Abstract
Rapid sensing of molecules is increasingly important in many studies and applications, such as DNA sequencing and protein identification. Here, beyond atomically thin 2D nanopores, we conceptualize, simulate and experimentally demonstrate coupled, guiding and reusable bilayer nanopore platforms, enabling advanced ultrafast detection of unmodified molecules. The bottom layer can collimate and decelerate the molecule before it enters the sensing zone, and the top 2D pore (~2 nm) enables position sensing. We varied the number of pores in the bottom layer from one to nine while fixing one 2D pore in the top layer. When the number of pores in the bottom layer is reduced to one, sensing is performed by both layers, and distinct T- and W-shaped translocation signals indicate the precise position of molecules and are sensitive to fragment lengths. This is uniquely enabled by microsecond resolution capabilities and precision nanofabrication. Coupled nanopores represent configurable multifunctional systems with inter- and intralayer structures for improved electromechanical control and prolonged dwell times in a 2D sensing zone.
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Data availability
Source data and analysis codes are available via the figshare repository at https://doi.org/10.6084/m9.figshare.26132701. Other details are also available upon request for purposes of reproducing or extending the work and analysis. If devices are requested such as 2D materials or GURU devices, this may be possible as well if resources for device nanomanufacturing are available.
References
Xue, L. et al. Solid-state nanopore sensors. Nat. Rev. Mater. 5, 931–951 (2020).
Manrao, E. A. et al. Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat. Biotechnol. 30, 349–353 (2012).
Danda, G. & Drndić, M. Two-dimensional nanopores and nanoporous membranes for ion and molecule transport. Curr. Opin. Biotechnol. 55, 124–133 (2019).
Healy, K., Schiedt, B., Morrison, I. P. & Morrison, A. P. Solid-state nanopore technologies for nanopore-based DNA analysis. Nanomedicine 2, 875–897 (2007).
Branton, D. et al. The potential and challenges of nanopore sequencing. Nat. Biotechnol. 26, 1146–1153 (2008).
Dekker, C. Solid-state nanopores. Nat. Nanotechnol. 2, 209–215 (2007).
Deamer, D. W. & Akeson, M. Nanopores and nucleic acids: prospects for ultrarapid sequencing. Trends Biotechnol. 18, 147–151 (2000).
Chen, K., Gularek, F., Liu, B., Weinhold, E. & Keyser, U. F. Electrical DNA sequence mapping using oligodeoxynucleotide labels and nanopores. ACS Nano 15, 2679–2685 (2021).
Chen, K. et al. Dynamics of driven polymer transport through a nanopore. Nat. Phys. 17, 1043–1049 (2021).
Niedzwiecki, D. J. et al. Devices for nanoscale guiding of DNA through a 2D nanopore. ACS Sens. 6, 2534–2545 (2021).
Cadinu, P. et al. Double barrel nanopores as a new tool for controlling single-molecule transport. Nano Lett. 18, 2738–2745 (2018).
Rand, A. et al. Electronic mapping of a bacterial genome with dual solid-state nanopores and active single-molecule control. ACS Nano 16, 5258–5273 (2022).
Pud, S. et al. Mechanical trapping of DNA in a double-nanopore system. Nano Lett. 16, 8021–8028 (2016).
Chou, Y.-C., Chen, J., Lin, C.-Y. & Drndić, M. Engineering adjustable two-pore devices for parallel ion transport and DNA translocations. J. Chem. Phys. 154, 105102 (2021).
Pedone, D., Langecker, M., Abstreiter, G. & Rant, U. A pore–cavity–pore device to trap and investigate single nanoparticles and DNA molecules in a femtoliter compartment: confined diffusion and narrow escape. Nano Lett. 11, 1561–1567 (2011).
Langecker, M., Pedone, D., Simmel, F. C. & Rant, U. Electrophoretic time-of-flight measurements of single DNA molecules with two stacked nanopores. Nano Lett. 11, 5002–5007 (2011).
Liu, X., Skanata, M. M. & Stein, D. Entropic cages for trapping DNA near a nanopore. Nat. Commun. 6, 6222 (2015).
Merchant, C. A. et al. DNA translocation through graphene nanopores. Nano Lett. 10, 2915–2921 (2010).
Masih Das, P. et al. Atomic-scale patterning in two-dimensional van der Waals superlattices. Nanotechnology 31, 105302 (2019).
Rodríguez-Manzo, J. A., Puster, M., Nicolaï, A., Meunier, V. & Drndić, M. DNA translocation in nanometer thick silicon nanopores. ACS Nano 9, 6555–6564 (2015).
Chien, C.-C., Shekar, S., Niedzwiecki, D. J., Shepard, K. L. & Drndić, M. Single-stranded DNA translocation recordings through solid-state nanopores on glass chips at 10 MHz measurement bandwidth. ACS Nano 13, 10545–10554 (2019).
Fischbein, M. D. & Drndić, M. Electron beam nanosculpting of suspended graphene sheets. Appl. Phys. Lett. 93, 113107 (2008).
Thiruraman, J. P., Masih Das, P. & Drndić, M. Stochastic ionic transport in single atomic zero-dimensional pores. ACS Nano 14, 11831–11845 (2020).
Masih Das, P. et al. Controlled sculpture of black phosphorus nanoribbons. ACS Nano 10, 5687–5695 (2016).
Briggs, K. et al. DNA translocations through nanopores under nanoscale preconfinement. Nano Lett. 18, 660–668 (2018).
Alibakhshi, M. A. et al. Scaled‐up synthesis of freestanding molybdenum disulfide membranes for nanopore sensing. Adv. Mater. 35, 2207089 (2023).
Lin, C.-Y. et al. Modulation of charge density and charge polarity of nanopore wall by salt gradient and voltage. ACS Nano 13, 9868–9879 (2019).
Wanunu, M. et al. Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors. Nat. Nanotechnol. 5, 807–814 (2010).
Kowalczyk, S. W., Tuijtel, M. W., Donkers, S. P. & Dekker, C. Unraveling single-stranded DNA in a solid-state nanopore. Nano Lett. 10, 1414–1420 (2010).
Brinkers, S., Dietrich, H. R. C., De Groote, F. H., Young, I. T. & Rieger, B. The persistence length of double stranded DNA determined using dark field tethered particle motion. J. Chem. Phys. 130, 215105 (2009).
Bell, N. A. W., Chen, K., Ghosal, S., Ricci, M. & Keyser, U. F. Asymmetric dynamics of DNA entering and exiting a strongly confining nanopore. Nat. Commun. 8, 380 (2017).
Carson, S., Wilson, J., Aksimentiev, A. & Wanunu, M. Smooth DNA transport through a narrowed pore geometry. Biophys. J. 107, 2381–2393 (2014).
Chou, Y.-C., Masih Das, P., Monos, D. S. & Drndić, M. Lifetime and stability of silicon nitride nanopores and nanopore arrays for ionic measurements. ACS Nano 14, 6715–6728 (2020).
Shekar, S. et al. Measurement of DNA translocation dynamics in a solid-state nanopore at 100 ns temporal resolution. Nano Lett. 16, 4483–4489 (2016).
Lin, C.-Y. et al. Ultrafast polymer dynamics through a nanopore. Nano Lett. 22, 8719–8727 (2022).
Venta, K. et al. Differentiation of short, single-stranded DNA homopolymers in solid-state nanopores. ACS Nano 7, 4629–4636 (2013).
Parkin, W. M. et al. Raman shifts in electron-irradiated monolayer MoS2. ACS Nano 10, 4134–4142 (2016).
Mlack, J. T. et al. Transfer of monolayer TMD WS2 and Raman study of substrate effects. Sci. Rep. 7, 43037 (2017).
Balan, A. et al. Improving signal-to-noise performance for DNA translocation in solid-state nanopores at MHz bandwidths. Nano Lett. 14, 7215–7220 (2014).
Acknowledgements
We acknowledge use of the JEOL F200 TEM and JEOL NEOARM in the NSF-MRSEC electron microscopy facility at the University of Pennsylvania. The work was performed in the David Rittenhouse Laboratory and at the Singh Center for Nanotechnology, an NNCI member supported by NSF grant no. ECCS-15421153. This work was partially funded by NSF grants 2002477 and 1905045, NIH grant R21 HG0101536 and CHOP institutional funds.
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Y.-C.C. and C.-Y.L. contributed equally to the work. Y.-C.C., D.M. and M.D. conceptualized and conceived the project. Y.-C.C., C.-Y.L., A.C., R.K. and P.Y. fabricated GURU devices and nanopores. Y.-C.C. and A.C. prepared DNA samples. Y.-C.C., C.-Y.L. and A.C. performed the ionic measurements. Y.-C.C. and C.-Y.L. performed gel electrophoresis and analysis. Y.-C.C., C.-Y.L., J.C. and A.C. performed data analysis. Y.-C.C., C.-Y.L., J.C., A.C., D.M. and M.D. constructed and approved the manuscripts. D.M. and M.D. supervised the project.
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Extended data
Extended Data Fig. 1 Schematic illustration of the fabrication process for the 2D-GURU devices with different configurations.
There are two complementary ways to make the pores in the underlying SiN layer. Electron beam lithography (EBL) is typically used to create nanopore arrays in the SiN layer, forming an [N, 1] configuration. The second way to make SiN pores is with transmission electron microscopy (TEM) drilling. Using TEM sculpting to drill a single pore in the SiN layer results in a device with a [1, 1] configuration. Some [N,1] devices with small N and small SiN pore diameter, dSiN (~ 10 nm or less in diameter) were also made with TEM sculpting (Fig. 2a in the main paper). After fabricating SiN pores in the trench region, we deposit the 2D material flake onto the trench, followed by AC-STEM drilling of the 2D pore. Supplementary Table 1 provides an index of TEM images for GURU devices with various configurations.
Extended Data Fig. 2 Nanopore size control throughout the AC-STEM drilling process.
Series of ADF-STEM (annular dark field scanning transmission electron microscopy) images of suspended monolayer MoS2 during the nanopore drilling process on two different devices. Some accumulation of atoms on the pore edges is visible and this can contribute to an increased effective thickness of the pore in some cases. (a) MoS2 lattice before drilling, (b) after a few seconds of drilling, a sub-nanometer pore is created (size ~ 0.85 nm x 0.85 nm), (c) same nanopore after a few additional seconds of drilling, yielding a final nanopore with a size adapted to ssDNA translocation measurements (~ 1.7 nm x 1.3 nm). This pore is a part of a [6,1] device configuration. (d-f) Images of the same process on another GURU device, aiming for a nanopore size adapted to translocation measurements of dsDNA. Pore sizes are ~ 1.29 nm x 1.47 nm, 1.81 nm x 1.89 nm, 2.17 nm x 3.15 nm for D, E and F, respectively. These sizes are extracted from two intensity profiles taken at the widest points of the pore vertically and horizontally, respectively. All scale bars are 2 nm.
Extended Data Fig. 3 Additional examples of 2D MoS2 nanopore drilling for three other GURU devices with varying geometries.
(a, b) [2,1], (c, d) [6,1], (e, f) [9,1]. ADF-STEM (annular dark field scanning transmission electron microscope) images of (a) RIE-thinned region of the SiN membrane containing two TEM-drilled nanopores (inset: closeup of the bottom nanopore covered by monolayer MoS2 prior to drilling; (b) 2D nanopore above the SiN pore; (c) pre-patterned RIE-thinned square in the SiN membrane containing six EBL-made nanopores, (d) closeup of pore highlighted by the blue dashed square in (c), showing the suspended monolayer MoS2 after AC-STEM drilling (inset: high resolution image of the 2D nanopore), (e) pre-patterned RIE-thinned square in the SiN membrane containing nine EBL-made nanopores, (f) closeup of pore highlighted by the blue dashed square in (e) showing the suspended monolayer MoS2 after AC-STEM drilling (inset: high resolution image of the 2D nanopore). (e) and (f) are images of the reused device shown in Fig. 2a in the main text, the STEM drilling step shown here corresponds to the fourth MoS2 transfer process, and third STEM drilling that this device underwent. Scale bars are 100 nm for (a), (b) and (c), 5 nm for (d), (e) and (f), and 2 nm in all inset images.
Extended Data Fig. 5 Reusability and Versatility of 2D-GURU Devices.
(a) TEM images showing two patterned windows on top of which 2D material is deposited. The 2D pores can be selectively drilled in multiple desired locations. (b) Series of TEM images (top) and optical images (bottom) after the same device was reused. On this device we deposited ALD (atomic layer deposition) HfO2 (~ 3 nm) after the first round of measurement, which can be seen as the white circles around the pore edges. The position of two patterned windows is highlighted in dotted red squares. Devices presented in the main text do not contain the HfO2 layer and this device in Extended Data Fig. 5b was used for wetting and ionic measurement tests.
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Supplementary Figs. 1–24, discussion and Tables 1 and 2.
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Chou, YC., Lin, CY., Castan, A. et al. Coupled nanopores for single-molecule detection. Nat. Nanotechnol. (2024). https://doi.org/10.1038/s41565-024-01746-7
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DOI: https://doi.org/10.1038/s41565-024-01746-7
