1
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Lee WY, Wen C, Pham NH, Khaksaran MH, Lee SK, Zhang SL. Brownian Motion Paving the Way for Molecular Translocation in Nanopores. SMALL METHODS 2024:e2400042. [PMID: 38593378 DOI: 10.1002/smtd.202400042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/15/2024] [Indexed: 04/11/2024]
Abstract
Tracing fast nanopore-translocating analytes requires a high-frequency measurement system that warrants a temporal resolution better than 1 µs. This constraint may practically shift the challenge from increasing the sampling bandwidth to dealing with the rapidly growing noise with frequencies typically above 10 kHz, potentially making it still uncertain if all translocation events are unambiguously captured. Here, a numerical simulation model is presented as an alternative to discern translocation events with different experimental settings including pore dimension, bias voltage, the charge state of the analyte, salt concentration, and electrolyte viscosity. The model allows for simultaneous analysis of forces exerting on a large analyte cohort along their individual trajectories; these forces are responsible for the analyte movement leading eventually to the nanopore translocation. Through tracing the analyte trajectories, the Brownian force is found to dominate the analyte movement in electrolytes until the last moment at which the electroosmotic force determines the final translocation act. The mean dwell time of analytes mimicking streptavidin decreases from ≈6 to ≈1 µs with increasing the bias voltage from ±100 to ±500 mV. The simulated translocation events qualitatively agree with the experimental data with streptavidin. The simulation model is also helpful for the design of new solid-state nanopore sensors.
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Affiliation(s)
- Won-Yong Lee
- Division of Solid-State Electronics, Department of Electrical Engineering, Uppsala University, Uppsala, 75103, Sweden
| | - Chenyu Wen
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629 HZ, The Netherlands
- Laboratory of Biophysics, Wageningen University, Wageningen, 6708 WE, The Netherlands
| | - Ngan Hoang Pham
- Division of Solid-State Electronics, Department of Electrical Engineering, Uppsala University, Uppsala, 75103, Sweden
| | - Mohammad Hadi Khaksaran
- Division of Solid-State Electronics, Department of Electrical Engineering, Uppsala University, Uppsala, 75103, Sweden
| | - Sang-Kwon Lee
- Department of Physics, Chung-Ang University, Seoul, 06974, South Korea
| | - Shi-Li Zhang
- Division of Solid-State Electronics, Department of Electrical Engineering, Uppsala University, Uppsala, 75103, Sweden
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2
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He P, Shao Y, Yu Z, Liang X, Liu J, Bian Y, Zhu Z, Li M, Pereira CM, Shao Y. Electrostatic-Gated Kinetics of Rapid Ion Transfers at a Nano-liquid/Liquid Interface. Anal Chem 2022; 94:9801-9810. [PMID: 35766488 DOI: 10.1021/acs.analchem.2c01574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Charge (ion and electron)-transfer reactions at a liquid/liquid interface are critical processes in many important biological and chemical systems. An ion-transfer (IT) process is usually very fast, making it difficult to accurately measure its kinetic parameters. Nano-liquid/liquid interfaces supported at nanopipettes are advantageous approaches to study the kinetics of such ultrafast IT processes due to their high mass transport rate. However, correct measurements of IT kinetic parameters at nanointerfaces supported at nanopipettes are inhibited by a lack of knowledge of the nanometer-sized interface geometry, influence of the electric double layer, wall charge polarity, etc. Herein, we propose a new electrochemical characterization equation for nanopipettes and make a suggestion on the shape of a nano-water/1,2-dichloroethane (nano-W/DCE) interface based on the characterization and calculation results. A theoretical model based on the Poisson-Nernst-Planck equation was applied to systematically study how the electric double layer influences the IT process of cations (TMA+, TEA+, TPrA+, ACh+) and anions (ClO4-, SCN-, PF6-, BF4-) at the nano-W/DCE interface. The relationships between the wall charge conditions and distribution of concentration and potential inside the nanopipette revealed that the measured standard rate constant (k0) was enhanced when the polarity of the ionic species was opposite to the pipette wall charge and reduced when the same. This work lays the right foundation to obtain the kinetics at the nano-liquid/liquid interfaces.
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Affiliation(s)
- Peng He
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yi Shao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhengyou Yu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xu Liang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Junjie Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yixuan Bian
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhiwei Zhu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Meixian Li
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Carlos M Pereira
- Centro de Investigação em Química da Universidade do Porto, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Porto 4099-002, Portugal
| | - Yuanhua Shao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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3
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Bush SN, Ken JS, Martin CR. The Ionic Composition and Chemistry of Nanopore-Confined Solutions. ACS NANO 2022; 16:8338-8346. [PMID: 35486898 DOI: 10.1021/acsnano.2c02597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
There is increasing interest in understanding the properties of solutions confined within nanotubes and synthetic or biological nanopores. How the ionic content of a nanopore-confined solution differs from that of a contacting bulk salt solution is of particular importance, for example, to water desalinization, industrial electrolysis, and all living systems. This paper explores ionic content, ionic interactions, and ion-transport properties of solutions confined within the 10 nm diameter pores of a synthetic polymer membrane. The membrane has a fixed negative pore-wall and surface charge due to ionizable carbonate groups. As a result, under some conditions, the nanopore-confined solution contains only cations and no anions or salt present in a contacting solution, ideal cation permselectivity. This anion- and salt-rejecting ability varies greatly with the cation of the salt, a result that is in contradiction to the prevailing model for permselectivity in nanopores. The extant model fails because it does not account for specific chemical interactions between the cation and the carbonate groups. The nature of these ion-selective interactions is discussed here.
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Affiliation(s)
- Stevie N Bush
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Jay S Ken
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Charles R Martin
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
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4
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Chang CC. Asymmetric Electrokinetic Energy Conversion in Slip Conical Nanopores. NANOMATERIALS 2022; 12:nano12071100. [PMID: 35407218 PMCID: PMC9000662 DOI: 10.3390/nano12071100] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 02/08/2023]
Abstract
Ion current rectification (ICR) phenomena in asymmetric nanofluidic structures, such as conical-shaped nanopores and funnel-shaped nanochannels, have been widely investigated in recent decades. To date, the effect of asymmetric nanofluidic structures on electrokinetic power generation driven by the streaming current/potential has not been explored. Accordingly, this study employed a numerical model based on the Poisson equation, Nernst–Planck equation, and Navier–Stokes equation to investigate the electrokinetic energy conversion (EKEC) in a conical nanopore while considering hydrodynamic slippage. The results indicated that the asymmetric characteristics of streaming current (short-circuit current), streaming potential (open-circuit voltage), maximum power generation, maximum conversion efficiency, and flow rate were observed in conical nanopores under the forward pressure bias (tip-to-base direction) and reverse pressure bias (base-to-tip direction) once the nonequilibrium ion concentration polarization (ICP) became considerable. The rectification behaviors in the streaming current, maximum power, and maximum conversion efficiency were all shown to be opposite to those of the well-known ICR in conical nanopores. In other words, the reverse pressure bias revealed a higher EKEC performance than the forward pressure bias. It was concluded that the asymmetric behavior in EKEC is attributed to the asymmetric electrical resistance resulting from asymmetric ion depletion and ion enrichment. Particularly, it was found that the decrease in electrical resistance (i.e., the change in electrical resistance dominated by the ion enrichment) observed in the reverse pressure bias enhanced the maximum power and maximum conversion efficiency. The asymmetric EKEC characteristics became more significant with increasing slip length, surface charge density, cone angle, and pressure bias, especially at lower salt concentrations. The present findings provide useful information for the future development of EKEC in engineered membranes with asymmetric nanopores.
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Affiliation(s)
- Chih-Chang Chang
- Department of Industrial Technology Education, National Kaohsiung Normal University, Kaohsiung 824, Taiwan
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5
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High‐Efficient and Dosage‐Controllable Intracellular Cargo Delivery through Electrochemical Metal–Organic Hybrid Nanogates. SMALL SCIENCE 2021. [DOI: 10.1002/smsc.202100069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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6
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Dutt S, Apel P, Lizunov N, Notthoff C, Wen Q, Trautmann C, Mota-Santiago P, Kirby N, Kluth P. Shape of nanopores in track-etched polycarbonate membranes. J Memb Sci 2021. [DOI: 10.1016/j.memsci.2021.119681] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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7
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Lucas FR, Sarthak K, Lenting EM, Coltan D, van der Heide NJ, Versloot RCA, Aksimentiev A, Maglia G. The Manipulation of the Internal Hydrophobicity of FraC Nanopores Augments Peptide Capture and Recognition. ACS NANO 2021; 15:9600-9613. [PMID: 34060809 PMCID: PMC8223486 DOI: 10.1021/acsnano.0c09958] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 05/21/2021] [Indexed: 05/21/2023]
Abstract
The detection of analytes and the sequencing of DNA using biological nanopores have seen major advances over recent years. The analysis of proteins and peptides with nanopores, however, is complicated by the complex physicochemical structure of polypeptides and the lack of understanding of the mechanism of capture and recognition of polypeptides by nanopores. In this work, we show that introducing aromatic amino acids at precise positions within the lumen of α-helical fragaceatoxin C (FraC) nanopores increased the capture frequency of peptides and largely improved the discrimination among peptides of similar size. Molecular dynamics simulations determined the sensing region of the nanopore, elucidated the microscopic mechanism enabling accurate characterization of the peptides via ionic current blockades in FraC, and characterized the effect of the pore modification on peptide discrimination. This work provides insights to improve the recognition and to augment the capture of peptides by nanopores, which is important for developing a real-time and single-molecule size analyzer for peptide recognition and identification.
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Affiliation(s)
| | - Kumar Sarthak
- Center
for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Erica Mariska Lenting
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - David Coltan
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Nieck Jordy van der Heide
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | | | - Aleksei Aksimentiev
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Giovanni Maglia
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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8
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Al Sulaiman D, Gatehouse A, Ivanov AP, Edel JB, Ladame S. Length-Dependent, Single-Molecule Analysis of Short Double-Stranded DNA Fragments through Hydrogel-Filled Nanopores: A Potential Tool for Size Profiling Cell-Free DNA. ACS APPLIED MATERIALS & INTERFACES 2021; 13:26673-26681. [PMID: 34085806 DOI: 10.1021/acsami.1c01145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Fast sampling followed by sequence-independent sensing and length-dependent detection of short double-stranded DNA fragments, the size of those found in blood and other bodily fluids, is achieved using engineered molecular sensors, dubbed hydrogel-filled nanopores (HFNs). Fragments as short as 100 base pairs were blindly sampled and concentrated at the tip of an HFN before reversing the applied potential to detect and distinguish individual molecules based on fragment length as they translocate out of the nanopore. A remarkable 16-fold increase in the signal-to-noise ratio was observed in the eject configuration compared to the load configuration, enabling the resolution of fragments with a size difference of 50 nucleotides in length. This fast and versatile technology offers great tunability for both sampling and detection. While increasing sampling time leads to an increase in the local DNA concentration at the tip prior to detection, a linear correlation between the peak current and DNA fragment size enables good resolution of fragments up to 250 bp long.
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Affiliation(s)
- Dana Al Sulaiman
- Department of Bioengineering, Imperial College London, Sir Michael Uren Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Alfie Gatehouse
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, London W12 0BZ, U.K
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, London W12 0BZ, U.K
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, London W12 0BZ, U.K
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, Sir Michael Uren Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
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9
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Marion S, Vučemilović-Alagić N, Špadina M, Radenović A, Smith AS. From Water Solutions to Ionic Liquids with Solid State Nanopores as a Perspective to Study Transport and Translocation Phenomena. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100777. [PMID: 33955694 DOI: 10.1002/smll.202100777] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/01/2021] [Indexed: 06/12/2023]
Abstract
Solid state nanopores are single-molecular devices governed by nanoscale physics with a broad potential for technological applications. However, the control of translocation speed in these systems is still limited. Ionic liquids are molten salts which are commonly used as alternate solvents enabling the regulation of the chemical and physical interactions on solid-liquid interfaces. While their combination can be challenging to the understanding of nanoscopic processes, there has been limited attempts on bringing these two together. While summarizing the state of the art and open questions in these fields, several major advances are presented with a perspective on the next steps in the investigations of ionic-liquid filled nanopores, both from a theoretical and experimental standpoint. By analogy to aqueous solutions, it is argued that ionic liquids and nanopores can be combined to provide new nanofluidic functionalities, as well as to help resolve some of the pertinent problems in understanding transport phenomena in confined ionic liquids and providing better control of the speed of translocating analytes.
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Affiliation(s)
- Sanjin Marion
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015, Lausanne, Switzerland
| | - Nataša Vučemilović-Alagić
- Group for Computational Life Sciences, Ruđer Bošković Institute, Division of Physical Chemistry, 10000, Zagreb, Croatia
- PULS Group, Physics Department, Interdisciplinary Center for Nanostructured Films, FAU Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Mario Špadina
- Group for Computational Life Sciences, Ruđer Bošković Institute, Division of Physical Chemistry, 10000, Zagreb, Croatia
| | - Aleksandra Radenović
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015, Lausanne, Switzerland
| | - Ana-Sunčana Smith
- Group for Computational Life Sciences, Ruđer Bošković Institute, Division of Physical Chemistry, 10000, Zagreb, Croatia
- PULS Group, Physics Department, Interdisciplinary Center for Nanostructured Films, FAU Erlangen-Nürnberg, 91058, Erlangen, Germany
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10
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Sharma V, Freedman KJ. Constricted Apertures for Dynamic Trapping and Micro-/Nanoscale Discrimination Based on Recapture Kinetics. NANO LETTERS 2021; 21:3364-3371. [PMID: 33861619 DOI: 10.1021/acs.nanolett.0c04392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Sensing via analyte passage through a constricted aperture is a powerful and robust technology which is being utilized broadly, from DNA sequencing to single virus and cell characterization. Micro- and nanoscale structures typically translocate a constricted aperture, or pore, using electrophoretic force. In the present work, we explore the advances in metrology which can be achieved through rapid directional switching of hydrodynamic forces. Interestingly, multipass measurements of microscale and nanoscale structures achieve cell discrimination. We explore this cell-discrimination phenomenon as well as other features of hydrodynamic focusing such as dynamic trapping and discrete interval sensing.
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Affiliation(s)
- Vinay Sharma
- University of California-Riverside, Department of Bioengineering, 900 University Avenue, Riverside, California 92521, United States
| | - Kevin J Freedman
- University of California-Riverside, Department of Bioengineering, 900 University Avenue, Riverside, California 92521, United States
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11
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Pal S, Ramkumar B, Jugade S, Rao A, Naik A, Chakraborty B, Varma MM. Effect of single nanoparticle-nanopore interaction strength on ionic current modulation. SENSORS AND ACTUATORS. B, CHEMICAL 2020; 325:128785. [PMID: 34321714 PMCID: PMC8312308 DOI: 10.1016/j.snb.2020.128785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Solid-state nanopores are rapidly emerging as promising platforms for developing various single molecule sensing applications. The modulation of ionic current through the pore due to translocation of the target molecule has been the dominant measurement modality in nanopore sensors. Here, we focus on the dwell time, which is the duration taken by the target molecule or particle to traverse the pore and study its dependence on the strength of interaction of the target with the pore using single gold nanoparticles (NPs) as targets interacting with a silicon nitride (SiN) nanopore. The strength of interaction, which in our case is electrostatic in nature, can be controlled by coating the nanoparticles with charged polymers. We report on an operating regime of this nanopore sensor, characterized by attractive interactions between the nanoparticle and the pore, where the dwell time is exponentially sensitive to the target-pore interaction. We used negatively and positively charged gold nanoparticles to control the strength of their interaction with the Silicon Nitride pore which is negatively charged. Our experiments revealed how this modulation of the electrostatic force greatly affects the dwell time. Positively charged NPs with strong attractive interactions with the pore resulted in increase of dwell times by 2-3 orders of magnitude, from 0.4 ms to 75.3 ms. This extreme sensitivity of the dwell time on the strength of interaction between a target and nanopore can be exploited in emerging nanopore sensor applications.
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Affiliation(s)
- Sohini Pal
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - B. Ramkumar
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Sanket Jugade
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, United States
| | - Akshay Naik
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Banani Chakraborty
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Manoj M. Varma
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India
- Corresponding author. (M.M. Varma)
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12
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Willems K, Ruić D, L R Lucas F, Barman U, Verellen N, Hofkens J, Maglia G, Van Dorpe P. Accurate modeling of a biological nanopore with an extended continuum framework. NANOSCALE 2020; 12:16775-16795. [PMID: 32780087 DOI: 10.1039/d0nr03114c] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Despite the broad success of biological nanopores as powerful instruments for the analysis of proteins and nucleic acids at the single-molecule level, a fast simulation methodology to accurately model their nanofluidic properties is currently unavailable. This limits the rational engineering of nanopore traits and makes the unambiguous interpretation of experimental results challenging. Here, we present a continuum approach that can faithfully reproduce the experimentally measured ionic conductance of the biological nanopore Cytolysin A (ClyA) over a wide range of ionic strengths and bias potentials. Our model consists of the extended Poisson-Nernst-Planck and Navier-Stokes (ePNP-NS) equations and a computationally efficient 2D-axisymmetric representation for the geometry and charge distribution of the nanopore. Importantly, the ePNP-NS equations achieve this accuracy by self-consistently considering the finite size of the ions and the influence of both the ionic strength and the nanoscopic scale of the pore on the local properties of the electrolyte. These comprise the mobility and diffusivity of the ions, and the density, viscosity and relative permittivity of the solvent. Crucially, by applying our methodology to ClyA, a biological nanopore used for single-molecule enzymology studies, we could directly quantify several nanofluidic characteristics difficult to determine experimentally. These include the ion selectivity, the ion concentration distributions, the electrostatic potential landscape, the magnitude of the electro-osmotic flow field, and the internal pressure distribution. Hence, this work provides a means to obtain fundamental new insights into the nanofluidic properties of biological nanopores and paves the way towards their rational engineering.
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Affiliation(s)
- Kherim Willems
- KU Leuven, Department of Chemistry, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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13
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Nouri R, Tang Z, Guan W. Quantitative Analysis of Factors Affecting the Event Rate in Glass Nanopore Sensors. ACS Sens 2019; 4:3007-3013. [PMID: 31612705 DOI: 10.1021/acssensors.9b01540] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
While the solid-state nanopore sensors have shown exceptional promise with their single-molecule sensitivity and label-free operations, one of the most significant challenges in the nanopore sensor is the limited analyte translocation event rate that leads to prolonged sensor response time. This issue is more pronounced when the analyte concentration is below the nanomolar (nM) range, owing to the diffusion-limited mass transport. In this work, we systematically studied the experimental factors beyond the intrinsic analyte concentration and electrophoretic mobility that affect the event rate in glass nanopore sensors. We developed a quantitative model to capture the impact of nanopore surface charge density, ionic strength, nanopore geometry, and translocation direction on the event rate. The synergistic effects of these factors on the event rates were investigated with the aim to find the optimized experimental conditions for operating the glass nanopore sensor from the response time standpoint. The findings in the study would provide useful and practical insight to enhance the device response time and achieve a lower detection limit for various glass nanopore-sensing experiments.
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14
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Pandey D, Bhattacharyya S, Ghosal S. A numerical study of the selectivity of an isolated cylindrical or conical nanopore to a charged macro-ion. BIOMICROFLUIDICS 2019; 13:054108. [PMID: 31592303 PMCID: PMC6773593 DOI: 10.1063/1.5124132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
The selectivity of a single nanopore in a uniformly charged solid membrane to a charged analyte ion is studied using numerical simulation. A continuum model is used where the ions are regarded as point particles and characterized by a continuously varying number density. The problem is described by the coupled equations for the electrostatic potential, ion-transport, and hydrodynamic flow, which are solved under appropriate boundary conditions using a finite volume method. The nanopore geometry is considered conical, the cylindrical pore being a special case where the cone angle is zero. The selectivity is characterized by a dimensionless parameter: the pore selectivity index. Results are presented showing how the pore selectivity index varies with the membrane surface charge and other parameters of the problem. The role of hydrodynamic flow on transport properties is examined and found to be consistent with theoretical results on electroosmotic flow through nanopores.
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Affiliation(s)
- Doyel Pandey
- Department of Mathematics, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Somnath Bhattacharyya
- Department of Mathematics, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sandip Ghosal
- Department of Mechanical Engineering and Engineering Sciences and Applied Mathematics, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
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15
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Malgaretti P, Janssen M, Pagonabarraga I, Rubi JM. Driving an electrolyte through a corrugated nanopore. J Chem Phys 2019; 151:084902. [DOI: 10.1063/1.5110349] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Paolo Malgaretti
- Max-Planck-Institut für Intelligente Systeme, Heisenbergstr. 3, D-70569 Stuttgart, Germany
- IV. Institut für Theoretische Physik, Universität Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Mathijs Janssen
- Max-Planck-Institut für Intelligente Systeme, Heisenbergstr. 3, D-70569 Stuttgart, Germany
- IV. Institut für Theoretische Physik, Universität Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Ignacio Pagonabarraga
- Departament de Fisica de la Materia Condensada, Universitat de Barcelona, Carrer Martí i Franqués, 08028 Barcelona, Spain
- CECAM, Centre Européeen de Calcul Atomique et Moléculaire, École Polytechnique Fédérale de Lausanne, Batochime, Avenue Forel 2, 1015 Lausanne, Switzerland
- Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, 08028 Barcelona, Spain
| | - J. Miguel Rubi
- Departament de Fisica de la Materia Condensada, Universitat de Barcelona, Carrer Martí i Franqués, 08028 Barcelona, Spain
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16
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Rabinowitz J, Edwards MA, Whittier E, Jayant K, Shepard KL. Nanoscale Fluid Vortices and Nonlinear Electroosmotic Flow Drive Ion Current Rectification in the Presence of Concentration Gradients. J Phys Chem A 2019; 123:8285-8293. [PMID: 31264868 DOI: 10.1021/acs.jpca.9b04075] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Ion current rectification (ICR) is a transport phenomenon in which an electrolyte conducts unequal currents at equal and opposite voltages. Here, we show that nanoscale fluid vortices and nonlinear electroosmotic flow (EOF) drive ICR in the presence of concentration gradients. The same EOF can yield negative differential resistance (NDR), in which current decreases with increasing voltage. A finite element model quantitatively reproduces experimental ICR and NDR recorded across glass nanopipettes under concentration gradients. The model demonstrates that spatial variations of electrical double layer properties induce the nanoscale vortices and nonlinear EOF. Experiments are performed in conditions directly related to scanning probe imaging and show that quantitative understanding of nanoscale transport under concentration gradients requires accounting for EOF. This characterization of nanopipette transport physics will benefit diverse experimentation, pushing the resolution limits of chemical and biophysical recordings.
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Affiliation(s)
| | - Martin A Edwards
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112 , United States
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17
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Zhou Y, Wang D, Li C, Hu P, Jin Y. Resistive-Pulse Sensing and Surface Charge Analysis of a Single Nanoparticle Collision at a Conical Glass Nanopore. Anal Chem 2019; 91:7648-7653. [DOI: 10.1021/acs.analchem.9b00553] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Ya Zhou
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, Jilin 130022, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Dandan Wang
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, Jilin 130022, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Chuanping Li
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Hu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, Jilin 130022, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yongdong Jin
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
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18
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Poggioli AR, Siria A, Bocquet L. Beyond the Tradeoff: Dynamic Selectivity in Ionic Transport and Current Rectification. J Phys Chem B 2019; 123:1171-1185. [DOI: 10.1021/acs.jpcb.8b11202] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Anthony R. Poggioli
- Laboratoire de Physique Statistique, Ecole Normale Supérieure, Paris 75005, France
- Centre National de la Recherche Scientifique, Paris 75005, France
| | - Alessandro Siria
- Laboratoire de Physique Statistique, Ecole Normale Supérieure, Paris 75005, France
- Centre National de la Recherche Scientifique, Paris 75005, France
| | - Lydéric Bocquet
- Laboratoire de Physique Statistique, Ecole Normale Supérieure, Paris 75005, France
- Centre National de la Recherche Scientifique, Paris 75005, France
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19
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Chinappi M, Malgaretti P. Charge polarization, local electroneutrality breakdown and eddy formation due to electroosmosis in varying-section channels. SOFT MATTER 2018; 14:9083-9087. [PMID: 30418463 DOI: 10.1039/c8sm01298a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We characterize the dynamics of an electrolyte embedded in a varying-section channel under the action of a constant external electrostatic field. By means of molecular dynamics simulations we determine the stationary density, charge and velocity profiles of the electrolyte. Our results show that when the Debye length is comparable to the width of the channel bottlenecks a concentration polarization along with two eddies sets inside the channel. Interestingly, upon increasing the external field, local electroneutrality breaks down and charge polarization sets leading to the onset of net dipolar field. This novel scenario, that cannot be captured by the standard approaches based on local electroneutrality, opens the route for the realization of novel micro and nano-fluidic devices.
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Affiliation(s)
- Mauro Chinappi
- Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, via del Politecnico 1, 00133 Roma, Italia.
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20
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Hulings ZK, Melnikov DV, Gracheva ME. Brownian dynamics simulations of the ionic current traces for a neutral nanoparticle translocating through a nanopore. NANOTECHNOLOGY 2018; 29:445204. [PMID: 30109992 DOI: 10.1088/1361-6528/aada64] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this work, the ionic current blockades due to the translocation of a neutral spherical nanoparticle through a nanopore in a solid state membrane are computed. We use a Brownian dynamics approach, in conjunction with a full three-dimensional self-consistent solution of the Poisson-Nernst-Planck and Navier-Stockes system of equations to describe realistic ionic current response arising due to the random motion of a nanoparticle through a nanopore. We find that in addition to the usual geometric blockade, the variations of the current along the axis of the pore are largely caused by a concentration polarization induced by the presence of the translocating nanoparticle in the nanopore while the current changes in the radial (perpendicular to the axis) direction occur because of the local build up of the ionic charge between the particle and the nanopore surface. By performing statistical analysis of the current traces, we also observe that, in general, smaller current blockade values correspond to faster translocation times, while increased dwell times result in a larger current decrease.
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Affiliation(s)
- Zachery K Hulings
- Department of Physics, Clarkson University, Potsdam, NY 13699, United States of America
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21
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Werkhoven BL, Everts JC, Samin S, van Roij R. Flow-Induced Surface Charge Heterogeneity in Electrokinetics due to Stern-Layer Conductance Coupled to Reaction Kinetics. PHYSICAL REVIEW LETTERS 2018; 120:264502. [PMID: 30004760 DOI: 10.1103/physrevlett.120.264502] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/18/2018] [Indexed: 06/08/2023]
Abstract
We theoretically study the electrokinetic problem of a pressure-induced liquid flow through a narrow long channel with charged walls, going beyond the classical Helmholtz-Schmolukowski picture by considering the surprisingly strong combined effect of (i) Stern-layer conductance and (ii) dynamic charge-regulating rather than fixed surface charges. We find that the water flow induces, apart from the well-known streaming potential, also a strongly heterogeneous surface charge and zeta potential on chemically homogeneous channel walls. Moreover, we identify a novel steady state with a nontrivial 3D electric flux with 2D surface charges acting as sources and sinks. For a pulsed pressure drop our findings also provide a first-principles explanation for ill-understood experiments on the effect of flow on interfacial chemistry [D. Lis et al., Science 344, 1138 (2014)SCIEAS0036-807510.1126/science.1253793].
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Affiliation(s)
- B L Werkhoven
- Institute for Theoretical Physics, Center for Extreme Matter and Emergent Phenomena, Utrecht University, Princetonplein 5, 3584 CC, Utrecht, The Netherlands
| | - J C Everts
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia
| | - S Samin
- Institute for Theoretical Physics, Center for Extreme Matter and Emergent Phenomena, Utrecht University, Princetonplein 5, 3584 CC, Utrecht, The Netherlands
| | - R van Roij
- Institute for Theoretical Physics, Center for Extreme Matter and Emergent Phenomena, Utrecht University, Princetonplein 5, 3584 CC, Utrecht, The Netherlands
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22
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Sen T, Barisik M. Size dependent surface charge properties of silica nano-channels: double layer overlap and inlet/outlet effects. Phys Chem Chem Phys 2018; 20:16719-16728. [PMID: 29881843 DOI: 10.1039/c8cp01906a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transport inside nano-channels and tubes is highly dependent on their surface charge properties. While previous studies assume that the charge density of a surface is a material property and independent of confinement size, this study properly characterized the surface charge of a nanochannel as a function of channel height and length under various solution conditions. By calculating the local surface charge based on local ionic concentrations, the surface charge of a nano-channel was studied by considering the effects of both overlapping electrical double layers (EDLs) and inlet/outlet regions. First, the surface charge of silica decreased with the increase in EDL overlap, which is characterized by the ratio of EDL thickness to channel height. Second, the local surface charge showed variation at the inlet/outlet regions where the channel's electrokinetics was in development. We defined a general entrance length as a function of EDL thickness for the electrokinetically developing part of different cases, after which the surface charge reached its equilibrium value and remained constant. Based on such length scales, we extended the existing theory to include nano-effects. A phenomenological model was developed, which can predict the average nano-channel surface charge as a function of EDL thickness, pH, channel length and channel height.
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Affiliation(s)
- Tumcan Sen
- Department of Mechanical Engineering, Izmir Institute of Technology, IZMIR, 35430, Turkey.
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23
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Wu X, Experton J, Xu W, Martin CR. Chemoresponsive Nanofluidic Pump That Turns Off in the Presence of Lead Ion. Anal Chem 2018; 90:7715-7720. [DOI: 10.1021/acs.analchem.8b01623] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Xiaojian Wu
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Juliette Experton
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Weihuang Xu
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Charles R. Martin
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
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24
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Zhang M, Ngampeerapong C, Redin D, Ahmadian A, Sychugov I, Linnros J. Thermophoresis-Controlled Size-Dependent DNA Translocation through an Array of Nanopores. ACS NANO 2018; 12:4574-4582. [PMID: 29648793 DOI: 10.1021/acsnano.8b00961] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Large arrays of nanopores can be used for high-throughput biomolecule translocation with applications toward size discrimination and sorting at the single-molecule level. In this paper, we propose to discriminate DNA length by the capture rate of the molecules to an array of relatively large nanopores (50-130 nm) by introducing a thermal gradient by laser illumination in front of the pores balancing the force from an external electric field. Nanopore arrays defined by photolithography were batch processed using standard silicon technology in combination with electrochemical etching. Parallel translocation of single, fluorophore-labeled dsDNA strands is recorded by imaging the array with a fast CMOS camera. The experimental data show that the capture rates of DNA molecules decrease with increasing DNA length due to the thermophoretic effect of the molecules. It is shown that the translocation can be completely turned off for the longer molecule using an appropriate bias, thus allowing a size discrimination of the DNA translocation through the nanopores. A derived analytical model correctly predicts the observed capture rate. Our results demonstrate that by combining a thermal and a potential gradient at the nanopores, such large nanopore arrays can potentially be used as a low-cost, high-throughput platform for molecule sensing and sorting.
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Affiliation(s)
- Miao Zhang
- Department of Applied Physics , KTH Royal Institute of Technology , Electrum 229 , 164 40 Kista , Sweden
| | - Chonmanart Ngampeerapong
- Department of Applied Physics , KTH Royal Institute of Technology , Electrum 229 , 164 40 Kista , Sweden
| | - David Redin
- School of Biotechnology, Division of Gene Technology, Science for Life Laboratory , KTH Royal Institute of Technology , SE-171 65 , Solna , Sweden
| | - Afshin Ahmadian
- School of Biotechnology, Division of Gene Technology, Science for Life Laboratory , KTH Royal Institute of Technology , SE-171 65 , Solna , Sweden
| | - Ilya Sychugov
- Department of Applied Physics , KTH Royal Institute of Technology , Electrum 229 , 164 40 Kista , Sweden
| | - Jan Linnros
- Department of Applied Physics , KTH Royal Institute of Technology , Electrum 229 , 164 40 Kista , Sweden
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25
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Abstract
Ion transporters in Nature exhibit a wealth of complex transport properties such as voltage gating, activation, and mechanosensitive behavior. When combined, such processes result in advanced ionic machines achieving active ion transport, high selectivity, or signal processing. On the artificial side, there has been much recent progress in the design and study of transport in ionic channels, but mimicking the advanced functionalities of ion transporters remains as yet out of reach. A prerequisite is the development of ionic responses sensitive to external stimuli. In the present work, we report a counterintuitive and highly nonlinear coupling between electric and pressure-driven transport in a conical nanopore, manifesting as a strong pressure dependence of the ionic conductance. This result is at odds with standard linear response theory and is akin to a mechanical transistor functionality. We fully rationalize this behavior on the basis of the coupled electrohydrodynamics in the conical pore by extending the Poisson-Nernst-Planck-Stokes framework. The model is shown to capture the subtle mechanical balance occurring within an extended spatially charged zone in the nanopore. The pronounced sensitivity to mechanical forcing offers leads in tuning ion transport by mechanical stimuli. The results presented here provide a promising avenue for the design of tailored membrane functionalities.
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26
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Xie G, Li P, Zhao Z, Zhu Z, Kong XY, Zhang Z, Xiao K, Wen L, Jiang L. Light- and Electric-Field-Controlled Wetting Behavior in Nanochannels for Regulating Nanoconfined Mass Transport. J Am Chem Soc 2018. [DOI: 10.1021/jacs.7b13136] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ganhua Xie
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Pei Li
- Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education School of Chemistry and Environment, Beihang University, Beijing 100191, P. R. China
| | - Zhiju Zhao
- College of Chemical Engineering and Biotechnology, Xingtai University, Xingtai 054001, P. R. China
| | - Zhongpeng Zhu
- Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xiang-Yu Kong
- Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Zhen Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Kai Xiao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Liping Wen
- Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education School of Chemistry and Environment, Beihang University, Beijing 100191, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Lei Jiang
- Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education School of Chemistry and Environment, Beihang University, Beijing 100191, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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27
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Abstract
We derive a general closed expression for the local pressure exerted onto the corrugated walls of a channel confining a fluid medium. When the fluid medium is at equilibrium, the local pressure is a functional of the shape of the walls. It is shown that, due to the intrinsic nonlocal character of the interactions among the particles forming the fluid, the applicability of approximate schemes such as the concept of a surface of tension or morphometric thermodynamics is limited to wall curvatures that are small compared to the range of particle-particle interactions.
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Affiliation(s)
- Paolo Malgaretti
- Max Planck Institute for Intelligent Systems, Heisenbergstrasse 3, 70569 Stuttgart, Germany and Institute for Theoretical Physics IV, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Markus Bier
- Max Planck Institute for Intelligent Systems, Heisenbergstrasse 3, 70569 Stuttgart, Germany and Institute for Theoretical Physics IV, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
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28
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Chaimanatsakun A, Japrung D, Pongprayoon P. Multiscale simulation studies of geometrical effects on solution transport through nanopores. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2017.1334881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Attaphon Chaimanatsakun
- Faculty of Engineering at Sriracha, Department of Mechanical Engineering, Kasetsart University, Sriracha, Thailand
| | - Deanpen Japrung
- National Nanotechnology Center, National Science and Technology Development Agency, Pathumthani, Thailand
| | - Prapasiri Pongprayoon
- Faculty of Science, Department of Chemistry, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Kasetsart University, Bangkok, Thailand
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29
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Martinez J, Ashby D, Zhu C, Dunn B, Baker LA, Siwy ZS. Probing ion current in solid-electrolytes at the meso- and nanoscale. Faraday Discuss 2018; 210:55-67. [DOI: 10.1039/c8fd00071a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The ionic conductivity of silica ionogel based solid electrolyte on meso and nanoscales is measured.
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Affiliation(s)
- Joseph Martinez
- Department of Physics and Astronomy
- University of California
- Irvine
- USA
| | - David Ashby
- Department of Materials Science and Engineering
- University of California
- Los Angeles
- USA
| | - Cheng Zhu
- Department of Chemistry
- Indiana University
- Bloomington
- USA
| | - Bruce Dunn
- Department of Materials Science and Engineering
- University of California
- Los Angeles
- USA
| | - Lane A. Baker
- Department of Chemistry
- Indiana University
- Bloomington
- USA
| | - Zuzanna S. Siwy
- Department of Physics and Astronomy
- University of California
- Irvine
- USA
- Department of Chemistry
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30
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Huang G, Willems K, Soskine M, Wloka C, Maglia G. Electro-osmotic capture and ionic discrimination of peptide and protein biomarkers with FraC nanopores. Nat Commun 2017; 8:935. [PMID: 29038539 PMCID: PMC5715100 DOI: 10.1038/s41467-017-01006-4] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/09/2017] [Indexed: 12/13/2022] Open
Abstract
Biological nanopores are nanoscale sensors employed for high-throughput, low-cost, and long read-length DNA sequencing applications. The analysis and sequencing of proteins, however, is complicated by their folded structure and non-uniform charge. Here we show that an electro-osmotic flow through Fragaceatoxin C (FraC) nanopores can be engineered to allow the entry of polypeptides at a fixed potential regardless of the charge composition of the polypeptide. We further use the nanopore currents to discriminate peptide and protein biomarkers from 25 kDa down to 1.2 kDa including polypeptides differing by one amino acid. On the road to nanopore proteomics, our findings represent a rationale for amino-acid analysis of folded and unfolded polypeptides with nanopores. Biological nanopore–based protein sequencing and recognition is challenging due to the folded structure or non-uniform charge of peptides. Here the authors show that engineered FraC nanopores can overcome these problems and recognize biomarkers in the form of oligopeptides, polypeptides and folded proteins.
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Affiliation(s)
- Gang Huang
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Kherim Willems
- KU Leuven Department of Chemistry, Celestijnenlaan 200G, 3001, Leuven, Belgium.,Imec, Kapeldreef 75, 3001, Leuven, Belgium
| | - Misha Soskine
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Carsten Wloka
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands.
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands.
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31
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Asandei A, Ciuca A, Apetrei A, Schiopu I, Mereuta L, Seo CH, Park Y, Luchian T. Nanoscale Investigation of Generation 1 PAMAM Dendrimers Interaction with a Protein Nanopore. Sci Rep 2017; 7:6167. [PMID: 28733599 PMCID: PMC5522495 DOI: 10.1038/s41598-017-06435-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/13/2017] [Indexed: 12/20/2022] Open
Abstract
Herein, we describe at uni-molecular level the interactions between poly(amidoamine) (PAMAM) dendrimers of generation 1 and the α-hemolysin protein nanopore, at acidic and neutral pH, and ionic strengths of 0.5 M and 1 M KCl, via single-molecule electrical recordings. The results indicate that kinetics of dendrimer-α-hemolysin reversible interactions is faster at neutral as compared to acidic pH, and we propose as a putative explanation the fine interplay among conformational and rigidity changes on the dendrimer structure, and the ionization state of the dendrimer and the α-hemolysin. From the analysis of the dendrimer's residence time inside the nanopore, we posit that the pH- and salt-dependent, long-range electrostatic interactions experienced by the dendrimer inside the ion-selective α-hemolysin, induce a non-Stokesian diffusive behavior of the analyte inside the nanopore. We also show that the ability of dendrimer molecules to adapt their structure to nanoscopic spaces, and control the flow of matter through the α-hemolysin nanopore, depends non-trivially on the pH- and salt-induced conformational changes of the dendrimer.
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Affiliation(s)
- Alina Asandei
- Interdisciplinary Research Department, Alexandru I. Cuza University, Iasi, Romania
| | - Andrei Ciuca
- Department of Physics, Alexandru I. Cuza University, Iasi, Romania
| | - Aurelia Apetrei
- Department of Physics, Alexandru I. Cuza University, Iasi, Romania
| | - Irina Schiopu
- Interdisciplinary Research Department, Alexandru I. Cuza University, Iasi, Romania
| | - Loredana Mereuta
- Department of Physics, Alexandru I. Cuza University, Iasi, Romania
| | - Chang Ho Seo
- Department of Bioinformatics, Kongju National University, Kongju, South Korea
| | - Yoonkyung Park
- Department of Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University, Gwangju, Korea.
| | - Tudor Luchian
- Department of Physics, Alexandru I. Cuza University, Iasi, Romania.
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32
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Chen K, Bell NAW, Kong J, Tian Y, Keyser UF. Direction- and Salt-Dependent Ionic Current Signatures for DNA Sensing with Asymmetric Nanopores. Biophys J 2017; 112:674-682. [PMID: 28256227 DOI: 10.1016/j.bpj.2016.12.033] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/06/2016] [Accepted: 12/21/2016] [Indexed: 11/18/2022] Open
Abstract
Solid-state nanopores are promising tools for single-molecule detection of both DNA and proteins. In this study, we investigated the patterns of ionic current blockades as DNA translocates into or out of the geometric confinement of conically shaped pores across a wide range of salt conditions. We studied how the geometry of a nanopore affects the detected ionic current signal of a translocating DNA molecule over a wide range of salt concentration. The blockade level in the ionic current depends on the translocation direction at a high salt concentration, and at lower salt concentrations we find a nonintuitive ionic current decrease and increase within each single event for the DNA translocations exiting from confinement. We use a recently developed method for synthesizing DNA molecules with multiple position markers, which provides further experimental characterization by matching the position of the DNA in the pore with the observed ionic current signal. Finally, we employ finite element calculations to explain the shapes of the signals observed at all salt concentrations and show that the unexpected current decrease and increase are due to the competing effects of ion concentration polarization and geometric exclusion of ions. Our analysis shows that over a wide range of geometries, voltages, and salt concentrations, we are able to understand the ionic current signals of DNA in asymmetric nanopores, enabling signal optimization in molecular sensing applications.
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Affiliation(s)
- Kaikai Chen
- Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom; State Key Laboratory of Tribology, Tsinghua University, Beijing, China
| | - Nicholas A W Bell
- Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Jinglin Kong
- Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Yu Tian
- State Key Laboratory of Tribology, Tsinghua University, Beijing, China
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom.
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33
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Shankla M, Aksimentiev A. Modulation of Molecular Flux Using a Graphene Nanopore Capacitor. J Phys Chem B 2017; 121:3724-3733. [PMID: 28009170 DOI: 10.1021/acs.jpcb.6b10574] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Modulation of ionic current flowing through nanoscale pores is one of the fundamental biological processes. Inspired by nature, nanopores in synthetic solid-state membranes are being developed to enable rapid analysis of biological macromolecules and to serve as elements of nanofludic circuits. Here, we theoretically investigate ion and water transport through a graphene-insulator-graphene membrane containing a single, electrolyte-filled nanopore. By means of all-atom molecular dynamics simulations, we show that the charge state of such a graphene nanopore capacitor can regulate both the selectivity and the magnitude of the nanopore ionic current. At a fixed transmembrane bias, the ionic current can be switched from being carried by an equal mixture of cations and anions to being carried almost exclusively by either cationic or anionic species, depending on the sign of the charge assigned to both plates of the capacitor. Assigning the plates of the capacitor opposite sign charges can either increase the nanopore current or reduce it substantially, depending on the polarity of the bias driving the transmembrane current. Facilitated by the changes of the nanopore surface charge, such ionic current modulations are found to occur despite the physical dimensions of the nanopore being an order of magnitude larger than the screening length of the electrolyte. The ionic current rectification is accompanied by a pronounced electro-osmotic effect that can transport neutral molecules such as proteins and drugs across the solid-state membrane and thereby serve as an interface between electronic and chemical signals.
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Affiliation(s)
- Manish Shankla
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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Bulushev RD, Marion S, Petrova E, Davis SJ, Maerkl SJ, Radenovic A. Single Molecule Localization and Discrimination of DNA-Protein Complexes by Controlled Translocation Through Nanocapillaries. NANO LETTERS 2016; 16:7882-7890. [PMID: 27960483 DOI: 10.1021/acs.nanolett.6b04165] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Through the use of optical tweezers we performed controlled translocations of DNA-protein complexes through nanocapillaries. We used RNA polymerase (RNAP) with two binding sites on a 7.2 kbp DNA fragment and a dCas9 protein tailored to have five binding sites on λ-DNA (48.5 kbp). Measured localization of binding sites showed a shift from the expected positions on the DNA that we explained using both analytical fitting and a stochastic model. From the measured force versus stage curves we extracted the nonequilibrium work done during the translocation of a DNA-protein complex and used it to obtain an estimate of the effective charge of the complex. In combination with conductivity measurements, we provided a proof of concept for discrimination between different DNA-protein complexes simultaneous to the localization of their binding sites.
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Affiliation(s)
- Roman D Bulushev
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
| | - Sanjin Marion
- Institute of Physics , Bijenička cesta 46, HR-10000 Zagreb, Croatia
| | - Ekaterina Petrova
- Laboratory of Biological Network Characterization, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
| | - Sebastian J Davis
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
| | - Sebastian J Maerkl
- Laboratory of Biological Network Characterization, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
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Lan WJ, Edwards MA, Luo L, Perera RT, Wu X, Martin CR, White HS. Voltage-Rectified Current and Fluid Flow in Conical Nanopores. Acc Chem Res 2016; 49:2605-2613. [PMID: 27689816 DOI: 10.1021/acs.accounts.6b00395] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ion current rectification (ICR) refers to the asymmetric potential-dependent rate of the passage of solution ions through a nanopore, giving rise to electrical current-voltage characteristics that mimic those of a solid-state electrical diode. Since the discovery of ICR in quartz nanopipettes two decades ago, synthetic nanopores and nanochannels of various geometries, fabricated in membranes and on wafers, have been extensively investigated to understand fundamental aspects of ion transport in highly confined geometries. It is now generally accepted that ICR requires an asymmetric electrical double layer within the nanopore, producing an accumulation or depletion of charge-carrying ions at opposite voltage polarities. Our research groups have recently explored how the voltage-dependent ion distributions and ICR within nanopores can induce novel nanoscale flow phenomena that have applications in understanding ionics in porous materials used in energy storage devices, chemical sensing, and low-cost electrical pumping of fluids. In this Account, we review our most recent investigations on this topic, based on experiments using conical nanopores (10-300 nm tip opening) fabricated in thin glass, mica, and polymer membranes. Measurable fluid flow in nanopores can be induced either using external pressure forces, electrically via electroosmotic forces, or by a combination of these two forces. We demonstrate that pressure-driven flow can greatly alter the electrical properties of nanopores and, vice versa, that the nonlinear electrical properties of conical nanopores can impart novel and useful flow phenomena. Electroosmotic flow (EOF), which depends on the magnitude of the ion fluxes within the double layer of the nanopore, is strongly coupled to the accumulation/depletion of ions. Thus, the same underlying cause of ICR also leads to EOF rectification, i.e., unequal flows occurring for the same voltage but opposite polarities. EOF rectification can be used to electrically pump fluids with very precise control across membranes containing conical pores via the application of a symmetric sinusoidal voltage. The combination of pressure and asymmetric EOF can also provide a means to generate new nanopore electrical behaviors, including negative differential resistance (NDR), in which the current through a conical pore decreases with increasing driving force (applied voltage), similar to solid-state tunnel diodes. NDR results from a positive feedback mechanism between the ion distributions and EOF, yielding a true bistability in both fluid flow and electrical current at a critical applied voltage. Nanopore-based NDR is extremely sensitive to the surface charge near the nanopore opening, suggesting possible applications in chemical sensing.
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Affiliation(s)
- Wen-Jie Lan
- Department
of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Martin A. Edwards
- Department
of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Long Luo
- Department
of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Rukshan T. Perera
- Department
of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Xiaojian Wu
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Charles R. Martin
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Henry S. White
- Department
of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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Rempfer G, Ehrhardt S, Holm C, de Graaf J. Nanoparticle Translocation through Conical Nanopores: A Finite Element Study of Electrokinetic Transport. MACROMOL THEOR SIMUL 2016. [DOI: 10.1002/mats.201600051] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Georg Rempfer
- Institute for Computational Physics (ICP); University of Stuttgart; Allmandring 3 70569 Stuttgart Germany
| | - Sascha Ehrhardt
- Institute for Computational Physics (ICP); University of Stuttgart; Allmandring 3 70569 Stuttgart Germany
| | - Christian Holm
- Institute for Computational Physics (ICP); University of Stuttgart; Allmandring 3 70569 Stuttgart Germany
| | - Joost de Graaf
- Institute for Computational Physics (ICP); University of Stuttgart; Allmandring 3 70569 Stuttgart Germany
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Hsu WL, Daiguji H. Manipulation of Protein Translocation through Nanopores by Flow Field Control and Application to Nanopore Sensors. Anal Chem 2016; 88:9251-8. [PMID: 27571138 DOI: 10.1021/acs.analchem.6b02513] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The control of biomolecule translocation through nanopores is important in nanopore protein detection. Improvement in current nanopore molecule control is desired to enhance capture rates, extend translocation times, and ensure the effective detection of various proteins in the same solutions. We present a method that simultaneously resolves these issues through the use of a gate-modulated conical nanopore coupled with solutions of varying salt concentration. Simulation results show that the presence of an induced reverse electroosmotic flow (IREOF) results in inlet flows from the two ends of the nanopore centerline entering into the nanopore in opposite directions, which simultaneously elevates the capture rate and immobilizes the protein in the nanopore, thus enabling steady current blockage measurements for a range of proteins. In addition, it is shown that proteins with different size/charge ratios can be trapped by a gate modulation intensified flow field at a similar location in the nanopore in the same solution conditions.
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Affiliation(s)
- Wei-Lun Hsu
- Department of Mechanical Engineering, University of Tokyo , Tokyo 113-8656, Japan
| | - Hirofumi Daiguji
- Department of Mechanical Engineering, University of Tokyo , Tokyo 113-8656, Japan
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Rempfer G, Ehrhardt S, Laohakunakorn N, Davies GB, Keyser UF, Holm C, de Graaf J. Selective Trapping of DNA Using Glass Microcapillaries. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:8525-8532. [PMID: 27479470 DOI: 10.1021/acs.langmuir.6b02071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We show experimentally that an inexpensive glass microcapillary can accumulate λ-phage DNA at its tip and deliver the DNA into the capillary using a combination of electro-osmotic flow, pressure-driven flow, and electrophoresis. We develop an efficient simulation model based on the electrokinetic equations and the finite-element method to explain this phenomenon. As a proof of concept for the generality of this trapping mechanism we use our numerical model to explore the effect of the salt concentration, the capillary surface charge, the applied voltage, the pressure difference, and the mobility of the analyte molecules. Our results indicate that the simple microcapillary system has the potential to capture a wide range of analyte molecules based on their electrophoretic mobility that extends well beyond our experimental example of λ-phage DNA. Our method for separation and preconcentration of analytes therefore has implications for the development of low-cost lab-on-a-chip devices.
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Affiliation(s)
- Georg Rempfer
- Institute for Computational Physics (ICP), University of Stuttgart , Allmandring 3, 70569 Stuttgart, Germany
| | - Sascha Ehrhardt
- Institute for Computational Physics (ICP), University of Stuttgart , Allmandring 3, 70569 Stuttgart, Germany
| | | | - Gary B Davies
- Institute for Computational Physics (ICP), University of Stuttgart , Allmandring 3, 70569 Stuttgart, Germany
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge , Cambridge CB3 0HE, United Kingdom
| | - Christian Holm
- Institute for Computational Physics (ICP), University of Stuttgart , Allmandring 3, 70569 Stuttgart, Germany
| | - Joost de Graaf
- Institute for Computational Physics (ICP), University of Stuttgart , Allmandring 3, 70569 Stuttgart, Germany
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Rempfer G, Davies GB, Holm C, de Graaf J. Reducing spurious flow in simulations of electrokinetic phenomena. J Chem Phys 2016; 145:044901. [DOI: 10.1063/1.4958950] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Georg Rempfer
- Institute for Computational Physics (ICP), University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Gary B. Davies
- Institute for Computational Physics (ICP), University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Christian Holm
- Institute for Computational Physics (ICP), University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Joost de Graaf
- School of Physics and Astronomy, University of Edinburgh, Scotland, Edinburgh EH9 3JL, United Kingdom
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Fahie MA, Yang B, Pham B, Chen M. Tuning the selectivity and sensitivity of an OmpG nanopore sensor by adjusting ligand tether length. ACS Sens 2016; 1:614-622. [PMID: 27500277 DOI: 10.1021/acssensors.6b00014] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We have previously shown that a biotin ligand tethered to the rim of an OmpG nanopore can be used to detect biotin-binding proteins. Here, we investigate the effect of the length of the polyethylene glycol tether on the nanopore's sensitivity and selectivity. When the tether length was increased from 2 to 45 ethylene repeats, sensitivity decreased substantially for a neutral protein streptavidin and slightly for a positively charged protein (avidin). In addition, we found that two distinct avidin binding conformations were possible when using a long tether. These conformations were sensitive to the salt concentration and applied voltage. Finally, a longer tether resulted in reduced sensitivity due to slower association for a monoclonal anti-biotin antibody. Our results highlight the importance of electrostatic, electroosmotic and electrophoretic forces on nanopore binding kinetics and sensor readout.
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Affiliation(s)
- Monifa A. Fahie
- Molecular and Cellular Biology Program and ‡Department of
Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Bib Yang
- Molecular and Cellular Biology Program and ‡Department of
Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Bach Pham
- Molecular and Cellular Biology Program and ‡Department of
Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Min Chen
- Molecular and Cellular Biology Program and ‡Department of
Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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Wu X, Ramiah Rajasekaran P, Martin CR. An Alternating Current Electroosmotic Pump Based on Conical Nanopore Membranes. ACS NANO 2016; 10:4637-43. [PMID: 27046145 DOI: 10.1021/acsnano.6b00939] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Electroosmotic flow (EOF) is used to pump solutions through microfluidic devices and capillary electrophoresis columns. We describe here an EOF pump based on membrane EOF rectification, an electrokinetic phenomenon we recently described. EOF rectification requires membranes with asymmetrically shaped pores, and conical pores in a polymeric membrane were used here. We show here that solution flow through the membrane can be achieved by applying a symmetrical sinusoidal voltage waveform across the membrane. This is possible because the alternating current (AC) carried by ions through the pore is rectified, and we previously showed that rectified currents yield EOF rectification. We have investigated the effect of both the magnitude and frequency of the voltage waveform on flow rate through the membrane, and we have measured the maximum operating pressure. Finally, we show that operating in AC mode offers potential advantages relative to conventional DC-mode EOF pumps.
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Affiliation(s)
- Xiaojian Wu
- Department of Chemistry, University of Florida , Gainesville, Florida 32611-7200, United States
| | | | - Charles R Martin
- Department of Chemistry, University of Florida , Gainesville, Florida 32611-7200, United States
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Bulushev RD, Marion S, Radenovic A. Relevance of the Drag Force during Controlled Translocation of a DNA-Protein Complex through a Glass Nanocapillary. NANO LETTERS 2015; 15:7118-25. [PMID: 26393370 DOI: 10.1021/acs.nanolett.5b03264] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Combination of glass nanocapillaries with optical tweezers allowed us to detect DNA-protein complexes in physiological conditions. In this system, a protein bound to DNA is characterized by a simultaneous change of the force and ionic current signals from the level observed for the bare DNA. Controlled displacement of the protein away from the nanocapillary opening revealed decay in the values of the force and ionic current. Negatively charged proteins EcoRI, RecA, and RNA polymerase formed complexes with DNA that experienced electrophoretic force lower than the bare DNA inside nanocapillaries. Force profiles obtained for DNA-RecA in our system were different than those in the system with nanopores in membranes and optical tweezers. We suggest that such behavior is due to the dominant impact of the drag force comparing to the electrostatic force acting on a DNA-protein complex inside nanocapillaries. We explained our results using a stochastic model taking into account the conical shape of glass nanocapillaries.
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Affiliation(s)
- Roman D Bulushev
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
| | - Sanjin Marion
- Institute of Physics , Bijenicka cesta 46, HR-10000 Zagreb, Croatia
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
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