Sizing DNA using a nanometer-diameter pore

Abstract

Each species from bacteria to human has a distinct genetic fingerprint. Therefore, a mechanism that detects a single molecule of DNA represents the ultimate analytical tool. As a first step in the development of such a tool, we have explored using a nanometer-diameter pore, sputtered in a nanometer-thick inorganic membrane with a tightly focused electron beam, as a transducer that detects single molecules of DNA and produces an electrical signature of the structure. When an electric field is applied across the membrane, a DNA molecule immersed in electrolyte is attracted to the pore, blocks the current through it, and eventually translocates across the membrane as verified unequivocally by gel electrophoresis. The relationship between DNA translocation and blocking current has been established through molecular dynamics simulations. By measuring the duration and magnitude of the blocking current transient, we can discriminate single-stranded from double-stranded DNA and resolve the length of the polymer.

FIGURE 1

Characterization of nanopore and translocation of DNA. The top inset in panel a is a TEM image of a nanopore (slightly out of focus to exaggerate the pore) in a nominally 10-nm-thick nitride membrane viewed at 0° tilt angle. The apparent radius of the pore is R_p = 0.5 ± 0.1 nm. The bottom inset is a schematic representation of the structure inferred from tilted TEM images of similar pores. The current-voltage characteristic of the nanopore is approximately linear. Panel a is a measurement of the I-V characteristic obtained in 1 M KCl, corresponding to the nanopore shown in the inset. The fit through the data (red dashed line) has a slope of 0.63 ± 0.03 nS. When DNA is inserted at the negative electrode, transients are observed in the ionic current through the nanopore associated with a blockade by DNA. Panel b shows the current through the same nanopore as a continuous function of time with 50-mer poly(dT) ssDNA inserted at the negative electrode (blue) and without it (red). Corresponding to the observation of transients, DNA is found at the positive electrode. Panel c illustrates the variety of transients observed in the same pore for an applied voltage of 200 mV (i–iii) and 500 mV (iv); all plot on the same linear scale, but each transient has been offset for clarity. The blocking current is observed to vary during the transient and from transient to transient as well. The width of the transients ranges from the bandwidth-limited 100 μs to 10 ms.

FIGURE 2

Verification of the translocation of DNA through the nanopore. Transients are observed in the ionic current through the nanopore that we associate with a blockade by DNA. The figure shows the current measured through the nanopore of Fig. 1, as a continuous function of time with 58-mer ssDNA inserted at the negative electrode (blue). Notice that a 24-s interval, which did not contain any transients above the noise level, was deleted from the trace to economically represent the data. The inset shows the results of gel electrophoresis on amplified 58-mer ssDNA found at the positive electrode, (+)58 mer, and at the negative electrode, (−)58 mer, along with a control with no DNA and 100-bp ladder for calibration of the polymer length. We unambiguously observe 58 mer at the positive electrode, which indicates that ssDNA has translocated through a R_p = 0.5 nm pore.

FIGURE 3

Deconvolution of the impulse response from a current transient. The figure shows an example of a measured current transient (i) obtained when 100-bp dsDNA (electrophoretically driven with 200 mV DC applied at the Ag-AgCl electrodes) interacts with a R_p = 1.75 ± 0.1 nm pore. Superimposed on a measured trace are two deconvolved signals obtained using an impulse response associated with (ii) a negatively charged Undecagold electrophoretically driven with a 200-mV DC applied at the Ag-AgCl electrodes and (iii) a 4-μs 200-mV pulse. Generally, the shape of the transient is preserved.

FIGURE 4

Sorting DNA with nanopore. Transients are observed in the ionic current through the nanopore associated with a blockade by the DNA. Panel a is a histogram showing the frequency of occurrence of transients with a particular width that develops when a 0.5-nm radius pore in a 10-nm thick Si₃N₄ membrane interacts with 50-mer ssDNA (polydT) (blue) and 50-bp dsDNA (red) under a 200-mV bias voltage. Both distributions have the same total number of events, but at least two peaks are apparent in the blue distribution with most probable transients at 150 μs and 1.4 ms. The long-duration high-percentage blocking current transients are associated with translocations across the membrane through the nanopore. The inset shows the percentage blocking current versus the transient width. Notice that ssDNA can be discriminated from dsDNA using the long-duration transients. Panel b is a histogram showing the frequency of occurrence of transients with a particular width that develops when a 1.2 ± 0.1 nm radius pore in a 30-nm thick Si₃N₄ membrane interacts with 100-bp (green), 600-bp (red), and 1500-bp (blue) dsDNA under a 200-mV bias voltage. At least two peaks are apparent in the blue distribution with a most probable transient at 210 μs and 1.65 ms. The long duration transients can be used to differentiate different length polymers.

FIGURE 5

Molecular dynamic simulations of a translocation. Simulations of the ion current through a nanopore in a silicon nitride membrane reveal that the current is substantially blocked as the molecule translocates through the pore. Panel a shows the ion current and DNA displacement obtained from a simulation in which the axis of the molecule is aligned with the pore axis. The vertical dashed line indicates the time at which the DNA molecule is introduced into the system. The open pore current (in the absence of a DNA molecule) is indicated by the horizontal dashed line. The electric field is 1.4 V/5.2 nm, which is 14× larger than that used in the experiments to economize on simulation time. Notice that the duration of the translocation in panel a is only ∼45 ns, and it ends with a positive current spike above the open pore current. The system configurations at 12 ns and 40 ns are indicated in the insets. Panel b shows the results of a simulation of the current through the same pore at the same field, but now the molecule is straddling the pore, lying along the membrane. Notice that the blocking current is ∼80% of the open pore current even though the molecule is not in the pore.

FIGURE 6

Voltage dependence of the current transient. A histogram showing the voltage dependence of the transients found in the electrolytic current through the 1-nm pore shown in Fig. 1 a. The same number of events was recorded for each voltage, but frequency of long-duration >1-ms events increase as the voltage increases.