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

Journal name:
Nature Nanotechnology
Year published:
Published online


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


  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.


  1. Zhang, X., Ju, H. & Wang, J. Electrochemical Sensors, Biosensors and their Biomedical Applications (Elsevier, 2008).
  2. Venkatesan, B. M. & Bashir, R. Nanopore sensors for nucleic acid analysis. Nature Nanotech. 6, 615624 (2011).
  3. Tegenfeldt, J. O. et al. The dynamics of genomic-length DNA molecules in 100-nm channels. Proc. Natl Acad. Sci. USA 101, 1097910983 (2004).
  4. Pang, P., He, J., Park, J., Krstic, P. S. & Lindsay, S. Origin of giant ionic currents in carbon nanotube channels. ACS Nano 5, 72777283 (2011).
  5. Guan, W., Fan, R. & Reed, M. A. Field-effect reconfigurable nanofluidic ionic diodes. Nature Commun. 2, 506 (2011).
  6. Dekker, C. Solid-state nanopores. Nature Nanotech. 2, 209215 (2007).
  7. Healy, K. Nanopore-based single-molecule DNA analysis. Nanomedicine 2, 459481 (2007).
  8. Wanunu, M. & Meller, A. in Laboratory Manual on Single Molecules (eds Ha, T. & Selvin, P.) 395420 (Cold Spring Harbor Press, 2008).
  9. Wong, C. T. A. & Muthukumar, M. Polymer capture by electro-osmotic flow of oppositely charged nanopores. J. Chem. Phys. 126, 164903 (2007).
  10. He, Y., Tsutsui, M., Fan, C., Taniguchi, M. & Kawai, T. Controlling DNA translocation through gate modulation of nanopore wall surface charges. ACS Nano 5, 55095518 (2011).
  11. Kejian, D., Weimin, S., Haiyan, Z., Xianglei, P. & Honggang, H. Dependence of zeta potential on polyelectrolyte moving through a solid-state nanopore. Appl. Phys. Lett. 94, 014101 (2009).
  12. Van Dorp, S., Keyser, U. F., Dekker, N. H., Dekker, C. & Lemay, S. G. Origin of the electrophoretic force on DNA in solid-state nanopores. Nature Phys. 5, 347351 (2009).
  13. Firnkes, M., Pedone, D., Knezevic, J., Döblinger, M. & Rant, U. Electrically facilitated translocations of proteins through silicon nitride nanopores: conjoint and competitive action of diffusion, electrophoresis, and electroosmosis. Nano Lett. 10, 21622167 (2010).
  14. Iqbal, S. M. & Bashir, R. (eds) Nanopores, Sensing and Foundamental Biological Interactions (Springer, 2011).
  15. Wanunu, M., Morrison, W., Rabin, Y., Grosberg, A. Y. & Meller, A. Electrostatic focusing of unlabelled DNA into nanoscale pores using a salt gradient. Nature Nanotech. 5, 160165 (2010).
  16. Nam, S-W., Rooks, M. J., Kim, K-B. & Rossnagel, S. M. Ionic field effect transistors with sub-10 nm multiple nanopores. Nano Lett. 9, 20442048 (2009).
  17. Jiang, Z. & Stein, D. Charge regulation in nanopore ionic field-effect transistors. Phys. Rev. E 83, 031203 (2011).
  18. Keyser, U. F. et al. Nanopore tomography of a laser focus. Nano Lett. 5, 22532256 (2005).
  19. Svoboda, K. & Block, S. M. Biological applications of optical forces. Annu. Rev. Biophys. Biomol. Struct. 23, 247285 (1994).
  20. Peterman, E. J. G., Gittes, F. & Schmidt, C. F. Laser-induced heating in optical traps. Biophys. J. 84, 13081316 (2003).
  21. Beamish, E., Kwok, H., Tabard-Cossa, V. & Godin, M. Precise control of the size and noise of solid-state nanopores using high electric fields. Nanotechnology 23, 405301 (2012).
  22. Talaga, D. S. & Li, J. Single-molecule protein unfolding in solid state nanopores. J. Am. Chem. Soc. 131, 92879297 (2009).
  23. Yusko, E. C. et al. Controlling protein translocation through nanopores with bio-inspired fluid walls. Nature Nanotech. 6, 253260 (2011).
  24. Plesa, C. et al. Fast translocation of proteins through solid state nanopores. Nano Lett. 13, 658663 (2013).
  25. Welchman, R. L., Gordon, C. & Mayer, R. J. Ubiquitin and ubiquitin-like proteins as multifunctional signals. Nature Rev. Mol. Cell. Biol. 6, 599609 (2005).
  26. Wanunu, M., Sutin, J., McNally, B., Chow, A. & Meller, A. DNA translocation governed by interactions with solid state nanopores. Biophys. J. 95, 47164725 (2008).
  27. Soni, G. V. & Dekker, C. Detection of nucleosomal substructures using solid-state nanopores. Nano Lett. 12, 31803186 (2012).
  28. Raillon, C. et al. Nanopore detection of single molecule RNAP–DNA transcription complex. Nano Lett. 12, 11571164 (2012).
  29. Ho, C. et al. Electrolytic transport through a synthetic nanometer-diameter pore. Proc. Natl Acad. Sci. USA 102, 1044510450 (2005).
  30. Hoogerheide, D. P., Garaj, S. & Golovchenko, J. A. Probing surface charge fluctuations with solid-state nanopores. Phys. Rev. Lett. 102, 256804 (2009).
  31. Smeets, R. et al. Salt dependence of ion transport and DNA translocation through solid-state nanopores. Nano Lett. 6, 8995 (2006).
  32. Chen, Y., Ni, Z. & Wang, G. Electroosmotic flow in nanotubes with high surface charge densities. Nano Lett. 8, 4248 (2008).
  33. Plecis, A., Schoch, R. B. & Renaud, P. Ionic transport phenomena in nanofluidics: experimental and theoretical study of the exclusion-enrichment effect on a chip. Nano Lett. 5, 11471155 (2005).
  34. He, Y., Tsutsui, M., Fan, C., Taniguchi, M. & Kawai, T. Gate manipulation of DNA capture into nanopores. ACS Nano 5, 83918397 (2011).
  35. Behrens, S. H. & Grier, D. G. The charge of glass and silica surfaces. J. Chem. Phys. 115, 67166721 (2001).
  36. Wu, M. et al. Control of shape and material composition of solid-state nanopores. Nano Lett. 9, 479484 (2009).
  37. Deshpande, S. V. & Gulari, E. Optical properties of silicon nitride films deposited by hot filament chemical vapor deposition. J. Appl. Phys. 77, 65346541 (1995).
  38. Moustakas, T. D. The role of extended defects on the performance of optoelectronic devices in nitride semiconductors. Phys. Status Solidi (a) 210, 169174 (2012).
  39. Robertson, J., Warren, W. L. & Kanicki, J. Nature of the Si and N dangling bonds in silicon nitride. J. Non-Cryst. Solids 187, 297300 (1995).
  40. Robertson, J. & Powell, M. J. Gap states in silicon nitride. Appl. Phys. Lett. 44, 415417 (1984).
  41. Singh, R., Molnar, R. J., Unlu, M. S. & Moustakas, T. D. Intensity dependence of photoluminescence in gallium nitride thin films. Appl. Phys. Lett. 64, 336338 (1994).
  42. Wu, M. Y., Krapf, D., Zandbergen, M., Zandbergen, H. & Batson, P. E. Formation of nanopores in a SiN/SiO2 membrane with an electron beam. Appl. Phys. Lett. 87, 113106 (2005).
  43. Venkatesan, B. M., Shah, A. B., Zuo, J-M. & Bashir, R. DNA sensing using nanocrystalline surface-enhanced Al2O3 nanopore sensors. Adv. Funct. Mater. 20, 12661275 (2010).
  44. Anderson, B. N., Muthukumar, M. & Meller, A. pH tuning of DNA translocation time through organically functionalized nanopores. ACS Nano 7, 14081414 (2013).
  45. Fologea, D., Uplinger, J., Thomas, B., McNabb, D. S. & Li, J. Slowing DNA translocation in a solid-state nanopore. Nano Lett. 5, 17341737 (2005).
  46. Kowalczyk, S. W., Wells, D. B., Aksimentiev, A. & Dekker, C. Slowing down DNA translocation through a nanopore in lithium chloride. Nano Lett. 12, 10381044 (2012).
  47. Singer, A., Rapireddy, S., Ly, D. H. & Meller, A. Electronic barcoding of a viral gene at the single-molecule level. Nano Lett. 12, 17221728 (2012).
  48. Shim, J. et al. Detection and quantification of methylation in DNA using solid-state nanopores. Sci. Rep. 3, 1389 (2013).
  49. Wanunu, M. et al. Discrimination of methylcytosine from hydroxymethylcytosine in DNA molecules. J. Am. Chem. Soc. 133, 486492 (2011).

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Author information


  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


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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