Microcarrier-Guided Nanopore Dielectrophoresis for Selective Nucleic Acid Detection

Abstract

Dielectrophoresis (DEP) is the motion of a polarizable particle in a non-uniform electric field due to an unbalanced electrostatic force on the particle's induced dipole. The DEP mechanism has been extensively utilized for manipulation of biological particles, from cancer cells and viruses to biomolecules such as DNAs and proteins, for their concentration, separation, sorting, and transport. However, current DEP approaches to molecular manipulation are not selective, as DEP is not sensitive enough to discriminate among the induced dipoles of different molecules. Here we explore a novel single-molecule DEP mechanism, carrier-guided nanopore dielectrophoresis, for selective nucleic acid sequence detection. Rather than rely on a target's native polarizability, we designed a polycationic carrier to impart a tunable synthetic dipole to the target nucleic acid molecule; carrier sensitivity and selectivity are both programmable. Such synthetic dipoles can be captured in an engineered nanopore, which acts as an ideal foul-free point source to generate an extremely high field gradient (ΔE∼107 V·m-1 per nanometer or ∼1016 V·m-2) for molecular dipole manipulation. Non-target nucleic acids do not bind the carriers and hence are repelled from the pore by electrophoresis. To elucidate the mechanism of the dipole capture by the nanopore, we took an all-atom molecular dynamics (MD) simulation approach to observe the movements of and forces on the dipole. Simulation results predicted significantly increased force attracting the probe into the engineered nanopore as opposed to the wild type, consistent with the increased capture rates observed in experiment. Most strikingly of all, we find that a carrier with only a few positive charges can drive any length of DNA or RNA with equal capture efficiency. Development of nanopore dielectrophoretic detection thus offers ready medical applications of nanopore technology.