Optoelectronic control of surface charge and translocation dynamics in solid-state nanopores

Journal name:
Nature Nanotechnology
Volume:
8,
Pages:
946–951
Year published:
DOI:
doi:10.1038/nnano.2013.221
Received
Accepted
Published online

Abstract

Nanopores can be used to detect and analyse biomolecules. However, controlling the translocation speed of molecules through a pore is difficult, which limits the wider application of these sensors. Here, we show that low-power visible light can be used to control surface charge in solid-state nanopores and can influence the translocation dynamics of DNA and proteins. We find that laser light precisely focused at a nanopore can induce reversible negative surface charge densities as high as 1 C m−2, and that the effect is tunable on submillisecond timescales by adjusting the photon density. By modulating the surface charge, we can control the amount of electroosmotic flow through the nanopore, which affects the speed of translocating biomolecules. In particular, a few milliwatts of green light can reduce the translocation speed of double-stranded DNA by more than an order of magnitude and the translocation speed of small globular proteins such as ubiquitin by more than two orders of magnitude. The laser light can also be used to unclog blocked pores. Finally, we discuss a mechanism to account for the observed optoelectronic phenomenon.

At a glance

Figures

  1. The photoconductive effect in solid-state nanopores.
    Figure 1: The photoconductive effect in solid-state nanopores.

    a, Cartoon illustrating the optical nanopore set-up. A solid-state nanopore is positioned at a laser beam focus by a nanopositioner, and the ion current flowing through the pore is measured before and during translocation of DNA molecules. Inset: high-resolution transmission electron micrographs of a typical pore (diameter, 10 nm). b, Left: surface plot showing nanopore ionic current enhancement as a 10 mW focused laser beam (λ = 532 nm) scans the 4 × 4 µm2 SiN membrane at 1 µm s−1. When the focused beam reaches the nanopore it produces a significant increase in measured current (2.4-fold increase for this pore). Right: line profile through y = 0, fitted using a Gaussian function with a FWHM of ~500 nm, consistent with the diffraction limit. c, Clearing a blocked solid-state nanopore with light. Left: a 5 mW laser intensity raster scan of the entire SiN window (30 × 30 µm2, lower left to top right). The colour map represents the current flowing through the pore at ΔV = 300 mV. As soon as the laser beam overlaps with the nanopore location, it clears the pore and, thereafter, the ionic current stabilizes at the open-pore level of 12 nA. Right: time trace of I during the laser scan.

  2. Slowing down DNA and protein translocation speed with light.
    Figure 2: Slowing down DNA and protein translocation speed with light.

    a, Representative translocation events with and without illumination, showing the increase in IO, IB and tD. b, Time traces showing the open-pore current IO, the blocked current amplitude ΔI (top panel) and the mean translocation time left fencetDright fence (lower panel). The net effect of the laser illumination is to increase IO and tD while keeping ΔI constant. All data points in left fencetDright fence represent a running average over 150 translocation events, initialized at the moment the laser is switched on/off. RF is defined as the mean tD in light divided by the mean tD in darkness. In this example, a factor of ~10 is obtained with P = 2 mW. c, Detection of the small-molecular-weight protein ubiquitin in its native state using a 5 nm nanopore, enabled by illumination of the chip with laser light. Typical translocation time traces are shown at P = 0 (red) and P = 4 mW (blue). With P = 4 mW we observe at least two orders of magnitude increase in the dwell times of the events. A typical translocation time distribution and fractional blockade current (IB) of the ubiquitin under 4 mW of focused light are shown at the bottom (N > 500). Under these conditions, we typically observe two prominent timescales for ubiquitin translocation (340 ± 5 µs and 890 ± 70 µs), as well as two peaks in the blockade currents (0.88 and 0.78), approximated by a sum of two Gaussians (red lines). Inset: cartoon of the crystallographic structure of wild-type human ubiquitin (PDB 1d3z).

  3. Ionic current enhancement as a function of laser power and pore diameter.
    Figure 3: Ionic current enhancement as a function of laser power and pore diameter.

    a, Plots of ionic current enhancement I(P)/I(0) as a function of laser power for 5, 10, 15 and 20 nm diameter pores, as indicated. b, Pore response to light, δI/δP, obtained from linear fits to plots of I(P), as a function of pore diameter. The dependence on pore size of the current enhancement shown in a and the pore response to light shown in b suggest that the origin of the photoconductance effect arises from the surface of the pore (that is, the pore walls) and not its volumetric content.

  4. Light-induced surface charge density modulates the EOF and DNA translocation speed.
    Figure 4: Light-induced surface charge density modulates the EOF and DNA translocation speed.

    a, Cartoons showing the bulk and surface ionic current terms discussed in the text, and the origin of the EOF acting to retard the DNA translocation for the same nanopore in darkness (left) and under laser illumination (right). Here, Isurface = IDL + IEOF (equation (1)). b, Left: RF as a function of laser intensity measured for different nanopore sizes, 4.3, 5.4, 5.6, 6.1 and 7.4 nm and DNA lengths, 400 bp, 3.5 kbp, 5 kbp and 10 kbp. Each data point was calculated from at least 1,000 events per laser intensity. Right: RF as a function of nanopore surface charge density calculated using the open-pore current versus laser intensity for each pore (equations (2)). Remarkably, all data points collapse onto a single curve, regardless of DNA length or nanopore diameter.

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Author information

Affiliations

  1. Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA

    • Nicolas Di Fiori,
    • Allison Squires &
    • Amit Meller
  2. Department of Biomedical Engineering, The Technion – Israel Institute of Technology, Haifa, Israel 32000

    • Daniel Bar,
    • Tal Gilboa &
    • Amit Meller
  3. Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, USA

    • Theodore D. Moustakas

Contributions

N.D.F. and A.M. conceived and designed the experiments. N.D.F., D.B. and T.G. performed the experiments. A.S. drilled all pores. N.D.F., A.S., D.B., T.G. and A.M. analysed the data. N.D.F., T.D.M. and A.M. developed the model. N.D.F., A.S., D.B., T.G., T.D.M. and A.M. co-wrote the paper.

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The authors declare no competing financial interests.

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