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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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2
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Sensale S, Wang C, Chang HC. Resistive amplitude fingerprints during translocation of linear molecules through charged solid-state nanopores. J Chem Phys 2020; 153:035102. [PMID: 32716192 PMCID: PMC7367690 DOI: 10.1063/5.0013195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We report the first analytical theory on the amplitude of resistive signals during molecular translocation through charged solid-state nanopores with variable cross-sectional area and piecewise-constant surface charge densities. By providing closed-form explicit algebraic expressions for the concentration profiles inside charged nanopores, this theory allows the prediction of baseline and translocation resistive signals without the need for numerical simulation of the electrokinetic phenomena. A transversely homogenized theory and an asymptotic expansion for weakly charged pores capture DC or quasi-static rectification due to field-induced intrapore concentration polarization (as a result of pore charge inhomogeneity or a translocating molecule). This theory, validated by simulations and experiments, is then used to explain why the amplitude of a single stranded DNA molecule can be twice as high as the amplitude of its double stranded counterpart. It also suggests designs for intrapore concentration polarization and volume exclusion effects that can produce biphasic and other amplitude fingerprints for high-throughput and yet discriminating molecular identification.
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Affiliation(s)
- Sebastian Sensale
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, Indiana 46556-5637, USA
| | - Ceming Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556-5637, USA
| | - Hsueh-Chia Chang
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, Indiana 46556-5637, USA
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3
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Timp W, Timp G. Beyond mass spectrometry, the next step in proteomics. SCIENCE ADVANCES 2020; 6:eaax8978. [PMID: 31950079 PMCID: PMC6954058 DOI: 10.1126/sciadv.aax8978] [Citation(s) in RCA: 167] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 11/19/2019] [Indexed: 05/08/2023]
Abstract
Proteins can be the root cause of a disease, and they can be used to cure it. The need to identify these critical actors was recognized early (1951) by Sanger; the first biopolymer sequenced was a peptide, insulin. With the advent of scalable, single-molecule DNA sequencing, genomics and transcriptomics have since propelled medicine through improved sensitivity and lower costs, but proteomics has lagged behind. Currently, proteomics relies mainly on mass spectrometry (MS), but instead of truly sequencing, it classifies a protein and typically requires about a billion copies of a protein to do it. Here, we offer a survey that illuminates a few alternatives with the brightest prospects for identifying whole proteins and displacing MS for sequencing them. These alternatives all boast sensitivity superior to MS and promise to be scalable and seem to be adaptable to bioinformatics tools for calling the sequence of amino acids that constitute a protein.
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Affiliation(s)
- Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Gregory Timp
- Departments of Electrical Engineering and Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
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4
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Zrehen A, Huttner D, Meller A. On-Chip Stretching, Sorting, and Electro-Optical Nanopore Sensing of Ultralong Human Genomic DNA. ACS NANO 2019; 13:14388-14398. [PMID: 31756076 PMCID: PMC6933818 DOI: 10.1021/acsnano.9b07873] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 11/22/2019] [Indexed: 05/22/2023]
Abstract
Solid-state nanopore sensing of ultralong genomic DNA molecules has remained challenging, as the DNA must be controllably delivered by its leading end for efficient entry into the nanopore. Herein, we introduce a nanopore sensor device designed for electro-optical detection and sorting of ultralong (300+ kilobase pair) genomic DNA. The fluidic device, fabricated in-silicon and anodically bonded to glass, uses pressure-induced flow and an embedded pillar array for controllable DNA stretching and delivery. Extremely low concentrations (50 fM) and sample volumes (∼1 μL) of DNA can be processed. The low height profile of the device permits high numerical aperture, high magnification imaging of DNA molecules, which remain in focus over extended distances. We demonstrate selective DNA sorting based on sequence-specific nick translation labeling and imaging at high camera frame rates. Nanopores are fabricated directly in the assembled device by laser etching. We show that uncoiling and stretching of the ultralong DNA molecules permits efficient nanopore capture and threading, which is simultaneously and synchronously imaged and electrically measured. Furthermore, our technique provides key insights into the translocation behavior of ultralong DNA and promotes the development of all-in-one micro/nanofluidic platforms for nanopore sensing of biomolecules.
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Affiliation(s)
- Adam Zrehen
- Department
of Biomedical Engineering, Technion −
IIT, Haifa 32000, Israel
| | - Diana Huttner
- Department
of Biomedical Engineering, Technion −
IIT, Haifa 32000, Israel
| | - Amit Meller
- Department
of Biomedical Engineering, Technion −
IIT, Haifa 32000, Israel
- Russell
Berrie Nanotechnology Institute, Technion
− IIT, Haifa 32000, Israel
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5
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Mamad-Hemouch H, Bacri L, Huin C, Przybylski C, Thiébot B, Patriarche G, Jarroux N, Pelta J. Versatile cyclodextrin nanotube synthesis with functional anchors for efficient ion channel formation: design, characterization and ion conductance. NANOSCALE 2018; 10:15303-15316. [PMID: 30069556 DOI: 10.1039/c8nr02623h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Biomimetic ion channels with different materials have been extensively designed to study the dynamics in a confined medium. These channels allow the development of several applications, such as ultra-fast sequencing and biomarker detection. When considering their synthesis, the use of cheap, non-cytotoxic and readily available materials is an increasing priority. Cyclodextrins, in supramolecular architectures, are widely utilized for pharmaceutical and biotechnological applications. Recent work has shown that short nanotubes (NTs) based on alpha-cyclodextrin (α-CD) assemble transient ion channels into membranes without cytotoxicity. In this study, we probe the influence of new cyclodextrin NT structural parameters and chemical modifications on channel formation, stability and electrical conductance. We report the successful synthesis of β- and γ-cyclodextrin nanotubes (β-CDNTs and γ-CDNTs), as evidenced by mass-spectrometry and high-resolution transmission electron microscopy. CDNTs were characterized by their length, diameter and number of CDs. Two hydrophobic groups, silylated or vinylated, were attached along the γ-CDNTs, improving the insertion time into the membrane. All NTs synthesized form spontaneous biomimetic ion channels. The hydrophobic NTs exhibit higher stability in membranes. Electrophysiological measurements show that ion transport is the main contribution of NT conductance and that the ion energy penalty for the entry into these NTs is similar to that of biological channels.
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Affiliation(s)
- Hajar Mamad-Hemouch
- LAMBE, Université Evry, CNRS, CEA, Université Paris-Saclay, 91025, Evry, France.
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6
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Kennedy E, Hokmabadi M, Dong Z, McKelvey K, Nelson EM, Timp G. Method for Dynamically Detecting Secretions from Single Cells Using a Nanopore. NANO LETTERS 2018; 18:4263-4272. [PMID: 29870666 DOI: 10.1021/acs.nanolett.8b01257] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Secreted proteins mediate cell-to-cell communications. Thus, eavesdropping on the secretome could reveal the cellular phenotype, but it is challenging to detect the proteins because they are secreted only in minute amounts and then diluted in blood plasma or contaminated by cell culture medium or the lysate. In this pilot study, it is demonstrated that secretions from single cancer cells can be detected and dynamically analyzed through measurements of blockades in the electrolytic current due to single molecules translocating through a nanopore in a thin inorganic membrane. It is established that the distribution of blockades can be used to differentiate three different cancer cell lines (U937, MDA-MB-231, and MCF-7) in real time and quickly (<20 s). Importantly, the distinctive blockades associated with the chemokine CCL5, a prognostic factor for disease progression in breast cancer, along with other low-mass biomarkers of breast cancer (PI3, TIMP1, and MMP1) were identified in the context of the secretome of these three cell types, tracked with time, and used to provide information on the cellular phenotype.
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7
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Shim J, Banerjee S, Qiu H, Smithe KKH, Estrada D, Bello J, Pop E, Schulten K, Bashir R. Detection of methylation on dsDNA using nanopores in a MoS 2 membrane. NANOSCALE 2017; 9:14836-14845. [PMID: 28795735 PMCID: PMC5890527 DOI: 10.1039/c7nr03092d] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Methylation at the 5-carbon position of the cytosine nucleotide base in DNA has been shown to be a reliable diagnostic biomarker for carcinogenesis. Early detection of methylation and intervention could drastically increase the effectiveness of therapy and reduce the cancer mortality rate. Current methods for detecting methylation involve bisulfite genomic sequencing, which are cumbersome and demand a large sample size of bodily fluids to yield accurate results. Hence, more efficient and cost effective methods are desired. Based on our previous work, we present a novel nanopore-based assay using a nanopore in a MoS2 membrane, and the methyl-binding protein (MBP), MBD1x, to detect methylation on dsDNA. We show that the dsDNA translocation was effectively slowed down using an asymmetric concentration of buffer and explore the possibility of profiling the position of methylcytosines on the DNA strands as they translocate through the 2D membrane. Our findings advance us one step closer towards the possible use of nanopore sensing technology in medical applications such as cancer detection.
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Affiliation(s)
- Jiwook Shim
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028
- Corresponding Authors: Jiwook Shim, Ph.D., Department of Biomedical Engineering, Henry M. Rowan College of Engineering, owan University, 201 Mullica Hill Road, Glassboro, NJ 08028, U.S.A., , Phone: 856-256-5393, Rashid Bashir, Ph.D., Department of Bioengineering, University of Illinois at Urbana – Champaign, 1270 Digital Computer Laboratory, Urbana, IL 61801, , Phone: 217-333-1867
| | - Shouvik Banerjee
- Department of Material Science and Engineering, University of Illinois at Urbana – Champaign, Urbana, IL 61801
| | - Hu Qiu
- State Key Laboratory of Mechanics and Control of Mechanical Structures, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China
| | - Kirby K. H. Smithe
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305
| | - David Estrada
- Department of Material Science and Engineering, Boise State University, Boise, ID 83725
| | - Julian Bello
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028
| | - Eric Pop
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305
| | - Klaus Schulten
- Department of Physics and Beckman Institute, University of Illinois at Urbana – Champaign, Urbana, IL 61801
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois at Urbana – Champaign, Urbana, IL 61801
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana – Champaign, Urbana, IL 61801
- Carle Illinois College of Medicine, University of Illinois at Urbana – Champaign, Urbana, IL 61801
- Corresponding Authors: Jiwook Shim, Ph.D., Department of Biomedical Engineering, Henry M. Rowan College of Engineering, owan University, 201 Mullica Hill Road, Glassboro, NJ 08028, U.S.A., , Phone: 856-256-5393, Rashid Bashir, Ph.D., Department of Bioengineering, University of Illinois at Urbana – Champaign, 1270 Digital Computer Laboratory, Urbana, IL 61801, , Phone: 217-333-1867
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8
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Tahvildari R, Beamish E, Briggs K, Chagnon-Lessard S, Sohi AN, Han S, Watts B, Tabard-Cossa V, Godin M. Manipulating Electrical and Fluidic Access in Integrated Nanopore-Microfluidic Arrays Using Microvalves. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1602601. [PMID: 28026148 DOI: 10.1002/smll.201602601] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/06/2016] [Indexed: 06/06/2023]
Abstract
On-chip microvalves regulate electrical and fluidic access to an array of nanopores integrated within microfluidic networks. This configuration allows for on-chip sequestration of biomolecular samples in various flow channels and analysis by independent nanopores.
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Affiliation(s)
- Radin Tahvildari
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Eric Beamish
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | | | - Ali Najafi Sohi
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Shuo Han
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Benjamin Watts
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | | | - Michel Godin
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Department of Mechanical Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Ottawa-Carleton Institute for Biomedical Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
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9
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Experton J, Wilson AG, Martin CR. Low-Voltage Flow-Through Electroporation in Gold-Microtube Membranes. Anal Chem 2016; 88:12445-12452. [PMID: 28193019 DOI: 10.1021/acs.analchem.6b03820] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Electroporation is used to create pores within the membrane of living cells in order to deliver a substance, for example, a gene, into the cytoplasm. To achieve the high electric field gradients required to porate the membrane, current electroporation devices deliver voltage pulses in the kV range to the cell medium. We describe a new device based on gold-microtube membranes that can accomplish electroporation with voltage pulses that are orders of magnitude smaller, ≤5 V. This is possible because the voltage pulses are applied to the gold microtubes resulting in large electric field gradients down the length of the tubes. We used COMSOL simulations to calculate the electric field gradients, and these theoretical results were compared with known experimental values required to electroporate Escherichia coli. We developed two fluorescence-based methods to demonstrate successful electroporation of E. coli. The percentages of electroporated bacteria were found to be more than an order of magnitude higher than obtained with a commercial electroporator, although the voltage employed was 500 times lower. Furthermore, this microtube membrane device is flow through and is therefore capable of continuous, as opposed to batch-wise, electroporation and cell analysis. Cell throughput of >30 million cells per min, higher than any previously reported device, were obtained.
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Affiliation(s)
- Juliette Experton
- Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States
| | - Aaron G Wilson
- Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States
| | - Charles R Martin
- Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States
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10
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Kennedy E, Dong Z, Tennant C, Timp G. Reading the primary structure of a protein with 0.07 nm 3 resolution using a subnanometre-diameter pore. NATURE NANOTECHNOLOGY 2016; 11:968-976. [PMID: 27454878 DOI: 10.1038/nnano.2016.120] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 06/06/2016] [Indexed: 05/02/2023]
Abstract
The primary structure of a protein consists of a sequence of amino acids and is a key factor in determining how a protein folds and functions. However, conventional methods for sequencing proteins, such as mass spectrometry and Edman degradation, suffer from short reads and lack sensitivity, so alternative approaches are sought. Here, we show that a subnanometre-diameter pore, sputtered through a thin silicon nitride membrane, can be used to detect the primary structure of a denatured protein molecule. When a denatured protein immersed in electrolyte is driven through the pore by an electric field, measurements of a blockade in the current reveal nearly regular fluctuations, the number of which coincides with the number of residues in the protein. Furthermore, the amplitudes of the fluctuations are highly correlated with the volumes that are occluded by quadromers (four residues) in the primary structure. Each fluctuation, therefore, represents a read of a quadromer. Scrutiny of the fluctuations reveals that the subnanometre pore is sensitive enough to read the occluded volume that is related to post-translational modifications of a single residue, measuring volume differences of ∼0.07 nm3, but it is not sensitive enough to discriminate between the volumes of all twenty amino acids.
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Affiliation(s)
- Eamonn Kennedy
- Electrical Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Zhuxin Dong
- Electrical Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Clare Tennant
- Chemical Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Gregory Timp
- Electrical Engineering and Biological Science, University of Notre Dame, Notre Dame, Indiana 46556, USA
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11
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Tahvildari R, Beamish E, Tabard-Cossa V, Godin M. Integrating nanopore sensors within microfluidic channel arrays using controlled breakdown. LAB ON A CHIP 2015; 15:1407-11. [PMID: 25631885 DOI: 10.1039/c4lc01366b] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Nanopore arrays are fabricated by controlled dielectric breakdown (CBD) in solid-state membranes integrated within polydimethylsiloxane (PDMS) microfluidic devices. This technique enables the scalable production of independently addressable nanopores. By confining the electric field within the microfluidic architecture, nanopore fabrication is precisely localized and electrical noise is significantly reduced. Both DNA and protein molecules are detected to validate the performance of this sensing platform.
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Affiliation(s)
- Radin Tahvildari
- Department of Physics, University of Ottawa, 150 Louis Pasteur, K1N 6N5, Canada
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12
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Liu S, Wall TA, Ozcelik D, Parks JW, Hawkins AR, Schmidt H. Electro-optical detection of single λ-DNA. Chem Commun (Camb) 2015; 51:2084-7. [PMID: 25533516 PMCID: PMC4304986 DOI: 10.1039/c4cc07591a] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single λ-DNA molecules are detected on a nanopore-gated optofluidic chip electrically and optically. Statistical variations in the single particle trajectories are used to predict the intensity distribution of the fluorescence signals.
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Affiliation(s)
- Shuo Liu
- School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
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13
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Steinbock LJ, Krishnan S, Bulushev RD, Borgeaud S, Blokesch M, Feletti L, Radenovic A. Probing the size of proteins with glass nanopores. NANOSCALE 2014; 6:14380-14387. [PMID: 25329813 DOI: 10.1039/c4nr05001k] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Single molecule studies using nanopores have gained attention due to the ability to sense single molecules in aqueous solution without the need to label them. In this study, short DNA molecules and proteins were detected with glass nanopores, whose sensitivity was enhanced by electron reshaping which decreased the nanopore diameter and created geometries with a reduced sensing length. Further, proteins having molecular weights (MW) ranging from 12 kDa to 480 kDa were detected, which showed that their corresponding current peak amplitude changes according to their MW. In the case of the 12 kDa ComEA protein, its DNA-binding properties to an 800 bp long DNA molecule was investigated. Moreover, the influence of the pH on the charge of the protein was demonstrated by showing a change in the translocation direction. This work emphasizes the wide spectrum of detectable molecules using nanopores from glass nanocapillaries, which stand out because of their inexpensive, lithography-free, and rapid manufacturing process.
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Affiliation(s)
- L J Steinbock
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015 Lausanne, Switzerland.
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14
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Göhring J, Fulcher N, Schilcher K, Barta A, Jacak J. Suitable transfection methods for single particle tracing in plant suspension cells. PLANT METHODS 2014; 10:15. [PMID: 24991230 PMCID: PMC4076440 DOI: 10.1186/1746-4811-10-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 05/15/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND A multitude of different imaging systems are already available to image genetically altered RNA species; however, only a few of these techniques are actually suitable to visualize endogenous RNA. One possibility is to use fluorescently-labelled and hybridization-sensitive probes. In order to yield more information about the exact localization and movement of a single RNA molecule, it is necessary to image such probes with highly sensitive microscope setups. More challenges arise if such experiments are conducted in plant cells due to their high autofluorescence and demanding transfection procedures. RESULTS Here, we report in planta imaging of single RNA molecules using fluorescently labeled molecular beacons. We tested three different transfection protocols in order to identify optimal conditions for transfection of fluorescent DNA probes and their subsequent detection at the single molecule level. CONCLUSIONS We found that an optimized heat shock protocol provided a vastly improved transfection method for small DNA molecules which were used for subsequent single RNA molecule detection in living plant suspension cells.
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Affiliation(s)
- Janett Göhring
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohrgasse 9/3, Vienna, Austria
| | - Nick Fulcher
- Gregor Mendel Institute, Dr. Bohrgasse 3, Vienna, Austria
| | - Kurt Schilcher
- Upper Austria University of Applied Sciences, Campus Linz, Linz, 4020, Austria
| | - Andrea Barta
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohrgasse 9/3, Vienna, Austria
| | - Jaroslaw Jacak
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohrgasse 9/3, Vienna, Austria
- Upper Austria University of Applied Sciences, Campus Linz, Linz, 4020, Austria
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15
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Movileanu L. Watching single proteins using engineered nanopores. Protein Pept Lett 2014; 21:235-46. [PMID: 24370252 PMCID: PMC3924890 DOI: 10.2174/09298665113209990078] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 11/03/2012] [Accepted: 11/10/2012] [Indexed: 12/22/2022]
Abstract
Recent studies in the area of single-molecule detection of proteins with nanopores show a great promise in fundamental science, bionanotechnology and proteomics. In this mini-review, I discuss a comprehensive array of examinations of protein detection and characterization using protein and solid-state nanopores. These investigations demonstrate the power of the single-molecule nanopore measurements to reveal a broad range of functional, structural, biochemical and biophysical features of proteins, such as their backbone flexibility, enzymatic activity, binding affinity as well as their concentration, size and folding state. Engineered nanopores in organic materials and in inorganic membranes coupled with surface modification and protein engineering might provide a new generation of sensing devices for molecular biomedical diagnostics.
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Affiliation(s)
- Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA.
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16
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Kurz V, Tanaka T, Timp G. Single cell transfection with single molecule resolution using a synthetic nanopore. NANO LETTERS 2014; 14:604-11. [PMID: 24471806 DOI: 10.1021/nl403789z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We report the development of a single cell gene delivery system based on electroporation using a synthetic nanopore, that is not only highly specific and very efficient but also transfects with single molecule resolution at low voltage (1 V) with minimal perturbation to the cell. Such a system can be used to control gene expression with unprecedented precision--no other method offers such capabilities.
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Affiliation(s)
- Volker Kurz
- Department of Electrical Engineering, University of Notre Dame , Notre Dame, Indiana 46556, United States
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17
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Abstract
Electroporation is a simple yet powerful technique for breaching the cell membrane barrier. The applications of electroporation can be generally divided into two categories: the release of intracellular proteins, nucleic acids and other metabolites for analysis and the delivery of exogenous reagents such as genes, drugs and nanoparticles with therapeutic purposes or for cellular manipulation. In this review, we go over the basic physics associated with cell electroporation and highlight recent technological advances on microfluidic platforms for conducting electroporation. Within the context of its working mechanism, we summarize the accumulated knowledge on how the parameters of electroporation affect its performance for various tasks. We discuss various strategies and designs for conducting electroporation at the microscale and then focus on analysis of intracellular contents and delivery of exogenous agents as two major applications of the technique. Finally, an outlook for future applications of microfluidic electroporation in increasingly diverse utilities is presented.
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Affiliation(s)
- Tao Geng
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA. Fax: +1-540-231-5022; Tel: +1-540-231-8681
- School of Biomedical Engineering and Sciences, Virginia Tech-Wake Forest University, Blacksburg, VA 24061, USA
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Kurz V, Nelson EM, Shim J, Timp G. Direct visualization of single-molecule translocations through synthetic nanopores comparable in size to a molecule. ACS NANO 2013; 7:4057-69. [PMID: 23607372 DOI: 10.1021/nn400182s] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A nanopore is the ultimate analytical tool. It can be used to detect DNA, RNA, oligonucleotides, and proteins with submolecular sensitivity. This extreme sensitivity is derived from the electric signal associated with the occlusion that develops during the translocation of the analyte across a membrane through a pore immersed in electrolyte. A larger occluded volume results in an improvement in the signal-to-noise ratio, and so the pore geometry should be made comparable to the size of the target molecule. However, the pore geometry also affects the electric field, the charge density, the electro-osmotic flow, the capture volume, and the response time. Seeking an optimal pore geometry, we tracked the molecular motion in three dimensions with high resolution, visualizing with confocal microscopy the fluorescence associated with DNA translocating through nanopores with diameters comparable to the double helix, while simultaneously measuring the pore current. Measurements reveal single molecules translocating across the membrane through the pore commensurate with the observation of a current blockade. To explain the motion of the molecule near the pore, finite-element simulations were employed that account for diffusion, electrophoresis, and the electro-osmotic flow. According to this analysis, detection using a nanopore comparable in diameter to the double helix represents a compromise between sensitivity, capture volume, the minimum detectable concentration, and response time.
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Affiliation(s)
- Volker Kurz
- Departments of Electrical Engineering and Biological Science, University of Notre Dame, Notre Dame, Indiana 46556, United States
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Wang S, Lee LJ. Micro-/nanofluidics based cell electroporation. BIOMICROFLUIDICS 2013; 7:11301. [PMID: 23405056 PMCID: PMC3555966 DOI: 10.1063/1.4774071] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 12/04/2012] [Indexed: 05/04/2023]
Abstract
Non-viral gene delivery has been extensively explored as the replacement for viral systems. Among various non-viral approaches, electroporation has gained increasing attention because of its easy operation and no restrictions on probe or cell type. Several effective systems are now available on the market with reasonably good gene delivery performance. To facilitate broader biological and medical applications, micro-/nanofluidics based technologies were introduced in cell electroporation during the past two decades and their advances are summarized in this perspective. Compared to the commercially available bulk electroporation systems, they offer several advantages, namely, (1) sufficiently high pulse strength generated by a very low potential difference, (2) conveniently concentrating, trapping, and regulating the position and concentration of cells and probes, (3) real-time monitoring the intracellular trafficking at single cell level, and (4) flexibility on cells to be transfected (from single cell to large scale cell population). Some of the micro-devices focus on cell lysis or fusion as well as the analysis of cellular properties or intracellular contents, while others are designed for gene transfection. The uptake of small molecules (e.g., dyes), DNA plasmids, interfering RNAs, and nanoparticles has been broadly examined on different types of mammalian cells, yeast, and bacteria. A great deal of progress has been made with a variety of new micro-/nanofluidic designs to address challenges such as electrochemical reactions including water electrolysis, gas bubble formation, waste of expensive reagents, poor cell viability, low transfection efficacy, higher throughput, and control of transfection dosage and uniformity. Future research needs required to advance micro-/nanofluidics based cell electroporation for broad life science and medical applications are discussed.
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Affiliation(s)
- Shengnian Wang
- Institute for Micromanufacturing, Louisiana Tech University, Ruston, Louisiana 71272, USA and Chemical Engineering Program, Louisiana Tech University, Ruston, Louisiana 71272, USA
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Trouillon R, Passarelli MK, Wang J, Kurczy ME, Ewing AG. Chemical Analysis of Single Cells. Anal Chem 2012; 85:522-42. [DOI: 10.1021/ac303290s] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Raphaël Trouillon
- University of Gothenburg, Department of Chemistry and Molecular
Biology, 41296 Gothenburg, Sweden
| | - Melissa K. Passarelli
- University of Gothenburg, Department of Chemistry and Molecular
Biology, 41296 Gothenburg, Sweden
| | - Jun Wang
- University of Gothenburg, Department of Chemistry and Molecular
Biology, 41296 Gothenburg, Sweden
| | - Michael E. Kurczy
- Chalmers University, Department of Chemistry
and Biological Engineering, 41296 Gothenburg, Sweden
| | - Andrew G. Ewing
- University of Gothenburg, Department of Chemistry and Molecular
Biology, 41296 Gothenburg, Sweden
- Chalmers University, Department of Chemistry
and Biological Engineering, 41296 Gothenburg, Sweden
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