1
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Roelen Z, Briggs K, Tabard-Cossa V. Analysis of Nanopore Data: Classification Strategies for an Unbiased Curation of Single-Molecule Events from DNA Nanostructures. ACS Sens 2023; 8:2809-2823. [PMID: 37436112 PMCID: PMC10913896 DOI: 10.1021/acssensors.3c00751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Nanopores are versatile single-molecule sensors that are being used to sense increasingly complex mixtures of structured molecules with applications in molecular data storage and disease biomarker detection. However, increased molecular complexity presents additional challenges to the analysis of nanopore data, including more translocation events being rejected for not matching an expected signal structure and a greater risk of selection bias entering this event curation process. To highlight these challenges, here, we present the analysis of a model molecular system consisting of a nanostructured DNA molecule attached to a linear DNA carrier. We make use of recent advances in the event segmentation capabilities of Nanolyzer, a graphical analysis tool provided for nanopore event fitting, and describe approaches to the event substructure analysis. In the process, we identify and discuss important sources of selection bias that emerge in the analysis of this molecular system and consider the complicating effects of molecular conformation and variable experimental conditions (e.g., pore diameter). We then present additional refinements to existing analysis techniques, allowing for improved separation of multiplexed samples, fewer translocation events rejected as false negatives, and a wider range of experimental conditions for which accurate molecular information can be extracted. Increasing the coverage of analyzed events within nanopore data is not only important for characterizing complex molecular samples with high fidelity but is also becoming essential to the generation of accurate, unbiased training data as machine-learning approaches to data analysis and event identification continue to increase in prevalence.
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Affiliation(s)
- Zachary Roelen
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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2
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Yanagi I, Akahori R, Takeda KI. Dwell Time Prolongation and Identification of Single Nucleotides Passing through a Solid-State Nanopore by Using Ammonium Sulfate Aqueous Solution. ACS OMEGA 2023; 8:21285-21292. [PMID: 37332803 PMCID: PMC10268630 DOI: 10.1021/acsomega.3c02703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023]
Abstract
The ionic current blockades when poly(dT)60 or dNTPs passed through SiN nanopores in an aqueous solution containing (NH4)2SO4 were investigated. The dwell time of poly(dT)60 in the nanopores in an aqueous solution containing (NH4)2SO4 was significantly longer compared to that in an aqueous solution that did not contain (NH4)2SO4. This dwell time prolongation effect due to the aqueous solution containing (NH4)2SO4 was also confirmed when dCTP passed through the nanopores. In addition, when the nanopores were fabricated via dielectric breakdown in the aqueous solution containing (NH4)2SO4, the dwell time prolongation effect for dCTP still occurred even after the aqueous solution was displaced with the aqueous solution without (NH4)2SO4. Furthermore, we measured the ionic current blockades when the four types of dNTPs passed through the same nanopore, and the four types of dNTPs could be statistically identified according to their current blockade values.
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Affiliation(s)
- Itaru Yanagi
- Center
for Exploratory Research, Research & Development Group, Hitachi, Ltd., 1-280, Higashi-koigakubo, Kokubunji, Tokyo 185-8603, Japan
| | - Rena Akahori
- Center
for Technology Innovation - Healthcare, Research & Development
Group, Hitachi, Ltd., 1-280, Higashi-koigakubo, Kokubunji, Tokyo 185-8603, Japan
| | - Ken-ichi Takeda
- Center
for Technology Innovation - Healthcare, Research & Development
Group, Hitachi, Ltd., 1-280, Higashi-koigakubo, Kokubunji, Tokyo 185-8603, Japan
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3
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Hu R, Zhu R, Wei G, Wang Z, Gu ZY, Wanunu M, Zhao Q. Solid-State Quad-Nanopore Array for High-Resolution Single-Molecule Analysis and Discrimination. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2211399. [PMID: 37037423 DOI: 10.1002/adma.202211399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/12/2023] [Indexed: 06/16/2023]
Abstract
The ability to detect and distinguish biomolecules at the single-molecule level is at the forefront of today's biomedicine and analytical chemistry research. Increasing the dwell time of individual biomolecules in the sensing spot can greatly enhance the sensitivity of single-molecule methods. This is particularly important in solid-state nanopore sensing, where the detection of small molecules is often limited by the transit dwell time and insufficient temporal resolution. Here, a quad-nanopore is introduced, a square array of four nanopores (with a space interval of 30-50 nm) to improve the detection sensitivity through electric field manipulation in the access region. It is shown that dwell times of short DNA strands (200 bp) are prolonged in quad-nanopores as compared to single nanopores of the same diameter. The dependence of dwell times on the quad-pore spacing is investigated and it is found that the "retarding effect" increases with decreasing space intervals. Furthermore, ultra-short DNA (50 bp) detection is demonstrated using a 10 nm diameter quad-nanopore array, which is hardly detected by a single nanopore. Finally, the general utility of quad-nanopores has been verified by successful discrimination of two kinds of small molecules, metal-organic cage and bovine serum albumin (BSA).
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Affiliation(s)
- Rui Hu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
| | - Rui Zhu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
| | - Guanghao Wei
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
| | - Zhan Wang
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Zhi-Yuan Gu
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, 02115, USA
| | - Qing Zhao
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu, 226010, China
- Collaborative Innovation Center of Quantum Matter, Beijing, 100084, China
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4
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Singh SL, Chauhan K, Bharadwaj AS, Kishore V, Laux P, Luch A, Singh AV. Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges. Int J Mol Sci 2023; 24:6153. [PMID: 37047125 PMCID: PMC10094227 DOI: 10.3390/ijms24076153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/01/2023] [Accepted: 02/28/2023] [Indexed: 03/31/2023] Open
Abstract
Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.
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Affiliation(s)
- Swarn Lata Singh
- Department of Physics, Mahila Mahavidyalaya (MMV), Banaras Hindu University, Varanasi 221005, UP, India
| | - Keerti Chauhan
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India
| | - Atul S. Bharadwaj
- Department of Physics, CMP Degree College, University of Allahabad, Prayagraj 211002, UP, India
| | - Vimal Kishore
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India
| | - Peter Laux
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Andreas Luch
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Ajay Vikram Singh
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
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5
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Tsutsui M, Arima A, Yokota K, Baba Y, Kawai T. Ionic heat dissipation in solid-state pores. SCIENCE ADVANCES 2022; 8:eabl7002. [PMID: 35148181 PMCID: PMC8836805 DOI: 10.1126/sciadv.abl7002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Energy dissipation in solid-state nanopores is an important issue for their use as a sensor for detecting and analyzing individual objects in electrolyte solution by ionic current measurements. Here, we report on evaluations of heating via diffusive ion transport in the nanoscale conduits using thermocouple-embedded SiNx pores. We found a linear rise in the nanopore temperature with the input electrical power suggestive of steady-state ionic heat dissipation in the confined nanospace. Meanwhile, the heating efficiency was elucidated to become higher in a smaller pore due to a rapid decrease in the through-water thermal conduction for cooling the fluidic channel. The scaling law suggested nonnegligible influence of the heating to raise the temperature of single-nanometer two-dimensional nanopores by a few kelvins under the standard cross-membrane voltage and ionic strength conditions. The present findings may be useful in advancing our understanding of ion and mass transport phenomena in nanopores.
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Affiliation(s)
- Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Akihide Arima
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya 464-8603, Japan
| | - Kazumichi Yokota
- National Institute of Advanced Industrial Science and Technology, Takamatsu, Kagawa 761-0395, Japan
| | - Yoshinobu Baba
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya 464-8603, Japan
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Institute of Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Anagawa 4-9-1, Inage-ku, Chiba 263-8555, Japan
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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6
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King S, Briggs K, Slinger R, Tabard-Cossa V. Screening for Group A Streptococcal Disease via Solid-State Nanopore Detection of PCR Amplicons. ACS Sens 2022; 7:207-214. [PMID: 34995448 DOI: 10.1021/acssensors.1c01972] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Single-molecule detection methods are becoming increasingly important for diagnostic applications. Practical early detection of disease requires sensitivity down to the level of single copies of the targeted biomarkers. Of the candidate technologies that can address this need, solid-state nanopores show great promise as digital sensors for single-molecule detection. Here, we present work detailing the use of solid-state nanopores as downstream sensors for a polymerase chain reaction (PCR)-based assay targeting group A streptococcus (strep A), which can be readily extended to detect any pathogen that can be identified with a short nucleic acid sequence. We demonstrate that with some simple modifications to the standard PCR reaction mixture, nanopores can be used to reliably identify strep A in clinical samples. We also discuss methodological best practices for both adapting PCR-based assays to solid-state nanopore readout and analytical approaches by which to decide on sample status.
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Affiliation(s)
- Simon King
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Robert Slinger
- Division of Microbiology and Infectious Disease, Children’s Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H 8L1, Canada
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7
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Li W, Zhou J, Maccaferri N, Krahne R, Wang K, Garoli D. Enhanced Optical Spectroscopy for Multiplexed DNA and Protein-Sequencing with Plasmonic Nanopores: Challenges and Prospects. Anal Chem 2022; 94:503-514. [PMID: 34974704 PMCID: PMC8771637 DOI: 10.1021/acs.analchem.1c04459] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Wang Li
- State
Key Laboratory of Analytical Chemistry for Life Science School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, P. R. China
| | - Juan Zhou
- State
Key Laboratory of Analytical Chemistry for Life Science School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, P. R. China
| | - Nicolò Maccaferri
- Department
of Physics and Materials Science, University
of Luxembourg, L-1511 Luxembourg, Luxembourg
- Department
of Physics, Umeå University, Linnaeus väg 20, SE-90736 Umeå, Sweden
| | - Roman Krahne
- Istituto
Italiano di Tecnologia, Optoelectronics
Research Line, Morego
30, I-16163 Genova, Italy
| | - Kang Wang
- State
Key Laboratory of Analytical Chemistry for Life Science School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, P. R. China
| | - Denis Garoli
- Istituto
Italiano di Tecnologia, Optoelectronics
Research Line, Morego
30, I-16163 Genova, Italy
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8
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Ding T, Yang J, Wang J, Pan V, Lu Z, Ke Y, Zhang C. Shaped DNA origami carrier nanopore translocation influenced by aptamer based surface modification. Biosens Bioelectron 2022; 195:113658. [PMID: 34706323 DOI: 10.1016/j.bios.2021.113658] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/16/2021] [Accepted: 09/18/2021] [Indexed: 01/19/2023]
Abstract
DNA origami is widely used as a translocation carrier to assist solid-state nanopore analysis, e.g., soft linear origami carrier and special-shaped origami structures. In the linear origami carriers based nanopore sensing, molecular modifications induced tiny structural and charge changes, can result in significant variations on translocation signals to facilitating single-molecule sensing. However, an understanding on the influences of surface modifications on special-shaped DNA origami structures during solid-state (SS) nanopores translocation is still far elusive. Herein, we reported a surface modification strategy using aptamer/target-binding to influence the translocation of the shaped origami ribbon carrier through SS-nanopore. Our measurements indicate that the translocation signal variations can respond to ATP/aptamer binding on the carrier surface, even to the surface modifications induced by spatial distributions and enzyme catalysis. Meanwhile, the results also suggest a possibility to identify small spatial and electronic changes on DNA origami by using SS-nanopore. We envision that the surface aptamer-binding influenced origami translocation strategy could find more applications in origami carrier assisted SS-nanopore sensing and detection.
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Affiliation(s)
- Taoli Ding
- Key Lab of High Confidence Software Technologies, Department of Computer Science and Technology, School of Electronics Engineering and Computer Science, Peking University, Beijing, 100871, China
| | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Juan Wang
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China; Bio-evidence Sciences Academy, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Victor Pan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Zuhong Lu
- The State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China, 211189.
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Emory University School of Medicine, Atlanta, GA 30322, United States; Department of Chemistry, Emory University, Atlanta, GA 30322, United States.
| | - Cheng Zhang
- Key Lab of High Confidence Software Technologies, Department of Computer Science and Technology, School of Electronics Engineering and Computer Science, Peking University, Beijing, 100871, China.
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9
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Marion S, Vučemilović-Alagić N, Špadina M, Radenović A, Smith AS. From Water Solutions to Ionic Liquids with Solid State Nanopores as a Perspective to Study Transport and Translocation Phenomena. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100777. [PMID: 33955694 DOI: 10.1002/smll.202100777] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/01/2021] [Indexed: 06/12/2023]
Abstract
Solid state nanopores are single-molecular devices governed by nanoscale physics with a broad potential for technological applications. However, the control of translocation speed in these systems is still limited. Ionic liquids are molten salts which are commonly used as alternate solvents enabling the regulation of the chemical and physical interactions on solid-liquid interfaces. While their combination can be challenging to the understanding of nanoscopic processes, there has been limited attempts on bringing these two together. While summarizing the state of the art and open questions in these fields, several major advances are presented with a perspective on the next steps in the investigations of ionic-liquid filled nanopores, both from a theoretical and experimental standpoint. By analogy to aqueous solutions, it is argued that ionic liquids and nanopores can be combined to provide new nanofluidic functionalities, as well as to help resolve some of the pertinent problems in understanding transport phenomena in confined ionic liquids and providing better control of the speed of translocating analytes.
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Affiliation(s)
- Sanjin Marion
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015, Lausanne, Switzerland
| | - Nataša Vučemilović-Alagić
- Group for Computational Life Sciences, Ruđer Bošković Institute, Division of Physical Chemistry, 10000, Zagreb, Croatia
- PULS Group, Physics Department, Interdisciplinary Center for Nanostructured Films, FAU Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Mario Špadina
- Group for Computational Life Sciences, Ruđer Bošković Institute, Division of Physical Chemistry, 10000, Zagreb, Croatia
| | - Aleksandra Radenović
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015, Lausanne, Switzerland
| | - Ana-Sunčana Smith
- Group for Computational Life Sciences, Ruđer Bošković Institute, Division of Physical Chemistry, 10000, Zagreb, Croatia
- PULS Group, Physics Department, Interdisciplinary Center for Nanostructured Films, FAU Erlangen-Nürnberg, 91058, Erlangen, Germany
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10
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Sharma V, Freedman KJ. Constricted Apertures for Dynamic Trapping and Micro-/Nanoscale Discrimination Based on Recapture Kinetics. NANO LETTERS 2021; 21:3364-3371. [PMID: 33861619 DOI: 10.1021/acs.nanolett.0c04392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Sensing via analyte passage through a constricted aperture is a powerful and robust technology which is being utilized broadly, from DNA sequencing to single virus and cell characterization. Micro- and nanoscale structures typically translocate a constricted aperture, or pore, using electrophoretic force. In the present work, we explore the advances in metrology which can be achieved through rapid directional switching of hydrodynamic forces. Interestingly, multipass measurements of microscale and nanoscale structures achieve cell discrimination. We explore this cell-discrimination phenomenon as well as other features of hydrodynamic focusing such as dynamic trapping and discrete interval sensing.
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Affiliation(s)
- Vinay Sharma
- University of California-Riverside, Department of Bioengineering, 900 University Avenue, Riverside, California 92521, United States
| | - Kevin J Freedman
- University of California-Riverside, Department of Bioengineering, 900 University Avenue, Riverside, California 92521, United States
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11
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Sohi AN, Beamish E, Tabard-Cossa V, Godin M. DNA Capture by Nanopore Sensors under Flow. Anal Chem 2020; 92:8108-8116. [DOI: 10.1021/acs.analchem.9b05778] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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12
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Luo MB, Wu F, Zhang S, Sun LZ. Effect of temperature on the escape of charged polymer chain from a repulsive nanopore. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1629435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Meng-Bo Luo
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Zhejiang University, Hangzhou, People’s Republic of China
| | - Fan Wu
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Zhejiang University, Hangzhou, People’s Republic of China
| | - Shuang Zhang
- College of Science, Beibu Gulf University, Qinzhou, People’s Republic of China
| | - Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou, People’s Republic of China
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13
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Charron M, Briggs K, King S, Waugh M, Tabard-Cossa V. Precise DNA Concentration Measurements with Nanopores by Controlled Counting. Anal Chem 2019; 91:12228-12237. [DOI: 10.1021/acs.analchem.9b01900] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Martin Charron
- Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
| | - Kyle Briggs
- Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
| | - Simon King
- Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
| | - Matthew Waugh
- Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
| | - Vincent Tabard-Cossa
- Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
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14
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Goto Y, Akahori R, Yanagi I, Takeda KI. Solid-state nanopores towards single-molecule DNA sequencing. J Hum Genet 2019. [PMID: 31420594 DOI: 10.1038/s10038-019-0655-8]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Nanopore DNA sequencing offers a new paradigm owing to its extensive potential for long-read, high-throughput detection of nucleotide modification and direct RNA sequencing. Given the remarkable advances in protein nanopore sequencing technology, there is still a strong enthusiasm in exploring alternative nanopore-sequencing techniques, particularly those based on a solid-state nanopore using a semiconductor material. Since solid-state nanopores provide superior material robustness and large-scale integrability with on-chip electronics, they have the potential to surpass the limitations of their biological counterparts. However, there are key technical challenges to be addressed: the creation of an ultrasmall nanopore, fabrication of an ultrathin membrane, control of the ultrafast DNA speed and detection of four nucleotides. Extensive research efforts have been devoted to resolving these issues over the past two decades. In this review, we briefly introduce recent updates regarding solid-state nanopore technologies towards DNA sequencing. It can be envisioned that emerging technologies will offer a brand new future in DNA-sequencing technology.
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Affiliation(s)
- Yusuke Goto
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan.
| | - Rena Akahori
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Itaru Yanagi
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Ken-Ichi Takeda
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
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15
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Goto Y, Akahori R, Yanagi I, Takeda KI. Solid-state nanopores towards single-molecule DNA sequencing. J Hum Genet 2019; 65:69-77. [PMID: 31420594 DOI: 10.1038/s10038-019-0655-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 12/19/2022]
Abstract
Nanopore DNA sequencing offers a new paradigm owing to its extensive potential for long-read, high-throughput detection of nucleotide modification and direct RNA sequencing. Given the remarkable advances in protein nanopore sequencing technology, there is still a strong enthusiasm in exploring alternative nanopore-sequencing techniques, particularly those based on a solid-state nanopore using a semiconductor material. Since solid-state nanopores provide superior material robustness and large-scale integrability with on-chip electronics, they have the potential to surpass the limitations of their biological counterparts. However, there are key technical challenges to be addressed: the creation of an ultrasmall nanopore, fabrication of an ultrathin membrane, control of the ultrafast DNA speed and detection of four nucleotides. Extensive research efforts have been devoted to resolving these issues over the past two decades. In this review, we briefly introduce recent updates regarding solid-state nanopore technologies towards DNA sequencing. It can be envisioned that emerging technologies will offer a brand new future in DNA-sequencing technology.
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Affiliation(s)
- Yusuke Goto
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan.
| | - Rena Akahori
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Itaru Yanagi
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Ken-Ichi Takeda
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
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16
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Goto Y, Matsui K, Yanagi I, Takeda KI. Silicon nitride nanopore created by dielectric breakdown with a divalent cation: deceleration of translocation speed and identification of single nucleotides. NANOSCALE 2019; 11:14426-14433. [PMID: 31334729 DOI: 10.1039/c9nr03563j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nanopore DNA sequencing with a solid-state nanopore requires deceleration of the ultrafast translocation speed of single-stranded DNA (ssDNA). We report an unexpected phenomenon: controlled dielectric breakdown (CBD) with a divalent metal cation, especially Ca2+, provides a silicon nitride nanopore with the ability to decelerate ssDNA speed to 100 μs per base even after solution replacement. This speed is two orders of magnitude slower than that for CBD with a conventional monovalent metal cation. Temperature dependence experiments revealed that the enthalpic barrier for a nanopore created via CBD with Ca2+ is 25-30kBT, comparable to that of a biological nanopore. The slowing effect originates from the strong interaction between ssDNA and divalent cations, which were coated on the sidewall of the nanopore during the CBD process. In addition, we found that the nanopore created via CBD with Ca2+ can decelerate the speed of even single-nucleotide monomers, dNMPs, to 0.1-10 ms per base. The four single nucleotides could be statistically identified according to their blockade currents. Our approach is simple and practical because it simultaneously allows nanopore fabrication, ssDNA deceleration and the identification of nucleotide monomers.
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Affiliation(s)
- Yusuke Goto
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd, 1-280 Higashi-Koigakubo, Kokubunji, Tokyo 185-8601, Japan.
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17
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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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18
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Spitzberg JD, Zrehen A, van Kooten XF, Meller A. Plasmonic-Nanopore Biosensors for Superior Single-Molecule Detection. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1900422. [PMID: 30941823 DOI: 10.1002/adma.201900422] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 02/19/2019] [Indexed: 05/26/2023]
Abstract
Plasmonic and nanopore sensors have separately received much attention for achieving single-molecule precision. A plasmonic "hotspot" confines and enhances optical excitation at the nanometer length scale sufficient to optically detect surface-analyte interactions. A nanopore biosensor actively funnels and threads analytes through a molecular-scale aperture, wherein they are interrogated by electrical or optical means. Recently, solid-state plasmonic and nanopore structures have been integrated within monolithic devices that address fundamental challenges in each of the individual sensing methods and offer complimentary improvements in overall single-molecule sensitivity, detection rates, dwell time and scalability. Here, the physical phenomena and sensing principles of plasmonic and nanopore sensing are summarized to highlight the novel complementarity in dovetailing these techniques for vastly improved single-molecule sensing. A literature review of recent plasmonic nanopore devices is then presented to delineate methods for solid-state fabrication of a range of hybrid device formats, evaluate the progress and challenges in the detection of unlabeled and labeled analyte, and assess the impact and utility of localized plasmonic heating. Finally, future directions and applications inspired by the present state of the art are discussed.
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Affiliation(s)
- Joshua D Spitzberg
- Department of Biomedical Engineering, Technion-IIT, Haifa, 32000, Israel
| | - Adam Zrehen
- Department of Biomedical Engineering, Technion-IIT, Haifa, 32000, Israel
| | | | - Amit Meller
- Department of Biomedical Engineering, Technion-IIT, Haifa, 32000, Israel
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
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19
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Shi X, Verschueren DV, Dekker C. Active Delivery of Single DNA Molecules into a Plasmonic Nanopore for Label-Free Optical Sensing. NANO LETTERS 2018; 18:8003-8010. [PMID: 30460853 PMCID: PMC6295923 DOI: 10.1021/acs.nanolett.8b04146] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/16/2018] [Indexed: 05/23/2023]
Abstract
Plasmon resonance biosensors provide ultimate sensitivity at the single-molecule level. This sensitivity is, however, associated with a nanometer-sized confined hotspot, and molecular transport toward the sensor relies on inefficient diffusion. Here, we combine a plasmonic nanoantenna with a solid-state nanopore and demonstrate that single DNA molecules can be efficiently delivered to the plasmonic hotspots and detected in a label-free manner at submillisecond acquisition rates by monitoring the backscattered light intensity from the plasmonic nanoantennas. Our method realizes a better than 200 μs temporal resolution together with a down to subsecond waiting time, which is orders of magnitude better than traditional single-molecule plasmonic resonance sensing methods. Furthermore, the electric field applied to the nanopore can actively drive biomolecules away from the hotspot, preventing molecules to permanently bind to the gold sensor surface and allowing efficient reuse of the sensor. Our plasmonic nanopore sensor thus significantly outperforms conventional plasmon resonance sensors and provides great opportunities for high-throughput optical single-molecule-sensing assays.
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Affiliation(s)
- Xin Shi
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
- Key
Laboratory for Advanced Materials & School of Chemistry and Molecular
Engineering, East China University of Science
and Technology, Shanghai 200237, People’s Republic
of China
| | - Daniel V. Verschueren
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
| | - Cees Dekker
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
- E-mail:
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20
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Cressiot B, Greive SJ, Mojtabavi M, Antson AA, Wanunu M. Thermostable virus portal proteins as reprogrammable adapters for solid-state nanopore sensors. Nat Commun 2018; 9:4652. [PMID: 30405123 PMCID: PMC6220183 DOI: 10.1038/s41467-018-07116-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/12/2018] [Indexed: 11/09/2022] Open
Abstract
Nanopore-based sensors are advancing the sensitivity and selectivity of single-molecule detection in molecular medicine and biotechnology. Current electrical sensing devices are based on either membrane protein pores supported in planar lipid bilayers or solid-state (SS) pores fabricated in thin metallic membranes. While both types of nanosensors have been used in a variety of applications, each has inherent disadvantages that limit its use. Hybrid nanopores, consisting of a protein pore supported within a SS membrane, combine the robust nature of SS membranes with the precise and simple engineering of protein nanopores. We demonstrate here a novel lipid-free hybrid nanopore comprising a natural DNA pore from a thermostable virus, electrokinetically inserted into a larger nanopore supported in a silicon nitride membrane. The hybrid pore is stable and easy to fabricate, and, most importantly, exhibits low peripheral leakage allowing sensing and discrimination among different types of biomolecules.
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Affiliation(s)
- Benjamin Cressiot
- Department of Physics, Northeastern University, Boston, MA, 02115, USA.,Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA.,LAMBE, Université d'Evry Val d'Essonne, Université de Cergy Pontoise, CNRS, CEA, Université Paris-Saclay, Evry, F-91025, France
| | - Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Mehrnaz Mojtabavi
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK.
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, 02115, USA. .,Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA.
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21
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Zhang M, Ngampeerapong C, Redin D, Ahmadian A, Sychugov I, Linnros J. Thermophoresis-Controlled Size-Dependent DNA Translocation through an Array of Nanopores. ACS NANO 2018; 12:4574-4582. [PMID: 29648793 DOI: 10.1021/acsnano.8b00961] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Large arrays of nanopores can be used for high-throughput biomolecule translocation with applications toward size discrimination and sorting at the single-molecule level. In this paper, we propose to discriminate DNA length by the capture rate of the molecules to an array of relatively large nanopores (50-130 nm) by introducing a thermal gradient by laser illumination in front of the pores balancing the force from an external electric field. Nanopore arrays defined by photolithography were batch processed using standard silicon technology in combination with electrochemical etching. Parallel translocation of single, fluorophore-labeled dsDNA strands is recorded by imaging the array with a fast CMOS camera. The experimental data show that the capture rates of DNA molecules decrease with increasing DNA length due to the thermophoretic effect of the molecules. It is shown that the translocation can be completely turned off for the longer molecule using an appropriate bias, thus allowing a size discrimination of the DNA translocation through the nanopores. A derived analytical model correctly predicts the observed capture rate. Our results demonstrate that by combining a thermal and a potential gradient at the nanopores, such large nanopore arrays can potentially be used as a low-cost, high-throughput platform for molecule sensing and sorting.
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Affiliation(s)
- Miao Zhang
- Department of Applied Physics , KTH Royal Institute of Technology , Electrum 229 , 164 40 Kista , Sweden
| | - Chonmanart Ngampeerapong
- Department of Applied Physics , KTH Royal Institute of Technology , Electrum 229 , 164 40 Kista , Sweden
| | - David Redin
- School of Biotechnology, Division of Gene Technology, Science for Life Laboratory , KTH Royal Institute of Technology , SE-171 65 , Solna , Sweden
| | - Afshin Ahmadian
- School of Biotechnology, Division of Gene Technology, Science for Life Laboratory , KTH Royal Institute of Technology , SE-171 65 , Solna , Sweden
| | - Ilya Sychugov
- Department of Applied Physics , KTH Royal Institute of Technology , Electrum 229 , 164 40 Kista , Sweden
| | - Jan Linnros
- Department of Applied Physics , KTH Royal Institute of Technology , Electrum 229 , 164 40 Kista , Sweden
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22
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Jou I, Muthukumar M. Effects of Nanopore Charge Decorations on the Translocation Dynamics of DNA. Biophys J 2017; 113:1664-1672. [PMID: 29045861 DOI: 10.1016/j.bpj.2017.08.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/11/2017] [Accepted: 08/21/2017] [Indexed: 12/14/2022] Open
Abstract
We have investigated the dynamics of single-stranded DNA as it translocates through charge-mutated protein nanopores. Translocation of DNA is a crucial step in nanopore-based sequencing platforms, where control over translocation speed remains one of the main challenges. Taking advantage of the interactions between negatively charged DNA and positively charged amino acid residues, the translocation speed of DNA can be manipulated by deliberate charge decorations inside the nanopore. We employed coarse-grained Langevin dynamics simulations to monitor the step-by-step movement of DNA through different mutations of α-hemolysin protein nanopores. We found that although the average translocation time per nucleotide is longer, in agreement with experiments, the DNA nucleotides do not translocate with a uniform speed. Furthermore, the location and spacing of the charge decorations can alter the translocation dynamics significantly, trapping DNA in some cases. Our findings can give insights when designing charge patterns in nanopores.
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Affiliation(s)
- Ining Jou
- Department of Polymer Science and Engineering, Conte Research Center, University of Massachusetts, Amherst, Massachusetts
| | - Murugappan Muthukumar
- Department of Polymer Science and Engineering, Conte Research Center, University of Massachusetts, Amherst, Massachusetts.
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23
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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
- E-mail:
| | - Joshua B. Edel
- Department
of Chemistry, Department of Bioengineering, Department of Medicine, Imperial College London, SW7 2AZ, United Kingdom
- E-mail: ; phone number: 020 7594 0754
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24
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Das PK. DNA translocation through polyelectrolyte modified hairy nanopores. Colloids Surf A Physicochem Eng Asp 2017. [DOI: 10.1016/j.colsurfa.2017.06.068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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25
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Luo MB, Tsehay DA, Sun LZ. Temperature dependence of the translocation time of polymer through repulsive nanopores. J Chem Phys 2017; 147:034901. [PMID: 28734304 DOI: 10.1063/1.4993217] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The forced translocation of a polymer chain through repulsive nanopores was studied by using Langevin dynamics simulations. The polymer is in the compact globule state at low temperature and in the random coil state at high temperature. Simulation results show that the mean translocation time 〈τ〉 is highly dependent on the temperature T and the minimal 〈τ〉 is located near the coil-globule transition temperature. Moreover, the scaling behaviors 〈τ〉 ∼ Nα and 〈τ〉 ∼ F-δ are studied, with N the polymer length and F the driving force inside the nanopore. Universal values α = 1.4 and δ = 0.85 are observed for the polymer in the random coil state. While for the polymer in the compact globule state, α decreases from α = 2 at weak driving to 1.2 at strong driving for short N and δ increases with decreasing T in the low F region, but we find universal exponents α = 1.6 for long N and δ = 0.85 in the large F region. Results show that polymer's conformation plays a much more important role than the diffusion coefficient in controlling the translocation time of the polymer chain.
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Affiliation(s)
- Meng-Bo Luo
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | | | - Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
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26
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Yao H, Zeng J, Zhai P, Li Z, Cheng Y, Liu J, Mo D, Duan J, Wang L, Sun Y, Liu J. Large Rectification Effect of Single Graphene Nanopore Supported by PET Membrane. ACS APPLIED MATERIALS & INTERFACES 2017; 9:11000-11008. [PMID: 28262018 DOI: 10.1021/acsami.6b16736] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Graphene is an ideal candidate for the development of solid state nanopores due to its thickness at the atomic scale and its high chemical and mechanical stabilities. A facile method was adopted to prepare single graphene nanopore supported by PET membrane (G/PET nanopore) within the three steps assisted by the swift heavy ion irradiation and asymmetric etching technology. The inversion of the ion rectification effect was confirmed in G/PET nanopore while comparing with bare PET nanopore in KCl electrolyte solution. By modifying the wall charge state of PET conical nanopore with hydrochloric acid from negative to positive, the ion rectification effect of G/PET nanopore was found to be greatly enhanced and the large rectification ratio up to 190 was obtained during this work. Moreover, the high ionic flux and high ion separation efficiency was also observed in the G/PET nanopore system. By comparing the "on" and "off" state conductance of G/PET nanopore while immersed in the solution with pH value lower than the isoelectric point of the etched PET (IEP, pH = 3.8), the voltage dependence of the off conductance was established and it was confirmed that the large rectification effect was strongly dependent on the particularly low off conductance at higher applied voltage.
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Affiliation(s)
- Huijun Yao
- Institute of Modern Physics, Chinese Academy of Sciences , Lanzhou 730000, China
| | - Jian Zeng
- Institute of Modern Physics, Chinese Academy of Sciences , Lanzhou 730000, China
| | - Pengfei Zhai
- Institute of Modern Physics, Chinese Academy of Sciences , Lanzhou 730000, China
| | - Zongzhen Li
- Institute of Modern Physics, Chinese Academy of Sciences , Lanzhou 730000, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Yaxiong Cheng
- Institute of Modern Physics, Chinese Academy of Sciences , Lanzhou 730000, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Jiande Liu
- Institute of Modern Physics, Chinese Academy of Sciences , Lanzhou 730000, China
| | - Dan Mo
- Institute of Modern Physics, Chinese Academy of Sciences , Lanzhou 730000, China
| | - Jinglai Duan
- Institute of Modern Physics, Chinese Academy of Sciences , Lanzhou 730000, China
| | - Lanxi Wang
- Science and Technology on Vacuum Technology and Physics Laboratory, Lanzhou Institute of Physics , Feiyan Street 100, Lanzhou 730000, China
| | - Youmei Sun
- Institute of Modern Physics, Chinese Academy of Sciences , Lanzhou 730000, China
| | - Jie Liu
- Institute of Modern Physics, Chinese Academy of Sciences , Lanzhou 730000, China
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27
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Affiliation(s)
- Wenqing Shi
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Alicia K. Friedman
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Lane A. Baker
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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28
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Piguet F, Ouldali H, Discala F, Breton MF, Behrends JC, Pelta J, Oukhaled A. High Temperature Extends the Range of Size Discrimination of Nonionic Polymers by a Biological Nanopore. Sci Rep 2016; 6:38675. [PMID: 27924860 PMCID: PMC5141499 DOI: 10.1038/srep38675] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/11/2016] [Indexed: 01/29/2023] Open
Abstract
We explore the effect of temperature on the interaction of polydisperse mixtures of nonionic poly(ethylene glycol) (PEG) polymers of different average molar masses with the biological nanopore α-hemolysin. In contrast with what has been previously observed with various nanopores and analytes, we find that, for PEGs larger than a threshold molar mass (2000 g/mol, PEG 2000), increasing temperature increases the duration of the PEG/nanopore interaction. In the case of PEG 3400 the duration increases by up to a factor of 100 when the temperature increases from 5 °C to 45 °C. Importantly, we find that increasing temperature extends the polymer size range of application of nanopore-based single-molecule mass spectrometry (Np-SMMS)-type size discrimination. Indeed, in the case of PEG 3400, discrimination of individual molecular species of different monomer number is impossible at room temperature but is achieved when the temperature is raised to 45 °C. We interpret our observations as the consequence of a decrease of PEG solubility and a collapse of PEG molecules with higher temperatures. In addition to expanding the range of application of Np-SMMS to larger nonionic polymers, our findings highlight the crucial role of the polymer solubility for the nanopore detection.
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Affiliation(s)
- Fabien Piguet
- LAMBE UMR 8587 CNRS, Cergy and Évry Universities, France.,LPTM UMR 8089 CNRS, Cergy University, France
| | - Hadjer Ouldali
- LAMBE UMR 8587 CNRS, Cergy and Évry Universities, France
| | | | | | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Faculty of Medicine, Department of Physiology, University of Freiburg, Germany.,Freiburg Materials Research Centre, University of Freiburg, Germany.,Centre for Interactive Materials and Bioinspired Technologies, University of Freiburg, Germany
| | - Juan Pelta
- LAMBE UMR 8587 CNRS, Cergy and Évry Universities, France
| | | |
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29
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Goto Y, Yanagi I, Matsui K, Yokoi T, Takeda KI. Integrated solid-state nanopore platform for nanopore fabrication via dielectric breakdown, DNA-speed deceleration and noise reduction. Sci Rep 2016; 6:31324. [PMID: 27499264 PMCID: PMC4976334 DOI: 10.1038/srep31324] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/18/2016] [Indexed: 02/06/2023] Open
Abstract
The practical use of solid-state nanopores for DNA sequencing requires easy fabrication of the nanopores, reduction of the DNA movement speed and reduction of the ionic current noise. Here, we report an integrated nanopore platform with a nanobead structure that decelerates DNA movement and an insulating polyimide layer that reduces noise. To enable rapid nanopore fabrication, we introduced a controlled dielectric breakdown (CDB) process into our system. DNA translocation experiments revealed that single nanopores were created by the CDB process without sacrificing performance in reducing DNA movement speed by up to 10 μs/base or reducing noise up to 600 pArms at 1 MHz. Our platform provides the essential components for proceeding to the next step in the process of DNA sequencing.
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Affiliation(s)
- Yusuke Goto
- Center for Technology Innovation - Healthcare, Research &Development Group, Hitachi Ltd.,1-280 Higashi-Koigakubo, Kokubunji, Tokyo 185-8601, Japan
| | - Itaru Yanagi
- Center for Technology Innovation - Healthcare, Research &Development Group, Hitachi Ltd.,1-280 Higashi-Koigakubo, Kokubunji, Tokyo 185-8601, Japan
| | - Kazuma Matsui
- Center for Technology Innovation - Healthcare, Research &Development Group, Hitachi Ltd.,1-280 Higashi-Koigakubo, Kokubunji, Tokyo 185-8601, Japan
| | - Takahide Yokoi
- Center for Technology Innovation - Healthcare, Research &Development Group, Hitachi Ltd.,1-280 Higashi-Koigakubo, Kokubunji, Tokyo 185-8601, Japan
| | - Ken-Ichi Takeda
- Center for Technology Innovation - Healthcare, Research &Development Group, Hitachi Ltd.,1-280 Higashi-Koigakubo, Kokubunji, Tokyo 185-8601, Japan
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30
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Belkin M, Aksimentiev A. Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores. ACS APPLIED MATERIALS & INTERFACES 2016; 8:12599-608. [PMID: 26963065 PMCID: PMC4880514 DOI: 10.1021/acsami.6b00463] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/10/2016] [Indexed: 05/20/2023]
Abstract
The integration of local heat sources with solid-state nanopores offers new means for controlling the transmembrane transport of charged biomacromolecules. In the case of electrophoretic transport of DNA, recent experimental studies revealed unexpected temperature dependences of the DNA capture rate, the DNA translocation velocity, and the ionic current blockades produced by the presence of DNA in the nanopore. Here, we report the results of all-atom molecular dynamics simulations that elucidated the effect of temperature on the key microscopic processes governing electric field-driven transport of DNA through nanopores. Mimicking the experimental setup, we simulated the capture and subsequent translocation of short DNA duplexes through a locally heated nanopore at several temperatures and electrolyte conditions. The temperature dependence of ion mobility at the DNA surface was found to cause the dependence of the relative conductance blockades on temperature. To the first order, the effective force on DNA in the nanopore was found to be independent of temperature, despite a considerable reduction of solution viscosity. The temperature dependence of the solution viscosity was found to make DNA translocations faster for a uniformly heated system but not in the case of local heating that does not affect viscosity of solution surrounding the untranslocated part of the molecule. Increasing solution temperature was also found to reduce the lifetime of bonds formed between cations and DNA. Using a flow suppression algorithm, we were able to separate the effects of electro-osmotic flow and direct ion binding, finding the reduced durations of DNA-ion bonds to increase, albeit weakly, the effective force experienced by DNA in an electric field. Unexpectedly, our simulations revealed a considerable temperature dependence of solvent velocity at the DNA surface-slip velocity, an effect that can alter hydrodynamic coupling between the motion of DNA and the surrounding fluid.
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31
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Angevine CE, Seashols-Williams SJ, Reiner JE. Infrared Laser Heating Applied to Nanopore Sensing for DNA Duplex Analysis. Anal Chem 2016; 88:2645-51. [DOI: 10.1021/acs.analchem.5b03631] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Christopher E. Angevine
- Department of Physics, and ‡Department of
Forensic Science, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Sarah J. Seashols-Williams
- Department of Physics, and ‡Department of
Forensic Science, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Joseph E. Reiner
- Department of Physics, and ‡Department of
Forensic Science, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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Kulkarni M, Mukherjee A. Ionic liquid prolongs DNA translocation through graphene nanopores. RSC Adv 2016. [DOI: 10.1039/c6ra07017e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Ionic liquid molecules interact strongly with DNA and effectively reduce its translocation speed via graphene nanopore.
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Affiliation(s)
- Mandar Kulkarni
- Department of Chemistry
- Indian Institute of Science Education and Research
- Pune-411008
- India
| | - Arnab Mukherjee
- Department of Chemistry
- Indian Institute of Science Education and Research
- Pune-411008
- India
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Zahid OK, Hall AR. Helium Ion Microscope Fabrication of Solid-State Nanopore Devices for Biomolecule Analysis. HELIUM ION MICROSCOPY 2016. [DOI: 10.1007/978-3-319-41990-9_18] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Demming A. DNA sequencing: nanotechnology unravels the code for life. NANOTECHNOLOGY 2015; 26:310201. [PMID: 26180041 DOI: 10.1088/0957-4484/26/31/310201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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