Mechanical Trapping of DNA in a Double-Nanopore System
Nanopores have become ubiquitous components of systems for single-molecule manipulation and detection, in particular DNA sequencing where electric field driven translocation of DNA through a nanopore is used to read out the DNA molecule. Here, we present a double-pore system where two nanopores are drilled in parallel through the same solid-state membrane, which offers new opportunities for DNA manipulation. Our experiments and molecular dynamics simulations show that simultaneous electrophoretic capture of a DNA molecule by the two nanopores mechanically traps the molecule, increasing its residence time within the nanopores by orders of magnitude. Remarkably, by using two unequal-sized nanopores, the pore of DNA entry and exit can be discerned from the ionic current blockades, and the translocation direction can be precisely controlled by small differences in the effective force applied to DNA. The mechanical arrest of DNA translocation using a double-pore system can be straightforwardly integrated into any solid-state nanopore platform, including those using optical or transverse-current readouts.
Coarse-grained molecular dynamics simulations of a single-pore DNA translocation event in a double-pore system. The simulation was carried out at a transmembrane bias of 125 mV. The P and B beads of DNA are shown as orange and pink spheres, respectively.
Coarse-grained molecular dynamics simulation of mechanical trapping of DNA in a double-pore system. The simulation was carried out at a transmembrane bias of 125 mV. The P and B beads of DNA are shown as orange and pink spheres, respectively. The DNA is seem captured simultaneously by two pores during the translocation process.
Ensemble of DNA conformations observed during coarse-grained MD simulations of DNA translocation in a double-pore system. Shown in grey are the 2000 instantaneous conformations of DNA overlaid with each other. The DNA molecules simultaneously captured by the two pores are highlighted using a darker shade of grey. The color contours specify the density of the CG beads computed from the position of beads projected onto the XZ plane, over a 1 nm2 grid.