101
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Bespalova MI, Mahanta S, Krishnan M. Single-molecule trapping and measurement in solution. Curr Opin Chem Biol 2019; 51:113-121. [DOI: 10.1016/j.cbpa.2019.05.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 05/01/2019] [Accepted: 05/13/2019] [Indexed: 01/27/2023]
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102
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Aramesh M, Forró C, Dorwling-Carter L, Lüchtefeld I, Schlotter T, Ihle SJ, Shorubalko I, Hosseini V, Momotenko D, Zambelli T, Klotzsch E, Vörös J. Localized detection of ions and biomolecules with a force-controlled scanning nanopore microscope. NATURE NANOTECHNOLOGY 2019; 14:791-798. [PMID: 31308500 DOI: 10.1038/s41565-019-0493-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 06/03/2019] [Indexed: 06/10/2023]
Abstract
Proteins, nucleic acids and ions secreted from single cells are the key signalling factors that determine the interaction of cells with their environment and the neighbouring cells. It is possible to study individual ion channels by pipette clamping, but it is difficult to dynamically monitor the activity of ion channels and transporters across the cellular membrane. Here we show that a solid-state nanopore integrated in an atomic force microscope can be used for the stochastic sensing of secreted molecules and the activity of ion channels in arbitrary locations both inside and outside a cell. The translocation of biomolecules and ions through the nanopore is observed in real time in live cells. The versatile nature of this approach allows us to detect specific biomolecules under controlled mechanical confinement and to monitor the ion-channel activities of single cells. Moreover, the nanopore microscope was used to image the surface of the nuclear membrane via high-resolution scanning ion conductance measurements.
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Affiliation(s)
- Morteza Aramesh
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland.
- Laboratory of Applied Mechanobiology, Department for Health Sciences and Technology, ETH Zürich, Zürich, Switzerland.
| | - Csaba Forró
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Livie Dorwling-Carter
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Ines Lüchtefeld
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Tilman Schlotter
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Stephan J Ihle
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Ivan Shorubalko
- Laboratory for Transport at Nanoscale Interfaces, Swiss Federal Laboratories for Materials Science and Technology (Empa), Dübendorf, Switzerland
| | - Vahid Hosseini
- Laboratory of Applied Mechanobiology, Department for Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Dmitry Momotenko
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Tomaso Zambelli
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Enrico Klotzsch
- Laboratory of Applied Mechanobiology, Department for Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
- Institute for Biology, Experimental Biophysics/ Mechanobiology, Humboldt University of Berlin, Berlin, Germany
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland.
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103
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Nouri R, Tang Z, Guan W. Calibration-Free Nanopore Digital Counting of Single Molecules. Anal Chem 2019; 91:11178-11184. [DOI: 10.1021/acs.analchem.9b01924] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Zifan Tang
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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104
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Goel M, Singh A, Bhola A, Gupta S. Size-Tunable Assembly of Gold Nanoparticles Using Competitive AC Electrokinetics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:8015-8024. [PMID: 30879298 DOI: 10.1021/acs.langmuir.8b03963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Alternating current (AC) electrokinetics is a facile way of patterning colloidal particles into advanced structures. We demonstrate the combined use of AC dielectrophoresis (AC-DEP) and AC electrohydrodynamics (AC-EHD) in a microwell electrode geometry for size-tunable assembly of gold nanoparticles (AuNPs) into one-dimensional microwires and two-dimensional films. The AC-DEP force scales with both particle size and field frequency, whereas the AC-EHD force depends only on the field frequency. So, a critical particle diameter ( dc) exists, below which the EHD phenomenon becomes more important and beyond which the DEP force is dominating. We performed theoretical and experimental studies to determine " dc" and how it gets affected by operating parameters like field frequency, voltage, particle number, electrolyte concentration, electrode size, and geometry. Our results show that the morphologies of the colloidal structures transition from films to microwires as the NP diameters vary from nanometers (< dc) to microns (> dc), and no assembly takes place at intermediate sizes (∼ dc). While the film formation is governed purely by surface EHD flows, microwire synthesis is a result of EHD-assisted DEP phenomenon. Also, a minimum particle number, a low salt concentration, and an optimum frequency range is required to initiate assembly.
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Affiliation(s)
- Meenal Goel
- Department of Chemical Engineering , Indian Institute of Technology Delhi (IITD) , New Delhi 110016 , India
| | - Akshay Singh
- Department of Chemical Engineering , Indian Institute of Technology Delhi (IITD) , New Delhi 110016 , India
| | - Ashwin Bhola
- Department of Chemical Engineering , Indian Institute of Technology Delhi (IITD) , New Delhi 110016 , India
| | - Shalini Gupta
- Department of Chemical Engineering , Indian Institute of Technology Delhi (IITD) , New Delhi 110016 , India
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105
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Albrecht T. Single-Molecule Analysis with Solid-State Nanopores. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:371-387. [PMID: 30707594 DOI: 10.1146/annurev-anchem-061417-125903] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Solid-state nanopores and nanopipettes are an exciting class of single-molecule sensors that has grown enormously over the last two decades. They offer a platform for testing fundamental concepts of stochasticity and transport at the nanoscale, for studying single-molecule biophysics and, increasingly, also for new analytical applications and in biomedical sensing. This review covers some fundamental aspects underpinning sensor operation and transport and, at the same time, it aims to put these into context as an analytical technique. It highlights new and recent developments and discusses some of the challenges lying ahead.
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Affiliation(s)
- Tim Albrecht
- School of Chemistry, University of Birmingham, Birmingham B15 2TT, United Kingdom;
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106
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Patrice FT, Qiu K, Ying YL, Long YT. Single Nanoparticle Electrochemistry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:347-370. [PMID: 31018101 DOI: 10.1146/annurev-anchem-061318-114902] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Experimental techniques to monitor and visualize the behaviors of single nanoparticles have not only revealed the significant spatial and temporal heterogeneity of those individuals, which are hidden in ensemble methods, but more importantly, they have also enabled researchers to elucidate the origin of such heterogeneity. In pursuing the intrinsic structure-function relations of single nanoparticles, the recently developed stochastic collision approach demonstrated some early promise. However, it was later realized that the appropriate sizing of a single nanoparticle by an electrochemical method could be far more challenging than initially expected owing to the dynamic motion of nanoparticles in electrolytes and complex charge-transfer characteristics at electrode surfaces. This clearly indicates a strong necessity to integrate single nanoparticle electrochemistry with high-resolution optical microscopy. Hence, this review aims to give a timely update of the latest progress for both electrochemically sensing and seeing single nanoparticles. A major focus is on collision-based measurements, where nanoparticles or single entities in solution impact on a collector electrode and the electrochemical response is recorded. These measurements are further enhanced with optical measurements in parallel. For completeness, advances in other related methods for single nanoparticle electrochemistry are also included.
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Affiliation(s)
- Fato Tano Patrice
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China; ;
| | - Kaipei Qiu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China; ;
| | - Yi-Lun Ying
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China; ;
| | - Yi-Tao Long
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China; ;
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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107
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Wang H, Tang H, Yang C, Li Y. Selective Single Molecule Nanopore Sensing of microRNA Using PNA Functionalized Magnetic Core-Shell Fe 3O 4-Au Nanoparticles. Anal Chem 2019; 91:7965-7970. [PMID: 31132236 DOI: 10.1021/acs.analchem.9b02025] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Solid-state nanopores have been employed as useful tools for single molecule analysis due to their advantages of easy fabrication and controllable diameter, but selectivity is always a big concern for complicated samples. In this work, functionalized magnetic core-shell Fe3O4-Au nanoparticles, which acted as a molecular carrier, were introduced into nanopore electrochemical system for microRNA sensing in complicated samples with high sensitivity, selectivity and signal-to-noise ratio (SNR). This strategy is based on the specific affinity between neutral peptide nucleic acids (PNA)-modified Fe3O4-Au nanoparticles and negative miRNA, and the formation of negative Fe3O4-Au-PNA-miRNA complex, which can pass through the nanopore by application of a positive potential and eliminate neutral Fe3O4-Au-PNA complex. To detect miRNA in complicated samples, a magnet has been used to separate Fe3O4-Au-PNA-miRNA complex with good selectivity. We think this is a facile and effective method for the detection of different targets at single molecular level, including nucleic acids, proteins, and other small molecules, which will open up a new approach in the nanopore sensing field.
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Affiliation(s)
- Hao Wang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science , Anhui Normal University , Wuhu 241000 , P. R. China
| | - Haoran Tang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science , Anhui Normal University , Wuhu 241000 , P. R. China
| | - Cheng Yang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science , Anhui Normal University , Wuhu 241000 , P. R. China
| | - Yongxin Li
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science , Anhui Normal University , Wuhu 241000 , P. R. China
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108
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Gao R, Lin Y, Ying YL, Hu YX, Xu SW, Ruan LQ, Yu RJ, Li YJ, Li HW, Cui LF, Long YT. Wireless nanopore electrodes for analysis of single entities. Nat Protoc 2019; 14:2015-2035. [PMID: 31168087 DOI: 10.1038/s41596-019-0171-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 04/02/2019] [Indexed: 11/09/2022]
Abstract
Measurements of a single entity underpin knowledge of the heterogeneity and stochastics in the behavior of molecules, nanoparticles, and cells. Electrochemistry provides a direct and fast method to analyze single entities as it probes electron/charge-transfer processes. However, a highly reproducible electrochemical-sensing nanointerface is often hard to fabricate because of a lack of control of the fabrication processes at the nanoscale. In comparison with conventional micro/nanoelectrodes with a metal wire inside, we present a general and easily implemented protocol that describes how to fabricate and use a wireless nanopore electrode (WNE). Nanoscale metal deposition occurs at the tip of the nanopipette, providing an electroactive sensing interface. The WNEs utilize a dynamic ionic flow instead of a metal wire to sense the interfacial redox process. WNEs provide a highly controllable interface with a 30- to 200-nm diameter. This protocol presents the construction and characterization of two types of WNEs-the open-type WNE and closed-type WNE-which can be used to achieve reproducible electrochemical measurements of single entities. Combined with the related signal amplification mechanisms, we also describe how WNEs can be used to detect single redox molecules/ions, analyze the metabolism of single cells, and discriminate single nanoparticles in a mixture. This protocol is broadly applicable to studies of living cells, nanomaterials, and sensors at the single-entity level. The total time required to complete the protocol is ~10-18 h. Each WNE costs ~$1-$3.
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Affiliation(s)
- Rui Gao
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Yao Lin
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Yi-Lun Ying
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China. .,School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China.
| | - Yong-Xu Hu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Su-Wen Xu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Lin-Qi Ruan
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Ru-Jia Yu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuan-Jie Li
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Hao-Wen Li
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Ling-Fei Cui
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Yi-Tao Long
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China.,School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
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109
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Chuah K, Wu Y, Vivekchand SRC, Gaus K, Reece PJ, Micolich AP, Gooding JJ. Nanopore blockade sensors for ultrasensitive detection of proteins in complex biological samples. Nat Commun 2019; 10:2109. [PMID: 31068594 PMCID: PMC6506515 DOI: 10.1038/s41467-019-10147-7] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 04/12/2019] [Indexed: 01/07/2023] Open
Abstract
Nanopore sensors detect individual species passing through a nanoscale pore. This experimental paradigm suffers from long analysis times at low analyte concentration and non-specific signals in complex media. These limit effectiveness of nanopore sensors for quantitative analysis. Here, we address these challenges using antibody-modified magnetic nanoparticles ((anti-PSA)-MNPs) that diffuse at zero magnetic field to capture the analyte, prostate-specific antigen (PSA). The (anti-PSA)-MNPs are magnetically driven to block an array of nanopores rather than translocate through the nanopore. Specificity is obtained by modifying nanopores with anti-PSA antibodies such that PSA molecules captured by (anti-PSA)-MNPs form an immunosandwich in the nanopore. Reversing the magnetic field removes (anti-PSA)-MNPs that have not captured PSA, limiting non-specific effects. The combined features allow detecting PSA in whole blood with a 0.8 fM detection limit. Our ‘magnetic nanoparticle, nanopore blockade’ concept points towards a strategy to improving nanopore biosensors for quantitative analysis of various protein and nucleic acid species. Nanopore sensors have long analysis times when analytes are at low concentration and non-specific signals in complex media. Here the authors use antibody-modified magnetic nanoparticles to detect prostate-specific antigen at sub-femtomolar concentrations in blood.
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Affiliation(s)
- Kyloon Chuah
- School of Chemistry, Australian Centre for NanoMedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Yanfang Wu
- School of Chemistry, Australian Centre for NanoMedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - S R C Vivekchand
- School of Chemistry, Australian Centre for NanoMedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Peter J Reece
- School of Physics, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Adam P Micolich
- School of Physics, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - J Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, NSW, 2052, Australia.
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110
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Tsutsui M, Yokota K, Nakada T, Arima A, Tonomura W, Taniguchi M, Washio T, Kawai T. Electric field interference and bimodal particle translocation in nano-integrated multipores. NANOSCALE 2019; 11:7547-7553. [PMID: 30793714 DOI: 10.1039/c8nr08632j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Parallel integration of multiple channels is a fundamental strategy for high-throughput particle detection in solid-state nanopores wherein understanding and control of crosstalk is an important issue for the post resistive pulse analysis. Here we report on a prominent effect of cross-channel electric field interference on the ionic current blockade by nanoparticles in nano-spaced pore arrays in a thin Si3N4 membrane. We systematically investigated the variations in resistive pulse profiles in multipore systems of various inter-channel distances. Although each pore acted independently when they were formed at excessively far distances, we observed significant cross-pore electrostatic interactions under close-integration that led the multipores to virtually act as a single-pore of equivalent area. As a result of the interference, the resistive pulse height demonstrated bimodal distributions due to the pronounced particle trajectory-dependence of the ionic blockade effects. Most importantly, the overcrowded multi-channel structure was found to deliver significant crosstalk with serious degradation of the sensor sensitivity to particle sizes. The present results provide a guide to design multipore structures regarding the trade-off between the detection throughput and sensor sensitivity.
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Affiliation(s)
- Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan.
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111
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Bae JH, Wang D, Hu K, Mirkin MV. Surface-Charge Effects on Voltammetry in Carbon Nanocavities. Anal Chem 2019; 91:5530-5536. [PMID: 30977642 DOI: 10.1021/acs.analchem.9b00426] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Ion transport controlled by electrostatic interactions is an important phenomenon in biological and artificial membranes, channels, and nanopores. Here, we employ carbon-coated nanopipets (CNPs) for studying permselective electrochemistry in a conductive nanopore. A significant accumulation (up to 2000-fold) of cationic redox species and anion depletion inside a CNP by diffuse-layer and surface-charge effects in a solution of low ionic strength were observed as well as the shift of the voltammetric midpeak potential. Finite-element simulations of electrostatic effects on CNP voltammograms show permselective ion transport in a single conducting nanopore and semiquantitatively explain our experimental data. The reported results are potentially useful for improving sensitivity and selectivity of CNP sensors for ionic analytes.
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Affiliation(s)
- Je Hyun Bae
- Department of Chemistry and Biochemistry , Queens College , Flushing , New York 11367 , United States
| | - Dengchao Wang
- Department of Chemistry and Biochemistry , Queens College , Flushing , New York 11367 , United States
| | - Keke Hu
- Department of Chemistry and Biochemistry , Queens College , Flushing , New York 11367 , United States.,The Graduate Center of CUNY , New York , New York 10016 , United States
| | - Michael V Mirkin
- Department of Chemistry and Biochemistry , Queens College , Flushing , New York 11367 , United States.,The Graduate Center of CUNY , New York , New York 10016 , United States
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112
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Small molecule electro-optical binding assay using nanopores. Nat Commun 2019; 10:1797. [PMID: 30996223 PMCID: PMC6470146 DOI: 10.1038/s41467-019-09476-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/12/2019] [Indexed: 01/12/2023] Open
Abstract
The identification of short nucleic acids and proteins at the single molecule level is a major driving force for the development of novel detection strategies. Nanopore sensing has been gaining in prominence due to its label-free operation and single molecule sensitivity. However, it remains challenging to detect small molecules selectively. Here we propose to combine the electrical sensing modality of a nanopore with fluorescence-based detection. Selectivity is achieved by grafting either molecular beacons, complementary DNA, or proteins to a DNA molecular carrier. We show that the fraction of synchronised events between the electrical and optical channels, can be used to perform single molecule binding assays without the need to directly label the analyte. Such a strategy can be used to detect targets in complex biological fluids such as human serum and urine. Future optimisation of this technology may enable novel assays for quantitative protein detection as well as gene mutation analysis with applications in next-generation clinical sample analysis. Nanopore detection of small molecules can be improved using molecular carriers, but separating a small analyte from the carrier signal can be challenging. Here the authors address this challenge using simultaneous electrical and optical readout in nanopore sensing to detect small molecules and quantify binding affinities.
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113
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Tonomura W, Tsutsui M, Arima A, Yokota K, Taniguchi M, Washio T, Kawai T. High-throughput single-particle detections using a dual-height-channel-integrated pore. LAB ON A CHIP 2019; 19:1352-1358. [PMID: 30907393 DOI: 10.1039/c8lc01371c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We report a proof-of-principle demonstration of particle concentration to achieve high-throughput resistive pulse detections of bacteria using a microfluidic-channel-integrated micropore. We fabricated polymeric nanochannels to trap micrometer-sized bioparticles via a simple water pumping mechanism that allowed aggregation-free size-selective particle concentration with negligible loss. Single-bioparticle detections by ionic current measurements were then implemented through releasing and transporting the thus-collected analytes to the micropore. As a result, we attained two orders of magnitude enhancement in the detection throughput by virtue of an accumulation effect via hydrodynamic control. The device concept presented may be useful in developing nanopores and nanochannels for high-throughput single-particle and -molecule analyses.
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Affiliation(s)
- Wataru Tonomura
- The Institute of Scientific and Industrial Research, Osaka University, Japan.
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114
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Yu R, Ying Y, Gao R, Long Y. Confined Nanopipette Sensing: From Single Molecules, Single Nanoparticles, to Single Cells. Angew Chem Int Ed Engl 2019; 58:3706-3714. [DOI: 10.1002/anie.201803229] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 05/25/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Ru‐Jia Yu
- Key Laboratory for Advanced MaterialsSchool of Chemistry & Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
| | - Yi‐Lun Ying
- Key Laboratory for Advanced MaterialsSchool of Chemistry & Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
| | - Rui Gao
- Key Laboratory for Advanced MaterialsSchool of Chemistry & Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
| | - Yi‐Tao Long
- Key Laboratory for Advanced MaterialsSchool of Chemistry & Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
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115
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Hu H, Yang X, Guo X, Khaliji K, Biswas SR, García de Abajo FJ, Low T, Sun Z, Dai Q. Gas identification with graphene plasmons. Nat Commun 2019; 10:1131. [PMID: 30850594 PMCID: PMC6408516 DOI: 10.1038/s41467-019-09008-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/24/2019] [Indexed: 11/09/2022] Open
Abstract
Identification of gas molecules plays a key role a wide range of applications extending from healthcare to security. However, the most widely used gas nano-sensors are based on electrical approaches or refractive index sensing, which typically are unable to identify molecular species. Here, we report label-free identification of gas molecules SO2, NO2, N2O, and NO by detecting their rotational-vibrational modes using graphene plasmon. The detected signal corresponds to a gas molecule layer adsorbed on the graphene surface with a concentration of 800 zeptomole per μm2, which is made possible by the strong field confinement of graphene plasmons and high physisorption of gas molecules on the graphene nanoribbons. We further demonstrate a fast response time (<1 min) of our devices, which enables real-time monitoring of gaseous chemical reactions. The demonstration and understanding of gas molecule identification using graphene plasmonic nanostructures open the door to various emerging applications, including in-breath diagnostics and monitoring of volatile organic compounds.
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Affiliation(s)
- Hai Hu
- Division of Nanophotonics, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, 100190, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiaoxia Yang
- Division of Nanophotonics, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, 100190, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiangdong Guo
- Division of Nanophotonics, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, 100190, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Kaveh Khaliji
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Sudipta Romen Biswas
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - F Javier García de Abajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860, Castelldefels (Barcelona), Spain.,ICREA-Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08010, Barcelona, Spain
| | - Tony Low
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Zhipei Sun
- Department of Electronics and Nanoengineering, Aalto University, Tietotie 3, FI-02150, Espoo, Finland. .,QTF Centre of Excellence, Department of Applied Physics, Aalto University, FI-00076, Aalto, Finland.
| | - Qing Dai
- Division of Nanophotonics, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, 100190, Beijing, China. .,University of Chinese Academy of Sciences, 100049, Beijing, China.
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116
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Chen Q, Yuan YJ. A review of polystyrene bead manipulation by dielectrophoresis. RSC Adv 2019; 9:4963-4981. [PMID: 35514668 PMCID: PMC9060650 DOI: 10.1039/c8ra09017c] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/14/2019] [Indexed: 01/18/2023] Open
Abstract
Exploitation of the intrinsic electrical properties of particles has recently emerged as an appealing approach for trapping and separating various scaled particles. Initiative particle manipulation by dielectrophoresis (DEP) showed remarkable advantages including high speed, ease of handling, high precision and being label-free. Herein, we provide a general overview of the manipulation of polystyrene (PS) beads and related particles via DEP; especially, the wide applications of these manipulated PS beads in the quantitative evaluation of device performance for model validation and standardization have been discussed. The motion and polarizability of the PS beads induced by DEP were analyzed and classified into two categories as positive and negative DEP within the time and space domains. The DEP techniques used for bioparticle manipulation were demonstrated, and their applications were conducted in four fields: trapping of single-sized PS beads, separation of multiple-sized PS beads by size, separation of PS beads and non-bioparticles, and separation of PS beads and bioparticles. Finally, future perspectives on DEP-on-a-chip have been proposed to discriminate bio-targets in the network of microfluidic channels.
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Affiliation(s)
- Qiaoying Chen
- Laboratory of Biosensing and MicroMechatronics, School of Materials Science and Engineering, Southwest Jiaotong University Chengdu Sichuan 610031 China
| | - Yong J Yuan
- Laboratory of Biosensing and MicroMechatronics, School of Materials Science and Engineering, Southwest Jiaotong University Chengdu Sichuan 610031 China
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117
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Nadappuram BP, Cadinu P, Barik A, Ainscough AJ, Devine MJ, Kang M, Gonzalez-Garcia J, Kittler JT, Willison KR, Vilar R, Actis P, Wojciak-Stothard B, Oh SH, Ivanov AP, Edel JB. Nanoscale tweezers for single-cell biopsies. NATURE NANOTECHNOLOGY 2019; 14:80-88. [PMID: 30510280 DOI: 10.1038/s41565-018-0315-8] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 10/19/2018] [Indexed: 05/19/2023]
Abstract
Much of the functionality of multicellular systems arises from the spatial organization and dynamic behaviours within and between cells. Current single-cell genomic methods only provide a transcriptional 'snapshot' of individual cells. The real-time analysis and perturbation of living cells would generate a step change in single-cell analysis. Here we describe minimally invasive nanotweezers that can be spatially controlled to extract samples from living cells with single-molecule precision. They consist of two closely spaced electrodes with gaps as small as 10-20 nm, which can be used for the dielectrophoretic trapping of DNA and proteins. Aside from trapping single molecules, we also extract nucleic acids for gene expression analysis from living cells without affecting their viability. Finally, we report on the trapping and extraction of a single mitochondrion. This work bridges the gap between single-molecule/organelle manipulation and cell biology and can ultimately enable a better understanding of living cells.
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Affiliation(s)
| | - Paolo Cadinu
- Department of Chemistry, Imperial College London, London, UK
| | - Avijit Barik
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Alexander J Ainscough
- Department of Chemistry, Imperial College London, London, UK
- Department of Experimental Medicine and Toxicology, Imperial College London, London, UK
| | - Michael J Devine
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Minkyung Kang
- Department of Chemistry, Imperial College London, London, UK
| | | | - Josef T Kittler
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | | | - Ramon Vilar
- Department of Chemistry, Imperial College London, London, UK
| | - Paolo Actis
- School of Electronic and Electrical Engineering, Pollard Institute, University of Leeds, Leeds, UK
| | | | - Sang-Hyun Oh
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
| | | | - Joshua B Edel
- Department of Chemistry, Imperial College London, London, UK.
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118
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Tsutsui M, Yokota K, Nakada T, Arima A, Tonomura W, Taniguchi M, Washio T, Kawai T. Particle Capture in Solid-State Multipores. ACS Sens 2018; 3:2693-2701. [PMID: 30421923 DOI: 10.1021/acssensors.8b01214] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Utilization of multiple-channel structure is a promising way of accomplishing high-throughput detections of analytes in solid-state pore sensors. Here we report on systematic investigation of particle capture efficiency in Si3N4 multipore systems of various array configurations. We demonstrated enhanced detection throughput with increasing numbers of pore channels in a membrane. Meanwhile, we also observed significant contributions of the interchannel crosstalk in closely integrated multipores that tended to deteriorate throughput performance by causing shrinkage of the absorption zone via the interference-derived weakening of the electric field around the pore orifice. At the same time, the interference-derived electric field distributions were also found to diminish the electroosmotic contributions to the particle capture efficiency. The present findings can be useful in designing pore arrays with optimal throughput performance.
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Affiliation(s)
- Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Kazumichi Yokota
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
- National Institute of Advanced Industrial Science and Technology, Takamatsu, Kagawa 761-0395, Japan
| | - Tomoko Nakada
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Akihide Arima
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Wataru Tonomura
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Takashi Washio
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
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119
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Yu R, Ying Y, Gao R, Long Y. Detektieren mit Nanopipetten im eingeschränkten Raum: von einzelnen Molekülen über Nanopartikel hin zu der Zelle. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803229] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Ru‐Jia Yu
- Key Laboratory for Advanced MaterialsSchool of Chemistry & Molecular EngineeringEast China University of Science and Technology Shanghai 200237 VR China
| | - Yi‐Lun Ying
- Key Laboratory for Advanced MaterialsSchool of Chemistry & Molecular EngineeringEast China University of Science and Technology Shanghai 200237 VR China
| | - Rui Gao
- Key Laboratory for Advanced MaterialsSchool of Chemistry & Molecular EngineeringEast China University of Science and Technology Shanghai 200237 VR China
| | - Yi‐Tao Long
- Key Laboratory for Advanced MaterialsSchool of Chemistry & Molecular EngineeringEast China University of Science and Technology Shanghai 200237 VR China
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120
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Wu Y, Tilley RD, Gooding JJ. Challenges and Solutions in Developing Ultrasensitive Biosensors. J Am Chem Soc 2018; 141:1162-1170. [PMID: 30463401 DOI: 10.1021/jacs.8b09397] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This Perspective focuses on the latest strategies and challenges for the development of bioanalytical sensors with sub-picomolar detection limits. Achieving sub-picomolar detection limits has three major challenges: (1) assay sensitivity, (2) response time, and (3) selectivity (including limiting background signals). Each of these challenges is discussed, along with how nanomaterials provide the solutions. One strategy to gain greater sensitivity involves confining the sensing volume to the nanoscale, as used in nanopore- or nanoparticle-based sensors, because nanoparticles are ubiquitous in amplification. Methods to improve response time typically focus on obtaining an intimate mixture between the sensor and the sample either by extending the length scale of nanoscale sensors using nanostructuring or by dispersing magnetic nanoparticles through the sample to capture the analyte. Loading nanoparticles with many biorecognition species is one solution to help address the challenge of selectivity. Many examples in this Perspective explore the detection of prostate-specific antigen which enables a comparison between strategies. Finally, exciting future opportunities in developing single-molecule sensors and the requirements to go even lower in concentration are explored.
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Affiliation(s)
- Yanfang Wu
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology , The University of New South Wales , Sydney , New South Wales 2052 , Australia
| | - Richard D Tilley
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology , The University of New South Wales , Sydney , New South Wales 2052 , Australia
| | - J Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology , The University of New South Wales , Sydney , New South Wales 2052 , Australia
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121
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Affiliation(s)
- Daihyun Kim
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Mukul Sonker
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
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122
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Xue L, Cadinu P, Paulose Nadappuram B, Kang M, Ma Y, Korchev Y, Ivanov AP, Edel JB. Gated Single-Molecule Transport in Double-Barreled Nanopores. ACS APPLIED MATERIALS & INTERFACES 2018; 10:38621-38629. [PMID: 30360085 PMCID: PMC6243394 DOI: 10.1021/acsami.8b13721] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Single-molecule methods have been rapidly developing with the appealing prospect of transforming conventional ensemble-averaged analytical techniques. However, challenges remain especially in improving detection sensitivity and controlling molecular transport. In this article, we present a direct method for the fabrication of analytical sensors that combine the advantages of nanopores and field-effect transistors for simultaneous label-free single-molecule detection and manipulation. We show that these hybrid sensors have perfectly aligned nanopores and field-effect transistor components making it possible to detect molecular events with up to near 100% synchronization. Furthermore, we show that the transport across the nanopore can be voltage-gated to switch on/off translocations in real time. Finally, surface functionalization of the gate electrode can also be used to fine tune transport properties enabling more active control over the translocation velocity and capture rates.
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Affiliation(s)
- Liang Xue
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
| | - Paolo Cadinu
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
| | | | - Minkyung Kang
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
| | - Ye Ma
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
| | - Yuri Korchev
- Department
of Medicine, Imperial College London, London W12 0NN, U.K.
| | - Aleksandar P. Ivanov
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
- E-mail: (A.P.I)
| | - Joshua B. Edel
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
- E-mail: (J.B.E.)
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123
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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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124
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Gao P, Ma Q, Ding D, Wang D, Lou X, Zhai T, Xia F. Distinct functional elements for outer-surface anti-interference and inner-wall ion gating of nanochannels. Nat Commun 2018; 9:4557. [PMID: 30385758 PMCID: PMC6212446 DOI: 10.1038/s41467-018-06873-z] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 10/02/2018] [Indexed: 12/18/2022] Open
Abstract
Over the decades, widespread advances have been achieved on nanochannels, including nanochannel-based DNA sequencing, single-molecule detection, smart sensors, and energy transfer and storage. However, most interest has been focused on the contribution from the functional elements (FEs) at the inner wall (IW) of nanochannels, whereas little attention has been paid to the contribution from the FEs at the nanochannels' outer surface (OS). Herein, we achieve explicit partition of FEOS and FEIW based on accurate regional-modification of OS and IW. The FEIW are served for ionic gating, and the chosen FEOS (hydrophobic or charged) are served for blocking interference molecules into the nanochannels, decreasing the false signals for the ionic gating in complex environments. Furthermore, we define a composite factor, areas of a radar map, to evaluate the FEOS performance for blocking interference molecules.
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Affiliation(s)
- Pengcheng Gao
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), 388 lumo Road, 430074, Wuhan, China
| | - Qun Ma
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), 388 lumo Road, 430074, Wuhan, China
| | - Defang Ding
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), 388 lumo Road, 430074, Wuhan, China
| | - Dagui Wang
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), 388 lumo Road, 430074, Wuhan, China
| | - Xiaoding Lou
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), 388 lumo Road, 430074, Wuhan, China
| | - Tianyou Zhai
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Material Sciences and Engineering, Huazhong University of Science and Technology (HUST), 430074, Wuhan, China
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), 388 lumo Road, 430074, Wuhan, China.
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125
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Neves MMPDS, Martín-Yerga D. Advanced Nanoscale Approaches to Single-(Bio)entity Sensing and Imaging. BIOSENSORS 2018; 8:E100. [PMID: 30373209 PMCID: PMC6316691 DOI: 10.3390/bios8040100] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/11/2018] [Accepted: 10/23/2018] [Indexed: 01/01/2023]
Abstract
Individual (bio)chemical entities could show a very heterogeneous behaviour under the same conditions that could be relevant in many biological processes of significance in the life sciences. Conventional detection approaches are only able to detect the average response of an ensemble of entities and assume that all entities are identical. From this perspective, important information about the heterogeneities or rare (stochastic) events happening in individual entities would remain unseen. Some nanoscale tools present interesting physicochemical properties that enable the possibility to detect systems at the single-entity level, acquiring richer information than conventional methods. In this review, we introduce the foundations and the latest advances of several nanoscale approaches to sensing and imaging individual (bio)entities using nanoprobes, nanopores, nanoimpacts, nanoplasmonics and nanomachines. Several (bio)entities such as cells, proteins, nucleic acids, vesicles and viruses are specifically considered. These nanoscale approaches provide a wide and complete toolbox for the study of many biological systems at the single-entity level.
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Affiliation(s)
| | - Daniel Martín-Yerga
- Department of Chemical Engineering, KTH Royal Institute of Technology, 100-44 Stockholm, Sweden.
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126
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Abstract
Sensitive and specific DNA biomarker detection is critical for accurately diagnosing a broad range of clinical conditions. However, the incorporation of such biosensing structures in integrated microfluidic devices is often complicated by the need for an additional labelling step to be implemented on the device. In this review we focused on presenting recent advances in label-free DNA biosensor technology, with a particular focus on microfluidic integrated devices. The key biosensing approaches miniaturized in flow-cell structures were presented, followed by more sophisticated microfluidic devices and higher integration examples in the literature. The option of full DNA sequencing on microfluidic chips via nanopore technology was highlighted, along with current developments in the commercialization of microfluidic, label-free DNA detection devices.
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127
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Wilson J, Aksimentiev A. Water-Compression Gating of Nanopore Transport. PHYSICAL REVIEW LETTERS 2018; 120:268101. [PMID: 30004740 PMCID: PMC6262874 DOI: 10.1103/physrevlett.120.268101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 04/18/2018] [Indexed: 05/22/2023]
Abstract
Electric field-driven motion of biomolecules is a process essential to many analytics methods, in particular, to nanopore sensing, where a transient reduction of nanopore ionic current indicates the passage of a biomolecule through the nanopore. However, before any molecule can be examined by a nanopore, the molecule must first enter the nanopore from the solution. Previously, the rate of capture by a nanopore was found to increase with the strength of the applied electric field. Here, we theoretically show that, in the case of narrow pores in graphene membranes, increasing the strength of the electric field can not only decrease the rate of capture, but also repel biomolecules from the nanopore. As the strong electric field polarizes water near and within the nanopore, the high gradient of the field also produces a strong dielectrophoretic force that compresses the water. The pressure difference caused by the sharp water density gradient produces a hydrostatic force that repels DNA or proteins from the nanopore, preventing, in certain conditions, their capture. We show that such local compression of fluid can regulate the transport of biomolecules through nanoscale passages in the absence of physical gates and sort proteins according to their phosphorylated states.
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Affiliation(s)
- James Wilson
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801 and Beckman Institute for Advanced Science and Technology
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128
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Silva J, Milne BF, Nogueira F. Theoretical Investigation of Single-Molecule Sensing Using Nanotube-Enhanced Circular Dichroism. J Phys Chem A 2018; 122:5666-5670. [DOI: 10.1021/acs.jpca.8b03676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jaime Silva
- CFisUC, Department of Physics, University of Coimbra, Rua Larga, 3004-516 Coimbra, Portugal
| | - Bruce F. Milne
- CFisUC, Department of Physics, University of Coimbra, Rua Larga, 3004-516 Coimbra, Portugal
- Coimbra Chemistry Centre, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
- Nano-Bio Spectroscopy Group, University of the Basque Country (UPV-EHU), Centro Joxe Mari Korta, Avenida de Tolosa, 72, 20018 Donostia-San Sebastian, Spain
| | - Fernando Nogueira
- CFisUC, Department of Physics, University of Coimbra, Rua Larga, 3004-516 Coimbra, Portugal
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129
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Zhang S, Li M, Su B, Shao Y. Fabrication and Use of Nanopipettes in Chemical Analysis. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2018; 11:265-286. [PMID: 29894227 DOI: 10.1146/annurev-anchem-061417-125840] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
This review summarizes progress in the fabrication, modification, characterization, and applications of nanopipettes since 2010. A brief history of nanopipettes is introduced, and the details of fabrication, modification, and characterization of nanopipettes are provided. Applications of nanopipettes in chemical analysis are the focus in several cases, including recent progress in imaging; in the study of single molecules, single nanoparticles, and single cells; in fundamental investigations of charge transfer (ion and electron) reactions at liquid/liquid interfaces; and as hyphenated techniques combined with other methods to study the mechanisms of complicated electrochemical reactions and to conduct bioanalysis.
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Affiliation(s)
- Shudong Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China;
| | - Mingzhi Li
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China;
| | - Bin Su
- Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, China;
| | - Yuanhua Shao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China;
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130
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Chang PL, Graf M, Hung CH, Radenovic A. Orthogonal Tip-to-Tip Nanocapillary Alignment Allows for Easy Detection of Fluorescent Emitters in Femtomolar Concentrations. NANO LETTERS 2018; 18:3165-3171. [PMID: 29616553 DOI: 10.1021/acs.nanolett.8b00831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Here we present the realization of a novel fluorescence detection method based on the electromigration of fluorescent molecules within a nanocapillary combined with the laser excitation through a platinum (Pt)-coated nanocapillary. By using the Pt nanocapillary assisted focusing of a laser beam, we completely remove the background scattering on the tip of the electrophoretic nanocapillary. In this excitation geometry, we demonstrate a 1000-fold sensitivity enhancement (1.0 nM to 1.0 pM) compared to the detection in microcapillaries with epifluorescence illumination and fluorescence spectrophotometry. Due to a significant electroosmotic flow, we observe a decelerating migration of DNA molecules close to the tip of the electrophoretic nanocapillary. The reduced DNA translocation velocity causes a two-step stacking process of molecules in the tip of the nanocapillary and can be used as a way to locally concentrate molecules. The sensitivity of our method is further improved by a continuous electrokinetic injection of DNA molecules followed by sample zone stacking on the tip of the nanocapillary. Concentrations ranging from 0.1 pM to 1.0 fM can be directly observed on the orifice of the electrophoretic nanocapillary. This is a 1000-fold improvement compared to traditional capillary electrophoresis with laser-induced fluorescence.
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Affiliation(s)
- Po-Ling Chang
- Department of Chemistry , Tunghai University , Taichung 40704 , Taiwan
| | - Michael Graf
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering , EPFL , 1015 Lausanne , Switzerland
| | - Chao-Hsuan Hung
- Department of Chemistry , Tunghai University , Taichung 40704 , Taiwan
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering , EPFL , 1015 Lausanne , Switzerland
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131
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Pandey P, Panday N, Chang S, Pang P, Garcia J, Wang X, Fu Q, He J. Probing Dynamic Events of Dielectric Nanoparticles by a Nanoelectrode‐Nanopore Nanopipette. ChemElectroChem 2018. [DOI: 10.1002/celc.201800163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Popular Pandey
- Physics Department Florida International University Miami 33199 United States
| | - Namuna Panday
- Physics Department Florida International University Miami 33199 United States
| | - Shuai Chang
- College of Materials and Metallurgy Wuhan University of Science and Technology Wuhan 430081 China
| | - Pei Pang
- Biodesign Institute Arizona State University Phoenix 85004 United States
| | - Javier Garcia
- Physics Department Florida International University Miami 33199 United States
| | - Xuewen Wang
- Physics Department Florida International University Miami 33199 United States
| | - Qiang Fu
- JiangXi College of Traditional Chinese Medicine Fuzhou 344000 China
| | - Jin He
- Physics Department Florida International University Miami 33199 United States
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132
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Shi L, Rana A, Esfandiari L. A low voltage nanopipette dielectrophoretic device for rapid entrapment of nanoparticles and exosomes extracted from plasma of healthy donors. Sci Rep 2018; 8:6751. [PMID: 29712935 PMCID: PMC5928082 DOI: 10.1038/s41598-018-25026-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/13/2018] [Indexed: 12/15/2022] Open
Abstract
An insulator-based dielectrophoresis (iDEP) is a label-free method that has been extensively utilized for manipulation of nanoparticles, cells, and biomolecules. Here, we present a new iDEP approach that can rapidly trap nanoparticles at the close proximity of a glass nanopipette’s tip by applying 10 V/cm direct current (DC) across the pipette’s length. The trapping mechanism was systemically studied using both numerical modeling and experimental observations. The results showed that the particle trapping was determined to be controlled by three dominant electrokinetic forces including dielectrophoretic, electrophoretic and electroosmotic force. Furthermore, the effect of the ionic strength, the pipette’s geometry, and the applied electric field on the entrapment efficiency was investigated. To show the application of our device in biomedical sciences, we demonstrated the successful entrapment of fluorescently tagged liposomes and unlabeled plasma-driven exosomes from the PBS solution. Also, to illustrate the selective entrapment capability of our device, 100 nm liposomes were extracted from the PBS solution containing 500 nm polystyrene particles at the tip of the pipette as the voltage polarity was reversed.
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Affiliation(s)
- Leilei Shi
- Department of Electrical Engineering and Computer Science, College of Engineering and Applied Science, University of Cincinnati, Ohio, 45221, United States
| | - Ankit Rana
- Department of Electrical Engineering and Computer Science, College of Engineering and Applied Science, University of Cincinnati, Ohio, 45221, United States
| | - Leyla Esfandiari
- Department of Electrical Engineering and Computer Science, College of Engineering and Applied Science, University of Cincinnati, Ohio, 45221, United States. .,Department of Biomedical Engineering, College of Engineering and Applied Science, University of Cincinnati, Ohio, 45221, United States.
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133
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Xiao K, Chen L, Xie G, Li P, Kong XY, Wen L, Jiang L. A bio-inspired dumbbell-shaped nanochannel with a controllable structure and ionic rectification. NANOSCALE 2018; 10:6850-6854. [PMID: 29616269 DOI: 10.1039/c8nr01191e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Inspired by the potassium ion channel, here, we firstly report a structure-tailorable dumbbell-shaped nanochannel with controllable ionic rectification. This system creates an ideal experimental and theoretical platform for the precision transportation of ions, which have potential applications in analytical sciences.
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Affiliation(s)
- Kai Xiao
- Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China.
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134
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Direct electrochemical observation of glucosidase activity in isolated single lysosomes from a living cell. Proc Natl Acad Sci U S A 2018; 115:4087-4092. [PMID: 29610324 PMCID: PMC5910846 DOI: 10.1073/pnas.1719844115] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The quantification of protein activity in individual lysosomes in living cells is realized using a nanocapillary designed to electrochemically analyze internal solution, in which a single lysosome is sorted from the cell and the target protein is reacted with the corresponding kit components to generate hydrogen peroxide for measurement. The ability to sort and assay multiple lysosomes from the same cell allows direct study of protein function at subcellular resolution and provides unprecedented information about the homogeneity within the lysosomal population of a single cell. The protein activity in individual intracellular compartments in single living cells must be analyzed to obtain an understanding of protein function at subcellular locations. The current methodology for probing activity is often not resolved to the level of an individual compartment, and the results provide an extent of reaction that is averaged from a group of compartments. To address this technological limitation, a single lysosome is sorted from a living cell via electrophoresis into a nanocapillary designed to electrochemically analyze internal solution. The activity of a protein specific to lysosomes, β-glucosidase, is determined by the electrochemical quantification of hydrogen peroxide generated from the reaction with its substrate and the associated enzymes preloaded in the nanocapillary. Sorting and assaying multiple lysosomes from the same cell shows the relative homogeneity of protein activity between different lysosomes, whereas the protein activity in single lysosomes from different cells of the same type is heterogeneous. Thus, this study for the analysis of protein activity within targeted cellular compartments allows direct study of protein function at subcellular resolution and provides unprecedented information about the homogeneity within the lysosomal population of a single cell.
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135
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Chen XZ, Jang B, Ahmed D, Hu C, De Marco C, Hoop M, Mushtaq F, Nelson BJ, Pané S. Small-Scale Machines Driven by External Power Sources. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1705061. [PMID: 29443430 DOI: 10.1002/adma.201705061] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/03/2017] [Indexed: 05/23/2023]
Abstract
Micro- and nanorobots have shown great potential for applications in various fields, including minimally invasive surgery, targeted therapy, cell manipulation, environmental monitoring, and water remediation. Recent progress in the design, fabrication, and operation of these miniaturized devices has greatly enhanced their versatility. In this report, the most recent progress on the manipulation of small-scale robots based on power sources, such as magnetic fields, light, acoustic waves, electric fields, thermal energy, or combinations of these, is surveyed. The design and propulsion mechanism of micro- and nanorobots are the focus of this article. Their fabrication and applications are also briefly discussed.
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Affiliation(s)
- Xiang-Zhong Chen
- Multi-Scale Robotics Lab (MSRL), Institute of Robotics and Intelligent Systems (IRIS), ETH Zurich, CH, 8092, Zurich, Switzerland
| | - Bumjin Jang
- Multi-Scale Robotics Lab (MSRL), Institute of Robotics and Intelligent Systems (IRIS), ETH Zurich, CH, 8092, Zurich, Switzerland
| | - Daniel Ahmed
- Multi-Scale Robotics Lab (MSRL), Institute of Robotics and Intelligent Systems (IRIS), ETH Zurich, CH, 8092, Zurich, Switzerland
| | - Chengzhi Hu
- Multi-Scale Robotics Lab (MSRL), Institute of Robotics and Intelligent Systems (IRIS), ETH Zurich, CH, 8092, Zurich, Switzerland
| | - Carmela De Marco
- Multi-Scale Robotics Lab (MSRL), Institute of Robotics and Intelligent Systems (IRIS), ETH Zurich, CH, 8092, Zurich, Switzerland
| | - Marcus Hoop
- Multi-Scale Robotics Lab (MSRL), Institute of Robotics and Intelligent Systems (IRIS), ETH Zurich, CH, 8092, Zurich, Switzerland
| | - Fajer Mushtaq
- Multi-Scale Robotics Lab (MSRL), Institute of Robotics and Intelligent Systems (IRIS), ETH Zurich, CH, 8092, Zurich, Switzerland
| | - Bradley J Nelson
- Multi-Scale Robotics Lab (MSRL), Institute of Robotics and Intelligent Systems (IRIS), ETH Zurich, CH, 8092, Zurich, Switzerland
| | - Salvador Pané
- Multi-Scale Robotics Lab (MSRL), Institute of Robotics and Intelligent Systems (IRIS), ETH Zurich, CH, 8092, Zurich, Switzerland
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136
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Ying YL, Hu YX, Gao R, Yu RJ, Gu Z, Lee LP, Long YT. Asymmetric Nanopore Electrode-Based Amplification for Electron Transfer Imaging in Live Cells. J Am Chem Soc 2018. [PMID: 29529376 DOI: 10.1021/jacs.7b12106] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Capturing real-time electron transfer, enzyme activity, molecular dynamics, and biochemical messengers in living cells is essential for understanding the signaling pathways and cellular communications. However, there is no generalizable method for characterizing a broad range of redox-active species in a single living cell at the resolution of cellular compartments. Although nanoelectrodes have been applied in the intracellular detection of redox-active species, the fabrication of nanoelectrodes to maximize the signal-to-noise ratio of the probe remains challenging because of the stringent requirements of 3D fabrication. Here, we report an asymmetric nanopore electrode-based amplification mechanism for the real-time monitoring of NADH in a living cell. We used a two-step 3D fabrication process to develop a modified asymmetric nanopore electrode with a diameter down to 90 nm, which allowed for the detection of redox metabolism in living cells. Taking advantage of the asymmetric geometry, the above 90% potential drop at the two terminals of the nanopore electrode converts the faradaic current response into an easily distinguishable bubble-induced transient ionic current pattern. Therefore, the current signal was amplified by at least 3 orders of magnitude, which was dynamically linked to the presence of trace redox-active species. Compared to traditional wire electrodes, this wireless asymmetric nanopore electrode exhibits a high signal-to-noise ratio by increasing the current resolution from nanoamperes to picoamperes. The asymmetric nanopore electrode achieves the highly sensitive and selective probing of NADH concentrations as low as 1 pM. Moreover, it enables the real-time nanopore monitoring of the respiration chain (i.e., NADH) in a living cell and the evaluation of the effects of anticancer drugs in an MCF-7 cell. We believe that this integrated wireless asymmetric nanopore electrode provides promising building blocks for the future imaging of electron transfer dynamics in live cells.
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Affiliation(s)
- Yi-Lun Ying
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , PR China
| | - Yong-Xu Hu
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , PR China
| | - Rui Gao
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , PR China
| | - Ru-Jia Yu
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , PR China
| | - Zhen Gu
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , PR China
| | - Luke P Lee
- Biomedical Institute for Global Health Research and Technology , National University of Singapore , 117599 Singapore.,Departments of Bioengineering, Electrical Engineering, and Computer Sciences , ∥Berkeley Sensor and Actuator Center , and ⊥Biophysics Graduate Program , University of California , Berkeley , California 94720 , United States
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , PR China
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137
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Abstract
Bioinspired smart asymmetric nanochannel membranes (BSANM) have been explored extensively to achieve the delicate ionic transport functions comparable to those of living organisms. The abiotic system exhibits superior stability and robustness, allowing for promising applications in many fields. In view of the abundance of research concerning BSANM in the past decade, herein, we present a systematic overview of the development of the state-of-the-art BSANM system. The discussion is focused on the construction methodologies based on raw materials with diverse dimensions (i.e. 0D, 1D, 2D, and bulk). A generic strategy for the design and construction of the BSANM system is proposed first and put into context with recent developments from homogeneous to heterogeneous nanochannel membranes. Then, the basic properties of the BSANM are introduced including selectivity, gating, and rectification, which are associated with the particular chemical and physical structures. Moreover, we summarized the practical applications of BSANM in energy conversion, biochemical sensing and other areas. In the end, some personal opinions on the future development of the BSANM are briefly illustrated. This review covers most of the related literature reported since 2010 and is intended to build up a broad and deep knowledge base that can provide a solid information source for the scientific community.
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Affiliation(s)
- 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
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138
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Bayley H. Single-molecule DNA sequencing: Getting to the bottom of the well. NATURE NANOTECHNOLOGY 2017; 12:1116-1117. [PMID: 28945241 DOI: 10.1038/nnano.2017.205] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Hagan Bayley
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
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139
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Larkin J, Henley RY, Jadhav V, Korlach J, Wanunu M. Length-independent DNA packing into nanopore zero-mode waveguides for low-input DNA sequencing. NATURE NANOTECHNOLOGY 2017; 12:1169-1175. [PMID: 28892102 PMCID: PMC5718969 DOI: 10.1038/nnano.2017.176] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 07/26/2017] [Indexed: 05/03/2023]
Abstract
Compared with conventional methods, single-molecule real-time (SMRT) DNA sequencing exhibits longer read lengths than conventional methods, less GC bias, and the ability to read DNA base modifications. However, reading DNA sequence from sub-nanogram quantities is impractical owing to inefficient delivery of DNA molecules into the confines of zero-mode waveguides-zeptolitre optical cavities in which DNA sequencing proceeds. Here, we show that the efficiency of voltage-induced DNA loading into waveguides equipped with nanopores at their floors is five orders of magnitude greater than existing methods. In addition, we find that DNA loading is nearly length-independent, unlike diffusive loading, which is biased towards shorter fragments. We demonstrate here loading and proof-of-principle four-colour sequence readout of a polymerase-bound 20,000-base-pair-long DNA template within seconds from a sub-nanogram input quantity, a step towards low-input DNA sequencing and mammalian epigenomic mapping of native DNA samples.
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Affiliation(s)
- Joseph Larkin
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - Robert Y Henley
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - Vivek Jadhav
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
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140
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Graphene-edge dielectrophoretic tweezers for trapping of biomolecules. Nat Commun 2017; 8:1867. [PMID: 29192277 PMCID: PMC5709377 DOI: 10.1038/s41467-017-01635-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 10/05/2017] [Indexed: 12/19/2022] Open
Abstract
The many unique properties of graphene, such as the tunable optical, electrical, and plasmonic response make it ideally suited for applications such as biosensing. As with other surface-based biosensors, however, the performance is limited by the diffusive transport of target molecules to the surface. Here we show that atomically sharp edges of monolayer graphene can generate singular electrical field gradients for trapping biomolecules via dielectrophoresis. Graphene-edge dielectrophoresis pushes the physical limit of gradient-force-based trapping by creating atomically sharp tweezers. We have fabricated locally backgated devices with an 8-nm-thick HfO2 dielectric layer and chemical-vapor-deposited graphene to generate 10× higher gradient forces as compared to metal electrodes. We further demonstrate near-100% position-controlled particle trapping at voltages as low as 0.45 V with nanodiamonds, nanobeads, and DNA from bulk solution within seconds. This trapping scheme can be seamlessly integrated with sensors utilizing graphene as well as other two-dimensional materials. The capability of positioning target molecules onto the edges of patterned graphene nanostructures is highly desirable. Here, the authors demonstrate that the atomically sharp edges of graphene can be used as dielectrophoretic tweezers for gradient-force-based trapping applications.
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141
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Zhang H, Hiratani M, Nagaoka K, Kawano R. MicroRNA detection at femtomolar concentrations with isothermal amplification and a biological nanopore. NANOSCALE 2017; 9:16124-16127. [PMID: 29043339 DOI: 10.1039/c7nr04215a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
One of the greatest challenges faced by chemists and biologists is the detection of molecules at extremely low concentrations. This paper describes a method to detect ultra-low concentrations (1 femtomole) of nucleotides using isothermal amplification and a biological nanopore.
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Affiliation(s)
- Haolin Zhang
- Laboratory of Veterinary Physiology, Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
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142
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Yu Y, Sundaresan V, Bandyopadhyay S, Zhang Y, Edwards MA, McKelvey K, White HS, Willets KA. Three-Dimensional Super-resolution Imaging of Single Nanoparticles Delivered by Pipettes. ACS NANO 2017; 11:10529-10538. [PMID: 28968077 DOI: 10.1021/acsnano.7b05902] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Controlled three-dimensional positioning of nanoparticles is achieved by delivering single fluorescent nanoparticles from a nanopipette and capturing them at well-defined regions of an electrified substrate. To control the position of single nanoparticles, the force of the pressure-driven flow from the pipette is balanced by the attractive electrostatic force at the substrate, providing a strategy by which nanoparticle trajectories can be manipulated in real time. To visualize nanoparticle motion, a resistive-pulse electrochemical setup is coupled with an optical microscope, and nanoparticle trajectories are tracked in three dimensions using super-resolution fluorescence imaging to obtain positional information with precision in the tens of nanometers. As the particles approach the substrate, the diffusion kinetics are analyzed and reveal either subdiffusive (hindered) or superdiffusive (directed) motion depending on the electric field at the substrate and the pressure-driven flow from the pipette. By balancing the effects of the forces exerted on the particle by the pressure and electric fields, controlled, real-time manipulation of single nanoparticle trajectories is achieved. The developed approach has implications for a variety of applications such as surface patterning and drug delivery using colloidal nanoparticles.
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Affiliation(s)
- Yun Yu
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Vignesh Sundaresan
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | | | - Yulun Zhang
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
| | - Martin A Edwards
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
| | - Kim McKelvey
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
| | - Henry S White
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
| | - Katherine A Willets
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
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143
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Cadinu P, Paulose Nadappuram B, Lee DJ, Sze JYY, Campolo G, Zhang Y, Shevchuk A, Ladame S, Albrecht T, Korchev Y, Ivanov AP, Edel JB. Single Molecule Trapping and Sensing Using Dual Nanopores Separated by a Zeptoliter Nanobridge. NANO LETTERS 2017; 17:6376-6384. [PMID: 28862004 PMCID: PMC5662926 DOI: 10.1021/acs.nanolett.7b03196] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/01/2017] [Indexed: 05/19/2023]
Abstract
There is a growing realization, especially within the diagnostic and therapeutic community, that the amount of information enclosed in a single molecule can not only enable a better understanding of biophysical pathways, but also offer exceptional value for early stage biomarker detection of disease onset. To this end, numerous single molecule strategies have been proposed, and in terms of label-free routes, nanopore sensing has emerged as one of the most promising methods. However, being able to finely control molecular transport in terms of transport rate, resolution, and signal-to-noise ratio (SNR) is essential to take full advantage of the technology benefits. Here we propose a novel solution to these challenges based on a method that allows biomolecules to be individually confined into a zeptoliter nanoscale droplet bridging two adjacent nanopores (nanobridge) with a 20 nm separation. Molecules that undergo confinement in the nanobridge are slowed down by up to 3 orders of magnitude compared to conventional nanopores. This leads to a dramatic improvement in the SNR, resolution, sensitivity, and limit of detection. The strategy implemented is universal and as highlighted in this manuscript can be used for the detection of dsDNA, RNA, ssDNA, and proteins.
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Affiliation(s)
- Paolo Cadinu
- Department
of Chemistry, Department of Bioengineering, Department of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Binoy Paulose Nadappuram
- Department
of Chemistry, Department of Bioengineering, Department of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Dominic J. Lee
- Department
of Chemistry, Department of Bioengineering, Department of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Jasmine Y. Y. Sze
- Department
of Chemistry, Department of Bioengineering, Department of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Giulia Campolo
- Department
of Chemistry, Department of Bioengineering, Department of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Yanjun Zhang
- Department
of Chemistry, Department of Bioengineering, Department of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Andrew Shevchuk
- Department
of Chemistry, Department of Bioengineering, Department of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Sylvain Ladame
- Department
of Chemistry, Department of Bioengineering, Department of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Tim Albrecht
- Department
of Chemistry, Department of Bioengineering, Department of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Yuri Korchev
- Department
of Chemistry, Department of Bioengineering, Department of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Aleksandar P. Ivanov
- Department
of Chemistry, Department of Bioengineering, Department of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Joshua B. Edel
- Department
of Chemistry, Department of Bioengineering, Department of Medicine, Imperial College London, SW7 2AZ, United Kingdom
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144
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Ren R, Zhang Y, Nadappuram BP, Akpinar B, Klenerman D, Ivanov AP, Edel JB, Korchev Y. Nanopore extended field-effect transistor for selective single-molecule biosensing. Nat Commun 2017; 8:586. [PMID: 28928405 PMCID: PMC5605549 DOI: 10.1038/s41467-017-00549-w] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/07/2017] [Indexed: 11/21/2022] Open
Abstract
There has been a significant drive to deliver nanotechnological solutions to biosensing, yet there remains an unmet need in the development of biosensors that are affordable, integrated, fast, capable of multiplexed detection, and offer high selectivity for trace analyte detection in biological fluids. Herein, some of these challenges are addressed by designing a new class of nanoscale sensors dubbed nanopore extended field-effect transistor (nexFET) that combine the advantages of nanopore single-molecule sensing, field-effect transistors, and recognition chemistry. We report on a polypyrrole functionalized nexFET, with controllable gate voltage that can be used to switch on/off, and slow down single-molecule DNA transport through a nanopore. This strategy enables higher molecular throughput, enhanced signal-to-noise, and even heightened selectivity via functionalization with an embedded receptor. This is shown for selective sensing of an anti-insulin antibody in the presence of its IgG isotype. Efficient detection of single molecules is vital to many biosensing technologies, which require analytical platforms with high selectivity and sensitivity. Ren et al. combine a nanopore sensor and a field-effect transistor, whereby gate voltage mediates DNA and protein transport through the nanopore.
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Affiliation(s)
- Ren Ren
- Department of Medicine, Imperial College London, London, W12 0NN, UK.,Department of Chemistry, Imperial College London, London, SW7 2AZ, UK
| | - Yanjun Zhang
- Department of Medicine, Imperial College London, London, W12 0NN, UK. .,Tianjin Neurological Institute, Tianjin Medical University General Hospital, Heping Qu, 300052, China.
| | | | - Bernice Akpinar
- Department of Chemistry, Imperial College London, London, SW7 2AZ, UK
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | | | - Joshua B Edel
- Department of Chemistry, Imperial College London, London, SW7 2AZ, UK.
| | - Yuri Korchev
- Department of Medicine, Imperial College London, London, W12 0NN, UK.,National University of Science & Technology MISIS, Moscow, 119049, Russia
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145
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Chen K, Juhasz M, Gularek F, Weinhold E, Tian Y, Keyser UF, Bell NAW. Ionic Current-Based Mapping of Short Sequence Motifs in Single DNA Molecules Using Solid-State Nanopores. NANO LETTERS 2017; 17:5199-5205. [PMID: 28829136 PMCID: PMC5599873 DOI: 10.1021/acs.nanolett.7b01009] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Nanopore sensors show great potential for rapid, single-molecule determination of DNA sequence information. Here, we develop an ionic current-based method for determining the positions of short sequence motifs in double-stranded DNA molecules with solid-state nanopores. Using the DNA-methyltransferase M.TaqI and a biotinylated S-adenosyl-l-methionine cofactor analogue we create covalently attached biotin labels at 5'-TCGA-3' sequence motifs. Monovalent streptavidin is then added to bind to the biotinylated sites giving rise to additional current blockade signals when the DNA passes through a conical quartz nanopore. We determine the relationship between translocation time and position along the DNA contour and find a minimum resolvable distance between two labeled sites of ∼200 bp. We then characterize a variety of DNA molecules by determining the positions of bound streptavidin and show that two short genomes can be simultaneously detected in a mixture. Our method provides a simple, generic single-molecule detection platform enabling DNA characterization in an electrical format suited for portable devices for potential diagnostic applications.
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Affiliation(s)
- Kaikai Chen
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
- State
Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China
| | - Matyas Juhasz
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Felix Gularek
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Elmar Weinhold
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Yu Tian
- State
Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China
| | - Ulrich F. Keyser
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
- E-mail:
| | - Nicholas A. W. Bell
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
- E-mail: . Fax: +44 (0)1223 337000
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146
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Wang D, Mirkin MV. Electron-Transfer Gated Ion Transport in Carbon Nanopipets. J Am Chem Soc 2017; 139:11654-11657. [DOI: 10.1021/jacs.7b05058] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Dengchao Wang
- Department of Chemistry and
Biochemistry, Queens College, City University of New York, Flushing, New York 11367, United States
| | - Michael V. Mirkin
- Department of Chemistry and
Biochemistry, Queens College, City University of New York, Flushing, New York 11367, United States
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147
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Chorsi HT, Zhu Y, Zhang JXJ. Patterned Plasmonic Surfaces-Theory, Fabrication, and Applications in Biosensing. JOURNAL OF MICROELECTROMECHANICAL SYSTEMS : A JOINT IEEE AND ASME PUBLICATION ON MICROSTRUCTURES, MICROACTUATORS, MICROSENSORS, AND MICROSYSTEMS 2017; 26:718-739. [PMID: 29276365 PMCID: PMC5736324 DOI: 10.1109/jmems.2017.2699864] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Low-profile patterned plasmonic surfaces are synergized with a broad class of silicon microstructures to greatly enhance near-field nanoscale imaging, sensing, and energy harvesting coupled with far-field free-space detection. This concept has a clear impact on several key areas of interest for the MEMS community, including but not limited to ultra-compact microsystems for sensitive detection of small number of target molecules, and "surface" devices for optical data storage, micro-imaging and displaying. In this paper, we review the current state-of-the-art in plasmonic theory as well as derive design guidance for plasmonic integration with microsystems, fabrication techniques, and selected applications in biosensing, including refractive-index based label-free biosensing, plasmonic integrated lab-on-chip systems, plasmonic near-field scanning optical microscopy and plasmonics on-chip systems for cellular imaging. This paradigm enables low-profile conformal surfaces on microdevices, rather than bulk material or coatings, which provide clear advantages for physical, chemical and biological-related sensing, imaging, and light harvesting, in addition to easier realization, enhanced flexibility, and tunability.
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Affiliation(s)
- Hamid T Chorsi
- Thayer School of engineering, Dartmouth College, Hanover, NH 03755 USA
| | - Ying Zhu
- Thayer School of engineering, Dartmouth College, Hanover, NH 03755 USA
| | - John X J Zhang
- Thayer School of engineering, Dartmouth College, Hanover, NH 03755 USA
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148
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Fujii S, Nobukawa A, Osaki T, Morimoto Y, Kamiya K, Misawa N, Takeuchi S. Pesticide vapor sensing using an aptamer, nanopore, and agarose gel on a chip. LAB ON A CHIP 2017; 17:2421-2425. [PMID: 28620670 DOI: 10.1039/c7lc00361g] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
A pesticide vapor sensor was developed using an agarose gel-based chip containing a nanopore sensing system. Vaporized omethoate was detected by the absorption into the gel, the complex formation with a DNA aptamer, and its obstruction at the nanopore. This strategy is applicable to other vapors, expanding the versatility of nanopore sensors.
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Affiliation(s)
- Satoshi Fujii
- Kanagawa Academy of Science and Technology (The current name is, Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology), 3-2-1 Sakado, Takatsu, 213-0012 Kawasaki, Japan.
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149
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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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150
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Bajaj H, Acosta Gutierrez S, Bodrenko I, Malloci G, Scorciapino MA, Winterhalter M, Ceccarelli M. Bacterial Outer Membrane Porins as Electrostatic Nanosieves: Exploring Transport Rules of Small Polar Molecules. ACS NANO 2017; 11:5465-5473. [PMID: 28485920 DOI: 10.1021/acsnano.6b08613] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Transport of molecules through biological membranes is a fundamental process in biology, facilitated by selective channels and general pores. The architecture of some outer membrane pores in Gram-negative bacteria, common to other eukaryotic pores, suggests them as prototypes of electrostatically regulated nanosieve devices. In this study, we sensed the internal electrostatics of the two most abundant outer membrane channels of Escherichia coli, using norfloxacin as a dipolar probe in single molecule electrophysiology. The voltage dependence of the association rate constant of norfloxacin interacting with these nanochannels follows an exponential trend, unexpected for neutral molecules. We combined electrophysiology, channel mutagenesis, and enhanced sampling molecular dynamics simulations to explain this molecular mechanism. Voltage and temperature dependent ion current measurements allowed us to quantify the transversal electric field inside the channel as well as the distance where the applied potential drops. Finally, we proposed a general model for transport of polar molecules through these electrostatic nanosieves. Our model helps to further understand the basis for permeability in Gram-negative pathogens, contributing to fill in the innovation gap that has limited the discovery of effective antibiotics in the last 20 years.
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Affiliation(s)
- Harsha Bajaj
- Jacobs University Bremen , Campus Ring 1, D-28759 Bremen, Germany
| | | | - Igor Bodrenko
- Department of Physics, University of Cagliari , 09124 Cagliari, Italy
| | - Giuliano Malloci
- Department of Physics, University of Cagliari , 09124 Cagliari, Italy
| | | | | | - Matteo Ceccarelli
- Department of Physics, University of Cagliari , 09124 Cagliari, Italy
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