1
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Wu Y, Gooding JJ. The application of single molecule nanopore sensing for quantitative analysis. Chem Soc Rev 2022; 51:3862-3885. [PMID: 35506519 DOI: 10.1039/d1cs00988e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Nanopore-based sensors typically work by monitoring transient pulses in conductance via current-time traces as molecules translocate through the nanopore. The unique property of being able to monitor single molecules gives nanopore sensors the potential as quantitative sensors based on the counting of single molecules. This review provides an overview of the concepts and fabrication of nanopore sensors as well as nanopore sensing with a view toward using nanopore sensors for quantitative analysis. We first introduce the classification of nanopores and highlight their applications in molecular identification with some pioneering studies. The review then shifts focus to recent strategies to extend nanopore sensors to devices that can rapidly and accurately quantify the amount of an analyte of interest. Finally, future prospects are provided and briefly discussed. The aim of this review is to aid in understanding recent advances, challenges, and prospects for nanopore sensors for quantitative analysis.
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Affiliation(s)
- Yanfang Wu
- School of Chemistry and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia.
| | - J Justin Gooding
- School of Chemistry and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia.
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2
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Fried JP, Wu Y, Tilley RD, Gooding JJ. Optical Nanopore Sensors for Quantitative Analysis. NANO LETTERS 2022; 22:869-880. [PMID: 35089719 DOI: 10.1021/acs.nanolett.1c03976] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nanopore sensors have received significant interest for the detection of clinically important biomarkers with single-molecule resolution. These sensors typically operate by detecting changes in the ionic current through a nanopore due to the translocation of an analyte. Recently, there has been interest in developing optical readout strategies for nanopore sensors for quantitative analysis. This is because they can utilize wide-field microscopy to independently monitor many nanopores within a high-density array. This significantly increases the amount of statistics that can be obtained, thus enabling the analysis of analytes present at ultralow concentrations. Here, we review the use of optical nanopore sensing strategies for quantitative analysis. We discuss optical nanopore sensing assays that have been developed to detect clinically relevant biomarkers, the potential for multiplexing such measurements, and techniques to fabricate high density arrays of nanopores with a view toward the use of these devices for clinical applications.
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Affiliation(s)
- Jasper P Fried
- 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
| | - 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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3
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Cai S, Pataillot-Meakin T, Shibakawa A, Ren R, Bevan CL, Ladame S, Ivanov AP, Edel JB. Single-molecule amplification-free multiplexed detection of circulating microRNA cancer biomarkers from serum. Nat Commun 2021; 12:3515. [PMID: 34112774 PMCID: PMC8192752 DOI: 10.1038/s41467-021-23497-y] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/30/2021] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) play essential roles in post-transcriptional gene expression and are also found freely circulating in bodily fluids such as blood. Dysregulated miRNA signatures have been associated with many diseases including cancer, and miRNA profiling from liquid biopsies offers a promising strategy for cancer diagnosis, prognosis and monitoring. Here, we develop size-encoded molecular probes that can be used for simultaneous electro-optical nanopore sensing of miRNAs, allowing for ultrasensitive, sequence-specific and multiplexed detection directly in unprocessed human serum, in sample volumes as small as 0.1 μl. We show that this approach allows for femtomolar sensitivity and single-base mismatch selectivity. We demonstrate the ability to simultaneously monitor miRNAs (miR-141-3p and miR-375-3p) from prostate cancer patients with active disease and in remission. This technology can pave the way for next generation of minimally invasive diagnostic and companion diagnostic tests for cancer.
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Affiliation(s)
- Shenglin Cai
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK
| | - Thomas Pataillot-Meakin
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK
- Department of Bioengineering, Imperial College London, Sir Michael Uren Hub, London, W12 0BZ, UK
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Akifumi Shibakawa
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Ren Ren
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK
| | - Charlotte L Bevan
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK.
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, Sir Michael Uren Hub, London, W12 0BZ, UK.
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK.
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK.
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4
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Fried JP, Swett JL, Nadappuram BP, Mol JA, Edel JB, Ivanov AP, Yates JR. In situ solid-state nanopore fabrication. Chem Soc Rev 2021; 50:4974-4992. [PMID: 33623941 DOI: 10.1039/d0cs00924e] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanopores in solid-state membranes are promising for a wide range of applications including DNA sequencing, ultra-dilute analyte detection, protein analysis, and polymer data storage. Techniques to fabricate solid-state nanopores have typically been time consuming or lacked the resolution to create pores with diameters down to a few nanometres, as required for the above applications. In recent years, several methods to fabricate nanopores in electrolyte environments have been demonstrated. These in situ methods include controlled breakdown (CBD), electrochemical reactions (ECR), laser etching and laser-assisted controlled breakdown (la-CBD). These techniques are democratising solid-state nanopores by providing the ability to fabricate pores with diameters down to a few nanometres (i.e. comparable to the size of many analytes) in a matter of minutes using relatively simple equipment. Here we review these in situ solid-state nanopore fabrication techniques and highlight the challenges and advantages of each method. Furthermore we compare these techniques by their desired application and provide insights into future research directions for in situ nanopore fabrication methods.
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Affiliation(s)
- Jasper P Fried
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | - Jacob L Swett
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | - Binoy Paulose Nadappuram
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - Jan A Mol
- School of Physics and Astronomy, Queen Mary University of London, Mile End Road, E1 4NS, UK
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - James R Yates
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
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5
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Huang Q, Li N, Zhang H, Che C, Sun F, Xiong Y, Canady TD, Cunningham BT. Critical Review: digital resolution biomolecular sensing for diagnostics and life science research. LAB ON A CHIP 2020; 20:2816-2840. [PMID: 32700698 PMCID: PMC7485136 DOI: 10.1039/d0lc00506a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
One of the frontiers in the field of biosensors is the ability to quantify specific target molecules with enough precision to count individual units in a test sample, and to observe the characteristics of individual biomolecular interactions. Technologies that enable observation of molecules with "digital precision" have applications for in vitro diagnostics with ultra-sensitive limits of detection, characterization of biomolecular binding kinetics with a greater degree of precision, and gaining deeper insights into biological processes through quantification of molecules in complex specimens that would otherwise be unobservable. In this review, we seek to capture the current state-of-the-art in the field of digital resolution biosensing. We describe the capabilities of commercially available technology platforms, as well as capabilities that have been described in published literature. We highlight approaches that utilize enzymatic amplification, nanoparticle tags, chemical tags, as well as label-free biosensing methods.
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Affiliation(s)
- Qinglan Huang
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Nantao Li
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Hanyuan Zhang
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Congnyu Che
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Department of Bioengineering, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Fu Sun
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Yanyu Xiong
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Taylor D. Canady
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Brian T. Cunningham
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Department of Bioengineering, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Illinois Cancer Center, University of Illinois at Urbana-Champaign Urbana, IL 61801
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6
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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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7
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Zambrana-Puyalto X, Maccaferri N, Ponzellini P, Giovannini G, De Angelis F, Garoli D. Site-selective functionalization of plasmonic nanopores for enhanced fluorescence emission rate and Förster resonance energy transfer. NANOSCALE ADVANCES 2019; 1:2454-2461. [PMID: 36131984 PMCID: PMC9419820 DOI: 10.1039/c9na00077a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/03/2019] [Indexed: 05/26/2023]
Abstract
In this work, we use a site-selective functionalization strategy to decorate plasmonic nanopores with fluorescent dyes. Using an easy and robust fabrication method, we manage to build plasmonic rings on top of dielectric nanotubes with different inner diameters. The modulation of the dimension of the nanopores allows us to tailor their field confinement and their Purcell factor in the visible spectral range. In order to investigate how the changes in geometry influence the fluorescence emission rate efficiency, thiol-conjugated dyes are anchored on the plasmonic ring, thus forming a functional nanopore. We study the lifetime of ATTO 520 and ATTO 590 attached in two different configurations: single dye and FRET pair. For the single dye configuration, we observe that the lifetime of both single dyes decreases as the size of the nanopore is reduced. The smallest nanopores yield an experimental Purcell factor of 6. For the FRET pair configuration, we measure two regimes. For large nanopore sizes, the FRET efficiency remains constant. Whereas for smaller sizes, the FRET efficiency increases from 30 up to 45% with a decrease of the nanopore size. These findings, which have been supported by numerical simulations, may open new perspectives towards energy transfer engineering in plasmonic nanopores with potential applications in photonics and biosensing, in particular in single-molecule detection and sequencing.
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Affiliation(s)
| | - Nicolò Maccaferri
- Istituto Italiano di Tecnologia Via Morego 30 16163 Genova Italy
- Physics and Materials Science Research Unit, University of Luxembourg L-1511 Luxembourg Luxembourg
| | - Paolo Ponzellini
- Istituto Italiano di Tecnologia Via Morego 30 16163 Genova Italy
| | | | | | - Denis Garoli
- Istituto Italiano di Tecnologia Via Morego 30 16163 Genova Italy
- Ab Analitica Via Svizzera 13 35027 Padova Italy
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8
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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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9
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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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10
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Lee K, Park KB, Kim HJ, Yu JS, Chae H, Kim HM, Kim KB. Recent Progress in Solid-State Nanopores. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1704680. [PMID: 30260506 DOI: 10.1002/adma.201704680] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 06/08/2018] [Indexed: 05/28/2023]
Abstract
The solid-state nanopore has attracted much attention as a next-generation DNA sequencing tool or a single-molecule biosensor platform with its high sensitivity of biomolecule detection. The platform has advantages of processability, robustness of the device, and flexibility in the nanopore dimensions as compared with the protein nanopore, but with the limitation of insufficient spatial and temporal resolution to be utilized in DNA sequencing. Here, the fundamental principles of the solid-state nanopore are summarized to illustrate the novelty of the device, and improvements in the performance of the platform in terms of device fabrication are explained. The efforts to reduce the electrical noise of solid-state nanopore devices, and thus to enhance the sensitivity of detection, are presented along with detailed descriptions of the noise properties of the solid-state nanopore. Applications of 2D materials including graphene, h-BN, and MoS2 as a nanopore membrane to enhance the spatial resolution of nanopore detection, and organic coatings on the nanopore membranes for the addition of chemical functionality to the nanopore are summarized. Finally, the recently reported applications of the solid-state nanopore are categorized and described according to the target biomolecules: DNA-bound proteins, modified DNA structures, proteins, and protein oligomers.
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Affiliation(s)
- Kidan Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyeong-Beom Park
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyung-Jun Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae-Seok Yu
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hongsik Chae
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun-Mi Kim
- Research Institute of Advanced Materials, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ki-Bum Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Research Institute of Advanced Materials, Seoul National University, Seoul, 08826, Republic of Korea
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11
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Fraccari RL, Carminati M, Piantanida G, Leontidou T, Ferrari G, Albrecht T. High-bandwidth detection of short DNA in nanopipettes. Faraday Discuss 2018; 193:459-470. [PMID: 27711887 DOI: 10.1039/c6fd00109b] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Glass or quartz nanopipettes have found increasing use as tools for studying the biophysical properties of DNA and proteins, and as sensor devices. The ease of fabrication, favourable wetting properties and low capacitance are some of the inherent advantages, for example compared to more conventional, silicon-based nanopore chips. Recently, we have demonstrated high-bandwidth detection of double-stranded (ds) DNA with microsecond time resolution in nanopipettes, using custom-designed electronics. The electronics design has now been refined to include more sophisticated control features, such as integrated bias reversal and other features. Here, we exploit these capabilities and probe the translocation of short dsDNA in the 100 bp range, in different electrolytes. Single-stranded (ss) DNA of similar length are in use as capture probes, so label-free detection of their ds counterparts could therefore be of relevance in disease diagnostics.
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Affiliation(s)
- Raquel L Fraccari
- Imperial College London, Department of Chemistry, Exhibition, Road, London SW7 2AZ, UK.
| | - Marco Carminati
- Politecnico di Milano, Dipartimento di Elettronica, Informazione e Bioingegneria, P.za, Leonardo da Vinci 32, Milano, Italy
| | - Giacomo Piantanida
- Politecnico di Milano, Dipartimento di Elettronica, Informazione e Bioingegneria, P.za, Leonardo da Vinci 32, Milano, Italy
| | - Tina Leontidou
- Imperial College London, Department of Chemistry, Exhibition, Road, London SW7 2AZ, UK.
| | - Giorgio Ferrari
- Politecnico di Milano, Dipartimento di Elettronica, Informazione e Bioingegneria, P.za, Leonardo da Vinci 32, Milano, Italy
| | - Tim Albrecht
- Imperial College London, Department of Chemistry, Exhibition, Road, London SW7 2AZ, UK.
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12
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Crouch GM, Han D, Bohn PW. Zero-Mode Waveguide Nanophotonic Structures for Single Molecule Characterization. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2018; 51:193001. [PMID: 34158676 PMCID: PMC8216246 DOI: 10.1088/1361-6463/aab8be] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Single-molecule characterization has become a crucial research tool in the chemical and life sciences, but limitations, such as limited concentration range, inability to control molecular distributions in space, and intrinsic phenomena, such as photobleaching, present significant challenges. Recent developments in non-classical optics and nanophotonics offer promising routes to mitigating these restrictions, such that even low affinity (K D ~ mM) biomolecular interactions can be studied. Here we introduce and review specific nanophotonic devices used to support single molecule studies. Optical nanostructures, such as zero-mode waveguides (ZMWs), are usually fabricated in thin gold or aluminum films and serve to confine the observation volume of optical microspectroscopy to attoliter to zeptoliter volumes. These simple nanostructures allow individual molecules to be isolated for optical and electrochemical analysis, even when the molecules of interest are present at high concentration (μM - mM) in bulk solution. Arrays of ZMWs may be combined with optical probes such as single molecule fluorescence, single molecule fluorescence resonance energy transfer (smFRET), and fluorescence correlation spectroscopy (FCS) for distributed analysis of large numbers of single-molecule reactions or binding events in parallel. Furthermore, ZMWs may be used as multifunctional devices, for example by combining optical and electrochemical functions in a single discrete architecture to achieve electrochemical ZMWs (E-ZMW). In this review, we will describe the optical properties, fabrication, and applications of ZMWs for single-molecule studies, as well as the integration of ZMWs into systems for chemical and biochemical analysis.
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Affiliation(s)
- Garrison M. Crouch
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Donghoon Han
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Paul W. Bohn
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
- Departmemt of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
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13
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Dwyer JR, Harb M. Through a Window, Brightly: A Review of Selected Nanofabricated Thin-Film Platforms for Spectroscopy, Imaging, and Detection. APPLIED SPECTROSCOPY 2017; 71:2051-2075. [PMID: 28714316 DOI: 10.1177/0003702817715496] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present a review of the use of selected nanofabricated thin films to deliver a host of capabilities and insights spanning bioanalytical and biophysical chemistry, materials science, and fundamental molecular-level research. We discuss approaches where thin films have been vital, enabling experimental studies using a variety of optical spectroscopies across the visible and infrared spectral range, electron microscopies, and related techniques such as electron energy loss spectroscopy, X-ray photoelectron spectroscopy, and single molecule sensing. We anchor this broad discussion by highlighting two particularly exciting exemplars: a thin-walled nanofluidic sample cell concept that has advanced the discovery horizons of ultrafast spectroscopy and of electron microscopy investigations of in-liquid samples; and a unique class of thin-film-based nanofluidic devices, designed around a nanopore, with expansive prospects for single molecule sensing. Free-standing, low-stress silicon nitride membranes are a canonical structural element for these applications, and we elucidate the fabrication and resulting features-including mechanical stability, optical properties, X-ray and electron scattering properties, and chemical nature-of this material in this format. We also outline design and performance principles and include a discussion of underlying material preparations and properties suitable for understanding the use of alternative thin-film materials such as graphene.
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Affiliation(s)
- Jason R Dwyer
- 1 Department of Chemistry, University of Rhode Island, Kingston, RI, USA
| | - Maher Harb
- 2 Department of Physics and Materials, Science & Engineering, Drexel University, Philadelphia, PA, USA
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14
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Dwyer JR, Bandara YMNDY, Whelan JC, Karawdeniya BI, Nichols JW. Silicon Nitride Thin Films for Nanofluidic Device Fabrication. NANOFLUIDICS 2016. [DOI: 10.1039/9781849735230-00190] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Silicon nitride is a ubiquitous and well-established nanofabrication material with a host of favourable properties for creating nanofluidic devices with a range of compelling designs that offer extraordinary discovery potential. Nanochannels formed between two thin silicon nitride windows can open up vistas for exploration by freeing transmission electron microscopy to interrogate static structures and structural dynamics in liquid-based samples. Nanopores present a strikingly different architecture—nanofluidic channels through a silicon nitride membrane—and are one of the most promising tools to emerge in biophysics and bioanalysis, offering outstanding capabilities for single molecule sensing. The constrained environments in such nanofluidic devices make surface chemistry a vital design and performance consideration. Silicon nitride has a rich and complex surface chemistry that, while too often formidable, can be tamed with new, robust surface functionalization approaches. We will explore how a simple structural element—a ∼100 nm-thick silicon nitride window—can be used to fabricate devices to wrest unprecedented insights from the nanoscale world. We will detail the intricacies of native silicon nitride surface chemistry, present surface chemical modification routes that leverage the richness of available surface moieties, and examine the effect of engineered chemical surface functionality on nanofluidic device character and performance.
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Affiliation(s)
- J. R. Dwyer
- University of Rhode Island, Department of Chemistry Kingston RI 02881 USA
| | | | - J. C. Whelan
- University of Rhode Island, Department of Chemistry Kingston RI 02881 USA
| | - B. I. Karawdeniya
- University of Rhode Island, Department of Chemistry Kingston RI 02881 USA
| | - J. W. Nichols
- University of Rhode Island, Department of Chemistry Kingston RI 02881 USA
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15
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Shi X, Gao R, Ying YL, Si W, Chen YF, Long YT. A Scattering Nanopore for Single Nanoentity Sensing. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00408] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xin Shi
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Rui Gao
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Wei Si
- Jiangsu
Key Laboratory for Design and Manufacture of Micro-Nano Biomedical
Instruments, Southeast University, Nanjing 210096, P. R. China
| | - Yun-Fei Chen
- Jiangsu
Key Laboratory for Design and Manufacture of Micro-Nano Biomedical
Instruments, Southeast University, Nanjing 210096, P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
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16
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Liu S, Hawkins AR, Schmidt H. Optofluidic devices with integrated solid-state nanopores. Mikrochim Acta 2016; 183:1275-1287. [PMID: 27046940 DOI: 10.1007/s00604-016-1758-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This review (with 90 refs.) covers the state of the art in optofluidic devices with integrated solid-state nanopores for use in detection and sensing. Following an introduction into principles of optofluidics and solid-state nanopore technology, we discuss features of solid-state nanopore based assays using optofluidics. This includes the incorporation of solid-state nanopores into optofluidic platforms based on liquid-core anti-resonant reflecting optical waveguides (ARROWs), methods for their fabrication, aspects of single particle detection and particle manipulation. We then describe the new functionalities provided by solid-state nanopores integrated into optofluidic chips, in particular acting as smart gates for correlated electro-optical detection and discrimination of nanoparticles. This enables the identification of viruses and λ-DNA, particle trajectory simulations, enhancing sensitivity by tuning the shape of nanopores. The review concludes with a summary and an outlook.
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Affiliation(s)
- Shuo Liu
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Aaron R Hawkins
- ECEn Department, 459 Clyde Building, Brigham Young University, Provo, UT 84602, USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
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17
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Visualizing nanopore blinkings in parallel: a high-throughput nanopore array potential for ultra-rapid DNA sequencing. Sci Bull (Beijing) 2015. [DOI: 10.1007/s11434-015-0943-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Kerman S, Chen C, Li Y, Van Roy W, Lagae L, Van Dorpe P. Raman fingerprinting of single dielectric nanoparticles in plasmonic nanopores. NANOSCALE 2015; 7:18612-8. [PMID: 26490057 DOI: 10.1039/c5nr05341b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Plasmonic nano-apertures are commonly used for the detection of small particles such as nanoparticles and proteins by exploiting electrical and optical techniques. Plasmonic nanopores are metallic nano-apertures sitting on a thin membrane with a tiny hole. It has been shown that plasmonic nanopores with a given geometry identify internal molecules using Surface Enhanced Raman Spectroscopy (SERS). However, label-free identification of a single dielectric nanoparticle requires a highly localized field comparable to the size of the particle. Additionally, the particle's Brownian motion can jeopardize the amount of photons collected from a single particle. Here, we demonstrate that the combination of optical trapping and SERS can be used for the detection and identification of 20 nm polystyrene nanoparticles in plasmonic nanopores. This work is anticipated to contribute to the detection of small bioparticles, optical trapping and nanotribology studies.
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Affiliation(s)
- Sarp Kerman
- imec, Kapeldreef 75, Leuven, B3001, Belgium.
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19
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Li J, Yu D, Zhao Q. Solid-state nanopore-based DNA single molecule detection and sequencing. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1542-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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20
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Zhang M, Schmidt T, Jemt A, Sahlén P, Sychugov I, Lundeberg J, Linnros J. Nanopore arrays in a silicon membrane for parallel single-molecule detection: DNA translocation. NANOTECHNOLOGY 2015; 26:314002. [PMID: 26180050 DOI: 10.1088/0957-4484/26/31/314002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Optical nanopore sensing offers great potential in single-molecule detection, genotyping, or DNA sequencing for high-throughput applications. However, one of the bottle-necks for fluorophore-based biomolecule sensing is the lack of an optically optimized membrane with a large array of nanopores, which has large pore-to-pore distance, small variation in pore size and low background photoluminescence (PL). Here, we demonstrate parallel detection of single-fluorophore-labeled DNA strands (450 bps) translocating through an array of silicon nanopores that fulfills the above-mentioned requirements for optical sensing. The nanopore array was fabricated using electron beam lithography and anisotropic etching followed by electrochemical etching resulting in pore diameters down to ∼7 nm. The DNA translocation measurements were performed in a conventional wide-field microscope tailored for effective background PL control. The individual nanopore diameter was found to have a substantial effect on the translocation velocity, where smaller openings slow the translocation enough for the event to be clearly detectable in the fluorescence. Our results demonstrate that a uniform silicon nanopore array combined with wide-field optical detection is a promising alternative with which to realize massively-parallel single-molecule detection.
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Affiliation(s)
- Miao Zhang
- Materials and Nano Physics, School of Information and Communication Technology, KTH Royal Institute of Technology, Electrum 229, SE-16440 Kista-Stockholm, Sweden
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21
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Mathwig K, Albrecht T, Goluch ED, Rassaei L. Challenges of Biomolecular Detection at the Nanoscale: Nanopores and Microelectrodes. Anal Chem 2015; 87:5470-5. [DOI: 10.1021/acs.analchem.5b01167] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Klaus Mathwig
- Pharmaceutical
Analysis, Groningen Research Institute of Pharmacy, University of Groningen, P.O. Box 196, 9700 AD Groningen, The Netherlands
| | - Tim Albrecht
- Department
of Chemistry, Imperial College London, Exhibition Road, South Kensington
Campus, London, SW7 2AZ, U.K
| | - Edgar D. Goluch
- Department
of Chemical Engineering, Northeastern University, 360 Huntington Avenue, 313SN, Boston, Massachusetts 02115, United States
| | - Liza Rassaei
- Department
of Chemical Engineering, Delft University of Technology, Julianalaan
136, 2628 BL Delft, The Netherlands
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22
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Aramesh M, Shimoni O, Fox K, Karle TJ, Lohrmann A, Ostrikov K, Prawer S, Cervenka J. Ultra-high-density 3D DNA arrays within nanoporous biocompatible membranes for single-molecule-level detection and purification of circulating nucleic acids. NANOSCALE 2015; 7:5998-6006. [PMID: 25744416 DOI: 10.1039/c4nr07351g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Extracellular nucleic acids freely circulating in blood and other physiologic fluids are important biomarkers for non-invasive diagnostics and early detection of cancer and other diseases, yet difficult to detect because they exist in very low concentrations and large volumes. Here we demonstrate a new broad-range sensor platform for ultrasensitive and selective detection of circulating DNA down to the single-molecule level. The biosensor is based on a chemically functionalized nanoporous diamond-like carbon (DLC) coated alumina membrane. The few nanometer-thick, yet perfect and continuous DLC-coating confers the chemical stability and biocompatibility of the sensor, allowing its direct application in biological conditions. The selective detection is based on complementary hybridization of a fluorescently-tagged circulating cancer oncomarker (a 21-mer nucleic acid) with covalently immobilized DNA on the surface of the membrane. The captured DNAs are detected in the nanoporous structure of the sensor using confocal scanning laser microscopy. The flow-through membrane sensor demonstrates broad-range sensitivity, spanning from 10(15) molecules per cm(2) down to single molecules, which is several orders of magnitude improvement compared to the flat DNA microarrays. Our study suggests that these flow-through type nanoporous sensors represent a new powerful platform for large volume sampling and ultrasensitive detection of different chemical biomarkers.
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Affiliation(s)
- M Aramesh
- School of Physics, The University of Melbourne, Melbourne, Victoria 3010, Australia.
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23
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Pitchford WH, Kim HJ, Ivanov AP, Kim HM, Yu JS, Leatherbarrow RJ, Albrecht T, Kim KB, Edel JB. Synchronized optical and electronic detection of biomolecules using a low noise nanopore platform. ACS NANO 2015; 9:1740-8. [PMID: 25635821 DOI: 10.1021/nn506572r] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In the past two decades there has been a tremendous amount of research into the use of nanopores as single molecule sensors, which has been inspired by the Coulter counter and molecular transport across biological pores. Recently, the desire to increase structural resolution and analytical throughput has led to the integration of additional detection methods such as fluorescence spectroscopy. For structural information to be probed electronically high bandwidth measurements are crucial due to the high translocation velocity of molecules. The most commonly used solid-state nanopore sensors consist of a silicon nitride membrane and bulk silicon substrate. Unfortunately, the photoinduced noise associated with illumination of these platforms limits their applicability to high-bandwidth, high-laser-power synchronized optical and electronic measurements. Here we present a unique low-noise nanopore platform, composed of a predominately Pyrex substrate and silicon nitride membrane, for synchronized optical and electronic detection of biomolecules. Proof of principle experiments are conducted showing that the Pyrex substrates have substantially lowers ionic current noise arising from both laser illumination and platform capacitance. Furthermore, using confocal microscopy and a partially metallic pore we demonstrate high signal-to-noise synchronized optical and electronic detection of dsDNA.
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Affiliation(s)
- William H Pitchford
- Department of Chemistry, Imperial College London, South Kensington Campus , London SW7 2AZ, U.K
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24
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25
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Rutkowska A, Freedman K, Skalkowska J, Kim MJ, Edel JB, Albrecht T. Electrodeposition and Bipolar Effects in Metallized Nanopores and Their Use in the Detection of Insulin. Anal Chem 2015; 87:2337-44. [DOI: 10.1021/ac504463r] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Agnieszka Rutkowska
- Department
of Chemistry, Imperial College London, South Kensington, SW7 2AZ, London, United Kingdom
| | - Kevin Freedman
- Department
of Chemistry, Imperial College London, South Kensington, SW7 2AZ, London, United Kingdom
- Department
of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Justyna Skalkowska
- Department
of Chemistry, Imperial College London, South Kensington, SW7 2AZ, London, United Kingdom
- Department
of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Min Jun Kim
- Department
of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Joshua B. Edel
- Department
of Chemistry, Imperial College London, South Kensington, SW7 2AZ, London, United Kingdom
| | - Tim Albrecht
- Department
of Chemistry, Imperial College London, South Kensington, SW7 2AZ, London, United Kingdom
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26
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Assad O, Di Fiori N, Squires AH, Meller A. Two color DNA barcode detection in photoluminescence suppressed silicon nitride nanopores. NANO LETTERS 2015; 15:745-52. [PMID: 25522780 PMCID: PMC4296929 DOI: 10.1021/nl504459c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 12/16/2014] [Indexed: 05/20/2023]
Abstract
Optical sensing of solid-state nanopores is a relatively new approach that can enable high-throughput, multicolor readout from a collection of nanopores. It is therefore highly attractive for applications such as nanopore-based DNA sequencing and genotyping using DNA barcodes. However, to date optical readout has been plagued by the need to achieve sufficiently high signal-to-noise ratio (SNR) for single fluorophore sensing, while still maintaining millisecond resolution. One of the main factors degrading the optical SNR in solid-state nanopores is the high photoluminescence (PL) background emanating from the silicon nitride (SiNx) membrane in which pores are commonly fabricated. Focusing on the optical properties of SiNx nanopores we show that the local membrane PL intensity is substantially reduced, and its spectrum is shifted toward shorter wavelengths with increasing e-beam dose. This phenomenon, which is correlated with a marked photocurrent enhancement in these nanopores, is utilized to perform for the first time single molecule fluorescence detection using both green and red laser excitations. Specifically, the reduction in PL and the concurrent measurement of the nanopore photocurrent enhancement allow us to maximize the background suppression and to detect a dual color, five-unit DNA barcode with high SNR levels.
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Affiliation(s)
- Ossama
N. Assad
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215 United States
| | - Nicolas Di Fiori
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215 United States
| | - Allison H. Squires
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215 United States
| | - Amit Meller
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215 United States
- Department
of Biomedical Engineering, Technion −
Israel Institute of Technology, Haifa, Israel 32000
- E-mail:
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27
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Abstract
The "$1000 Genome" project has been drawing increasing attention since its launch a decade ago. Nanopore sequencing, the third-generation, is believed to be one of the most promising sequencing technologies to reach four gold standards set for the "$1000 Genome" while the second-generation sequencing technologies are bringing about a revolution in life sciences, particularly in genome sequencing-based personalized medicine. Both of protein and solid-state nanopores have been extensively investigated for a series of issues, from detection of ionic current blockage to field-effect-transistor (FET) sensors. A newly released protein nanopore sequencer has shown encouraging potential that nanopore sequencing will ultimately fulfill the gold standards. In this review, we address advances, challenges, and possible solutions of nanopore sequencing according to these standards.
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Affiliation(s)
- Yue Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| | - Qiuping Yang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| | - Zhimin Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
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28
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Ivanov AP, Actis P, Jönsson P, Klenerman D, Korchev Y, Edel JB. On-demand delivery of single DNA molecules using nanopipets. ACS NANO 2015; 9:3587-95. [PMID: 25794527 DOI: 10.1021/acsnano.5b00911] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Understanding the behavioral properties of single molecules or larger scale populations interacting with single molecules is currently a hotly pursued topic in nanotechnology. This arises from the potential such techniques have in relation to applications such as targeted drug delivery, early stage detection of disease, and drug screening. Although label and label-free single molecule detection strategies have existed for a number of years, currently lacking are efficient methods for the controllable delivery of single molecules in aqueous environments. In this article we show both experimentally and from simulations that nanopipets in conjunction with asymmetric voltage pulses can be used for label-free detection and delivery of single molecules through the tip of a nanopipet with "on-demand" timing resolution. This was demonstrated by controllable delivery of 5 kbp and 10 kbp DNA molecules from solutions with concentrations as low as 3 pM.
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Affiliation(s)
- Aleksandar P Ivanov
- †Department of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom
| | - Paolo Actis
- ‡Department of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Peter Jönsson
- §Department of Chemistry, Lund University, Lund SE-221 00, Sweden
- ∥Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - David Klenerman
- ∥Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Yuri Korchev
- ‡Department of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Joshua B Edel
- †Department of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom
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29
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Hauer P, Le Ru EC, Willmott GR. Co-ordinated detection of microparticles using tunable resistive pulse sensing and fluorescence spectroscopy. BIOMICROFLUIDICS 2015; 9:014110. [PMID: 25713692 PMCID: PMC4312361 DOI: 10.1063/1.4905874] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/01/2015] [Indexed: 05/09/2023]
Abstract
Tunable resistive pulse sensing (TRPS) has emerged as a useful tool for particle-by-particle detection and analysis of microparticles and nanoparticles as they pass through a pore in a thin stretchable membrane. We have adapted a TRPS device in order to conduct simultaneous optical measurements of particles passing through the pore. High-resolution fluorescence emission spectra have been recorded for individual 1.9 μm diameter particles at a sampling period of 4.3 ms. These spectra are time-correlated with RPS pulses in a current trace sampled every 20 μs. The flow rate through the pore, controlled by altering the hydrostatic pressure, determines the rate of particle detection. At pressures below 1 kPa, more than 90% of fluorescence and RPS events were matching. At higher pressures, some peaks were missed by the fluorescence technique due to the difference in sampling rates. This technique enhances the particle-by-particle specificity of conventional RPS measurements and could be useful for a range of particle characterization and bioanalysis applications.
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Affiliation(s)
- Peter Hauer
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Chemical and Physical Sciences, Victoria University of Wellington , P.O. Box 600, Wellington 6140, New Zealand
| | - Eric C Le Ru
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Chemical and Physical Sciences, Victoria University of Wellington , P.O. Box 600, Wellington 6140, New Zealand
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30
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Al Balushi AA, Kotnala A, Wheaton S, Gelfand RM, Rajashekara Y, Gordon R. Label-free free-solution nanoaperture optical tweezers for single molecule protein studies. Analyst 2015; 140:4760-78. [DOI: 10.1039/c4an02213k] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Recent advances in nanoaperture optical tweezers have enabled studies of single nanoparticles like proteins in label-free, free-solution environments.
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Affiliation(s)
- Ahmed A. Al Balushi
- Department of Electrical and Computer Engineering
- University of Victoria
- Victoria
- Canada V8P5C2
| | - Abhay Kotnala
- Department of Electrical and Computer Engineering
- University of Victoria
- Victoria
- Canada V8P5C2
| | - Skyler Wheaton
- Department of Electrical and Computer Engineering
- University of Victoria
- Victoria
- Canada V8P5C2
| | - Ryan M. Gelfand
- Department of Electrical and Computer Engineering
- University of Victoria
- Victoria
- Canada V8P5C2
| | - Yashaswini Rajashekara
- Department of Electrical and Computer Engineering
- University of Victoria
- Victoria
- Canada V8P5C2
| | - Reuven Gordon
- Department of Electrical and Computer Engineering
- University of Victoria
- Victoria
- Canada V8P5C2
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31
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Shi X, Gao R, Ying YL, Si W, Chen Y, Long YT. An integrated system for optical and electrical detection of single molecules/particles inside a solid-state nanopore. Faraday Discuss 2015; 184:85-99. [DOI: 10.1039/c5fd00060b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Nanopore techniques have proven to be useful tools for single-molecule detection. The combination of optical detection and ionic current measurements enables a new possibility for the parallel readout of multiple nanopores without complex nanofluidics and embedded electrodes. In this study, we developed a new integrated system for the label-free optical and electrical detection of single molecules based on a metal-coated nanopore. The entire system, containing a dark-field microscopy system and an ultralow current detection system with high temporal resolution, was designed and fabricated. An Au-coated nanopore was used to generate the optical signal. Light scattering from a single Au-coated nanopore was measured under a dark-field microscope. A lab-built ultralow current detection system was designed for the correlated optical and electrical readout. This integrated system might provide more direct and detailed information on single analytes inside the nanopore compared with classical ionic current measurements.
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Affiliation(s)
- Xin Shi
- Key Laboratory for Advanced Materials
- Department of Chemistry
- East China University of Science and Technology
- Shanghai
- P. R. China
| | - Rui Gao
- Key Laboratory for Advanced Materials
- Department of Chemistry
- East China University of Science and Technology
- Shanghai
- P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials
- Department of Chemistry
- East China University of Science and Technology
- Shanghai
- P. R. China
| | - Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments
- Southeast University
- Nanjing 210096
- P. R. China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments
- Southeast University
- Nanjing 210096
- P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials
- Department of Chemistry
- East China University of Science and Technology
- Shanghai
- P. R. China
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32
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Nicoli F, Verschueren D, Klein M, Dekker C, Jonsson MP. DNA translocations through solid-state plasmonic nanopores. NANO LETTERS 2014; 14:6917-25. [PMID: 25347403 PMCID: PMC4264857 DOI: 10.1021/nl503034j] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/22/2014] [Indexed: 05/19/2023]
Abstract
Nanopores enable label-free detection and analysis of single biomolecules. Here, we investigate DNA translocations through a novel type of plasmonic nanopore based on a gold bowtie nanoantenna with a solid-state nanopore at the plasmonic hot spot. Plasmonic excitation of the nanopore is found to influence both the sensor signal (nanopore ionic conductance blockade during DNA translocation) and the process that captures DNA into the nanopore, without affecting the duration time of the translocations. Most striking is a strong plasmon-induced enhancement of the rate of DNA translocation events in lithium chloride (LiCl, already 10-fold enhancement at a few mW of laser power). This provides a means to utilize the excellent spatiotemporal resolution of DNA interrogations with nanopores in LiCl buffers, which is known to suffer from low event rates. We propose a mechanism based on plasmon-induced local heating and thermophoresis as explanation of our observations.
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33
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Anderson BN, Assad ON, Gilboa T, Squires AH, Bar D, Meller A. Probing solid-state nanopores with light for the detection of unlabeled analytes. ACS NANO 2014; 8:11836-45. [PMID: 25363680 PMCID: PMC4334260 DOI: 10.1021/nn505545h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Nanopore sensing has enabled label-free single-molecule measurements on a wide variety of analytes, including DNA, RNA, and protein complexes. Much progress has been made toward biotechnological applications; however, electrically probing the ion current introduces nonideal noise components. Here we further develop a method to couple an ionic current to a photon-by-photon counting of fluorescent signal from Ca(2+)-sensitive dyes and demonstrate label-free optical detection of biopolymer translocation through solid-state nanopores using TIRF and confocal microscopy. We show that by fine adjustment of the CaCl2 gradient, EGTA concentration, and voltage, the optical signals can be localized to the immediate vicinity of the pore. Consequently, the noise spectral density distribution in the optical signal exhibits a nearly flat distribution throughout the entire frequency range. With the use of high-speed photon counting devices in confocal microscopy and higher photon count rates using stronger light sources, we can improve the signal-to-noise ratio of signal acquisition, while the use of wide-field imaging in TIRF can allow for simultaneous quantitative imaging of large arrays of nanopores.
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Affiliation(s)
- Brett N. Anderson
- Department of Biomedical Engineering Boston University Boston, Massachusetts 02215, United States
| | - Ossama N. Assad
- Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel 32000
| | - Tal Gilboa
- Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel 32000
| | - Allison H. Squires
- Department of Biomedical Engineering Boston University Boston, Massachusetts 02215, United States
| | - Daniel Bar
- Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel 32000
| | - Amit Meller
- Department of Biomedical Engineering Boston University Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel 32000
- Address correspondence to
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34
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Ivankin A, Henley RY, Larkin J, Carson S, Toscano ML, Wanunu M. Label-free optical detection of biomolecular translocation through nanopore arrays. ACS NANO 2014; 8:10774-81. [PMID: 25232895 PMCID: PMC4212781 DOI: 10.1021/nn504551d] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
In recent years, nanopores have emerged as exceptionally promising single-molecule sensors due to their ability to detect biomolecules at subfemtomole levels in a label-free manner. Development of a high-throughput nanopore-based biosensor requires multiplexing of nanopore measurements. Electrical detection, however, poses a challenge, as each nanopore circuit must be electrically independent, which requires complex nanofluidics and embedded electrodes. Here, we present an optical method for simultaneous measurements of the ionic current across an array of solid-state nanopores, requiring no additional fabrication steps. Proof-of-principle experiments are conducted that show simultaneous optical detection and characterization of ssDNA and dsDNA using an array of pores. Through a comparison with electrical measurements, we show that optical measurements are capable of accessing equivalent transmembrane current information.
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Affiliation(s)
- Andrey Ivankin
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Robert Y. Henley
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Joseph Larkin
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Spencer Carson
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Michael L. Toscano
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
- Address correspondence to
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35
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Nam S, Choi I, Fu CC, Kim K, Hong S, Choi Y, Zettl A, Lee LP. Graphene nanopore with a self-integrated optical antenna. NANO LETTERS 2014; 14:5584-9. [PMID: 25203166 DOI: 10.1021/nl503159d] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We report graphene nanopores with integrated optical antennae. We demonstrate that a nanometer-sized heated spot created by photon-to-heat conversion of a gold nanorod resting on a graphene membrane forms a nanoscale pore with a self-integrated optical antenna in a single step. The distinct plasmonic traits of metal nanoparticles, which have a unique capability to concentrate light into nanoscale regions, yield the significant advantage of parallel nanopore fabrication compared to the conventional sequential process using an electron beam. Tunability of both the nanopore dimensions and the optical characteristics of plasmonic nanoantennae are further achieved. Finally, the key optical function of our self-integrated optical antenna on the vicinity of graphene nanopore is manifested by multifold fluorescent signal enhancement during DNA translocation.
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Affiliation(s)
- SungWoo Nam
- Department of Bioengineering, ‡Berkeley Sensor and Actuator Center, §Department of Physics, ⊥Center of Integrated Nanomechanical Systems, ∇Department of Electrical Engineering and Computer Sciences, and ■Biophysics Graduate Program, University of California , Berkeley, California 94720, United States
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36
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Al Balushi AA, Gordon R. A label-free untethered approach to single-molecule protein binding kinetics. NANO LETTERS 2014; 14:5787-91. [PMID: 25211555 DOI: 10.1021/nl502665n] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Single molecule approaches provide rich real-time dynamics of molecular interactions that are not accessible to ensemble measurements. Previous single molecule studies have relied on labeling and tethering, which alters the natural state of the protein. Here we use the double-nanohole (DNH) optical tweezer approach to measure protein binding kinetics at the single molecule level in a label-free, free-solution (untethered) way. The binding kinetics of human serum albumin (HSA) to tolbutamide and to phenytoin are in quantitative agreement with previous measurements, and our single-molecule approach reveals a biexponential behavior characteristic of a multistep process. The DNH optical tweezer is an inexpensive platform for studying the real-time binding kinetics of protein-small molecule interactions in a label-free, free-solution environment, which will be of interest to future studies including drug discovery.
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Affiliation(s)
- Ahmed A Al Balushi
- Department of Electrical Engineering, University of Victoria , Victoria, British Columbia V8W 3P6, Canada
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37
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Japrung D, Bahrami A, Nadzeyka A, Peto L, Bauerdick S, Edel JB, Albrecht T. SSB binding to single-stranded DNA probed using solid-state nanopore sensors. J Phys Chem B 2014; 118:11605-12. [PMID: 25222770 DOI: 10.1021/jp506832u] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Single-stranded DNA (ssDNA) binding protein plays an important role in the DNA replication process in a wide range of organisms. It binds to ssDNA to prevent premature reannealing and to protect it from degradation. Current understanding of SSB/ssDNA interaction points to a complex mechanism, including SSB motion along the DNA strand. We report on the first characterization of this interaction at the single-molecule level using solid-state nanopore sensors, namely without any labeling or surface immobilization. Our results show that the presence of SSB on the ssDNA can control the speed of nanopore translocation, presumably due to strong interactions between SSB and the nanopore surface. This enables nanopore-based detection of ssDNA fragments as short as 37 nt, which is normally very difficult with solid-state nanopore sensors, due to constraints in noise and bandwidth. Notably, this fragment is considerably shorter than the 65 nt binding motif, typically required for SSB binding at high salt concentrations. The nonspecificity of SSB binding to ssDNA further suggests that this approach could be used for fragment sizing of short ssDNA.
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Affiliation(s)
- Deanpen Japrung
- Department of Chemistry, Imperial College London , Exhibition Road, South Kensington Campus, London SW7 2AZ, U.K
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38
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Zhang M, Schmidt T, Sangghaleh F, Roxhed N, Sychugov I, Linnros J. Oxidation of nanopores in a silicon membrane: self-limiting formation of sub-10 nm circular openings. NANOTECHNOLOGY 2014; 25:355302. [PMID: 25116147 DOI: 10.1088/0957-4484/25/35/355302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We describe a simple but reliable approach to shrink silicon nanopores with nanometer precision for potential high throughput biomolecular sensing and parallel DNA sequencing. Here, nanopore arrays on silicon membranes were fabricated by a self-limiting shrinkage of inverted pyramidal pores using dry thermal oxidation at 850 °C. The shrinkage rate of the pores with various initial sizes saturated after 4 h of oxidation. In the saturation regime, the shrinkage rate is within ± 2 nm h(-1). Oxidized pores with an average diameter of 32 nm were obtained with perfect circular shape. By careful design of the initial pore size, nanopores with diameters as small as 8 nm have been observed. Statistics of the pore width show that the shrinkage process did not broaden the pore size distribution; in most cases the distribution even decreased slightly. The progression of the oxidation and the deformation of the oxide around the pores were characterized by focused ion beam and electron microscopy. Cross-sectional imaging of the pores suggests that the initial inverted pyramidal geometry is most likely the determining factor for the self-limiting shrinkage.
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Affiliation(s)
- Miao Zhang
- Materials and Nano Physics, School of Information and Communication Technology, KTH Royal Institute of Technology, Electrum 229, SE-16440 Kista-Stockholm, Sweden
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39
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Howorka S, Hesse J. Microarrays and single molecules: an exciting combination. SOFT MATTER 2014; 10:931-41. [PMID: 24651891 DOI: 10.1039/c3sm52561a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Biomolecules positioned at interfaces have spawned many applications in bioanalysis, biophysics, and cell biology. This Highlight describes recent developments in the research areas of protein and DNA arrays, and single-molecule sensing. We cover the ultrasensitive scanning of conventional microarrays as well as the generation of arrays composed of individual molecules. The combination of these tools has improved the detection limits and the dynamic range of microarray analysis, helped develop powerful single-molecule sequencing approaches, and offered biophysical examination with high throughput and molecular detail. The topic of this Highlight integrates several disciplines and is written for interested chemists, biophysicists and nanotechnologists.
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Affiliation(s)
- Stefan Howorka
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London WC1H 0AJ, UK.
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40
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Brucale M, Schuler B, Samorì B. Single-molecule studies of intrinsically disordered proteins. Chem Rev 2014; 114:3281-317. [PMID: 24432838 DOI: 10.1021/cr400297g] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Marco Brucale
- Institute for the Study of Nanostructured Materials (ISMN), Italian National Council of Research (CNR) , Area della Ricerca Roma1, Via Salaria km 29.3 00015 Monterotondo (Rome), Italy
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41
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Barik A, Otto LM, Yoo D, Jose J, Johnson T, Oh SH. Dielectrophoresis-enhanced plasmonic sensing with gold nanohole arrays. NANO LETTERS 2014; 14:2006-12. [PMID: 24646075 PMCID: PMC4083195 DOI: 10.1021/nl500149h] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 03/18/2014] [Indexed: 05/17/2023]
Abstract
We experimentally demonstrate dielectrophoretic concentration of biological analytes on the surface of a gold nanohole array, which concurrently acts as a nanoplasmonic sensor and gradient force generator. The combination of nanohole-enhanced dielectrophoresis, electroosmosis, and extraordinary optical transmission through the periodic gold nanohole array enables real-time label-free detection of analyte molecules in a 5 μL droplet using concentrations as low as 1 pM within a few minutes, which is more than 1000 times faster than purely diffusion-based binding. The nanohole-based optofluidic platform demonstrated here is straightforward to construct, applicable to both charged and neutral molecules, and performs a novel function that cannot be accomplished using conventional surface plasmon resonance sensors.
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Affiliation(s)
- Avijit Barik
- Department of Electrical and Computer
Engineering and Department of Biomedical Engineering, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Lauren M. Otto
- Department of Electrical and Computer
Engineering and Department of Biomedical Engineering, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Daehan Yoo
- Department of Electrical and Computer
Engineering and Department of Biomedical Engineering, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jincy Jose
- Department of Electrical and Computer
Engineering and Department of Biomedical Engineering, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Timothy
W. Johnson
- Department of Electrical and Computer
Engineering and Department of Biomedical Engineering, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Sang-Hyun Oh
- Department of Electrical and Computer
Engineering and Department of Biomedical Engineering, University
of Minnesota, Minneapolis, Minnesota 55455, United States
- E-mail:
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42
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Cecchini MP, Wiener A, Turek VA, Chon H, Lee S, Ivanov AP, McComb DW, Choo J, Albrecht T, Maier SA, Edel JB. Rapid ultrasensitive single particle surface-enhanced Raman spectroscopy using metallic nanopores. NANO LETTERS 2013; 13:4602-9. [PMID: 24021086 DOI: 10.1021/nl402108g] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nanopore sensors embedded within thin dielectric membranes have been gaining significant interest due to their single molecule sensitivity and compatibility of detecting a large range of analytes, from DNA and proteins, to small molecules and particles. Building on this concept we utilize a metallic Au solid-state membrane to translocate and rapidly detect single Au nanoparticles (NPs) functionalized with 589 dye molecules using surface-enhanced resonance Raman spectroscopy (SERRS). We show that, due to the plasmonic coupling between the Au metallic nanopore surface and the NP, signal intensities are enhanced when probing analyte molecules bound to the NP surface. Although not single molecule, this nanopore sensing scheme benefits from the ability of SERRS to provide rich vibrational information on the analyte, improving on current nanopore-based electrical and optical detection techniques. We show that the full vibrational spectrum of the analyte can be detected with ultrahigh spectral sensitivity and a rapid temporal resolution of 880 μs.
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Affiliation(s)
- Michael P Cecchini
- Department of Chemistry, Imperial College London , South Kensington Campus, London, SW7 2AZ, United Kingdom
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43
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Holzmeister P, Acuna GP, Grohmann D, Tinnefeld P. Breaking the concentration limit of optical single-molecule detection. Chem Soc Rev 2013; 43:1014-28. [PMID: 24019005 DOI: 10.1039/c3cs60207a] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over the last decade, single-molecule detection has been successfully utilized in the life sciences and materials science. Yet, single-molecule measurements only yield meaningful results when working in a suitable, narrow concentration range. On the one hand, diffraction limits the minimal size of the observation volume in optical single-molecule measurements and consequently a sample must be adequately diluted so that only one molecule resides within the observation volume. On the other hand, at ultra-low concentrations relevant for sensing, the detection volume has to be increased in order to detect molecules in a reasonable timespan. This in turn results in the loss of an optimal signal-to-noise ratio necessary for single-molecule detection. This review discusses the requirements for effective single-molecule fluorescence applications, reflects on the motivation for the extension of the dynamic concentration range of single-molecule measurements and reviews various approaches that have been introduced recently to solve these issues. For the high-concentration limit, we identify four promising strategies including molecular confinement, optical observation volume reduction, temporal separation of signals and well-conceived experimental designs that specifically circumvent the high concentration limit. The low concentration limit is addressed by increasing the measurement speed, parallelization, signal amplification and preconcentration. The further development of these ideas will expand our possibilities to interrogate research questions with the clarity and precision provided only by the single-molecule approach.
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Affiliation(s)
- Phil Holzmeister
- Braunschweig University of Technology, Institute for Physical & Theoretical Chemistry, Hans-Sommer-Str. 10, 38106 Braunschweig, Germany.
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44
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Li Y, Chen C, Kerman S, Neutens P, Lagae L, Groeseneken G, Stakenborg T, Van Dorpe P. Harnessing plasmon-induced ionic noise in metallic nanopores. NANO LETTERS 2013; 13:1724-1729. [PMID: 23458167 DOI: 10.1021/nl4003188] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The ionic properties of a metal-coated silicon nanopore were examined in a nanofluidic system. We observed a strong increase of the ionic noise upon laser light illumination. The effect appeared to be strongly mediated by the resonant excitation of surface plasmons in the nanopore as was demonstrated by means of ionic mapping of the plasmonic electromagnetic field. Evidence from both simulations and experiments ruled out plasmonic heating as the main source of the noise, and point toward photoinduced electrochemical catalysis at the semiconductor-electrolyte interface. This ionic mapping technique described is opening up new opportunities on noninvasive applications ranging from biosensing to energy conversion.
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Affiliation(s)
- Yi Li
- IMEC, Kapeldreef 75, Leuven, Belgium
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45
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A theoretical study on entropy-driven polymer translocation through a finite-sized nanochannel. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.02.059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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46
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Japrung D, Dogan J, Freedman KJ, Nadzeyka A, Bauerdick S, Albrecht T, Kim MJ, Jemth P, Edel JB. Single-molecule studies of intrinsically disordered proteins using solid-state nanopores. Anal Chem 2013; 85:2449-56. [PMID: 23327569 DOI: 10.1021/ac3035025] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Partially or fully disordered proteins are instrumental for signal-transduction pathways; however, many mechanistic aspects of these proteins are not well-understood. For example, the number and nature of intermediate states along the binding pathway is still a topic of intense debate. To shed light on the conformational heterogeneity of disordered protein domains and their complexes, we performed single-molecule experiments by translocating disordered proteins through a nanopore embedded within a thin dielectric membrane. This platform allows for single-molecule statistics to be generated without the need of fluorescent labels or other modification groups. These studies were performed on two different intrinsically disordered protein domains, a binding domain from activator of thyroid hormone and retinoid receptors (ACTR) and the nuclear coactivator binding domain of CREB-binding protein (NCBD), along with their bimolecular complex. Our results demonstrate that both ACTR and NCBD populate distinct conformations upon translocation through the nanopore. The folded complex of the two disordered domains, on the other hand, translocated as one conformation. Somewhat surprisingly, we found that NCBD undergoes a charge reversal under high salt concentrations. This was verified by both translocation statistics as well as by measuring the ζ-potential. Electrostatic interactions have been previously suggested to play a key role in the association of intrinsically disordered proteins, and the observed behavior adds further complexity to their binding reactions.
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Affiliation(s)
- Deanpen Japrung
- Department of Chemistry, Imperial College London, South Kensington, SW7 2AZ, London, United Kingdom
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47
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Miles BN, Ivanov AP, Wilson KA, Doğan F, Japrung D, Edel JB. Single molecule sensing with solid-state nanopores: novel materials, methods, and applications. Chem Soc Rev 2013; 42:15-28. [DOI: 10.1039/c2cs35286a] [Citation(s) in RCA: 362] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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48
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Kumar S, Wittenberg NJ, Oh SH. Nanopore-induced spontaneous concentration for optofluidic sensing and particle assembly. Anal Chem 2012; 85:971-7. [PMID: 23214989 DOI: 10.1021/ac302690w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Metallic nanopore arrays have emerged as optofluidic platforms with multifarious sensing and analytical capabilities such as label-free surface plasmon resonance (SPR) sensing of molecular binding interactions and surface-enhanced Raman spectroscopy (SERS). However, directed delivery of analytes through open nanopores using traditional methods such as external electric fields or pressure gradients still remains difficult. We demonstrate that nanopore arrays have an intrinsic ability to promote flow through them via capillary flow and evaporation. This passive "nano-drain" mechanism is utilized to concentrate biomolecules on the surface of nanopores for improved detection sensitivity or create ordered nanoscale arrays of beads and liposomes. Without using any external pump or fluidic interconnects, we can concentrate and detect the presence of less than a femtomole of streptavidin in 10 μL of sample using fluorescence imaging. Liposome nanoarrays are also prepared in less than 5 min and used to detect lipid-protein interactions. We also demonstrate label-free SPR detection of analytes using metallic nanopore arrays. This method provides a fast, simple, transportable, and small-volume platform for labeled as well as label-free plasmonic analysis while improving the detection time and sensitivity.
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Affiliation(s)
- Shailabh Kumar
- Laboratory of Nanostructures and Biosensing, Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
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49
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Xie Q, Zhou Q, Xie F, Sang J, Wang W, Zhang HA, Wu W, Li Z. Wafer-scale fabrication of high-aspect ratio nanochannels based on edge-lithography technique. BIOMICROFLUIDICS 2012; 6:16502-165028. [PMID: 22396721 PMCID: PMC3293387 DOI: 10.1063/1.3683164] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Accepted: 01/15/2012] [Indexed: 05/15/2023]
Abstract
This paper introduced a wafer-scale fabrication approach for the preparation of nanochannels with high-aspect ratio (the ratio of the channel depth to its width). Edge lithography was used to pattern nanogaps in an aluminum film, which was functioned as deep reactive ion etching mask thereafter to form the nanochannel. Nanochannels with aspect ratio up to 172 and width down to 44 nm were successfully fabricated on a 4-inch Si wafer with width nonuniformity less than 13.6%. A microfluidic chip integrated with nanometer-sized filters was successfully fabricated by utilizing the present method for geometric-controllable nanoparticle packing.
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50
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Lindquist NC, Nagpal P, McPeak KM, Norris DJ, Oh SH. Engineering metallic nanostructures for plasmonics and nanophotonics. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2012; 75:036501. [PMID: 22790420 PMCID: PMC3396886 DOI: 10.1088/0034-4885/75/3/036501] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Metallic nanostructures now play an important role in many applications. In particular, for the emerging fields of plasmonics and nanophotonics, the ability to engineer metals on nanometric scales allows the development of new devices and the study of exciting physics. This review focuses on top-down nanofabrication techniques for engineering metallic nanostructures, along with computational and experimental characterization techniques. A variety of current and emerging applications are also covered.
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Affiliation(s)
- Nathan C Lindquist
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, U.S.A
- Physics Department, Bethel University, St. Paul, MN, U.S.A
| | | | - Kevin M McPeak
- Optical Materials Engineering Laboratory, ETH Zürich, Zürich, Switzerland
| | - David J Norris
- Optical Materials Engineering Laboratory, ETH Zürich, Zürich, Switzerland
| | - Sang-Hyun Oh
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, U.S.A
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