, 283, 391-398.). Binding of the positive analyte ions attracts more anions in the pore thus increasing the current. The asymmetric nature of the pore results in an additional device function, rectification. Our model, therefore, is a dual response device. Using a reduced model of the nanopore studied by a hybrid computer simulation method (Local Equilibrium Monte Carlo coupled to the Nernst-Planck equation) we show that we can create a sensor whose underlying mechanisms are based on the changes of the local electric field as a response to changing thermodynamic conditions. The change of the electric field results in changes in the local ionic concentrations (depletion zones), and, thus, changes in ionic currents.

Cryo-EM structure of the octameric pore of Clostridium perfringens β-toxin

“…Our PMF profiles indicate that the NBP should constitute an energy barrier for cations while the transmembrane barrel has the opposite effect. The asymmetric, bipolar, nature of the CPB channel surface charge is a unique feature, which has not been observed to other hemolysin pores (Madai et al , 2019). This peculiar charge distribution could results in an increased flux of cations due to binding of anions to the NBP which could also explain the very low LD50 of CPB compared to other hemolysin pores.…”

Rectification of bipolar nanopores in multivalent electrolytes: effect of charge inversion and strong ionic correlations

“…In our nanopore studies, we always tended to define quantities of unit dimensions put together from current values. [28,30,29,31,35,33,32] We called these quantities device functions. In the case of a bipolar nanopore studied here, the trivial device function is rectification that is defined as I ON /I OFF , where the absolute values of the total currents in the forward-and reverse-biased states are denoted by I ON and I OFF respectively (the OFF-state current is negative).…”

“…[55,56] LEMC has successfully described transport through membranes [55,57], calcium channels, [56,58] bipolar nanopores [30,28,59,32], transistors [31,34], and sensors. [29,33,35] Poisson-Nernst-Planck theory…”

“…[25] In that system, the principal device function is selectivity. Here, as in our previous studies, [28,29,30,31,32,33,34,35,36] by device function we mean (often dimensionless) quantities that are put together from output signals of the device, which are ionic currents in the case of nanopores. Selectivity, for example, can be defined as I i /I, where I i is the ionic current carried by ionic species i and I is the total current.…”

Bipolar Nanochannels: A Systematic Approach to Asymmetric Problems

“…In biosensing, protein adsorption onto the channel surface neutralizes the surface charge density, which in turn changes the response . Other mechanisms that can vary the surface charge (including switching the sign of the charge) include pH regulation, , multivalent ion interactions with the surface, , and selective binding molecules attached to the surface. − …”