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Chou YC, Chen J, Lin CY, Drndić M. Engineering adjustable two-pore devices for parallel ion transport and DNA translocations. J Chem Phys 2021; 154:105102. [PMID: 33722020 PMCID: PMC7952139 DOI: 10.1063/5.0044227] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 02/19/2021] [Indexed: 12/26/2022] Open
Abstract
We report ionic current and double-stranded DNA (dsDNA) translocation measurements through solid-state membranes with two TEM-drilled ∼3-nm diameter silicon nitride nanopores in parallel. Nanopores are fabricated with similar diameters but varying in effective thicknesses (from 2.6 to 10 nm) ranging from a thickness ratio of 1:1 to 1:3.75, producing distinct conductance levels. This was made possible by locally thinning the silicon nitride membrane to shape the desired topography with nanoscale precision using electron beam lithography (EBL). Two nanopores are engineered and subsequently drilled in either the EBL-thinned or the surrounding membrane region. By designing the interpore separation a few orders of magnitude larger than the pore diameter (e.g., ∼900 vs 3 nm), we show analytically, numerically, and experimentally that the total conductance of the two pores is the sum of the individual pore conductances. For a two-pore device with similar diameters yet thicknesses in the ratio of 1:3, a ratio of ∼1:2.2 in open-pore conductances and translocation current signals is expected, as if they were measured independently. Introducing dsDNA as analytes to both pores simultaneously, we detect more than 12 000 events within 2 min and trace them back with a high likelihood to which pore the dsDNA translocated through. Moreover, we monitor translocations through one active pore only when the other pore is clogged. This work demonstrates how two-pore devices can fundamentally open up a parallel translocation reading system for solid-state nanopores. This approach could be creatively generalized to more pores with desired parameters given a sufficient signal-to-noise ratio.
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Affiliation(s)
- Yung-Chien Chou
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Joshua Chen
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Chih-Yuan Lin
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Marija Drndić
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Chou YC, Masih Das P, Monos DS, Drndić M. Lifetime and Stability of Silicon Nitride Nanopores and Nanopore Arrays for Ionic Measurements. ACS NANO 2020; 14:6715-6728. [PMID: 32275381 PMCID: PMC9547353 DOI: 10.1021/acsnano.9b09964] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Nanopores are promising for many applications including DNA sequencing and molecular filtration. Solid-state nanopores are preferable over their biological counterparts for applications requiring durability and operation under a wider range of external parameters, yet few studies have focused on optimizing their robustness. We report the lifetime and durability of pores and porous arrays in 10 to 100 nm-thick, low-stress silicon nitride (SiNx) membranes. Pores are fabricated using a transmission electron microscope (TEM) and/or electron beam lithography (EBL) and reactive ion etching (RIE), with diameters from 2 to 80 nm. We store them in various electrolyte solutions (KCl, LiCl, MgCl2) and record open pore conductance over months to quantify pore stability. Pore diameters increase with time, and diameter etch rate increases with electrolyte concentration from Δd/Δt ∼ 0.2 to ∼ 3 nm/day for 0.01 to 3 M KCl, respectively. TEM confirms the range of diameter etch rates from ionic measurements. Using electron energy loss spectroscopy (EELS), we observe a N-deficient region around the edges of TEM-drilled pores. Pore expansion is caused by etching of the Si/SiO2 pore walls, which resembles the dissolution of silicon found in minerals such as silica (SiO2) in salty ocean water. The etching process occurs where the membrane was exposed to the electron beam and can result in pore formation. However, coating pores with a conformal 1 nm-thick hafnium oxide layer prevents expansion in 1 M KCl, in stark contrast to bare SiNx pores (∼ 1.7 nm/day). EELS data reveal the atomic composition of bare and HfO2-coated pores.
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Affiliation(s)
- Yung-Chien Chou
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Paul Masih Das
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Dimitri S Monos
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania and The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
- Immunogenetics Laboratory, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
| | - Marija Drndić
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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A Novel Profiled Multi-Pin Electrospinning System for Nanofiber Production and Encapsulation of Nanoparticles into Nanofibers. Sci Rep 2020; 10:4302. [PMID: 32152364 PMCID: PMC7062762 DOI: 10.1038/s41598-020-60752-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 02/17/2020] [Indexed: 11/25/2022] Open
Abstract
Electrospinning with various machine configurations is being used to produce polymer nanofibers with different rates of output. The use of polymers with high viscosity and the encapsulation of nanoparticles for achieving functionalities are some of the limitations of the existing methods. A profiled multi-pin electrospinning (PMES) setup is demonstrated in this work that overcomes the limitations in the needle and needleless electrospinning like needle clogging, particle settling, and uncontrolled/uneven Taylor cone formation, the requirement of very high voltage and uncontrolled distribution of nanoparticles in nanofibers. The key feature of the current setup is the use of profiled pin arrangement that aids in the formation of spherical shape polymer droplet and hence ensures uniform Taylor cone formation throughout the fiber production process. With a 10 wt% of Polyvinyl Alcohol (PVA) polymer solution and at an applied voltage of 30 kV, the production rate was observed as 1.690 g/h and average fiber diameter obtained was 160.5 ± 48.9 nm for PVA and 124.9 ± 49.8 nm for Cellulose acetate (CA) respectively. Moreover, the setup also provides the added advantage of using high viscosity polymer solutions in electrospinning. This approach is expected to increase the range of multifunctional electrospun nanofiber applications.
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Fam Y, Sheppard TL, Becher J, Scherhaufer D, Lambach H, Kulkarni S, Keller TF, Wittstock A, Wittwer F, Seyrich M, Brueckner D, Kahnt M, Yang X, Schropp A, Stierle A, Schroer CG, Grunwaldt JD. A versatile nanoreactor for complementary in situ X-ray and electron microscopy studies in catalysis and materials science. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:1769-1781. [PMID: 31490169 PMCID: PMC6732905 DOI: 10.1107/s160057751900660x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/08/2019] [Indexed: 05/04/2023]
Abstract
Two in situ `nanoreactors' for high-resolution imaging of catalysts have been designed and applied at the hard X-ray nanoprobe endstation at beamline P06 of the PETRA III synchrotron radiation source. The reactors house samples supported on commercial MEMS chips, and were applied for complementary hard X-ray ptychography (23 nm spatial resolution) and transmission electron microscopy, with additional X-ray fluorescence measurements. The reactors allow pressures of 100 kPa and temperatures of up to 1573 K, offering a wide range of conditions relevant for catalysis. Ptychographic tomography was demonstrated at limited tilting angles of at least ±35° within the reactors and ±65° on the naked sample holders. Two case studies were selected to demonstrate the functionality of the reactors: (i) annealing of hierarchical nanoporous gold up to 923 K under inert He environment and (ii) acquisition of a ptychographic projection series at ±35° of a hierarchically structured macroporous zeolite sample under ambient conditions. The reactors are shown to be a flexible and modular platform for in situ studies in catalysis and materials science which may be adapted for a range of sample and experiment types, opening new characterization pathways in correlative multimodal in situ analysis of functional materials at work. The cells will presently be made available for all interested users of beamline P06 at PETRA III.
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Affiliation(s)
- Yakub Fam
- Institute for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology, Engesserstraße 20, Karlsruhe, Baden Württemberg 76131, Germany
| | - Thomas L. Sheppard
- Institute for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology, Engesserstraße 20, Karlsruhe, Baden Württemberg 76131, Germany
- Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, Eggenstein-Leopoldshafen, Baden Württemberg 76344, Germany
| | - Johannes Becher
- Institute for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology, Engesserstraße 20, Karlsruhe, Baden Württemberg 76131, Germany
| | - Dennis Scherhaufer
- Institute for Micro Process Engineering, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, Eggenstein-Leopoldshafen, Baden Württemberg 76344, Germany
| | - Heinz Lambach
- Institute for Micro Process Engineering, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, Eggenstein-Leopoldshafen, Baden Württemberg 76344, Germany
| | | | - Thomas F. Keller
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg 22607, Germany
- Department Physik, Universität Hamburg, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Arne Wittstock
- Institute of Applied and Physical Chemistry, University of Bremen, Bremen 28359, Germany
| | - Felix Wittwer
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg 22607, Germany
- Department Physik, Universität Hamburg, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Martin Seyrich
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg 22607, Germany
- Department Physik, Universität Hamburg, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Dennis Brueckner
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg 22607, Germany
- Department Physik, Universität Hamburg, Luruper Chaussee 149, Hamburg 22761, Germany
- Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Universitätsstraße 150, Bochum 44801, Germany
| | - Maik Kahnt
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg 22607, Germany
- Department Physik, Universität Hamburg, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Xiaogang Yang
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg 22607, Germany
| | - Andreas Schropp
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg 22607, Germany
| | - Andreas Stierle
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg 22607, Germany
- Department Physik, Universität Hamburg, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Christian G. Schroer
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg 22607, Germany
- Department Physik, Universität Hamburg, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Jan-Dierk Grunwaldt
- Institute for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology, Engesserstraße 20, Karlsruhe, Baden Württemberg 76131, Germany
- Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, Eggenstein-Leopoldshafen, Baden Württemberg 76344, Germany
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Lam MH, Briggs K, Kastritis K, Magill M, Madejski GR, McGrath JL, de Haan HW, Tabard-Cossa V. Entropic Trapping of DNA with a Nanofiltered Nanopore. ACS APPLIED NANO MATERIALS 2019; 2:4773-4781. [PMID: 32577609 PMCID: PMC7310961 DOI: 10.1021/acsanm.9b00606] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Elucidating the kinetics of DNA passage through a solid-state nanopore is a fertile field of research, and mechanisms for controlling capture, passage, and trapping of biopolymers are likely to find numerous technological applications. Here we present a nanofiltered nanopore device, which forms an entropic cage for DNA following first passage through the nanopore, trapping the translocated DNA and permitting recapture for subsequent reanalysis and investigation of kinetics of passage under confinement. We characterize the trapping properties of this nanodevice by driving individual DNA polymers into the nanoscale gap separating the nanofilter and the pore, forming an entropic cage similar to a "two pores in series" device, leaving polymers to diffuse in the cage for various time lengths, and attempting to recapture the same molecule. We show that the cage results in effectively permanent trapping when the radius of gyration of the target polymer is significantly larger than the radii of the pores in the nanofilter. We also compare translocation dynamics as a function of translocation direction in order to study the effects of confinement on DNA just prior to translocation, providing further insight into the nanopore translocation process. This nanofiltered nanopore device realizes simple fabrication of a femtoliter nanoreactor in which to study fundamental biophysics and biomolecular reactions on the single-molecule level. The device provides an electrically-permeable single-molecule trap with a higher entropic barrier to escape than previous attempts to fabricate similar structures.
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Affiliation(s)
- Michelle H. Lam
- Department of Physics, University of Ottawa, Ottawa, ON, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, ON, Canada
| | | | - Martin Magill
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON, Canada
| | - Gregory R. Madejski
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
| | - James L. McGrath
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
| | - Hendrick W. de Haan
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON, Canada
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