1
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Sampad MJN, Saiduzzaman SM, Walker ZJ, Wells TN, Wayment JX, Ong EM, Mdaki SD, Tamhankar MA, Yuzvinsky TD, Patterson JL, Hawkins AR, Schmidt H. Label-free and amplification-free viral RNA quantification from primate biofluids using a trapping-assisted optofluidic nanopore platform. Proc Natl Acad Sci U S A 2024; 121:e2400203121. [PMID: 38598338 PMCID: PMC11032468 DOI: 10.1073/pnas.2400203121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/07/2024] [Indexed: 04/12/2024] Open
Abstract
Viral outbreaks can cause widespread disruption, creating the need for diagnostic tools that provide high performance and sample versatility at the point of use with moderate complexity. Current gold standards such as PCR and rapid antigen tests fall short in one or more of these aspects. Here, we report a label-free and amplification-free nanopore sensor platform that overcomes these challenges via direct detection and quantification of viral RNA in clinical samples from a variety of biological fluids. The assay uses an optofluidic chip that combines optical waveguides with a fluidic channel and integrates a solid-state nanopore for sensing of individual biomolecules upon translocation through the pore. High specificity and low limit of detection are ensured by capturing RNA targets on microbeads and collecting them by optical trapping at the nanopore location where targets are released and rapidly detected. We use this device for longitudinal studies of the viral load progression for Zika and Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infections in marmoset and baboon animal models, respectively. The up to million-fold trapping-based target concentration enhancement enables amplification-free RNA quantification across the clinically relevant concentration range down to the assay limit of RT-qPCR as well as cases in which PCR failed. The assay operates across all relevant biofluids, including semen, urine, and whole blood for Zika and nasopharyngeal and throat swab, rectal swab, and bronchoalveolar lavage for SARS-CoV-2. The versatility, performance, simplicity, and potential for full microfluidic integration of the amplification-free nanopore assay points toward a unique approach to molecular diagnostics for nucleic acids, proteins, and other targets.
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Affiliation(s)
| | - S. M. Saiduzzaman
- School of Engineering, University of California, Santa Cruz, CA95064
| | - Zach J. Walker
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT84602
| | - Tanner N. Wells
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT84602
| | - Jesse X. Wayment
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT84602
| | - Ephraim M. Ong
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT84602
| | | | | | | | | | - Aaron R. Hawkins
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT84602
| | - Holger Schmidt
- School of Engineering, University of California, Santa Cruz, CA95064
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2
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Stransky F, Kostrz D, Follenfant M, Pomplun S, Meyners C, Strick T, Hausch F, Gosse C. Use of DNA forceps to measure receptor-ligand dissociation equilibrium constants in a single-molecule competition assay. Methods Enzymol 2024; 694:51-82. [PMID: 38492958 DOI: 10.1016/bs.mie.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2024]
Abstract
The ability of biophysicists to decipher the behavior of individual biomolecules has steadily improved over the past thirty years. However, it still remains unclear how an ensemble of data acquired at the single-molecule level compares with the data acquired on an ensemble of the same molecules. We here propose an assay to tackle this question in the context of dissociation equilibrium constant measurements. A sensor is built by engrafting a receptor and a ligand onto a flexible dsDNA scaffold and mounting this assembly on magnetic tweezers. This way, looking at the position of the magnetic bead enables one to determine in real-time if the two molecular partners are associated or not. Next, to quantify the affinity of the scrutinized single-receptor for a given competitor, various amounts of the latter molecule are introduced in solution and the equilibrium response of the sensor is monitored throughout the titration protocol. Proofs of concept are established for the binding of three rapamycin analogs to the FKBP12 cis-trans prolyl isomerase. For each of these drugs the mean affinity constant obtained on a ten of individual receptors agrees with the one previously determined in a bulk assay. Furthermore, experimental contingencies are sufficient to explain the dispersion observed over the single-molecule values.
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Affiliation(s)
- François Stransky
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
| | - Dorota Kostrz
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
| | - Maryne Follenfant
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
| | - Sebastian Pomplun
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Christian Meyners
- Department of Chemistry and Biochemistry, Technical University Darmstadt, Darmstadt, Germany
| | - Terence Strick
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
| | - Felix Hausch
- Department of Chemistry and Biochemistry, Technical University Darmstadt, Darmstadt, Germany; Centre for Synthetic Biology, Technical University Darmstadt, Darmstadt, Germany
| | - Charlie Gosse
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France.
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3
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He L, Charron M, Mensing P, Briggs K, Adams J, de Haan H, Tabard-Cossa V. DNA origami characterized via a solid-state nanopore: insights into nanostructure dimensions, rigidity and yield. NANOSCALE 2023; 15:14043-14054. [PMID: 37580994 DOI: 10.1039/d3nr01873c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Due to their programmability via specific base pairing, self-assembled DNA origami structures have proven to be useful for a wide variety of applications, including diagnostics, molecular computation, drug delivery, and therapeutics. Measuring and characterizing these structures is therefore of great interest and an important part of quality control. Here, we show the extent to which DNA nanostructures can be characterized by a solid-state nanopore; a non-destructive, label-free, single-molecule sensor capable of electrically detecting and characterizing charged biomolecules. We demonstrate that in addition to geometrical dimensions, nanopore sensing can provide information on the mechanical properties, assembly yield, and stability of DNA nanostructures. For this work, we use a model structure consisting of a 3 helix-bundle (3HB), i.e. three interconnected DNA double helices using a M13 scaffold folded twice on itself by short DNA staple strands, and translocate it through solid-state nanopores fabricated by controlled breakdown. We present detailed analysis of the passage characteristics of 3HB structures through nanopores under different experimental conditions which suggest that segments of locally higher flexibility are present along the nanostructure contour that allow for the otherwise rigid 3HB to fold inside nanopores. By characterizing partially melted 3HB structures, we find that locally flexible segments are likely due to short staple oligomers missing from the fully assembled structure. The 3HB used herein is a prototypical example to establish nanopores as a sensitive, non-destructive, and label-free alternative to conventional techniques such as gel electrophoresis with which to characterize DNA nanostructures.
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Affiliation(s)
- Liqun He
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
| | - Martin Charron
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
| | - Philipp Mensing
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
| | - Jonathan Adams
- Faculty of Science, Ontario Tech University, Oshawa, Ontario, Canada
| | - Hendrick de Haan
- Faculty of Science, Ontario Tech University, Oshawa, Ontario, Canada
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4
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Xing Y, Rottensteiner A, Ciccone J, Howorka S. Functional Nanopores Enabled with DNA. Angew Chem Int Ed Engl 2023; 62:e202303103. [PMID: 37186432 DOI: 10.1002/anie.202303103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/17/2023]
Abstract
Membrane-spanning nanopores are used in label-free single-molecule sensing and next-generation portable nucleic acid sequencing, and as powerful research tools in biology, biophysics, and synthetic biology. Naturally occurring protein and peptide pores, as well as synthetic inorganic nanopores, are used in these applications, with their limitations. The structural and functional repertoire of nanopores can be considerably expanded by functionalising existing pores with DNA strands and by creating an entirely new class of nanopores with DNA nanotechnology. This review outlines progress in this area of functional DNA nanopores and outlines developments to open up new applications.
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Affiliation(s)
- Yongzheng Xing
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Alexia Rottensteiner
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Jonah Ciccone
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Stefan Howorka
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
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5
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Zhu J, Tivony R, Bošković F, Pereira-Dias J, Sandler SE, Baker S, Keyser UF. Multiplexed Nanopore-Based Nucleic Acid Sensing and Bacterial Identification Using DNA Dumbbell Nanoswitches. J Am Chem Soc 2023. [PMID: 37220424 DOI: 10.1021/jacs.3c01649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Multiplexed nucleic acid sensing methods with high specificity are vital for clinical diagnostics and infectious disease control, especially in the postpandemic era. Nanopore sensing techniques have developed in the past two decades, offering versatile tools for biosensing while enabling highly sensitive analyte measurements at the single-molecule level. Here, we establish a nanopore sensor based on DNA dumbbell nanoswitches for multiplexed nucleic acid detection and bacterial identification. The DNA nanotechnology-based sensor switches from an "open" into a "closed" state when a target strand hybridizes to two sequence-specific sensing overhangs. The loop in the DNA pulls two groups of dumbbells together. The change in topology results in an easily recognized peak in the current trace. Simultaneous detection of four different sequences was achieved by assembling four DNA dumbbell nanoswitches on one carrier. The high specificity of the dumbbell nanoswitch was verified by distinguishing single base variants in DNA and RNA targets using four barcoded carriers in multiplexed measurements. By combining multiple dumbbell nanoswitches with barcoded DNA carriers, we identified different bacterial species even with high sequence similarity by detecting strain specific 16S ribosomal RNA (rRNA) fragments.
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Affiliation(s)
- Jinbo Zhu
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, U.K
- School of Biomedical Engineering, Faculty of Medicine, Dalian University of Technology, No. 2, Linggong Road, Dalian 116024, China
| | - Ran Tivony
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, U.K
| | - Filip Bošković
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, U.K
| | - Joana Pereira-Dias
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffery Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, U.K
| | - Sarah E Sandler
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, U.K
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffery Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, U.K
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, U.K
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6
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Bošković F, Zhu J, Tivony R, Ohmann A, Chen K, Alawami MF, Đorđević M, Ermann N, Pereira-Dias J, Fairhead M, Howarth M, Baker S, Keyser UF. Simultaneous identification of viruses and viral variants with programmable DNA nanobait. NATURE NANOTECHNOLOGY 2023; 18:290-298. [PMID: 36646828 PMCID: PMC10020084 DOI: 10.1038/s41565-022-01287-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/07/2022] [Indexed: 05/31/2023]
Abstract
Respiratory infections are the major cause of death from infectious disease worldwide. Multiplexed diagnostic approaches are essential as many respiratory viruses have indistinguishable symptoms. We created self-assembled DNA nanobait that can simultaneously identify multiple short RNA targets. The nanobait approach relies on specific target selection via toehold-mediated strand displacement and rapid readout via nanopore sensing. Here we show that this platform can concurrently identify several common respiratory viruses, detecting a panel of short targets of viral nucleic acids from multiple viruses. Our nanobait can be easily reprogrammed to discriminate viral variants with single-nucleotide resolution, as we demonstrated for several key SARS-CoV-2 variants. Last, we show that the nanobait discriminates between samples extracted from oropharyngeal swabs from negative- and positive-SARS-CoV-2 patients without preamplification. Our system allows for the multiplexed identification of native RNA molecules, providing a new scalable approach for the diagnostics of multiple respiratory viruses in a single assay.
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Affiliation(s)
- Filip Bošković
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Jinbo Zhu
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Ran Tivony
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | | | - Kaikai Chen
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | | | - Milan Đorđević
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Niklas Ermann
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Joana Pereira-Dias
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
| | | | - Mark Howarth
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Stephen Baker
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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7
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Confederat S, Sandei I, Mohanan G, Wälti C, Actis P. Nanopore fingerprinting of supramolecular DNA nanostructures. Biophys J 2022; 121:4882-4891. [PMID: 35986518 PMCID: PMC9808562 DOI: 10.1016/j.bpj.2022.08.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/05/2022] [Accepted: 08/16/2022] [Indexed: 01/07/2023] Open
Abstract
DNA nanotechnology has paved the way for new generations of programmable nanomaterials. Utilizing the DNA origami technique, various DNA constructs can be designed, ranging from single tiles to the self-assembly of large-scale, complex, multi-tile arrays. This technique relies on the binding of hundreds of short DNA staple strands to a long single-stranded DNA scaffold that drives the folding of well-defined nanostructures. Such DNA nanostructures have enabled new applications in biosensing, drug delivery, and other multifunctional materials. In this study, we take advantage of the enhanced sensitivity of a solid-state nanopore that employs a poly-ethylene glycol enriched electrolyte to deliver real-time, non-destructive, and label-free fingerprinting of higher-order assemblies of DNA origami nanostructures with single-entity resolution. This approach enables the quantification of the assembly yields for complex DNA origami nanostructures using the nanostructure-induced equivalent charge surplus as a discriminant. We compare the assembly yield of four supramolecular DNA nanostructures obtained with the nanopore with agarose gel electrophoresis and atomic force microscopy imaging. We demonstrate that the nanopore system can provide analytical quantification of the complex supramolecular nanostructures within minutes, without any need for labeling and with single-molecule resolution. We envision that the nanopore detection platform can be applied to a range of nanomaterial designs and enable the analysis and manipulation of large DNA assemblies in real time.
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Affiliation(s)
- Samuel Confederat
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom
| | - Ilaria Sandei
- School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Gayathri Mohanan
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom
| | - Christoph Wälti
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom.
| | - Paolo Actis
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom.
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8
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Li F, Luo Y, Xi G, Fu J, Tu J. Single-Molecule Analysis of DNA structures using nanopore sensors. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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9
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King S, Briggs K, Slinger R, Tabard-Cossa V. Screening for Group A Streptococcal Disease via Solid-State Nanopore Detection of PCR Amplicons. ACS Sens 2022; 7:207-214. [PMID: 34995448 DOI: 10.1021/acssensors.1c01972] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Single-molecule detection methods are becoming increasingly important for diagnostic applications. Practical early detection of disease requires sensitivity down to the level of single copies of the targeted biomarkers. Of the candidate technologies that can address this need, solid-state nanopores show great promise as digital sensors for single-molecule detection. Here, we present work detailing the use of solid-state nanopores as downstream sensors for a polymerase chain reaction (PCR)-based assay targeting group A streptococcus (strep A), which can be readily extended to detect any pathogen that can be identified with a short nucleic acid sequence. We demonstrate that with some simple modifications to the standard PCR reaction mixture, nanopores can be used to reliably identify strep A in clinical samples. We also discuss methodological best practices for both adapting PCR-based assays to solid-state nanopore readout and analytical approaches by which to decide on sample status.
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Affiliation(s)
- Simon King
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Robert Slinger
- Division of Microbiology and Infectious Disease, Children’s Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H 8L1, Canada
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10
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He L, Tessier DR, Briggs K, Tsangaris M, Charron M, McConnell EM, Lomovtsev D, Tabard-Cossa V. Digital immunoassay for biomarker concentration quantification using solid-state nanopores. Nat Commun 2021; 12:5348. [PMID: 34504071 PMCID: PMC8429538 DOI: 10.1038/s41467-021-25566-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 08/12/2021] [Indexed: 12/05/2022] Open
Abstract
Single-molecule counting is the most accurate and precise method for determining the concentration of a biomarker in solution and is leading to the emergence of digital diagnostic platforms enabling precision medicine. In principle, solid-state nanopores—fully electronic sensors with single-molecule sensitivity—are well suited to the task. Here we present a digital immunoassay scheme capable of reliably quantifying the concentration of a target protein in complex biofluids that overcomes specificity, sensitivity, and consistency challenges associated with the use of solid-state nanopores for protein sensing. This is achieved by employing easily-identifiable DNA nanostructures as proxies for the presence (“1”) or absence (“0”) of the target protein captured via a magnetic bead-based sandwich immunoassay. As a proof-of-concept, we demonstrate quantification of the concentration of thyroid-stimulating hormone from human serum samples down to the high femtomolar range. Further optimization to the method will push sensitivity and dynamic range, allowing for development of precision diagnostic tools compatible with point-of-care format. The concentration of a biomarker in solution can be determined by counting single molecules. Here the authors report a digital immunoassay scheme with solid-state nanopore readout to quantify a target protein and use this to measure thyroid-stimulating hormone from human serum.
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Affiliation(s)
- Liqun He
- Department of Physics, University of Ottawa, Ottawa, Canada
| | | | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Canada
| | | | - Martin Charron
- Department of Physics, University of Ottawa, Ottawa, Canada
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11
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Chen J, Chen X, Sun LZ, Xu XJ, Luo MB. Translocation of a looped polymer threading through a nanopore. SOFT MATTER 2021; 17:4342-4351. [PMID: 33908563 DOI: 10.1039/d1sm00007a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recent experiments reported that the complicated translocation dynamics of a looped DNA chain through a nanopore can be detected by ionic current blockade profiles. Inspired by the experimental results, we systematically study the translocation dynamics of a looped polymer, formed by three building blocks of a loop in the middle and two tails of the same length connected with the loop, by using Langevin dynamics simulations. Based on two entering modes (tail-leading and loop-leading) and three translocation orders (loop-tail-tail, tail-loop-tail, and tail-tail-loop), the translocation of the looped polymer is classified into six translocation pathways, corresponding to different current blockade profiles. The probabilities of the six translocation pathways are dependent on the loop length, polymer length, and pore radius. Moreover, the translocation times of the entire polymer and the loop are investigated. We find that the two translocation times show different dependencies on the translocation pathways and on the lengths of the loop and the entire polymer.
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Affiliation(s)
- Jia Chen
- Department of Physics, Zhejiang University, Hangzhou 310027, China.
| | - Xian Chen
- Department of Physics, Zhejiang University, Hangzhou 310027, China.
| | - Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Xiao-Jun Xu
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - Meng-Bo Luo
- Department of Physics, Zhejiang University, Hangzhou 310027, China.
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12
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Chandrasekaran AR, MacIsaac M, Vilcapoma J, Hansen CH, Yang D, Wong WP, Halvorsen K. DNA Nanoswitch Barcodes for Multiplexed Biomarker Profiling. NANO LETTERS 2021; 21:469-475. [PMID: 33395311 PMCID: PMC8059342 DOI: 10.1021/acs.nanolett.0c03929] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Molecular biomarkers play a key role in the clinic, aiding in diagnostics and prognostics, and in the research laboratory, contributing to our basic understanding of diseases. Detecting multiple and diverse molecular biomarkers within a single accessible assay would have great utility, providing a more comprehensive picture for clinical evaluation and research, but is a challenge with standard methods. Here, we report programmable DNA nanoswitches for multiplexed detection of up to 6 biomarkers at once with each combination of biomarkers producing a unique barcode signature among 64 possibilities. As a defining feature of our method, we show "mixed multiplexing" for simultaneous barcoded detection of different types of biomolecules, for example, DNA, RNA, antibody, and protein in a single assay. To demonstrate clinical potential, we show multiplexed detection of a prostate cancer biomarker panel in serum that includes two microRNA sequences and prostate specific antigen.
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Affiliation(s)
- Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, New York, New York 12222, United States
| | - Molly MacIsaac
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Javier Vilcapoma
- The RNA Institute, University at Albany, State University of New York, New York, New York 12222, United States
| | - Clinton H Hansen
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Darren Yang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Wesley P Wong
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, New York, New York 12222, United States
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13
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Qiao L, Ignacio M, Slater GW. An efficient kinetic Monte Carlo to study analyte capture by a nanopore: transients, boundary conditions and time-dependent fields. Phys Chem Chem Phys 2021; 23:1489-1499. [PMID: 33400742 DOI: 10.1039/d0cp03638b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
To better understand the capture process by a nanopore, we introduce an efficient Kinetic Monte Carlo (KMC) algorithm that can simulate long times and large system sizes by mapping the dynamic of a point-like particle in a 3D spherically symmetric system onto the 1D biased random walk. Our algorithm recovers the steady-state analytical solution and allows us to study time-dependent processes such as transients. Simulation results show that the steady-state depletion zone near pore is barely larger than the pore radius and narrows at higher field intensities; as a result, the time to reach steady-state is much smaller than the time required to empty a zone of the size of the capture radius λe. When the sample reservoir has a finite size, a second depletion region propagates inward from the outer wall, and the capture rate starts decreasing when it reaches the capture radius λe. We also note that the flatness of the electric field near the pore, which is often neglected, induces a traffic jam that can increase the transient time by several orders of magnitude. Finally, we propose a new proof-of-concept scheme to separate two analytes of the same mobility but different diffusion coefficients using time-varying fields.
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Affiliation(s)
- Le Qiao
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
| | - Maxime Ignacio
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
| | - Gary W Slater
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
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14
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Yuan X, Yang C, He Q, Chen J, Yu D, Li J, Zhai S, Qin Z, Du K, Chu Z, Qin P. Current and Perspective Diagnostic Techniques for COVID-19. ACS Infect Dis 2020; 6:1998-2016. [PMID: 32677821 PMCID: PMC7409380 DOI: 10.1021/acsinfecdis.0c00365] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Indexed: 02/08/2023]
Abstract
Since late December 2019, the coronavirus pandemic (COVID-19; previously known as 2019-nCoV) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been surging rapidly around the world. With more than 1,700,000 confirmed cases, the world faces an unprecedented economic, social, and health impact. The early, rapid, sensitive, and accurate diagnosis of viral infection provides rapid responses for public health surveillance, prevention, and control of contagious diffusion. More than 30% of the confirmed cases are asymptomatic, and the high false-negative rate (FNR) of a single assay requires the development of novel diagnostic techniques, combinative approaches, sampling from different locations, and consecutive detection. The recurrence of discharged patients indicates the need for long-term monitoring and tracking. Diagnostic and therapeutic methods are evolving with a deeper understanding of virus pathology and the potential for relapse. In this Review, a comprehensive summary and comparison of different SARS-CoV-2 diagnostic methods are provided for researchers and clinicians to develop appropriate strategies for the timely and effective detection of SARS-CoV-2. The survey of current biosensors and diagnostic devices for viral nucleic acids, proteins, and particles and chest tomography will provide insight into the development of novel perspective techniques for the diagnosis of COVID-19.
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Affiliation(s)
- Xi Yuan
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong 518055, China
| | - Chengming Yang
- Southern
University of Science and Technology Hospital, Shenzhen, Guangdong 518055, China
| | - Qian He
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong 518055, China
| | - Junhu Chen
- National
Institute of Parasitic Diseases, Chinese
Center for Disease Control and Prevention, Shanghai 200025, China
| | - Dongmei Yu
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong 518055, China
- Department
of Mechanics and Aerospace Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Jie Li
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong 518055, China
- Kunming
Dog Base of Police Security, Ministry of Public Security, Kunming, Yunnan 650204, China
| | - Shiyao Zhai
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong 518055, China
| | - Zhifeng Qin
- Animal &
Plant Inspection and Quarantine Technology Center, Shenzhen Customs District People’s Republic of China, Shenzhen, Guangdong 518045, China
| | - Ke Du
- Department
of Mechanical Engineering, Rochester Institute
of Technology, Rochester, New York 14623, United States
| | - Zhenhai Chu
- Southern
University of Science and Technology Hospital, Shenzhen, Guangdong 518055, China
| | - Peiwu Qin
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong 518055, China
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15
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Esbin MN, Whitney ON, Chong S, Maurer A, Darzacq X, Tjian R. Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection. RNA (NEW YORK, N.Y.) 2020; 26:771-783. [PMID: 32358057 PMCID: PMC7297120 DOI: 10.1261/rna.076232.120] [Citation(s) in RCA: 334] [Impact Index Per Article: 83.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The current COVID-19 pandemic presents a serious public health crisis, and a better understanding of the scope and spread of the virus would be aided by more widespread testing. Nucleic-acid-based tests currently offer the most sensitive and early detection of COVID-19. However, the "gold standard" test pioneered by the U.S. Centers for Disease Control and Prevention takes several hours to complete and requires extensive human labor, materials such as RNA extraction kits that could become in short supply, and relatively scarce qPCR machines. It is clear that a huge effort needs to be made to scale up current COVID-19 testing by orders of magnitude. There is thus a pressing need to evaluate alternative protocols, reagents, and approaches to allow nucleic-acid testing to continue in the face of these potential shortages. There has been a tremendous explosion in the number of papers written within the first weeks of the pandemic evaluating potential advances, comparable reagents, and alternatives to the "gold-standard" CDC RT-PCR test. Here we present a collection of these recent advances in COVID-19 nucleic acid testing, including both peer-reviewed and preprint articles. Due to the rapid developments during this crisis, we have included as many publications as possible, but many of the cited sources have not yet been peer-reviewed, so we urge researchers to further validate results in their own laboratories. We hope that this review can urgently consolidate and disseminate information to aid researchers in designing and implementing optimized COVID-19 testing protocols to increase the availability, accuracy, and speed of widespread COVID-19 testing.
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Affiliation(s)
- Meagan N Esbin
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, USA
| | - Oscar N Whitney
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, USA
| | - Shasha Chong
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, USA
- The Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California 94720, USA
| | - Anna Maurer
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, USA
- The Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California 94720, USA
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16
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Sohi AN, Beamish E, Tabard-Cossa V, Godin M. DNA Capture by Nanopore Sensors under Flow. Anal Chem 2020; 92:8108-8116. [DOI: 10.1021/acs.analchem.9b05778] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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Qiao L, Slater GW. Capture of rod-like molecules by a nanopore: Defining an "orientational capture radius". J Chem Phys 2020; 152:144902. [PMID: 32295359 DOI: 10.1063/5.0002044] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Both the translational diffusion coefficient D and the electrophoretic mobility μ of a short rod-like molecule (such as dsDNA) that is being pulled toward a nanopore by an electric field should depend on its orientation. Since a charged rod-like molecule tends to orient in the presence of an inhomogeneous electric field, D and μ will change as the molecule approaches the nanopore, and this will impact the capture process. We present a simplified study of this problem using theoretical arguments and Langevin dynamics simulations. In particular, we introduce a new orientational capture radius, which we compare to the capture radius for the equivalent point-like particle, and we discuss the different physical regimes of orientation during capture and the impact of initial orientations on the capture time.
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Affiliation(s)
- Le Qiao
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Gary W Slater
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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