Mechanical Trapping of DNA in a Double-Nanopore System

Abstract

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 read-outs.

Controlling DNA Tug‐of‐War in a Dual Nanopore Device

“…Interpore distances for devices used in this paper are all less than 0.8 µm (Supporting Information). Note that the probability of dual‐pore cocapture in our devices in the absence of active control is very low, comparable to the capture probabilities observed by Pud et al . For devices with pore‐to‐pore spacing greater than 500 nm and pore diameters comparable to the diameters used here the cocapture probability in the absence of active control does not exceed 0.35% …”

“…The FPGA logic adjusts the voltage bias applied at the pores in response to triggers arising from sensing DNA translocation at pore 1 and pore 2. The active logic can catch molecules in the act of crossing between the two pores, reversing the bias at one pore so that the molecule is caught in a tug‐of‐war ( Figure ) . The active logic greatly increases the number of molecules that are caught in a tug‐of‐war state, from ≈0.1% in our previous study (for a similar device without active control) to 76.8% here.…”

“…Previous two‐pore approaches that lack active control fail to achieve a combination of high two‐pore cocapture rate and significant translocation slow‐down during two‐pore cocapture. While the method reported by Pud et al achieves a significant slowing down of DNA translocation speed (with trapping times in the two pores of up to 10 s, for pore diameters of 10 nm and pore‐to‐pore spacing of 280 nm), this method lacks a consistent way of capturing a single molecule in the two‐pore architecture, leading to a very low two‐pore event rate (0.5% of the total events). The double‐barreled glass pipette architecture reported by Cadinu et al does increase the two‐pore capture rate to a maximum of around 60% for λ‐DNA, likely due to the very small pore‐to‐pore spacing used in this device (pore diameter and a pore‐to‐pore spacing of 20 nm).…”

“…In addition, for large diameter (>5 nm) pores that enable efficient capture of long (>10 kbp) DNA, the occurrence of folds during translocation greatly reduces the number of usable events featuring a linear correspondence between translocation time and sequence position . Recently, a new class of “two‐pore” devices has been developed that enables simultaneous capture of a single DNA molecule by two closely spaced pores . Two‐pore devices, in principle, enable independent control of the DNA sensing bias and the bias driving DNA translocation.…”

Nanopore Sensing of Protein Folding

“…A similar model was previously used to predict ionic current blockades produced by DNA in a double nanopore system. 61 …”