Abstract
Solid-state nanopore technology presents an emerging single-molecule-based analytical tool for the separation and analysis of nanoparticles. Different approaches have been pursued to attain the anticipated detection performance. Here, we report the rectification behaviour of protein translocation through silicon-based truncated pyramidal nanopores. When the size of translocating proteins is comparable to the smallest physical constriction of the nanopore, the frequency of translocation events observed is lower for proteins that travel from the larger to the small opening of the nanopore than for those that travel in the reverse direction. When the proteins are appreciably smaller than the nanopore, an opposite rectification in the frequency of translocation events is evident. The maximum rectification factor achieved is around ten. Numerical simulations reveal the formation of an electro-osmotic vortex in such asymmetric nanopores. The vortex–protein interaction is found to play a decisive role in rectifying the translocation in terms of polarity and amplitude. The reported phenomenon can be potentially exploitable for the discrimination of various nanoparticles.
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The data that support the plots within this paper and other findings of this study are available from the corresponding author upon reasonable request.
References
Dekker, C. Solid-state nanopores. Nat. Nanotechnol. 2, 209–215 (2007).
Iqbal, S. M., Akin, D. & Bashir, R. Solid-state nanopore channels with DNA selectivity. Nat. Nanotechnol. 2, 243–248 (2007).
Venkatesan, B. M. & Bashir, R. Nanopore sensors for nucleic acid analysis. Nat. Nanotechnol. 6, 615–624 (2011).
Muthukumar, M., Plesa, C. & Dekker, C. Single-molecule sensing with nanopores. Phys. Today 68, 40–46 (2015).
Feng, J. et al. Identification of single nucleotides in MoS2 nanopores. Nat. Nanotechnol. 10, 1070–1076 (2015).
Yusko, E. C. et al. Controlling protein translocation through nanopores with bio-inspired fluid walls. Nat. Nanotechnol. 6, 253–260 (2011).
Yusko, E. C. et al. Real-time shape approximation and fingerprinting of single proteins using a nanopore. Nat. Nanotechnol. 12, 360–367 (2017).
Restrepo-Pérez, L., Joo, C. & Dekker, C. Paving the way to single-molecule protein sequencing. Nat. Nanotechnol. 13, 786–796 (2018).
Montagne, F., Blondiaux, N., Bojko, A. & Pugin, R. Molecular transport through nanoporous silicon nitride membranes produced from self-assembling block copolymers. Nanoscale 4, 5880–5886 (2012).
Kovarik, M. L. & Jacobson, S. C. Nanofluidics in lab-on-a-chip devices. Anal. Chem. 81, 7133–7140 (2009).
Walker, M. I. et al. Extrinsic cation selectivity of 2D membranes. ACS Nano 11, 1340–1346 (2017).
Rollings, R. C., Kuan, A. T. & Golovchenko, J. A. Ion selectivity of graphene nanopores. Nat. Commun. 7, 11408 (2016).
O’Hern, S. C. et al. Nanofiltration across defect-sealed nanoporous monolayer graphene. Nano Lett. 15, 3254–3260 (2015).
Amadei, C. A., Montessori, A., Kadow, J. P., Succi, S. & Vecitis, C. D. Role of oxygen functionalities in graphene oxide architectural laminate subnanometer spacing and water transport. Environ. Sci. Technol. 51, 4280–4288 (2017).
Feng, J. et al. Single-layer MoS2 nanopores as nanopower generators. Nature 536, 197–200 (2016).
Aksu, S. et al. High-throughput nanofabrication of infrared plasmonic nanoantenna arrays for vibrational nanospectroscopy. Nano Lett. 10, 2511–2518 (2010).
Byun, J., Lee, J. I., Kwon, S., Jeon, G. & Kim, J. K. Highly ordered nanoporous alumina on conducting substrates with adhesion enhanced by surface modification: universal templates for ultrahigh-density arrays of nanorods. Adv. Mater. 22, 2028–2032 (2010).
Schneider, G. F. & Dekker, C. DNA sequencing with nanopores. Nat. Biotechnol. 30, 326–328 (2012).
Garaj, S. et al. Graphene as a subnanometre trans-electrode membrane. Nature 467, 190–193 (2010).
Schneider, G. F. et al. DNA translocation through graphene nanopores. Nano Lett. 10, 3163–3167 (2010).
Liu, K., Feng, J., Kis, A. & Radenovic, A. Atomically thin molybdenum disulfide nanopores with high sensitivity for DNA translocation. ACS Nano 8, 2504–2511 (2014).
Zhou, Z. et al. DNA translocation through hydrophilic nanopore in hexagonal boron nitride. Sci. Rep. 3, 3287 (2013).
Wanunu, M. et al. Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors. Nat. Nanotechnol. 5, 807–814 (2010).
Arjmandi‐Tash, H. et al. Zero-depth interfacial nanopore capillaries. Adv. Mater. 30, 1703602 (2018).
Kong, Z. et al. Charge-tunable absorption behavior of DNA on graphene. J. Mater. Chem. B 3, 4814–4820 (2015).
Wells, D. B., Belkin, M., Comer, J. & Aksimentiev, A. Assessing graphene nanopores for sequencing DNA. Nano Lett. 12, 4117–4123 (2012).
Heerema, S. J. et al. 1/f noise in graphene nanopores. Nanotechnology 26, 074001 (2015).
Kowalczyk, S. W., Wells, D. B., Aksimentiev, A. & Dekker, C. Slowing down DNA translocation through a nanopore in lithium chloride. Nano Lett. 12, 1038–1044 (2012).
Sha, J. et al. Salt gradient improving signal-to-noise ratio in solid-state nanopore. ACS Sens. 2, 506–512 (2017).
Fologea, D., Uplinger, J., Thomas, B., McNabb, D. S. & Li, J. Slowing DNA translocation in a solid-state nanopore. Nano Lett. 5, 1734–1737 (2005).
Di Fiori, N. et al. Optoelectronic control of surface charge and translocation dynamics in solid-state nanopores. Nat. Nanotechnol. 8, 946–951 (2013).
Wei, R., Gatterdam, V., Wieneke, R., Tampé, R. & Rant, U. Stochastic sensing of proteins with receptor-modified solid-state nanopores. Nat. Nanotechnol. 7, 257–263 (2012).
Emilsson, G. et al. Polymer brushes in solid-state nanopores form an impenetrable entropic barrier for proteins. Nanoscale 10, 4663–4669 (2018).
Emilsson, G. et al. Gating protein transport in solid state nanopores by single molecule recognition. ACS Cent. Sci. 4, 1007–1014 (2018).
Storm, A. J., Chen, J. H., Ling, X. S., Zandbergen, H. W. & Dekker, C. Fabrication of solid-state nanopores with single-nanometre precision. Nat. Mater. 2, 537–540 (2003).
Chen, Q., Wang, Y., Deng, T. & Liu, Z. Fabrication of nanopores and nanoslits with feature sizes down to 5 nm by wet etching method. Nanotechnology 29, 085301 (2018).
Wen, C., Zhang, Z. & Zhang, S.-L. Physical model for rapid and accurate determination of nanopore size via conductance measurement. ACS Sens. 2, 1523–1530 (2017).
Tagliazucchi, M. & Szleifer, I. Transport mechanisms in nanopores and nanochannels: can we mimic nature? Mater. Today 18, 131–142 (2015).
Kosmulski, M. The pH-dependent surface charging and the points of zero charge. J. Colloid Interface Sci. 253, 77–87 (2002).
Smeets, R. M. M. et al. Salt dependence of ion transport and DNA translocation through solid-state nanopores. Nano Lett. 6, 89–95 (2006).
Ivanov, A. P. et al. DNA tunneling detector embedded in a nanopore. Nano Lett. 11, 279–285 (2011).
Anderson, B. N., Muthukumar, M. & Meller, A. pH tuning of DNA translocation time through organically functionalized nanopores. ACS Nano 7, 1408–1414 (2013).
Kox, R. et al. Local solid-state modification of nanopore surface charges. Nanotechnology 21, 335703 (2010).
Luan, B. & Stolovitzky, G. An electro-hydrodynamics-based model for the ionic conductivity of solid-state nanopores during DNA translocation. Nanotechnology 24, 195702 (2013).
Larkin, J., Henley, R. Y., Muthukumar, M., Rosenstein, J. K. & Wanunu, M. High-bandwidth protein analysis using solid-state nanopores. Biophys. J. 106, 696–704 (2014).
Yamazaki, H., Hu, R., Zhao, Q. & Wanunu, M. Photothermally assisted thinning of silicon nitride membranes for ultrathin asymmetric nanopores. ACS Nano 26, 12472–12481 (2018).
Qiu, Y., Siwy, Z. S. & Wanunu, M. Abnormal ionic–current rectification caused by reversed electroosmotic flow under viscosity gradients across thin nanopores. Anal. Chem. 91, 996–1004 (2019).
Seidel, H., Csepregi, L., Heuberger, A. & Baumgärtel, H. Anisotropic etching of crystalline silicon in alkaline solutions. I. Orientation dependence and behavior of passivation layers. J. Electrochem. Soc. 137, 3612–3626 (1990).
Zubel, I. & Barycka, I. Silicon anisotropic etching in alkaline solutions. I. The geometric description of figures developed under etching Si(100) in various solutions. Sens. Actuators A 70, 250–259 (1998).
Acknowledgements
The authors thank R. Scheicher, S. Cardoch, U. F. Keyser and S. Li for fruitful discussions. This work was financially supported by the Swedish Research Council (621-2014-6300) and Stiftelsen Olle Engkvist Byggmästare (2016/39).
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S.Z., C.W., S.-L.Z. and Z.Z. designed the experiments. P.S. and Z.Z. conceived the idea of silicon nanopores. S.Z. fabricated and characterized the nanopore devices under the supervision of Z.Z. C.W. performed the translocation experiments and finite element simulations under the supervision of S.-L.Z. S.Z., C.W., S.-L.Z. and Z.Z. co-wrote the manuscript. All the authors analyzed the data, discussed the results and commented on the manuscript.
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Zeng, S., Wen, C., Solomon, P. et al. Rectification of protein translocation in truncated pyramidal nanopores. Nat. Nanotechnol. 14, 1056–1062 (2019). https://doi.org/10.1038/s41565-019-0549-0
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DOI: https://doi.org/10.1038/s41565-019-0549-0
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