Electrochemical Confinement Effects for Innovating New Nanopore Sensing Mechanisms

Abstract

By mimicking confined pore-forming proteins in nature, the development of nanopores offers opportunities to explore a variety of dynamic processes in a confined space at a single-molecule level. In general, the nanopore positions in between two electrolyte solutions act as the only connection for mass transfer. [4][5][6] The application of an electric potential difference via two Ag/ AgCl electrodes generates an ionic current that drives individual biomolecule into the pore. If the internal dimensions of the nanopore are comparable to those of single target molecules, the transient stay of each individual mole cule in the confined nanopores will block the ionic current flow through the pore. Such a dynamic action leads to a blockage current, which is called the volume-exclusion effect. In this process, strong nanopore-analyte interactions are required to convert transient single-molecule actions into detectable ionic signals, [7][8][9] which can therefore reflect the key structural information of analytes, such as size, shape, and conformation. Taking this feature, nanopores act as a promising sensor to evaluate ssDNA with a single base difference, [10][11][12][13] discriminate the recognitions between different targets, [6,7,[14][15][16][17] study the unfolding mechanism of peptides, [18][19][20] peer into enzymology [21,22] at the single-molecule level, etc. [23] Broadly speaking, nanopores are divided into biological and solid-state ones. Although biological nanopores provide a well-defined constriction, they are accessible to limited kinds of molecules due to their fixed pore geometry. Moreover, the nonuniform charge distribution inside the nanopore attributed to the undesirable high energy barrier prevents the entrance of certain analytes. For example, aerolysin nanopore with a positive charged interior of ≈1.0 nm exhibits a preference for the ultrasensitive detection of negatively charged short oligonucleotide rather than the positively charged proteins. [24][25][26][27] With regard to solid-state nanopores, a rapid and in situ fabrication method such the dielectric-breakdown technique makes it more feasible to become a general method for single-molecule analysis. [28][29][30][31][32] To enhance the sensitivity and efficiency of solid-state nanopore analysis, quite a few different sensing mechanisms have been proposed, including tunneling measurement, [33,34] the modulation of electrophoresis and electro-osmosis, [35,36] Nanopores employ a confined space for electrochemical sensing of highthroughput individual biomolecules in solution. Tremendous research efforts over the last two decades have made nanopore techniques become a powerful single-molecule tool in nanotechnology and biotechnology. The most general mechanism of nanopore sensing is based on a volumeexclusion effect. However, the increasing demands on revealing the singlemolecule chemistry and biophysics require that nanopores not only provide structural/conformational/sequencing information but also directly read the dynamic functional properties ...

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