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Surface Charge Density Dependent DNA Capture Through Polymer Planar Nanopores Zheng Jia, Junseo Choi, and Sunggook Park ACS Appl. Mater. Interfaces, Just Accepted Manuscript • DOI: 10.1021/acsami.8b14423 • Publication Date (Web): 29 Oct 2018 Downloaded from http://pubs.acs.org on November 1, 2018
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ACS Applied Materials & Interfaces
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Surface Charge Density Dependent DNA Capture
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Through Polymer Planar Nanopores
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Zheng Jia‡, Junseo Choi‡ and Sunggook Park*
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Mechanical & Industrial Engineering Department and Center for BioModular Multiscale
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Systems for Precision Medicine, Louisiana State University, USA
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‡These authors contributed equally to this work.
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* CORRESPONDING AUTHOR.
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Prof. Sunggook Park
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Mechanical & Industrial Engineering Department and Center for Bio-Modular Multiscale
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Systems for Precision Medicine
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3290M Patrick F. Taylor Hall, Louisiana State University, Baton Rouge, LA70803, USA
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Fax: +1 225 578 5924; Tel: +1 225 578 0279; E-mail:
[email protected] 15
KEYWORDS: polymer planar nanopore · nanoimprint lithography (NIL) · DNA translocation
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· surface charge density · effective driving force
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ABSTRACT: Surface charge density of nanopore walls plays a critical role in DNA capture in
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nanopore-based sensing platforms. This paper studied the effect of surface charge density on
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the capture of double-stranded (ds) DNA molecules into a polymer planar nanopore
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numerically and experimentally. First, we simulated the effective driving force (𝐹𝑒𝑓𝑓) for the
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translocation of a dsDNA through a planar nanopore with different sizes and surface charge
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densities. Focus was given on the capture stage from the nanopore mouth into the nanopore
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by placing a rod-like DNA at the nanopore mouth rather than inside the nanopore. For
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negatively charged DNA and nanopore walls, electrophoretic driving force (𝐹𝐸𝑃) under an
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electric field is opposed by the viscous drag force by electroosmotic flow (𝐹𝐸𝑂𝐹). As the surface
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charge density of the nanopore wall becomes more negative, 𝐹𝐸𝑂𝐹 exceeds 𝐹𝐸𝑃 beyond a
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threshold surface charge density, 𝜎𝑡ℎ𝑟𝑒𝑠ℎ𝑜𝑙𝑑, where DNA molecules cannot be driven through
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the nanopore via electrophoretic motion. For a 10 nm diameter nanopore filled with 1× TE
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buffer, 𝜎𝑡ℎ𝑟𝑒𝑠ℎ𝑜𝑙𝑑 was determined to be -50 mC/m2. The simulation results were verified by
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performing dsDNA translocation experiments using a planar nanopore with 10 nm equivalent
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diameter imprinted on three polymer substrates with different surface charge densities. Both
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fluorescence observation and ionic current measurement confirmed that only nanopore
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devices with the surface charge density less negative than 𝜎𝑡ℎ𝑟𝑒𝑠ℎ𝑜𝑙𝑑 allowed DNA
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translocation, indicating that the simulated 𝜎𝑡ℎ𝑟𝑒𝑠ℎ𝑜𝑙𝑑 value can be used as a parameter to
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estimate the translocation of biopolymers in the design of nanopore devices.
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ACS Applied Materials & Interfaces
INTRODUCTION
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Nanopore-based fluidic devices are promising tools for DNA sensing due to their label-free,
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high throughput and low cost features.1-2 The sensing mechanism is straightforward: when a
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negatively charged DNA molecule passes a nanopore filled with electrolyte, ion transport
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through the nanopore is temporarily blocked, giving rise to a transient current signal as a
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molecular signature. The biophysical information can be deduced from the electrical signal.
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The nanopore-based DNA sensing platforms can be classified into two categories: biological
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nanopores and solid-state nanopores. Biological nanopores are pore-forming proteins with
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well-defined pore sizes and they can easily be modified by advanced biology technologies.3-4
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Solid-state nanopores are usually fabricated in a thin membrane of an inorganic material (e.g.
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SiO2, Si3N4, and glass) using high energy electron and ion beams.5-7 Compared with biological
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nanopores, solid-state nanopores can have controllable pore sizes ranging from sub-nanometer
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scale to tens of nanometers depending on the types of biomolecules to be interrogated and the
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target applications.4,
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experimental conditions (e.g. electrolyte concentrations, pH and temperature),8 which makes
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solid-state nanopores a good alternative to biological nanopores. However, due to the
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requirement of high-ends nanofabrication tools in the fabrication of solid-state nanopores with
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nanometer precision, it is still challenging and time consuming to produce nanopore devices
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in large scale.
8-9
They are also mechanically robust and stable under various
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Irrespective of the types of nanopore sensing platforms used, efficient capture of DNA
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molecules into nanopores is the basic but challenging operational requirement.10-13 DNA
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capture into a nanopore involves two stages. In the first stage, DNA molecules far from the
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nanopore are driven to nanopore mouth by diffusion and drift under an electric field extending
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out of the nanopore capture radius.14-16 The first stage is dominated by DNA molecule
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diffusion, and several methods have been proposed to facilitate the DNA capture in this stage,
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which include application of higher driving voltage,17-18 use of a buffer system with a salt
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gradient15, 19 and metal layer deposition on the nanopore wall.10 Once a DNA molecule reaches
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the nanopore mouth, in the second stage the coiled DNA molecule has to overcome the
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entropic barrier by putting a portion of its chain, sometimes the chain end or folded chain,
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into the nanopore.14, 16, 20-21 To overcome the entropic barrier, a sufficient driving force needs
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to be provided on the DNA molecule in the direction from the nanopore mouth to the
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nanopore. In order to facilitate DNA translocation at this stage, a tapered gradient inlet22-23 or
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pillar arrays24-25 have been integrated prior to a nanopore or nanochannel. For vertical nanopore
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membranes a threshold driving voltage of less than 100 mV is usually required to overcome the
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entropic barrier26, while for planar nanopore/nanochannel devices, the threshold driving voltage
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varies depending on the fluidic structures formed prior and past the nanopore/nanochannel. It
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should also be noted that, usually, the capture of long chain DNA molecules in vertical nanopores
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is limited by the diffusion in the first capture stage, whereas short chain DNA capture is limited
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by the entropy barrier in the second capture stage.12, 15
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This paper focuses on the study of DNA capture in the second capture stage, i.e. introduction of
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DNA molecules from the nanopore mouth into the nanopore, where the entropic barrier needs to
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be overcome by a sufficient driving force. Commonly used nanopores are negatively charged; for
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example, silicon (Si) based nanopores and most thermoplastics such as polymethyl methacrylate
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(PMMA). Electroosmotic flow (EOF) induced by negative surface charge of the nanopore wall is
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the intrinsic resistance to the electrophoretic motion of DNA for both capture stages.11-12, 27-29 In
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particular, for DNA molecules delivered to the nanopore mouth, a strong EOF leads to a high
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hydrodynamic drag force, 𝐹𝐸𝑂𝐹 against the electrophoretic force, 𝐹𝐸𝑃, on the unscreened DNA
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molecule in electric field. Both 𝐹𝐸𝑂𝐹 and 𝐹𝐸𝑃 correspond to the force in the direction of the
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nanopore axis. Therefore, the effective driving force, 𝐹𝑒𝑓𝑓, on a DNA molecule at the pore mouth
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in a negatively charged nanopore can be expressed as the difference of 𝐹𝐸𝑃 and 𝐹𝐸𝑂𝐹,28, 30-32
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𝐹𝑒𝑓𝑓 = 𝐹𝐸𝑃 ― 𝐹𝐸𝑂𝐹
(1)
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The effect of diffusion on the motion of DNA is negligible because the molecule is already in
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the confined zone of the nanopore mouth. Based on Equation (1), a high 𝐹𝐸𝑂𝐹 results in a low 𝐹𝑒𝑓𝑓,
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which may hinder the DNA molecule from overcoming the entropic barrier. If 𝐹𝑒𝑓𝑓 has a positive
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value, DNA can be pulled into the pore, and vice versa. The threshold surface charge density,
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𝜎𝑡ℎ𝑟𝑒𝑠ℎ𝑜𝑙𝑑, for DNA translocation is defined as the surface charge density of the nanopore wall
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where 𝐹𝐸𝑃 is balanced by 𝐹𝐸𝑂𝐹, namely 𝐹𝑒𝑓𝑓 = 0. It should also be noted that for positively charged
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nanopore devices, the directions of 𝐹𝐸𝑃 and 𝐹𝐸𝑂𝐹 are identical.
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In order to facilitate the design of solid-state nanopore devices and material selection for the
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devices, it is important to gain extensive knowledge on the effect of the surface charge on 𝐹𝑒𝑓𝑓
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for DNA translocation. The inversion of 𝐹𝑒𝑓𝑓 for DNA translocation by controlling the surface 5
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charge density of nanopores was first predicted by Luan et al. by means of all atom molecular
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dynamic simulations with a rod-like stretched poly(dA20)poly(dT20) DNA duplex in a Si3N4
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nanopore.33 𝜎𝑡ℎ𝑟𝑒𝑠ℎ𝑜𝑙𝑑 was also predicted based on continuum model simulation28,
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calculating 𝐹𝑒𝑓𝑓 of a rod-like stretched DNA molecule positioned inside nanopore. However,
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such models are not applicable for studying the capture of DNA for the second capture stage
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from the nanopore mouth to the nanopore because of the impractical assumption of the DNA
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position. Their results only helped understand 𝐹𝑒𝑓𝑓 on the DNA translocating inside the
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nanopore32, and DNA translocation kinetics and interactions within nanopore.36 To study the
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DNA capture at the second capture stage, 𝐹𝑒𝑓𝑓 should be calculated with a partially stretched
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DNA located in front of the nanopore. Moreover, the simulation results were rarely
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demonstrated by translocation experiments due to low throughput and time-consuming device
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fabrication. For example, He et al. simulated that DNA capture can also be manipulated by surface
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charge modulation using a gate electrode.11
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by
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In this work, we systematically studied the effect of surface charge density on 𝐹𝑒𝑓𝑓 for DNA
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capture through polymer planar nanopores by numerical simulation and experimentation.
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Compared to traditional vertical nanopores formed in a thin membrane, planar nanopores are
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ideal platforms for optical observation of the DNA translocation, because no additional
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structure (for example, zero-mode waveguide) is required to enhance the signal-to-noise ratio
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for the observation.37-38 Besides, the entire translocation process can be observed, including
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diffusion, drift and threading.39-40 Another important advantage of the planar design is that 6
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multiple nanopore devices41 can be formed on polymer substrates with various surface
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properties via a single step molding process, for example nanoimprint lithography (NIL),
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which can alleviate the scale-up issue of solid-state nanopore manufacturing.42-44 Using
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COMSOL 5.0 (COMSOL, Inc.), we first simulated 𝐹𝑒𝑓𝑓 on a rod-like double stranded (ds) DNA
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located at the pore mouth of a planar 10 nm pore with different surface charge density values.
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In order to verify the simulation results, optical observation and electrical detection were
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carried out for λ-DNA translocation through a 10 nm equivalent diameter nanopore imprinted
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in polymer substrates with different surface charge densities: poly(ethylene glycol) diacrylate
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(PEGDA), poly(methyl methacrylate) (PMMA) and cyclic olefin copolymer (COC).
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Experimental results were in good agreement with the simulation results in that the DNA
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translocation was observed only for the polymer nanopore with positive 𝐹𝑒𝑓𝑓.
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RESULTS AND DISCUSSION
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Numerical simulation on effective driving force for DNA translocation
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DNA molecules can be driven into a nanopore by electrophoretic motion only when the
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surface charge density of the nanopore wall is less negative than 𝜎𝑡ℎ𝑟𝑒𝑠ℎ𝑜𝑙𝑑 due to a lower
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hydrodynamic drag force caused by weaker EOF.31-33 𝜎𝑡ℎ𝑟𝑒𝑠ℎ𝑜𝑙𝑑 of the nanopore device can be
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predicted by performing COMSOL simulation on the electrokinetic behavior of a DNA
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molecule in the nanopore device with different surface charge density values.31, 7
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Our
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structural model consists of a planar nanopore with 10 nm diameter and 60 nm length
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connected to a tapered inlet and outlet structure. The surface charge density of the entire
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device wall varied from -20 to -80 mC/m2. To simulate 𝐹𝑒𝑓𝑓 of a rod-like, double-stranded λ-
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DNA molecule into a planar nanopore, a cylindrical rod with a diameter of 2 nm and the
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surface charge density of -0.15 C/m2 31, 45 was placed at the nanopore mouth. This initial DNA
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location assumes that one of the DNA chain ends was pre-stretched and approached the
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nanopore mouth. 1× TE buffer was chosen as electrolyte in consideration of the subsequent
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fluorescence observation. Supporting Information (SI) Figure S1 shows the axisymmetric
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structural model and boundary conditions used for the simulation. It should be noted that this
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model is similar to the planar nanopore structure used for experimental verification. With the
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model, 𝐹𝐸𝑃 and 𝐹𝐸𝑂𝐹 were calculated by solving the coupled Poisson-Nernst-Planck (PNP) and
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Navier–Stokes equations, which gives 𝐹𝑒𝑓𝑓 from Equation (1). Details regarding the simulation
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model and parameters used can be found in the method section and in SI Table S1.
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Figure 1 shows 𝐹𝐸𝑂𝐹 and 𝐹𝐸𝑃 exerting on the DNA molecule surface placed in front of a 10
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nm pore as a function of surface charge density of the nanopore wall. It should be reminded
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that 𝐹𝐸𝑂𝐹 and 𝐹𝐸𝑃 correspond to the force in the direction of the nanopore axis. 𝐹𝐸𝑂𝐹 was obtained
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by contour integration of 𝐹𝐸𝑂𝐹, 𝑖𝑧 around the DNA contour surface, 𝐹𝐸𝑂𝐹 = ∮𝐹𝐸𝑂𝐹,𝑖𝑧, where
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𝐹𝐸𝑂𝐹, 𝑖𝑧 is the hydrodynamic drag force at a given DNA surface. As shown in Figure 1a, 𝐹𝐸𝑂𝐹
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increases as the surface charge density of the nanopore wall becomes more negative. Figure 1b
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shows the spatial distribution of the simulated EOF velocity in the direction of the nanopore 8
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axis for three representative surface charge density values of -20 mC/m2, -30 mC/m2 and -80
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mC/m2, respectively. More negative surface charge density leads to a higher EOF velocity
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against the electrophoretic motion of the molecule.
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On the other hand, as shown in Figure 1c, 𝐹𝐸𝑃 initially increases, shows a maximum at -30
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mC/m2 and then decreases as the surface charge density value becomes more negative.
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According to the Coulomb’s law, 𝐹𝐸𝑃 applied on the DNA surface depends on the electric field
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in the nanopore axis direction (i.e. z-axis in simulation model), 𝐸𝑧, by 𝐹𝐸𝑃 = ∮𝑞𝐸𝑧 around the
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DNA surface contour. While a constant external voltage of 1 V is applied between top and
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bottom sides of the nanopore, different surface charges on the device wall modify 𝐸𝑧, leading
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to a dependence of 𝐹𝐸𝑃 on the surface charge density. Figure 1d shows the horizontal
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distribution of 𝐸𝑧 at z = -45 nm, which is 15 nm away from the front end of the DNA molecule.
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The direction of 𝐸𝑧 near the tapered wall was reversed from the direction of the electric field
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by applied voltage due to the negative surface charge of the wall. The reversed electric field
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decays with the distance from the tapered wall. As the surface charge density becomes more
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negative, the magnitude of the reversed 𝐸𝑧 near the tapered wall increases, resulting in a
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reduction of 𝐸𝑧 at and near the DNA molecule and thus 𝐹𝐸𝑃. This accounts for the behavior of
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𝐹𝐸𝑃 for the surface charge density ranging from -30 mC/m2 to -80 mC/m2.
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Figure 1. (a) 𝐹𝐸𝑂𝐹 for a rod-like DNA placed at the mouth of a 10 nm diameter nanopore having
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various surface charge densities; (b) Spatial distribution the simulated EOF velocity in the
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direction of the nanopore axis for three representative surface charge density values of -20
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mC/m2, -30 mC/m2 and -80 mC/m2, respectively; higher surface charge density (absolute value)
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leads to a higher EOF velocity at or near the DNA molecule. (c) 𝐹𝐸𝑃 for a rod-like DNA placed
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at the mouth of a 10 nm diameter nanopore having various surface charge densities; (d)
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Horizontal distribution of electric field in nanopore axis direction, 𝐸𝑧, at z = -45 nm for three
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representative surface charge density values of -20 mC/m2, -30 mC/m2 and -80 mC/m2,
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respectively. Higher surface charge (absolute value) density leads to stronger built up electric field
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near tapered wall and it has negative effect on 𝐸𝑧 at DNA surface. 10
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The behavior of 𝐹𝐸𝑃 for the surface charge density below -30 mC/m2 can be explained by
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the enlarged Debye length (or electric double layer) resulting from the surface charge of the
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device walls. As shown in SI Figure S2, The nanopore device with more negative surface charge
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density has a higher number of charge carriers inside the nanopore. The increased number of
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charge carriers inside the nanopore results in a decreased nanopore resistance and thus a lower
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𝐸𝑧 within nanopore, which subsequently leads to a higher 𝐸𝑧 outside the nanopore. This
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explains the behavior of 𝐹𝐸𝑃 for the surface charge density below -30 mC/m2.
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Figure 2a presents 𝐹𝑒𝑓𝑓 obtained from the simulated 𝐹𝐸𝑃 and 𝐹𝐸𝑂𝐹 using Equation (1) as a
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function of surface charge density for different nanopore diameters. The solid triangle of
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Figure 2a presents 𝐹𝑒𝑓𝑓 for a 10 nm diameter nanopore obtained from Figure 1a and 1c.
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Overall, 𝐹𝑒𝑓𝑓 decreases as the surface charge density becomes more negative. Interestingly, the
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sign of 𝐹𝑒𝑓𝑓 is reversed at a threshold surface charge density of -50 mC/m2, indicating that the
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DNA molecule cannot be driven into the nanopore when the surface charge density is more
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negative than this threshold surface charge density value.
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Figure 2. (a) 𝐹𝑒𝑓𝑓 for a rod-like DNA placed at the mouth nanopores with different pore sizes
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and various surface charge densities; (b) 𝐹𝑒𝑓𝑓 for a rod-like DNA placed inside nanopores with
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different pore sizes and various surface charge densities. A positive value of 𝐹𝑒𝑓𝑓 indicates a
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favor of DNA entrance into the nanopore, and vice versa. Insets indicate DNA location in
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simulation model.
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We further simulated 𝐹𝑒𝑓𝑓 versus surface charge density for different nanopore diameters of
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3 nm and 5 nm which is also shown in Figure 2a. For nanopores with the same surface charge
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density, 𝐹𝑒𝑓𝑓 decreases with decreasing the nanopore size, indicating that it is more difficult
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to drive the DNA molecule through smaller nanopores by electrophoretic motion. The
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negative effect of the tapered inlet structure on 𝐸𝑍 and 𝐹𝑒𝑓𝑓 becomes smaller for larger
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nanopores because the DNA is further away from the tapered wall. 𝜎𝑡ℎ𝑟𝑒𝑠ℎ𝑜𝑙𝑑 is reduced from
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-50 mC/m2 to -41 mC/m2 as the pore diameter decreases from 10 nm to 5 nm. For the 3 nm 12
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nanopore, 𝐹𝑒𝑓𝑓 is always negative irrespective of the magnitude of the negative surface charge
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density, indicating that it is not possible to drive the DNA molecule through the pore (when
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1× TE buffer is used).
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Our results indicate that the negative effect from the tapered inlet structure on 𝐹𝑒𝑓𝑓 can be
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reduced with a flat inlet structure. SI Figure S3 shows the simulation model with a flat inlet
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structure, and 𝐹𝐸𝑃, F𝐸𝑂𝐹 and 𝐹𝑒𝑓𝑓 versus surface charge density for a nanopore of 10 nm
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diameter. Both 𝐸𝐸𝑃 and 𝐸𝐸𝑂𝐹 increase with surface charge density. While 𝐹𝑒𝑓𝑓 decreases with
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the surface charge density, the 𝐹𝑒𝑓𝑓 values are always positive irrespective of the surface charge
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density used for the simulation, indicating that DNA molecules reaching at the nanopore
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mouth are readily introduced into the nanopore. An interesting conclusion can be deduced
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from the simulation results; a tapered inlet structure built prior to a nanopore or nanochannel
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has been known to be helpful to reduce the entropic barrier to capture DNA molecules into a
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nanopore or nanochannel.22-24 However, this merit is compromised by the negative effect of
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reduced or even inverted 𝐹𝑒𝑓𝑓. Therefore, this trade-off needs to be considered in the design
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of nanopore or nanochannel devices to improve the capture of the DNA molecules.
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For comparison, we also simulated 𝐹𝑒𝑓𝑓 for a DNA molecule placed inside the nanopore of
17
different diameters as shown in Figure 2b. The simulation model is shown in SI Figure S4.
18
Similar to the previous case of DNA at nanopore mouth, 𝐹𝑒𝑓𝑓 decreases as the surface charge
19
density becomes more negative and increases along with the nanopore size. Bringing the DNA
20
molecule in the nanopore leads to an increase in both 𝐹𝐸𝑃 and 𝐹𝐸𝑂𝐹 compared to those values for 13
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1
the DNA at the nanopore entrance. But the magnitude of this increase for 𝐹𝐸𝑃 and 𝐹𝐸𝑂𝐹 varies with
2
the pore size. As the pore size becomes smaller, the increase of 𝐹𝐸𝑂𝐹 becomes dominant over the
3
increase of 𝐹𝐸𝑃, leading to an increase in the negative slope of the 𝐹𝑒𝑓𝑓 vs 𝜎 curves (Figure 2b).
4
The 𝜎𝑡ℎ𝑟𝑒𝑠ℎ𝑜𝑙𝑑 values for 3 and 5 nm pores are -22 and -61 mC/m2, respectively. For the 10 nm
5
pore, 𝐹𝑒𝑓𝑓 show always positive values within the range of the surface charge density values
6
investigated. Consequently, for a certain combination of 𝜎 and nanopore size, a DNA molecule
7
inside the nanopore may be pulled out of the nanopore easily while the same DNA is hard to enter
8
the nanopore because it is repelled from the nanopore at the pore entrance. This is the case for 10
9
nm nanopore and with the surface charge density less than -50 mC/m2. It is not easy to
10
experimentally verify the easy pull-out of DNA from the nanopore because it is difficult to
11
introduce the DNA into the nanopore. An optical tweezer may help to reveal the forces of DNA at
12
the nanopore entrance and within nanopore.32 Nevertheless, the results clearly show that the
13
location of the DNA molecule is critical to properly understand the capture behavior of the
14
molecule from the nanopore mouth into the nanopore through the numerical simulation.
15
It is worthwhile to compare our results with 𝜎𝑡ℎ𝑟𝑒𝑠ℎ𝑜𝑙𝑑 calculated from the MD simulation by
16
Luan et al. For a rod-like stretched poly(dA20)poly(dT20) DNA duplex placed in the center of a
17
Si3N4 nanopore of 6 nm diameter and 6.4 nm length, the MD simulation resulted in a 𝜎𝑡ℎ𝑟𝑒𝑠ℎ𝑜𝑙𝑑 of
18
-29 mC/m2 (-0.18 e/nm2), which was less negative than the 𝜎𝑡ℎ𝑟𝑒𝑠ℎ𝑜𝑙𝑑 of -41 mC/m2 for 5 nm
19
nanopore in our continuum COMSOL simulation. The different 𝜎𝑡ℎ𝑟𝑒𝑠ℎ𝑜𝑙𝑑 values can be attributed
20
to the different nanopore lengths (6.4 nm vs. 60 nm) and ion concentrations used for the two
21
simulations (1 M KCl vs. 10 mM KCl).
22 14
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1
Experimental verification
2
Fabrication of polymer planar nanopore devices. In order to verify the simulation results,
3
DNA translocation experiments were designed and conducted using polymer nanopore devices
4
with different surface charge densities. Previous studies show that the surface charge density
5
of O2 plasma treated COC substrates is higher than that of O2 plasma treated PMMA.46 Also,
6
poly-ethylene glycol (PEG) is a well-known coating material to suppress EOF on a target
7
surface.47-48 Therefore, in this study we chose PEGDA, PMMA and COC as substrates for
8
device fabrication. We used the procedure developed in our group to produce polymer
9
nanopore and nanochannel devices, as illustrated in SI Figure S5.49-50 First, a Si master mold
10
with microchannel fluidic networks and planar nanopore was fabricated by a combination of
11
photolithography, wet etching of Si, and focused ion beam (FIB) milling. The patterns on the
12
Si mater were then transferred to a UV curable resin mold, which exerts excellent demolding
13
features. Finally, the planar nanopore device patterns were imprinted on target polymer
14
substrates via UV- or thermal-NIL.
15
Figure 3 shows SEM images of imprinted planar nanopores on different polymer substrates.
16
In comparison with the original Si mater mold, imprinted nanopores show good replication
17
fidelity. It should be mentioned that planar nanopore formed by FIB milling has a parabolic
18
shape, not circular. Thus, their equivalent circular pore diameter was calculated with the pore
19
width and depth measured from the SEM images, which amounts to 25 ± 5.3 nm before
20
thermal bonding to a cover plate. Also, tapered inlet /outlet and pillar arrays were built at both 15
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1
sides of the nanopore to pre-stretch DNA. It should be mentioned that our numerical
2
simulation model is 2D axisymmetric, therefore representing 3D nature of DNA molecules and
3
nanopore structures. On the other hand, the planar nanopore that were used in our
4
experimental work is a quasi-2D system in that it was machined in a top-down manner.
5 6
Figure 3. SEM images of Si master mold (a, e) and imprinted planar nanopore on PEGDA (b,
7
f), PMMA (c, g) and COC (d, h) substrates. Nanopillar arrays with 300 nm gap and tapered
8
inlet/outlet with an angle of 60 ° are designed to pre-stretch DNA. Nanopore length is 60 nm,
9
defined by AFM and SEM measurements and this value was used for all COMSOL simulation.
10
Images were taken under 5 kV, 5.9 pA by FEI Quanta 3D instrument. Despite deposition of a
11
4 nm Au/Pd layer on polymer chips to avoid charging effect, the nanopore feature on PMMA
12
substrate was deformed (enlarged and bent) under high magnification by electron beams (g).
16
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Compared with original Si master mold, all imprinted nanopores have good replication fidelity.
2
Scale bars, 3 µm in white and 100 nm red.
3 4
For all imprinted substrates, we used O2 plasma treated COC sheets as cover plate for bonding
5
at 70°C, 1 MPa for 15 min.51 These hybrid devices are denoted as PEGDA-COC, PMMA-COC
6
and COC-COC, respectively. The thermal fusion bonding process intrinsically utilizes mixing
7
of polymer chains between the imprinted substrate and the cover plate. Thus, we took
8
advantage of the thermal fusion bonding process as a process to reduce the nanopore size
9
further. The pore sizes for the enclosed planar nanopore devices after thermal fusion bonding
10
were estimated by measuring their conductance filled with 1 M KCl solution and comparing
11
the measured conductance values with the simulated conductance values of different nanopore
12
sizes. The equivalent pore diameters estimated for all the polymer devices showed similar
13
values of 10.3 ± 3.3 nm as shown in SI Table S2 and SI Figure S6.
14 15
Surface charge density measurement. Prior to DNA translocation experiments, surface charge
16
densities of PEGDA-COC, PMMA-COC and COC-COC devices were experimentally
17
determined by measuring conductance through the nanochannel devices for different KCl
18
concentration. The surface charges on polymer substrates are determined by several factors
19
including the diploe formation induced by the molecular structure at the surface, the ability
20
to deprotonate from the polymer chains, and dissociation of surface chemical groups such as 17
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1
carboxyl group. Also, the oxygen plasma treatment performed prior to the cover plate bonding
2
further modifies the ability to produce surface charges. The polyethylene glycol (PEG) group
3
in PEGDA is known to be close to neutral in aqueous solution while the carboxylic group
4
present in methyl methacrylate monomer makes PMMA highly negatively charged. When the
5
KCl concentration is greater than 10-2 M, measured conductance fits linearly to the theoretical
6
bulk conductance. At lower salt concentration, however, conductance saturates at a value
7
which is dependent on the surface charge density and device geometry. From the transition
8
point on the plot, the effective surface charge density, 𝜎𝑠 , can be calculated through the
9
following equation46, 52
10
𝜎𝑠 =
103𝑁𝐴 ∗ 𝑒 ∗ 𝑤 ∗ ℎ ∗ 2𝜇𝑜𝑝𝑝 ∗ 𝑐𝑡
(2)
(𝑤 + ℎ)(𝜇𝐾 + + 𝜇𝐶𝑙 ― )
11
, where 𝑁𝐴 is the Avogadro constant, 𝑒 is the elementary charge, 𝑤 and ℎ are the width and
12
height (depth) of the nanochannel, 𝜇𝐾 + and 𝜇𝐶𝑙 ― are the ion mobilities of 𝐾 + and 𝐶𝑙 ― ions,
13
𝜇𝑜𝑝𝑝 is the mobility of the counterions, and 𝑐𝑡 is the transition concentration between the two
14
regimes. Details on the derivation of Equation (2) are shown in SI.
15
The hybrid devices with five nanochannels were fabricated for this purpose as shown in
16
Figure 4a-d. Figure 4e shows the nanochannel conductance as a function of salt concentrations
17
for different hybrid devices. The effective surface charge densities obtained from Equation (2)
18
were -24.1 mC/m², -51.7 mC/m², and -73.8 mC/m² for PEGDA-COC, PMMA-COC and COC-
19
COC devices, respectively.52 Surface charge density of O2 plasma treated PMMA and COC are
20
close to the values reported in the previous studies.51,
53
18
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simulated 𝜎𝑡ℎ𝑟𝑒𝑠ℎ𝑜𝑙𝑑 of the 10 nm pore (filled with 1× TE) was -50 mC/m2, from which we
2
hypothesize that DNA molecules could only be driven through the nanopore made of PEGDA-
3
COC, not devices made of PMMA-COC and COC-COC.
4
It should be mentioned that different experimental conditions will change surface charge
5
density of polymer substrate. For example, surface charge becomes more negative with an
6
increase in the pH value. The understanding of surface charges on different polymer substrates,
7
i.e. polymer atomic structure-surface charge correlations, under various experimental
8
conditions requires atomistic modeling approaches such as molecular dynamic simulation or
9
quantum mechanical modeling such as density functional theory. But this is beyond the scope
10
of this work.
11 12
Figure 4. SEM images of nanochannel devices for surface charge density calculation and surface
13
charge density calculation results; (a) Si master mold, (b) UV imprinted nanochannels on PEGDA 19
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1
substrate, (c) thermal imprinted nanochannels on PMMA substrate, and (d) thermal imprinted
2
nanochannels on COC substrate. (e) Nanochannel conductance for PEGDA-COC, PMMA-
3
COC and COC-COC as a function of salt concentration. At high salt concentration,
4
nanochannel conductance is dependent on bulk solution concentration. At low salt
5
concentration, nanochannel conductance saturates at a value, which is dependent on surface
6
charge density of nanochannel walls. The transition concentration, 𝑐𝑡, between these two
7
regimes is indicated in graph.
8 9
Optical and electrical detection of λ-DNA translocation. In order to verify the surface
10
charge dependent DNA capture behavior in nanopores, we conducted optical observation
11
and electrical measurements for λ-DNA translocation through nanopore devices with tapered
12
inlet/outlet made of different hybrid substrates. We used 1× TE buffer to ensure enough
13
binding strength between YOYO-1 dye and λ-DNA backbones.54 Figure 5 shows
14
fluorescence images when the stained λ-DNA molecules were driven towards the nanopore
15
electrophoretically. For all the devices, fluorescence signals from λ-DNA molecules were
16
seen in the nanopillar array region up the nanopore mouth, indicating that DNA molecules
17
captured from the microchannels were accumulated in the nanopillar array region. However,
18
their translocation behavior through the nanopore was different. For PEGDA-COC device,
19
λ-DNA molecules translocated through the nanopore under bias voltage as low as 100-400
20
mV, which is similar to driving voltages reported for λ-DNA translocation through vertical 20
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1
nanopores.20, 26, 55 We also observed that stretched λ-DNA molecules hesitated for a short
2
time prior to entering into the nanopore, similar to a previous report for DNA translocation
3
through a planar nanochannel.23 When applying high driving voltage, this phenomenon
4
became more obvious as λ-DNA molecules piled up at the nanopore entrance region while
5
the molecule can still enter into the nanopore. For PMMA-COC and COC-COC devices, on
6
the other hand, λ-DNA molecules were stretched by pillar arrays and delivered to the
7
nanopore mouth, but could not enter into the nanopore. We reversed the bias several times
8
and also increased the driving voltage up to 10 V. However, no translocation events were
9
observed while the molecules piled up prior to the nanopore.
21
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1 2
Figure 5. Sequential fluorescence images of stained λ-DNA translocation through planar
3
single nanopore devices fabricated on (a) PEGDA (-24.1 mC/m2), (b) PMMA (-51.7 mC/m2)
4
and (c) COC (-73.8 mC/m2). λ-DNA molecules passed through PEGDA nanopore under bias
5
voltage as low as 100 mV but they could not do through PMMA and COC nanopore even
6
under 10 V. The white arrows in Figure 5a indicate translocated λ-DNA molecules through
7
PEGDA nanopore. Scale bar, 5 µm in white.
8
22
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Immediately after fluorescence observation, we used the same nanopore devices for
2
electrical detection of DNA translocation by using the same 1× TE buffer as electrolyte. Figure
3
6a shows ionic current traces measured from PEGDA-COC, PMMA-COC and COC-COC
4
devices under a driving voltage of 1 V, which is the maximum value that can be applied with
5
a commercial patch clamp used. Electrical measurement results were in an agreement with the
6
optical observation. Current blockage events from translocated λ-DNA molecules occurred
7
only for PEGDA-COC device, while no current blockage events were observed for PMMA-
8
COC and COC-COC devices. Both the optical and electrical measurements support our
9
hypothesis set based on the simulation results that λ-DNA molecules can be threaded into the
10
planar nanopore only when the surface charge density of the device is less negative than
11
𝜎𝑡ℎ𝑟𝑒𝑠ℎ𝑜𝑙𝑑. In other words, the simulated 𝜎𝑡ℎ𝑟𝑒𝑠ℎ𝑜𝑙𝑑 value may be the parameter that can be used
12
as a guide to estimate the translocation of biopolymers through planar nanopore in the
13
geometrical design and material selection of nanopore devices in consideration of nanopore
14
geometry and surface charge density.
23
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1 2
Figure 6. (a) Long duration current trace for stained λ-DNA translocation through PEGDA,
3
PMMA and COC based planar nanopores; (b) Scatter plot of DNA translocation events in
4
PEGDA device; (c) Typical unstretched, partially stretched and fully stretched current
5
blockade events.
6 7
For vertical nanopore membranes, the blockade event of a nanopore by a DNA molecule at
8
low salt concentration usually gives rise to an increased transient current peak due to the
9
enhanced flow of counterions along the DNA molecular chain.56 In our experiments, despite 24
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1
the use of 1× TE buffer with low salt concentration, all the transient current peaks were
2
downward. The reason of decreased transient current peaks at low salt concentration is still
3
not clear, but such opposite results have been reported for DNA translocation through
4
transverse electrodes57-58 and carbon nanotubes.59 One possible explanation is that our planar
5
nanopore is a quasi-2D structure and the DNA molecule may block more efficiently the
6
nanopore entrance, as compared to the 3D nature of vertical nanopores. The tapered inlet may
7
also help the DNA molecule to block the nanopore entrance efficiently. Moreover, the event
8
rate of λ-DNA translocation in PEGDA device (0.15 event/ 10 s for 5 ng/μl λ-DNA under a
9
1000 mV driving voltage) was significantly low compared to that reported for vertical
10
nanopores (> 1 event/ 10 s for 5 ng/μl λ-DNA under a 200 mV driving voltage).10, 15 Possible
11
explanation for the low event rate maybe thicker EDLs at the DNA molecule and the nanopore
12
surfaces that make DNA translocation more difficult.10, 60-61 As presented in SI Figure S7a,
13
𝐹𝑒𝑓𝑓 was simulated with different electrolyte concentration, higher concentration KCl leads to
14
higher 𝐹𝑒𝑓𝑓 due to thinner EDL, especially for nanopore with more negative surface charge
15
density. Ionic current measurement confirmed a higher event rate of 1.6 event/ 10 s for the
16
same PEGDA device filled with 1 M KCl, as shown in SI Figure S7b.
17
We further analyzed the current transient peaks from λ-DNA translocation events in
18
PEGDA-COC device. Figure 6b shows a scattered plot for the current drop and dwell time.
19
Three regimes can be identified: (1) short dwell time regime, (2) short current drop regime,
20
and (3) transition between (1) and (2) regimes. In Figure 6c is shown a representative current 25
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1
transient peak corresponding to each regime. Different current transient peaks indicate that
2
λ-DNA molecules translocated through the nanopore in different translocation modes, i.e.
3
unstretched, partially stretched, and fully stretched, which is similar to λ-DNA translocation
4
observed in vertical solid-state nanopores.20-21 Generally speaking, fully stretched
5
translocation events lead to a smaller current drop, longer dwelling time. Partially stretched
6
or unstretched (e.g. single local folded, double local folded or fully folded) events show a larger
7
current drop and shorter dwelling time. In addition to high rate fabrication modalities,
8
polymer planar nanopores are advantageous in that both optical and electrical measurements
9
can be performed in a single chip and that high throughput manufacturing modalities are
10
readily available. Our results indicate that polymer planar nanopores can be an alternative
11
platform to vertical nanopore membranes in obtaining biophysical information of
12
biopolymers.
13
The conformation of a DNA molecule in nanoscale confinement depends on the relative size of
14
the nanoscale confinement to the characteristic molecular scales such as the radius of gyration and
15
persistence length.62 The diameter of the axisymmetric tapered nanopore inlet up to the length of
16
the cylinder DNA used in the numerical simulation varies from 10 to 80 nm while the persistence
17
length of a double stranded DNA at 10 mM salt concentration amounts to 50 - 80 nm. Therefore,
18
the DNA in this region will have the conformation in the classical Odijk regime, meaning that the
19
DNA chain can only store contour through a serious of successive deflections with the wall,
20
characterized by the deflection length63 and that the use of a cylinder to model the DNA in the
21
simulation is justified. On the other hand, both the width and depth of the tapered inlet used for 26
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1
DNA translocation experiments varies from tens of nanometers to several hundred nanometers.
2
Therefore, only the small portion of the -DNA molecule adjacent to the nanopore would have
3
conformation in the Odijk regime while most of the DNA chain in the tail will be in the de Gennes
4
regime with the diameter of the DNA blobs varying along the nanopore axis.
5
It should be noted that DNA transport dynamics depends not only on nanopore material and
6
nanopore design and diameter, but also on other parameters such as electrolyte concentration, pH.
7
temperature, light illumination, voltage, etc. This is a topic of research that needs to be performed
8
to fully develop planar nanopore devices. We performed the verification experiments with the
9
planar nanopore of 10 nm diameter because it is still challenging to manufacture sub-10 nm planar
10
nanopores in a controllable manner in different polymer substrates. Despite such a shortcoming,
11
we believe that our work provides a new insight on the capture of DNA in planar polymer nanopore
12
devices.
13 14
CONCLUSIONS
15
The effect of the surface charge density of planar nanopore devices with tapered inlet/outlet
16
on the capture of λ-DNA molecules was studied numerically and experimentally. In our
17
continuum model, DNA was positioned in front of nanopore rather than inside nanopore. The
18
simulation results indicate that 𝐹𝑒𝑓𝑓 can be lowered or even reversed when the nanopore
19
device is made of materials with highly negative surface charge, hindering DNA translocation
20
by electrophoretic motion. This effect becomes more significant for smaller nanopores and
21
nanopores with a tapered inlet structure. The simulated 𝜎𝑡ℎ𝑟𝑒𝑠ℎ𝑜𝑙𝑑 at which the sign of 𝐹𝑒𝑓𝑓 is
22
reversed can be used as an indicator to determine the molecular translocation through 27
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1
nanopore devices, as verified by DNA translocation experiments where devices with the
2
measured surface charge density more negative than the simulated 𝜎𝑡ℎ𝑟𝑒𝑠ℎ𝑜𝑙𝑑 did not allow
3
translocation of λ-DNA translocation. Compared with PMMA and COC based devices, PEGDA
4
based nanopore fabricated by UV-NIL has the potential to replace Si based solid-state nanopore
5
in the future due to its low surface charge, hydrophilic nature and large-scale fabrication
6
possibility.
7 8
EXPERIMENTAL SECTION
9
Effective driving forces simulation. A 2-D axisymmetric dimensional model was built in
10
COMSOL 5.0 (COMSOL, Inc.) to investigate the effect of surface charge density on 𝐹𝑒𝑓𝑓 for
11
DNA capture.64-65 Electrostatic module, transport of diluted species module and
12
incompressible Navier–Stokes module were used to solve the coupled Poisson-Nernst-Planck
13
(PNP) and Navier–Stokes equations. We assume that a dsDNA is partially pre-stretched by a
14
nanopillar array and reaches the nanopore mouth with no initial velocity. Thus, the DNA
15
molecule can be modeled as a 2 nm diameter cylinder. Since the electric field is strong near
16
nanopore mouth, the end of the cylinder near the nanopore makes a major contribution to
17
𝐹𝑒𝑓𝑓.28 In our model, we placed a 30 nm long cylinder (which is shorter than dsDNA
18
persistence length, 50-80 nm) with no velocity in front of the nanopore to calculate 𝐹𝐸𝑂𝐹 and
19
𝐹𝐸𝑃. 𝐹𝑒𝑓𝑓 was obtained by Equation (1). For the negatively charged DNA, we used the DNA’s
20
bare surface charge density of -0.15 C/m2 (2e per base pair).31, 45 28
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ACS Applied Materials & Interfaces
For most DNA translocation simulation, KCl solution was the common electrolyte
65-67.
In
2
our experiment, we used 1× TE buffer (Sigma-Aldrich, containing 10 mM Tris-HCl, 1mM
3
EDTA, pH 8.0) as electrolyte for both fluorescence observation and electrical measurement.
4
For COMSOL simulation, therefore, we used 10 mM Tris-HCl concentration as the KCl
5
concentration, making sure that they have the same Debye length (ionic strength). All
6
parameters for COMSOL simulation are shown in SI Table S1.
7 8
Polymer device fabrication. Fluidic devices with a planar nanopore was produced by UV- or
9
thermal-NIL into three different polymer substrates: PEGDA (MW = 200, Sigma-Aldrich),
10
PMMA (ePlastics) and COC (COC6013, Tg = 142 °C, TOPAS) as shown in Figure 3. In order to
11
cure, PEGDA was exposed to flash-type UV light (250-400 nm) for 1 min at an intensity of
12
~1.8 W/cm2 after adding 1 wt% of the UV initiator (2,2-dimethoxy-2-phenylacetophenone,
13
Sigma-Aldrich). PMMA and COC were thermally imprinted at 135 °C, 3.5 MPa and 160 °C, 5
14
MPa for 15 min, respectively. For bonding at 70 °C, 1 MPa for 15 min, a low Tg thin COC sheet
15
(COC8007, Tg = 78 °C, TOPAS) was used as the cover plate for all three nanopore substrates.
16
The use of a low Tg cover plate minimize the deformation of the nanostructured substrate.51
17
Details on the device fabrication can be found in SI and our previous work.22, 50-51
18
In order to enhance wetting of the nanopore device and reduce hydrophobic interaction
19
between DNA and the nanopore wall, the patterned substrates (except for PEGDA) and cover
20
sheets were modified to become hydrophilic by O2 plasma prior to bonding.68 Water contact 29
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angles of these materials before and after O2 plasma treatment are shown in SI Figure S8. The
2
bare PEGDA substrate has a similar water contact angle to O2 plasma treated PMMA and COC
3
substrates.
4 5
Measurement of surface charge density. Nanofluidic devices with an array of nanochannels
6
with the width and height of 154 and 203 nm, respectively, were used to measure surface
7
charge density of different polymer substrates. SEM images of the Si master and imprinted
8
polymer nanochannel substrates used for the surface charge density measurements are shown
9
in Figure 4a-d. Conductance through these nanochannel arrays at each KCl concentration was
10
determined by measuring I-V curves using Axopatch 200B (Molecular Devices). The
11
measurement was repeated for different salt concentrations ranging from 10-6 M to 1 M. The
12
current-voltage measurements were performed after the baseline current became stable during
13
current-time measurement. 10 devices were measured for each substrate material. At high salt
14
concentration the nanochannel conductance is dependent on the salt concentration while at
15
low salt concentration the conductance is governed by surface charge density on the wall,46,
16
52, 69
17
be obtained from the transition point between these two regimes. Details on the determination
18
of the surface charge density can be found in SI.
as shown in Figure 4e. The effective surface charge density of a nanochannel substrate can
19
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1
Optical and electrical detection of λ-DNA translocation. Prior to introducing DNA molecules,
2
all devices were filled with 1 M KCl solution (Sigma-Aldrich) containing 1× TE (Sigma-
3
Aldrich), pH 8.0 at room temperature and ionic current (conductance) across the nanopore
4
was measured via Axopatch 200B (Molecular Devices) to make sure that all testing devices
5
have similar pore sizes. The nanopore size was determined by comparing the measured
6
conductance through the nanopore with the simulated conductance for a given nanopore
7
size.56, 70 The average ionic current prior to introducing DNA molecules was 150 ± 31 nA
8
under 1 V, which equals to 150 ± 31 nS in conductance. The estimated equivalent nanopore
9
diameter was 10.3 ± 3.3 nm (See SI Figure S6).
10
Then, 1 M KCl solution containing 1× TE was replaced to 1× TE buffer (Sigma-Aldrich) and a
11
solution of 5 ng/μL double-strand λ-DNA (New England BioLabs) stained with YOYO-1 dye
12
(ThermoFisher Scientific) was added to the cis side of the microchannel. Pt electrodes were
13
used to drive DNA molecules with a commercial power supply (BK Precision DC power supply
14
1735). The DNA movement was observed under a fluorescence microscope (Olympus IX70)
15
with a 100× oil immersion objective (Olympus). Fluorescence images and videos were captured
16
by a CCD camera (Photon Max, Princeton Instruments).
17
Immediately after fluorescence observation, we used the same nanopore device for electrical
18
detection of DNA translocation by using same 1× TE buffer as electrolyte. In order to reduce
19
the noise level, the device was kept in a homemade Faraday cage during electrical
20
measurement. Ag/AgCl electrodes were placed in inlet/outlet reservoirs to drive stained DNA 31
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molecules. Ionic transient current signal was recorded at a sampling rate of 250 kHz and low-
2
pass filtered at 10 kHz.
3 4
ASSOCIATED CONTENT
5
Supporting Information. Additional results including COMSOL simulation, polymer
6
nanofluidic device fabrication, nanopore size estimation, surface charge density measurement
7
and DNA translocation videos are supplied as Supporting Information.
8 9
AUTHOR INFORMATION
10
Corresponding Author
11
*E-mail:
[email protected] 12
ORCID
13
Zheng Jia: 0000-0003-2476-2969
14
Junseo Choi: 0000-0002-3461-3820
15
Sunggook Park: 0000-0003-0424-6318
16 17
Notes
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ACS Applied Materials & Interfaces
The authors declare no competing financial interest.
2 3 4 5
ACKNOWLEDGMENTS This research was supported by the P41 Center for BioModular Multiscale Systems for Precision Medicine (P41EB020594) from the National Institutes of Health.
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REFERENCES
8
(1) Carson, S.; Wanunu, M. Challenges in DNA Motion Control and Sequence Readout Using
9
Nanopore Devices. Nanotechnology 2015, 26, 074004.
10
(2) Haque, F.; Li, J.; Wu, H. C.; Liang, X. J.; Guo, P. Solid-State and Biological Nanopore for
11
Real-Time Sensing of Single Chemical and Sequencing of DNA. Nano today 2013, 8, 56-74.
12
(3) Maglia, G.; Restrepo, M. R.; Mikhailova, E.; Bayley, H. Enhanced Translocation of Single
13
DNA Molecules through Alpha-Hemolysin Nanopores by Manipulation of Internal Charge.
14
Proceedings of the National Academy of Sciences of the United States of America 2008, 105,
15
19720-5.
16
(4) Dekker, C. Solid-State Nanopores. Nature nanotechnology 2007, 2, 209-15.
17
(5) Li, J.; Stein, D.; McMullan, C.; Branton, D. Ion-Beam Sculpting at Nanometre Length
18
Scales. Nature 2001, 412, 166.
19
(6) Storm, A. J.; Chen, J. H.; Ling, X. S.; Zandbergen, H. W.; Dekker, C. Fabrication of Solid-
20
State Nanopores with Single-Nanometre Precision. Nature materials 2003, 2, 537-40. 33
ACS Paragon Plus Environment
ACS Applied Materials & Interfaces 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
1
(7) Wanunu, M.; Dadosh, T.; Ray, V.; Jin, J.; McReynolds, L.; Drndić, M. Rapid Electronic
2
Detection of Probe-Specific Micrornas Using Thin Nanopore Sensors. Nature nanotechnology
3
2010, 5, 807-814.
4
(8) Venkatesan, B. M.; Bashir, R. Nanopore Sensors for Nucleic Acid Analysis. Nature
5
nanotechnology 2011, 6, 615-24.
6
(9) Haque, F.; Li, J.; Wu, H.-C.; Liang, X.-J.; Guo, P. Solid-State and Biological Nanopore for
7
Real-Time Sensing of Single Chemical and Sequencing of DNA. Nano today 2013, 8, 56-74.
8
(10) Chen, P.; Mitsui, T.; Farmer, D. B.; Golovchenko, J.; Gordon, R. G.; Branton, D. Atomic
9
Layer Deposition to Fine-Tune the Surface Properties and Diameters of Fabricated Nanopores.
10
Nano letters 2004, 4, 1333-1337.
11
(11) He, Y.; Tsutsui, M.; Fan, C.; Taniguchi, M.; Kawai, T. Gate Manipulation of DNA Capture
12
into Nanopores. Acs Nano 2011, 5, 8391-8397.
13
(12) He, Y.; Tsutsui, M.; Taniguchi, M.; Kawai, T. DNA Capture in Nanopores for Genome
14
Sequencing: Challenges and Opportunities. Journal of Materials Chemistry 2012, 22, 13423-
15
13427.
16
(13) Bayley, H. Nanopore Sequencing: From Imagination to Reality. Clinical chemistry 2015,
17
61, 25-31.
18
(14) Grosberg, A. Y.; Rabin, Y. DNA Capture into a Nanopore: Interplay of Diffusion and
19
Electrohydrodynamics. The Journal of chemical physics 2010, 133, 10B617.
20
(15) Wanunu, M.; Morrison, W.; Rabin, Y.; Grosberg, A. Y.; Meller, A. Electrostatic Focusing
21
of Unlabelled DNA into Nanoscale Pores Using a Salt Gradient. Nature nanotechnology 2010, 5,
22
160-165.
34
ACS Paragon Plus Environment
Page 34 of 42
Page 35 of 42 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
ACS Applied Materials & Interfaces
1
(16) Kumar, R.; Muthukumar, M. Origin of Translocation Barriers for Polyelectrolyte Chains.
2
The Journal of chemical physics 2009, 131, 11B610.
3
(17) Maitra, R. D.; Kim, J.; Dunbar, W. B. Recent Advances in Nanopore Sequencing.
4
Electrophoresis 2012, 33, 3418-3428.
5
(18) Luan, B.; Stolovitzky, G.; Martyna, G. Slowing and Controlling the Translocation of DNA
6
in a Solid-State Nanopore. Nanoscale 2012, 4, 1068-1077.
7
(19) Feng, J.; Liu, K.; Bulushev, R. D.; Khlybov, S.; Dumcenco, D.; Kis, A.; Radenovic, A.
8
Identification of Single Nucleotides in Mos2 Nanopores. Nature nanotechnology 2015, 10, 1070-
9
6.
10
(20) Storm, A. J.; Storm, C.; Chen, J.; Zandbergen, H.; Joanny, J.-F.; Dekker, C. Fast DNA
11
Translocation through a Solid-State Nanopore. Nano letters 2005, 5, 1193-1197.
12
(21) Chen, P.; Gu, J.; Brandin, E.; Kim, Y.-R.; Wang, Q.; Branton, D. Probing Single DNA
13
Molecule Transport Using Fabricated Nanopores. Nano letters 2004, 4, 2293-2298.
14
(22) Wu, J.; Chantiwas, R.; Amirsadeghi, A.; Soper, S. A.; Park, S. Complete Plastic Nanofluidic
15
Devices for DNA Analysis Via Direct Imprinting with Polymer Stamps. Lab on a chip 2011, 11,
16
2984-2989.
17
(23) Zhou, J.; Wang, Y.; Menard, L. D.; Panyukov, S.; Rubinstein, M.; Ramsey, J. M. Enhanced
18
Nanochannel Translocation and Localization of Genomic DNA Molecules Using Three-
19
Dimensional Nanofunnels. Nature communications 2017, 8, 807.
20
(24) Cao, H.; Tegenfeldt, J. O.; Austin, R. H.; Chou, S. Y. Gradient Nanostructures for
21
Interfacing Microfluidics and Nanofluidics. Applied Physics Letters 2002, 81, 3058-3060.
35
ACS Paragon Plus Environment
ACS Applied Materials & Interfaces 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
1
(25) Wang, C.; Bruce, R. L.; Duch, E. A.; Patel, J. V.; Smith, J. T.; Astier, Y.; Wunsch, B. H.;
2
Meshram, S.; Galan, A.; Scerbo, C. Hydrodynamics of Diamond-Shaped Gradient Nanopillar
3
Arrays for Effective DNA Translocation into Nanochannels. ACS nano 2015, 9, 1206-1218.
4
(26) Zhang, J.; Shklovskii, B. Effective Charge and Free Energy of DNA inside an Ion Channel.
5
Physical Review E 2007, 75, 021906.
6
(27) Wong, C. T.; Muthukumar, M. Polymer Capture by Electro-Osmotic Flow of Oppositely
7
Charged Nanopores. The Journal of chemical physics 2007, 126, 164903.
8
(28) Chen, L.; Conlisk, A. Forces Affecting Double-Stranded DNA Translocation through
9
Synthetic Nanopores. Biomedical microdevices 2011, 13, 403-414.
10
(29) Muthukumar, M. Theory of Capture Rate in Polymer Translocation. The Journal of
11
chemical physics 2010, 132, 05B605.
12
(30) Keyser, U. F.; Koeleman, B. N.; van Dorp, S.; Krapf, D.; Smeets, R. M. M.; Lemay, S. G.;
13
Dekker, N. H.; Dekker, C. Direct Force Measurements on DNA in a Solid-State Nanopore.
14
Nature Physics 2006, 2, 473-477.
15
(31) Chen, L.; Conlisk, A. In Modeling of DNA Translocation in Nanopores, 47th AIAA
16
Aerospace Sciences Meeting including The New Horizons Forum and Aerospace Exposition,
17
2009; p 1121.
18
(32) van Dorp, S.; Keyser, U. F.; Dekker, N. H.; Dekker, C.; Lemay, S. G. Origin of the
19
Electrophoretic Force on DNA in Solid-State Nanopores. Nature Physics 2009, 5, 347-351.
20
(33) Luan, B.; Aksimentiev, A. Control and Reversal of the Electrophoretic Force on DNA in a
21
Charged Nanopore. Journal of Physics: Condensed Matter 2010, 22, 454123.
36
ACS Paragon Plus Environment
Page 36 of 42
Page 37 of 42 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
ACS Applied Materials & Interfaces
1
(34) Keyser, U. F.; Koeleman, B. N.; Van Dorp, S.; Krapf, D.; Smeets, R. M.; Lemay, S. G.;
2
Dekker, N. H.; Dekker, C. Direct Force Measurements on DNA in a Solid-State Nanopore.
3
Nature Physics 2006, 2, 473.
4
(35) Ghosal, S. Electrokinetic-Flow-Induced Viscous Drag on a Tethered DNA inside a
5
Nanopore. Physical Review E 2007, 76, 061916.
6
(36) Sathe, C.; Zou, X.; Leburton, J.-P.; Schulten, K. Computational Investigation of DNA
7
Detection Using Graphene Nanopores. ACS nano 2011, 5, 8842-8851.
8
(37) Levene, M. J.; Korlach, J.; Turner, S. W.; Foquet, M.; Craighead, H. G.; Webb, W. W.
9
Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations. Science 2003,
10
299, 682-686.
11
(38) Miles, B. N.; Ivanov, A. P.; Wilson, K. A.; Doğan, F.; Japrung, D.; Edel, J. B. Single
12
Molecule Sensing with Solid-State Nanopores: Novel Materials, Methods, and Applications.
13
Chemical Society reviews 2013, 42, 15-28.
14
(39) Das, S. K.; Austin, M. D.; Akana, M. C.; Deshpande, P.; Cao, H.; Xiao, M. Single Molecule
15
Linear Analysis of DNA in Nano-Channel Labeled with Sequence Specific Fluorescent Probes.
16
Nucleic acids research 2010, 38, e177-e177.
17
(40) Mannion, J. T.; Reccius, C. H.; Cross, J. D.; Craighead, H. G. Conformational Analysis of
18
Single DNA Molecules Undergoing Entropically Induced Motion in Nanochannels. Biophysical
19
journal 2006, 90, 4538-45.
20
(41) Harms, Z. D.; Mogensen, K. B.; Nunes, P. S.; Zhou, K.; Hildenbrand, B. W.; Mitra, I.; Tan,
21
Z.; Zlotnick, A.; Kutter, J. P.; Jacobson, S. C. Nanofluidic Devices with Two Pores in Series for
22
Resistive-Pulse Sensing of Single Virus Capsids. Analytical chemistry 2011, 83, 9573-9578.
37
ACS Paragon Plus Environment
ACS Applied Materials & Interfaces 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
1
(42) Chou, S. Y.; Krauss, P. R.; Renstrom, P. J. Imprint of Sub‐25 Nm Vias and Trenches in
2
Polymers. Applied physics letters 1995, 67, 3114-3116.
3
(43) Chou, S. Y.; Krauss, P. R.; Renstrom, P. J. Nanoimprint Lithography. Journal of Vacuum
4
Science & Technology B: Microelectronics and Nanometer Structures Processing, Measurement,
5
and Phenomena 1996, 14, 4129-4133.
6
(44) Choi, J.; Farshchian, B.; Kim, J.; Park, S. Fabrication of Perforated Micro/Nanopore
7
Membranes Via a Combination of Nanoimprint Lithography and Pressed Self-Perfection Process
8
for Size Reduction. Journal of nanoscience and nanotechnology 2013, 13, 4129-4133.
9
(45) Luan, B.; Aksimentiev, A. Electro-Osmotic Screening of the DNA Charge in a Nanopore.
10
Physical Review E 2008, 78, 021912.
11
(46) Uba, F. I.; Pullagurla, S. R.; Sirasunthorn, N.; Wu, J.; Park, S.; Chantiwas, R.; Cho, Y. K.;
12
Shin, H.; Soper, S. A. Surface Charge, Electroosmotic Flow and DNA Extension in Chemically
13
Modified Thermoplastic Nanoslits and Nanochannels. The Analyst 2015, 140, 113-26.
14
(47) Stiufiuc, R.; Iacovita, C.; Nicoara, R.; Stiufiuc, G.; Florea, A.; Achim, M.; Lucaciu, C. M.
15
One-Step Synthesis of Pegylated Gold Nanoparticles with Tunable Surface Charge. Journal of
16
Nanomaterials 2013, 2013, 88.
17
(48) Lee, C. S.; Blanchard, W. C.; Wu, C. T. Direct Control of the Electroosmosis in Capillary
18
Zone Electrophoresis by Using an External Electric Field. Analytical chemistry 1990, 62, 1550-
19
1552.
20
(49) Choi, J.; Jia, Z.; Park, S. Fabrication of Polymeric Dual-Scale Nanoimprint Molds Using a
21
Polymer Stencil Membrane. Microelectronic Engineering 2018.
22
(50) Jia, Z.; Choi, J.; Park, S. Selection of Uv Resins for Nanostructured Molds for Thermal-Nil.
23
Nanotechnology 2018. 38
ACS Paragon Plus Environment
Page 38 of 42
Page 39 of 42 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
ACS Applied Materials & Interfaces
1
(51) Uba, F. I.; Hu, B.; Weerakoon-Ratnayake, K.; Oliver-Calixte, N.; Soper, S. A. High Process
2
Yield Rates of Thermoplastic Nanofluidic Devices Using a Hybrid Thermal Assembly
3
Technique. Lab on a chip 2015, 15, 1038-1049.
4
(52) Schoch, R. B.; Renaud, P. Ion Transport through Nanoslits Dominated by the Effective
5
Surface Charge. Applied Physics Letters 2005, 86, 253111.
6
(53) ONeil, C. E.; Jackson, J. M.; Shim, S.-H.; Soper, S. A. Interrogating Surface Functional
7
Group Heterogeneity of Activated Thermoplastics Using Super-Resolution Fluorescence
8
Microscopy. Analytical chemistry 2016, 88, 3686-3696.
9
(54) Günther, K.; Mertig, M.; Seidel, R. Mechanical and Structural Properties of Yoyo-1
10
Complexed DNA. Nucleic acids research 2010, 38, 6526-6532.
11
(55) Maglia, G.; Restrepo, M. R.; Mikhailova, E.; Bayley, H. Enhanced Translocation of Single
12
DNA Molecules through Α-Hemolysin Nanopores by Manipulation of Internal Charge.
13
Proceedings of the National Academy of Sciences 2008, 105, 19720-19725.
14
(56) Smeets, R. M.; Keyser, U. F.; Krapf, D.; Wu, M.-Y.; Dekker, N. H.; Dekker, C. Salt
15
Dependence of Ion Transport and DNA Translocation through Solid-State Nanopores. Nano
16
letters 2006, 6, 89-95.
17
(57) Menard, L. D.; Mair, C. E.; Woodson, M. E.; Alarie, J. P.; Ramsey, J. M. A Device for
18
Performing Lateral Conductance Measurements on Individual Double-Stranded DNA Molecules.
19
ACS nano 2012, 6, 9087-9094.
20
(58) Liang, X.; Chou, S. Y. Nanogap Detector inside Nanofluidic Channel for Fast Real-Time
21
Label-Free DNA Analysis. Nano letters 2008, 8, 1472-1476.
39
ACS Paragon Plus Environment
ACS Applied Materials & Interfaces 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
1
(59) Liu, H.; He, J.; Tang, J.; Liu, H.; Pang, P.; Cao, D.; Krstic, P.; Joseph, S.; Lindsay, S.;
2
Nuckolls, C. Translocation of Single-Stranded DNA through Single-Walled Carbon Nanotubes.
3
Science 2010, 327, 64-67.
4
(60) Zhou, K.; Kovarik, M. L.; Jacobson, S. C. Surface-Charge Induced Ion Depletion and
5
Sample Stacking near Single Nanopores in Microfluidic Devices. Journal of the American
6
Chemical Society 2008, 130, 8614-8616.
7
(61) Schoch, R. B.; Van Lintel, H.; Renaud, P. Effect of the Surface Charge on Ion Transport
8
through Nanoslits. Physics of Fluids 2005, 17, 100604.
9
(62) Reisner, W.; Beech, J. P.; Larsen, N. B.; Flyvbjerg, H.; Kristensen, A.; Tegenfeldt, J. O.
10
Nanoconfinement-Enhanced Conformational Response of Single DNA Molecules to Changes in
11
Ionic Environment. Physical review letters 2007, 99, 058302.
12
(63) Reisner, W.; Pedersen, J. N.; Austin, R. H. DNA Confinement in Nanochannels: Physics
13
and Biological Applications. Reports on Progress in Physics 2012, 75, 106601.
14
(64) Ai, Y.; Liu, J.; Zhang, B.; Qian, S. Field Effect Regulation of DNA Translocation through a
15
Nanopore. Analytical chemistry 2010, 82, 8217-8225.
16
(65) Movahed, S.; Li, D. Electrokinetic Transport through Nanochannels. Electrophoresis 2011,
17
32, 1259-1267.
18
(66) Movahed, S.; Li, D. Electrokinetic Motion of a Rectangular Nanoparticle in a Nanochannel.
19
Journal of Nanoparticle Research 2012, 14, 1-15.
20
(67) Liu, H.; Qian, S.; Bau, H. H. The Effect of Translocating Cylindrical Particles on the Ionic
21
Current through a Nanopore. Biophysical journal 2007, 92, 1164-1177.
22
(68) Chen, Y.; Zhang, L.; Chen, G. Fabrication, Modification, and Application of Poly (Methyl
23
Methacrylate) Microfluidic Chips. Electrophoresis 2008, 29, 1801-1814. 40
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ACS Applied Materials & Interfaces
1
(69) Stein, D.; Kruithof, M.; Dekker, C. Surface-Charge-Governed Ion Transport in Nanofluidic
2
Channels. Physical review letters 2004, 93, 035901.
3
(70) Kowalczyk, S. W.; Grosberg, A. Y.; Rabin, Y.; Dekker, C. Modeling the Conductance and
4
DNA Blockade of Solid-State Nanopores. Nanotechnology 2011, 22, 315101.
5
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