1
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Wang Y, Yu Z, Smith CS, Caneva S. Site-Specific Integration of Hexagonal Boron Nitride Quantum Emitters on 2D DNA Origami Nanopores. NANO LETTERS 2024; 24:8510-8517. [PMID: 38856705 PMCID: PMC11261624 DOI: 10.1021/acs.nanolett.4c00673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 06/05/2024] [Accepted: 06/05/2024] [Indexed: 06/11/2024]
Abstract
Optical emitters in hexagonal boron nitride (hBN) are promising probes for single-molecule sensing platforms. When engineered in nanoparticle form, they can be integrated as detectors in nanodevices, yet positional control at the nanoscale is lacking. Here we demonstrate the functionalization of DNA origami nanopores with optically active hBN nanoparticles (NPs) with nanometer precision. The NPs are active under three wavelengths of visible illumination and display both stable and blinking emission, enabling their accurate localization by using wide-field optical nanoscopy. Correlative opto-structural characterization reveals deterministic binding of bright, multicolor hBN NPs at the pore rim due to π-π stacking interactions at site-specific locations on the DNA origami. Our work provides a scalable, bottom-up approach toward deterministic assembly of solid-state emitters on arbitrary structural elements based on DNA origami. Such a nanoscale arrangement of optically active components can advance the development of single-molecule platforms, including optical nanopores and nanochannel sensors.
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Affiliation(s)
- Yabin Wang
- Department
of Precision and Microsystems Engineering, Delft University of Technology, Mekelweg 2, 2628
CD, Delft, The Netherlands
- Delft
Center for Systems and Control, Delft University
of Technology, Mekelweg 2, 2628 CD Delft, Netherlands
| | - Ze Yu
- Department
of Precision and Microsystems Engineering, Delft University of Technology, Mekelweg 2, 2628
CD, Delft, The Netherlands
| | - Carlas S. Smith
- Delft
Center for Systems and Control, Delft University
of Technology, Mekelweg 2, 2628 CD Delft, Netherlands
| | - Sabina Caneva
- Department
of Precision and Microsystems Engineering, Delft University of Technology, Mekelweg 2, 2628
CD, Delft, The Netherlands
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2
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Stuber A, Schlotter T, Hengsteler J, Nakatsuka N. Solid-State Nanopores for Biomolecular Analysis and Detection. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:283-316. [PMID: 38273209 DOI: 10.1007/10_2023_240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Advances in nanopore technology and data processing have rendered DNA sequencing highly accessible, unlocking a new realm of biotechnological opportunities. Commercially available nanopores for DNA sequencing are of biological origin and have certain disadvantages such as having specific environmental requirements to retain functionality. Solid-state nanopores have received increased attention as modular systems with controllable characteristics that enable deployment in non-physiological milieu. Thus, we focus our review on summarizing recent innovations in the field of solid-state nanopores to envision the future of this technology for biomolecular analysis and detection. We begin by introducing the physical aspects of nanopore measurements ranging from interfacial interactions at pore and electrode surfaces to mass transport of analytes and data analysis of recorded signals. Then, developments in nanopore fabrication and post-processing techniques with the pros and cons of different methodologies are examined. Subsequently, progress to facilitate DNA sequencing using solid-state nanopores is described to assess how this platform is evolving to tackle the more complex challenge of protein sequencing. Beyond sequencing, we highlight the recent developments in biosensing of nucleic acids, proteins, and sugars and conclude with an outlook on the frontiers of nanopore technologies.
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Affiliation(s)
- Annina Stuber
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Tilman Schlotter
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Julian Hengsteler
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland.
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3
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de Blois C, Engel M, Rejou MA, Molcrette B, Favier A, Montel F. Optical single molecule characterisation of natural and synthetic polymers through nanopores. NANOSCALE 2023; 16:138-151. [PMID: 38054974 DOI: 10.1039/d3nr04915a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Nanopore techniques are now widely used to sequence DNA, RNA and even oligopeptide molecules at the base pair level by measuring the ionic current. In order to build a more versatile characterisation system, optical methods for the detection of a single molecule translocating through a nanopore have been developed, achieving very promising results. In this work, we developed a series of tools to interpret the optical signals in terms of the physical behaviour of various types of natural and synthetic polymers, with high throughput. We show that the measurement of the characteristic time of a translocation event gives access to the apparent molecular weight of an object, and allows us to quantify the concentration ratio of two DNA samples of different molecular weights in solution. Using the same tools for smaller synthetic polymers, we were able to obtain information about their molecular weight distribution depending on the synthesis method.
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Affiliation(s)
- Charlotte de Blois
- Univ. Lyon, ENS de Lyon, CNRS, Laboratoire de Physique, F-69342 Lyon, France.
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, INSA Lyon, Université Jean Monnet, UMR 5233, Ingénierie des Matériaux Polymères, F-69621 Villeurbanne, France.
| | - Marie Engel
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, INSA Lyon, Université Jean Monnet, UMR 5233, Ingénierie des Matériaux Polymères, F-69621 Villeurbanne, France.
| | - Marie-Amélie Rejou
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, INSA Lyon, Université Jean Monnet, UMR 5233, Ingénierie des Matériaux Polymères, F-69621 Villeurbanne, France.
| | - Bastien Molcrette
- Univ. Lyon, ENS de Lyon, CNRS, Laboratoire de Physique, F-69342 Lyon, France.
| | - Arnaud Favier
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, INSA Lyon, Université Jean Monnet, UMR 5233, Ingénierie des Matériaux Polymères, F-69621 Villeurbanne, France.
| | - Fabien Montel
- Univ. Lyon, ENS de Lyon, CNRS, Laboratoire de Physique, F-69342 Lyon, France.
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4
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Moazemi F, Ghanbari-Kashan S, Moharaminezhad F, Nikoofard N. Ejection dynamics of a semiflexible polymer from a nanosphere. Phys Rev E 2023; 108:044501. [PMID: 37978688 DOI: 10.1103/physreve.108.044501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/27/2023] [Indexed: 11/19/2023]
Abstract
Polymer ejection has been of interest due to its relation to the viral genome ejection. However, the ejection dynamics of a semiflexible polymer from a nanosphere is not yet understood. Here, a theory is developed for the ejection dynamics of a polymer with total length L_{0} and persistence length l from a sphere of diameter D. These length scales define different confinement regimes to study the polymer dynamics. The polymer sometimes undergoes between two to three regimes during its ejection. The rate of change of the free energy of confinement is balanced by the rate of energy dissipation, in each regime. The polymer experiences a final stage in which the free energy of polymer attachment to the sphere governs the ejection. The total ejection time τ depends on the polymer dynamics in the various regimes that it passes through in the phase space. Dependence of the ejection time on the polymer length, the persistence length, and the sphere diameter τ∝L_{0}^{α}D^{β}l^{γ} is obtained from the theory. It is shown that α changes between 1 and 1.7, β between 3 and 5, and γ takes a zero or positive value often smaller than 1. Agreement of these exponents with other theory and simulations are discussed.
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Affiliation(s)
- Farzaneh Moazemi
- Institute of Nanoscience and Nanotechnology, University of Kashan, Kashan 87317-53153, Iran
| | | | - Fatemeh Moharaminezhad
- Institute of Nanoscience and Nanotechnology, University of Kashan, Kashan 87317-53153, Iran
| | - Narges Nikoofard
- Institute of Nanoscience and Nanotechnology, University of Kashan, Kashan 87317-53153, Iran
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5
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Yang K, Yin Z, Sun L. Fabrication of High Aspect Ratio Nano-Channels by Thermal Nano-Imprinting and Parylene Deposition. MICROMACHINES 2023; 14:1430. [PMID: 37512741 PMCID: PMC10384472 DOI: 10.3390/mi14071430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/10/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023]
Abstract
A low-cost method of fabrication of high aspect ratio nano-channels by thermal nano-imprinting and Parylene deposition is proposed. SU-8 photoresist nano-channels were first manufactured by thermal nano-imprinting, and Parylene deposition was carried out to reduce the width of the nano-channels and increase the aspect ratio. During the process, the side walls of the SU-8 nano-channels were covered with the Parylene film, reducing the width of the nano-channels, and the depth of the channels increased due to the thickness of the Parylene film deposited on the surface of the SU-8 nano-channels, more so than that at the bottom. The influence of Parylene mass on the size of nano-channels was studied by theoretical analysis and experiments, and the deposition pressure of Parylene was optimized. The final high aspect ratio nano-channels are 46 nm in width and 746 nm in depth, of which the aspect ratio is 16. This simple and efficient method paves the way for the production of high aspect ratio nano-channels.
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Affiliation(s)
- Kun Yang
- Shanxi Key Laboratory of Micro Nano Sensors & Artificial Intelligence Perception, College of Information and Computer, Taiyuan University of Technology, Taiyuan 030024, China
| | - Zhifu Yin
- State Key Laboratory of Electrical Insulation and Power Equipment, Xi'an Jiaotong University, Xi'an 710049, China
- The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Lei Sun
- Shanxi Key Laboratory of Micro Nano Sensors & Artificial Intelligence Perception, College of Information and Computer, Taiyuan University of Technology, Taiyuan 030024, China
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6
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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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7
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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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8
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Li W, Zhou J, Maccaferri N, Krahne R, Wang K, Garoli D. Enhanced Optical Spectroscopy for Multiplexed DNA and Protein-Sequencing with Plasmonic Nanopores: Challenges and Prospects. Anal Chem 2022; 94:503-514. [PMID: 34974704 PMCID: PMC8771637 DOI: 10.1021/acs.analchem.1c04459] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Wang Li
- State
Key Laboratory of Analytical Chemistry for Life Science School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, P. R. China
| | - Juan Zhou
- State
Key Laboratory of Analytical Chemistry for Life Science School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, P. R. China
| | - Nicolò Maccaferri
- Department
of Physics and Materials Science, University
of Luxembourg, L-1511 Luxembourg, Luxembourg
- Department
of Physics, Umeå University, Linnaeus väg 20, SE-90736 Umeå, Sweden
| | - Roman Krahne
- Istituto
Italiano di Tecnologia, Optoelectronics
Research Line, Morego
30, I-16163 Genova, Italy
| | - Kang Wang
- State
Key Laboratory of Analytical Chemistry for Life Science School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, P. R. China
| | - Denis Garoli
- Istituto
Italiano di Tecnologia, Optoelectronics
Research Line, Morego
30, I-16163 Genova, Italy
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9
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Rahman M, Sampad MJN, Hawkins A, Schmidt H. Recent advances in integrated solid-state nanopore sensors. LAB ON A CHIP 2021; 21:3030-3052. [PMID: 34137407 PMCID: PMC8372664 DOI: 10.1039/d1lc00294e] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The advent of single-molecule probing techniques has revolutionized the biomedical and life science fields and has spurred the development of a new class of labs-on-chip based on powerful biosensors. Nanopores represent one of the most recent and most promising single molecule sensing paradigms that is seeing increased chip-scale integration for improved convenience and performance. Due to their physical structure, nanopores are highly sensitive, require low sample volume, and offer label-free, amplification-free, high-throughput real-time detection and identification of biomolecules. Over the last 25 years, nanopores have been extensively employed to detect a variety of biomolecules with a growing range of applicatons ranging from nucleic acid sequencing to ultrasensitive diagnostics to single-molecule biophysics. Nanopores, in particular those in solid-state membranes, also have the potential for integration with other technologies such as optics, plasmonics, microfluidics, and optofluidics to perform more complex tasks for an ever-expanding demand. A number of breakthrough results using integrated nanopore platforms have already been reported, and more can be expected as nanopores remain the focus of innovative research and are finding their way into commercial instruments. This review provides an overview of different aspects and challenges of nanopore technology with a focus on chip-scale integration of solid-state nanopores for biosensing and bioanalytical applications.
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Affiliation(s)
- Mahmudur Rahman
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064 USA. and Dhaka University of Engineering & Technology, Gazipur, Bangladesh
| | | | - Aaron Hawkins
- ECEn Department, Brigham Young University, 459 Clyde Building, 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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10
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Sun L, Zou H, Sang S. Effect of temperature on the
SU
‐8 photoresist filling behavior during thermal nanoimprinting. POLYM ENG SCI 2021. [DOI: 10.1002/pen.25751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lei Sun
- MicroNano System Research Center Key Lab of Advanced Transducers and Intelligent Control System of the Ministry of Education & College of Information Engineering, Taiyuan University of Technology Jinzhong China
| | - Helin Zou
- Key Laboratory for Precision and Non‐traditional Machining Technology of Ministry of Education Dalian University of Technology Dalian China
- Key Laboratory for Micro/Nano Technology and Systems of Liaoning Province Dalian University of Technology Dalian China
| | - Shengbo Sang
- MicroNano System Research Center Key Lab of Advanced Transducers and Intelligent Control System of the Ministry of Education & College of Information Engineering, Taiyuan University of Technology Jinzhong China
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11
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Zvuloni E, Zrehen A, Gilboa T, Meller A. Fast and Deterministic Fabrication of Sub-5 Nanometer Solid-State Pores by Feedback-Controlled Laser Processing. ACS NANO 2021; 15:12189-12200. [PMID: 34219449 PMCID: PMC8320231 DOI: 10.1021/acsnano.1c03773] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/28/2021] [Indexed: 05/26/2023]
Abstract
Nanopores are single-molecule sensors capable of detecting and quantifying a broad range of unlabeled biomolecules including DNA and proteins. Nanopores' generic sensing principle has permitted the development of a vast range of biomolecular applications in genomics and proteomics, including single-molecule DNA sequencing and protein fingerprinting. Owing to their superior mechanical and electrical stability, many of the recent studies involved synthetic nanopores fabricated in thin solid-state membranes such as freestanding silicon nitride. However, to date, one of the bottlenecks in this field is the availability of a fast, reliable, and deterministic fabrication method capable of repeatedly forming small nanopores (i.e., sub 5 nm) in situ. Recently, it was demonstrated that a tightly focused laser beam can induce controlled etching of silicon nitride membranes suspended in buffered aqueous solutions. Herein, we demonstrate that nanopore laser drilling (LD) can produce nanopores deterministically to a prespecified size without user intervention. By optimizing the optical apparatus, and by designing a multistep control algorithm for the LD process, we demonstrate a fully automatic fabrication method for any user-defined nanopore size within minutes. The LD process results in a double bowl-shaped structure having a typical size of the laser point-spread function (PSF) at its openings. Numerical simulations of the characteristic LD nanopore shape provide conductance curves that fit the experimental result and support the idea that the pore is produced at the thinnest area formed by the back-to-back facings bowls. The presented LD fabrication method significantly enhances nanopore fabrication throughput and accuracy and hence can be adopted for a large range of biomolecular sensing applications.
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Affiliation(s)
- Eran Zvuloni
- Department
of Biomedical Engineering, Technion-IIT, Haifa 32000, Israel
| | - Adam Zrehen
- Department
of Biomedical Engineering, Technion-IIT, Haifa 32000, Israel
| | - Tal Gilboa
- Department
of Pathology, Brigham and Women’s
Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Amit Meller
- Department
of Biomedical Engineering, Technion-IIT, Haifa 32000, Israel
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12
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Niedzwiecki DJ, DiPaolo B, Lin CY, Castan A, Keneipp R, Drndić M. Devices for Nanoscale Guiding of DNA through a 2D Nanopore. ACS Sens 2021; 6:2534-2545. [PMID: 34228425 DOI: 10.1021/acssensors.1c00829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We fabricate on-chip solid-state nanofluidic-2D nanopore systems that can limit the range of motion for DNA in the sensing region of a nanopore. We do so by creating devices containing one or more silicon nitride pores and silicon nitride pillars supporting a 2D pore that orient DNA within a nanopore device to a restricted geometry, yet allow the free motion of ions to maintain a high signal-to-noise ratio. We discuss two concepts with two and three independent electrical connections and corresponding nanopore chip device architectures to achieve this goal in practice. Here, we describe device fabrication and transmission electron microscope (TEM) images, and provide simulated translocations based on the finite element analysis in 3D to demonstrate its merit. In both methods, there is a main 2D nanopore which we refer to as a "sensing" nanopore (monolayer MoS2 in this paper). A secondary layer is either an array of guiding pores sharing the same electrode pair as the sensing pore (Method 1) or a single, independently contacted, guiding pore (Method 2). These pores are constructed parallel to the "sensing" pore and serve as "guiding" elements to stretch and feed DNA into the atomically thin sensing pore. We discuss the practical implementation of these concepts with nanofluidic and Si-based technology, including detailed fabrication steps and challenges involved for DNA applications in solution.
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Affiliation(s)
- David J. Niedzwiecki
- Goeppert LLC, Pennovation, 3401 Grays Ferry Avenue, Philadelphia, Pennsylvania 19146, United States
| | - Brian DiPaolo
- Goeppert LLC, Pennovation, 3401 Grays Ferry Avenue, Philadelphia, Pennsylvania 19146, United States
| | - Chih-Yuan Lin
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Alice Castan
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Rachael Keneipp
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Marija Drndić
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
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13
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Seth S, Bhattacharya A. DNA barcode by flossing through a cylindrical nanopore. RSC Adv 2021; 11:20781-20787. [PMID: 34178311 PMCID: PMC8190898 DOI: 10.1039/d1ra00349f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
We report an accurate method to determine DNA barcodes from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive theoretical scheme which improves the measurements to almost 100% accuracy. The heavier protein tags along the DNA backbone introduce a large speed variation in the chain that can be understood using the idea of non-equilibrium tension propagation theory. However, from an initial rough characterization of velocities into “fast” (nucleotides) and “slow” (protein tags) domains, we introduce a physically motivated interpolation scheme that enables us to determine the barcode velocities rather accurately. Our theoretical analysis of the motion of the DNA through a cylindrical nanopore opens up the possibility of its experimental realization and carries over to multi-nanopore devices used for barcoding. We report a method for DNA barcoding from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive scheme to improve the measurements to almost 100% accuracy.![]()
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Affiliation(s)
- Swarnadeep Seth
- Department of Physics, University of Central Florida Orlando FL 32816-2385 USA
| | - Aniket Bhattacharya
- Department of Physics, University of Central Florida Orlando FL 32816-2385 USA
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14
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Cao C, Krapp LF, Al Ouahabi A, König NF, Cirauqui N, Radenovic A, Lutz JF, Peraro MD. Aerolysin nanopores decode digital information stored in tailored macromolecular analytes. SCIENCE ADVANCES 2020; 6:eabc2661. [PMID: 33298438 PMCID: PMC7725454 DOI: 10.1126/sciadv.abc2661] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/26/2020] [Indexed: 05/23/2023]
Abstract
Digital data storage is a growing need for our society and finding alternative solutions than those based on silicon or magnetic tapes is a challenge in the era of "big data." The recent development of polymers that can store information at the molecular level has opened up new opportunities for ultrahigh density data storage, long-term archival, anticounterfeiting systems, and molecular cryptography. However, synthetic informational polymers are so far only deciphered by tandem mass spectrometry. In comparison, nanopore technology can be faster, cheaper, nondestructive and provide detection at the single-molecule level; moreover, it can be massively parallelized and miniaturized in portable devices. Here, we demonstrate the ability of engineered aerolysin nanopores to accurately read, with single-bit resolution, the digital information encoded in tailored informational polymers alone and in mixed samples, without compromising information density. These findings open promising possibilities to develop writing-reading technologies to process digital data using a biological-inspired platform.
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Affiliation(s)
- Chan Cao
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Lucien F Krapp
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Abdelaziz Al Ouahabi
- Université de Strasbourg, Centre national de la recherche scientifique (CNRS), Institute Charles Sadron UPR22, 23 rue du Loess, 67034 Strasbourg Cedex 2, France
| | - Niklas F König
- Université de Strasbourg, Centre national de la recherche scientifique (CNRS), Institute Charles Sadron UPR22, 23 rue du Loess, 67034 Strasbourg Cedex 2, France
| | - Nuria Cirauqui
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Department of Pharmaceutical Biotechnology, Universidade Federal do Rio de Janeiro, 21941-902 Rio de Janeiro, Brazil
- CNRS, UMR5086, "Molecular Microbiology and Structural Biochemistry", University of Lyon, 7 Passage du Vercors, 69367 Lyon, France
| | - Aleksandra Radenovic
- Institute of Bioengineering, School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Jean-François Lutz
- Université de Strasbourg, Centre national de la recherche scientifique (CNRS), Institute Charles Sadron UPR22, 23 rue du Loess, 67034 Strasbourg Cedex 2, France.
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
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15
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Zrehen A, Ohayon S, Huttner D, Meller A. On-chip protein separation with single-molecule resolution. Sci Rep 2020; 10:15313. [PMID: 32943759 PMCID: PMC7498591 DOI: 10.1038/s41598-020-72463-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/27/2020] [Indexed: 01/15/2023] Open
Abstract
Accurate identification of both abundant and rare proteins hinges on the development of single-protein sensing methods. Given the immense variation in protein expression levels in a cell, separation of proteins by weight would improve protein classification strategies. Upstream separation facilitates sample binning into smaller groups while also preventing sensor overflow, as may be caused by highly abundant proteins in cell lysates or clinical samples. Here, we scale a bulk analysis method for protein separation, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), to the single-molecule level using single-photon sensitive widefield imaging. Single-molecule sensing of the electrokinetically moving proteins is achieved by in situ polymerization of the PAGE in a low-profile fluidic channel having a depth of only ~ 0.6 µm. The polyacrylamide gel restricts the Brownian kinetics of the proteins, while the low-profile channel ensures that they remain in focus during imaging, allowing video-rate monitoring of single-protein migration. Calibration of the device involves separating a set of Atto647N-covalently labeled recombinant proteins in the size range of 14-70 kDa, yielding an exponential dependence of the proteins' molecular weights on the measured mobilities, as expected. Subsequently, we demonstrate the ability of our fluidic device to separate and image thousands of proteins directly extracted from a human cancer cell line. Using single-particle image analysis methods, we created detailed profiles of the separation kinetics of lysine and cysteine -labeled proteins. Downstream coupling of the device to single-protein identification sensors may provide superior protein classification and improve our ability to analyze complex biological and medical protein samples.
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Affiliation(s)
- Adam Zrehen
- Technion Israel Institute of Technology, Haifa, Israel
| | - Shilo Ohayon
- Technion Israel Institute of Technology, Haifa, Israel
| | - Diana Huttner
- Technion Israel Institute of Technology, Haifa, Israel
| | - Amit Meller
- Technion Israel Institute of Technology, Haifa, Israel.
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16
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Agrawal P, Reifenberger JG, Dorfman KD. 3D Printing-Enabled DNA Extraction for Long-Read Genomics. ACS OMEGA 2020; 5:20817-20824. [PMID: 32875216 PMCID: PMC7450497 DOI: 10.1021/acsomega.0c01912] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/02/2020] [Indexed: 05/05/2023]
Abstract
Long-read genomics technologies such as nanopore sequencing and genome mapping in nanochannels extract genomic information in the kilobase to megabase pair range from single DNA molecules, thereby overcoming read-length limitations in next-generation DNA sequencing. Long-read technologies start with long DNA molecules as the input and thus benefit from universal sample preparation methods that are fast and shear-free and present a scope of automation and direct upstream integration. We describe a 3D printing-assisted poly(dimethylysiloxane)-based DNA sample preparation device, where diffusive chemical lysis followed by electrophoresis produces circa 100 ng of long DNA directly from cells with less than 5 min of labor. Assessment of the product DNA by confinement in nanochannels reveals that the DNA sizes are commensurate with the requirements for long-read single-molecule technologies. Microfluidics not only expedites sample preparation, but also offers the opportunity for integration with genomics technologies to eliminate DNA fragmentation and loss during transfer to the genomic device.
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Affiliation(s)
- Paridhi Agrawal
- Department
of Chemical Engineering and Materials Science, University of Minnesota—Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, United States
| | - Jeffrey G. Reifenberger
- Bionano
Genomics, Inc., 9540
Towne Centre Drive, Suite 100, San Diego, California 92121, United States
| | - Kevin D. Dorfman
- Department
of Chemical Engineering and Materials Science, University of Minnesota—Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, United States
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17
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Zhang Y, Zhao J, Kan Y, Ji R, Pan J, Huang W, Xu Z, Si W, Sha J. Concentration effects on capture rate and translocation configuration of nanopore-based DNA detection. Electrophoresis 2020; 41:1523-1528. [PMID: 32529653 DOI: 10.1002/elps.202000016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 01/21/2023]
Abstract
Nanopore is a kind of powerful tool to detect single molecules and investigate fundamental biological processes. In biological cells or real detection systems, concentration of DNA molecules is various. Here, we report an experimental study of the effects of DNA concentration on capture rate and translocation configuration with different sized nanopores and applied voltages. Three classes of DNA translocation configurations have been observed including linear translocation, folded translocation, and cotranslocation. In the case of relatively large sized nanopore or high applied voltage, considerable cotranslocation events have been detected. The percentage of cotranslocation events also increases with DNA concentration, which leads to the relationship between capture rate and DNA concentration deviates from linearity. Therefore, in order to reflect the number of translocation molecules accurately, the capture rate should be corrected by double-counting cotranslocation events. These results will provide a valuable reference for the design of nanopore sensors.
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Affiliation(s)
- Yin Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, P. R. China
| | - Jiabin Zhao
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, P. R. China
| | - Yajing Kan
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, P. R. China
| | - Rui Ji
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, P. R. China
| | - Jianqiang Pan
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, P. R. China
| | - Weichi Huang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, P. R. China
| | - Zheng Xu
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian, P. R. China
| | - Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, P. R. China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, P. R. China
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18
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Fu J, Wu L, Qiao Y, Tu J, Lu Z. Microfluidic Systems Applied in Solid-State Nanopore Sensors. MICROMACHINES 2020; 11:mi11030332. [PMID: 32210148 PMCID: PMC7142662 DOI: 10.3390/mi11030332] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/08/2020] [Accepted: 03/20/2020] [Indexed: 01/04/2023]
Abstract
Microfluidic system, as a kind of miniature integrated operating platform, has been applied to solid-state nanopore sensors after many years of experimental study. In the process of introducing microfluidic into solid-state nanopore sensors, many novel device structures are designed due to the abundance of analytes and the diversity of detection methods. Here we review the fundamental setup of nanopore-based microfluidic systems and the developments and advancements that have been taking place in the field. The microfluidic systems with a multichannel strategy to elevate the throughput and efficiency of nanopore sensors are then presented. Multifunctional detection represented by optical-electrical detection, which is realized by microfluidic integration, is also described. A high integration microfluidic system with nanopore is further discussed, which shows the prototype of commercialization.
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Affiliation(s)
| | | | | | - Jing Tu
- Correspondence: (J.T.); (Z.L.); Tel.: +86-25-8379-2396 (J.T.); +86-25-8379-3779 (Z.L.)
| | - Zuhong Lu
- Correspondence: (J.T.); (Z.L.); Tel.: +86-25-8379-2396 (J.T.); +86-25-8379-3779 (Z.L.)
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19
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Affiliation(s)
- Si-Min Lu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yue-Yi Peng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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