Nanopore Resistive Pulse Sensing with Multiple Alpha-Hemolysin Pores Improves the Detection Limit of Microrna

Abstract

The concentration profile of microRNAs in body fluids has been related to a variety of diseases, including specific cancers. By conjugation with a complementary DNA probe, specific miRNA species can be enumerated by nanopore resistive pulsing. This is possible because a miRNA-DNA probe duplex temporarily blocks a nanopore of ∼1.5 nm diameter, causing a decrease in the electrical current by displacing electrolyte ions. Under the influence of the electrophoretic driving force, the duplex dissociates after ∼10-1000 ms, and both the miRNA and the DNA molecules transit through the pore. The pore is now open again and can capture another duplex, with the frequency of the duplex pore translocations corresponding to the miRNA concentration in the solution. Biological porins are attractive because of their reproducible self-assembly, but the lipid bilayer matrix prevents the application of voltages >120 mV. It has previously been shown that the electrophoretic driving force can also be enhanced by an electrolyte concentration gradient of 0.5 / 4 M KCl, but few pulses were observed below 1 nM duplex concentration. Here, we demonstrate that the frequency can be further increased by incorporating multiple pores in the same bilayer. With an electrolyte gradient of 0.2 / 1 M KCl, it was possible to perform resistive pulse sensing with up to 100 alpha-hemolysin pores in an aperture-suspended DPhPC bilayer. We characterize the effect of electrolyte salt gradients on the stability of bilayer-incorporated alpha-hemolysin and quantify the resistive pulses for duplex concentrations in the range 0.01-100 nM. The achieved ∼10-fold increase in frequency, with respect to single-pore sensing with a 0.5 / 4 M KCl gradient, demonstrates the potential of multi-pore sensing to achieve miRNA detection at clinically relevant concentrations.