1
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Chau CC, Maffeo CM, Aksimentiev A, Radford SE, Hewitt EW, Actis P. Single molecule delivery into living cells. Nat Commun 2024; 15:4403. [PMID: 38782907 PMCID: PMC11116494 DOI: 10.1038/s41467-024-48608-3] [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: 02/12/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
Controlled manipulation of cultured cells by delivery of exogenous macromolecules is a cornerstone of experimental biology. Here we describe a platform that uses nanopipettes to deliver defined numbers of macromolecules into cultured cell lines and primary cells at single molecule resolution. In the nanoinjection platform, the nanopipette is used as both a scanning ion conductance microscope (SICM) probe and an injection probe. The SICM is used to position the nanopipette above the cell surface before the nanopipette is inserted into the cell into a defined location and to a predefined depth. We demonstrate that the nanoinjection platform enables the quantitative delivery of DNA, globular proteins, and protein fibrils into cells with single molecule resolution and that delivery results in a phenotypic change in the cell that depends on the identity of the molecules introduced. Using experiments and computational modeling, we also show that macromolecular crowding in the cell increases the signal-to-noise ratio for the detection of translocation events, thus the cell itself enhances the detection of the molecules delivered.
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Affiliation(s)
- Chalmers C Chau
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, LS2 9JT, UK
- Bragg Centre for Materials Research, University of Leeds, Leeds, UK
| | - Christopher M Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sheena E Radford
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Eric W Hewitt
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Paolo Actis
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, LS2 9JT, UK.
- Bragg Centre for Materials Research, University of Leeds, Leeds, UK.
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2
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Patiño-Guillén G, Pešović J, Panić M, Savić-Pavićević D, Bošković F, Keyser UF. Single-molecule RNA sizing enables quantitative analysis of alternative transcription termination. Nat Commun 2024; 15:1699. [PMID: 38402271 PMCID: PMC10894232 DOI: 10.1038/s41467-024-45968-8] [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: 07/18/2023] [Accepted: 02/01/2024] [Indexed: 02/26/2024] Open
Abstract
Transcription, a critical process in molecular biology, has found many applications in RNA synthesis, including mRNA vaccines and RNA therapeutics. However, current RNA characterization technologies suffer from amplification and enzymatic biases that lead to loss of native information. Here, we introduce a strategy to quantitatively study both transcription and RNA polymerase behaviour by sizing RNA with RNA nanotechnology and nanopores. To begin, we utilize T7 RNA polymerase to transcribe linear DNA lacking termination sequences. Surprisingly, we discover alternative transcription termination in the origin of replication sequence. Next, we employ circular DNA without transcription terminators to perform rolling circle transcription. This allows us to gain valuable insights into the processivity and transcription behaviour of RNA polymerase at the single-molecule level. Our work demonstrates how RNA nanotechnology and nanopores may be used in tandem for the direct and quantitative analysis of RNA transcripts. This methodology provides a promising pathway for accurate RNA structural mapping by enabling the study of full-length RNA transcripts at the single-molecule level.
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Affiliation(s)
| | - Jovan Pešović
- University of Belgrade - Faculty of Biology, Centre for Human Molecular Genetics, Belgrade, Serbia
| | - Marko Panić
- University of Belgrade - Faculty of Biology, Centre for Human Molecular Genetics, Belgrade, Serbia
- Institute of Virology, Vaccines and Sera "Torlak", Belgrade, Serbia
| | - Dušanka Savić-Pavićević
- University of Belgrade - Faculty of Biology, Centre for Human Molecular Genetics, Belgrade, Serbia
| | - Filip Bošković
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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3
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Acharjee MC, Ledden B, Thomas B, He X, Messina T, Giurleo J, Talaga D, Li J. Aggregation and Oligomerization Characterization of ß-Lactoglobulin Protein Using a Solid-State Nanopore Sensor. SENSORS (BASEL, SWITZERLAND) 2023; 24:81. [PMID: 38202943 PMCID: PMC10781269 DOI: 10.3390/s24010081] [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: 11/08/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024]
Abstract
Protein aggregation is linked to many chronic and devastating neurodegenerative human diseases and is strongly associated with aging. This work demonstrates that protein aggregation and oligomerization can be evaluated by a solid-state nanopore method at the single molecule level. A silicon nitride nanopore sensor was used to characterize both the amyloidogenic and native-state oligomerization of a model protein ß-lactoglobulin variant A (βLGa). The findings from the nanopore measurements are validated against atomic force microscopy (AFM) and dynamic light scattering (DLS) data, comparing βLGa aggregation from the same samples at various stages. By calibrating with linear and circular dsDNA, this study estimates the amyloid fibrils' length and diameter, the quantity of the βLGa aggregates, and their distribution. The nanopore results align with the DLS and AFM data and offer additional insight at the level of individual protein molecular assemblies. As a further demonstration of the nanopore technique, βLGa self-association and aggregation at pH 4.6 as a function of temperature were measured at high (2 M KCl) and low (0.1 M KCl) ionic strength. This research highlights the advantages and limitations of using solid-state nanopore methods for analyzing protein aggregation.
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Affiliation(s)
- Mitu C. Acharjee
- Material Science and Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Brad Ledden
- Material Science and Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Brian Thomas
- Department of Physics, University of Arkansas, Fayetteville, AR 72701, USA
| | - Xianglan He
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (X.H.); (J.G.)
| | - Troy Messina
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (X.H.); (J.G.)
- Department of Physics, Berea College, Berea, KY 40404, USA
| | - Jason Giurleo
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (X.H.); (J.G.)
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - David Talaga
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (X.H.); (J.G.)
- Department of Chemistry, Sokol Institute, Montclair State University, Montclair, NJ 07043, USA
| | - Jiali Li
- Material Science and Engineering, University of Arkansas, Fayetteville, AR 72701, USA
- Department of Physics, University of Arkansas, Fayetteville, AR 72701, USA
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4
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Yang J, Wang J, Liu X, Chen Y, Liang Y, Wang Q, Jiang S, Zhang C. Translocation of Proteins through Solid-State Nanopores Using DNA Polyhedral Carriers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2303715. [PMID: 37496044 DOI: 10.1002/smll.202303715] [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: 05/03/2023] [Revised: 07/11/2023] [Indexed: 07/28/2023]
Abstract
The detection of biomolecules at the single molecule level has important applications in the fields of biosensing and biomedical diagnosis. The solid-state nanopore (SS nanopore) is a sensitive tool for detecting single molecules because of its unique label-free and low sample consumption properties. SS nanopore translocation of small biomolecules is typically driven by an electronic field force and is thus influenced by the charge, shape, and size of the target molecules. Therefore, it remains challenging to control the translocation of biomolecules through SS nanopores, particularly for different proteins with complex conformations and unique charges. Toward this problem, a DNA polyhedral carrier coating strategy to assist protein translocation through SS nanopores is developed, which facilitates target protein detection. The current signal-to-noise ratios are improved significantly using this DNA carrier loading strategy. The proposed method should aid the detection of proteins, which are difficult to translocate through nanopores. This coating-assisted method offers a wide range of applications for SS nanopore detection and promotes the development of single-molecule detection.
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Affiliation(s)
- Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Juan Wang
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Xuan Liu
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Yiming Chen
- School of Electronics Engineering and Computer Science, Peking University, Beijing, 100871, China
| | - Yuan Liang
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Qi Wang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Shuoxing Jiang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Cheng Zhang
- School of Electronics Engineering and Computer Science, Peking University, Beijing, 100871, China
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5
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Kitta K, Sakamoto M, Hayakawa K, Nukazuka A, Kano K, Yamamoto T. Nanopore Impedance Spectroscopy Reveals Electrical Properties of Single Nanoparticles for Detecting and Identifying Pathogenic Viruses. ACS OMEGA 2023; 8:14684-14693. [PMID: 37125101 PMCID: PMC10134219 DOI: 10.1021/acsomega.3c00628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
In the conventional nanopore method, direct current (DC) is used to study molecules and nanoparticles; however, it cannot easily discriminate between materials with similarly sized particles. Herein, we developed an alternating current (AC)-based nanopore method to measure the impedance of a single nanoparticle and distinguish between particles of the same size based on their material characteristics. We demonstrated the performance of this method using impedance measurements to determine the size and frequency characteristics of various particles, ranging in diameter from 200 nm to 1 μm. Furthermore, the alternating current method exhibited high accuracy for biosensing applications, identifying viruses with over 85% accuracy using single-particle measurement and machine learning. Therefore, this novel nanopore method is useful for applications in materials science, biology, and medicine.
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Affiliation(s)
- Kazuki Kitta
- Mechanical
Engineering, Tokyo Institute of Technology, Ishikawadai 1-314, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Maami Sakamoto
- Mechanical
Engineering, Tokyo Institute of Technology, Ishikawadai 1-314, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Kei Hayakawa
- Material
Research and Innovation Division, DENSO
CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Akira Nukazuka
- Material
Research and Innovation Division, DENSO
CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Kazuhiko Kano
- Material
Research and Innovation Division, DENSO
CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Takatoki Yamamoto
- Mechanical
Engineering, Tokyo Institute of Technology, Ishikawadai 1-314, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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6
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Xu X, Valavanis D, Ciocci P, Confederat S, Marcuccio F, Lemineur JF, Actis P, Kanoufi F, Unwin PR. The New Era of High-Throughput Nanoelectrochemistry. Anal Chem 2023; 95:319-356. [PMID: 36625121 PMCID: PMC9835065 DOI: 10.1021/acs.analchem.2c05105] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Xiangdong Xu
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | | | - Paolo Ciocci
- Université
Paris Cité, ITODYS, CNRS, F-75013 Paris, France
| | - Samuel Confederat
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.,Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.
| | - Fabio Marcuccio
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.,Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.,Faculty
of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Paolo Actis
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.,Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.,
| | | | - Patrick R. Unwin
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.,
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7
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Maheshwaram SK, Shet D, David SR, Lakshminarayana MB, Soni GV. Nanopore Sensing of DNA-Histone Complexes on Nucleosome Arrays. ACS Sens 2022; 7:3876-3884. [PMID: 36441954 DOI: 10.1021/acssensors.2c01865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The location of nucleosomes in DNA and their structural stability are critical in regulating DNA compaction, site accessibility, and epigenetic gene regulation. Here, we combine the nanopore platform-based fast and label-free single-molecule detection technique with a voltage-dependent force rupture assay to detect distinct structures on nucleosomal arrays and then to induce breakdown of individual nucleosome complexes. Specifically, we demonstrate direct measurement of distinct nucleosome structures present on individual 12-mer arrays. A detailed event analysis showed that nucleosomes are present as a combination of complete and partial structures, during translocation through the pore. By comparing with the voltage-dependent translocation of the mononucleosomes, we find that the partial nucleosomes result from voltage-dependent structural disintegration of nucleosomes. High signal-to-noise detection of heterogeneous levels in translocation of 12-mer array molecules quantifies the heterogeneity and nucleosomal substructure sizes on the arrays. These results facilitate the understanding of electrostatic interactions responsible for the integrity of the nucleosome structure and possible mechanisms of its unraveling by chromatin remodeling enzymes. This study also has potential applications in chromatin profiling.
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Affiliation(s)
| | - Divya Shet
- Raman Research Institute, Bangalore, Karnataka 560080, India
| | - Serene R David
- Raman Research Institute, Bangalore, Karnataka 560080, India
| | | | - Gautam V Soni
- Raman Research Institute, Bangalore, Karnataka 560080, India
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8
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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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9
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Sun Z, Liu X, Liu W, Li J, Yang J, Qiao F, Ma J, Sha J, Li J, Xu LQ. AutoNanopore: An Automated Adaptive and Robust Method to Locate Translocation Events in Solid-State Nanopore Current Traces. ACS OMEGA 2022; 7:37103-37111. [PMID: 36312336 PMCID: PMC9608407 DOI: 10.1021/acsomega.2c02927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Solid-state nanopore sequencing has shown impressive performances in several research scenarios but is still challenging, mainly due to the ultrafast speed of DNA translocation and significant noises embedded in raw signals. Hence, event detection, aiming to locate precisely these translocation events, is the fundamental step of data analysis. However, existing event detection methods use either a user-defined global threshold or an adaptive threshold determined by the data, assuming the baseline current to be stable over time. These disadvantages limit their applications in real-world application scenarios, especially considering that the results of different methods are often inconsistent. In this study, we develop an automated adaptive method called AutoNanopore, for fast and accurate event detection in current traces. The method consists of three consecutive steps: current trace segmentation, current amplitude outlier identification by straightforward statistical analyses, and event characterization. Then we propose ideas/metrics on how to quantitatively evaluate the performance of an event detection method, followed by comparing the performance of AutoNanopore against two state-of-the-art methods, OpenNanopore and EventPro. Finally, we examine if one method can detect the overlapping events detected by the other two, demonstrating that AutoNanopore has the highest coverage ratio. Moreover, AutoNanopore also performs well in detecting challenging events: e.g., those with significantly varying baselines.
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Affiliation(s)
- Zepeng Sun
- China
Mobile (Chengdu) Industrial Research Institute, Chengdu610000, People’s Republic of China
| | - Xinlong Liu
- China
Mobile (Chengdu) Industrial Research Institute, Chengdu610000, People’s Republic of China
| | - Wei Liu
- Jiangsu
Key Laboratory for Design and Manufacture of Micro-Nano Biomedical
Instruments, School of Mechanical Engineering, Southeast University, Nanjing210096, People’s Republic
of China
| | - Jiahui Li
- China
Mobile (Chengdu) Industrial Research Institute, Chengdu610000, People’s Republic of China
| | - Jing Yang
- Key
Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing210096, People’s Republic of China
| | - Feng Qiao
- China
Mobile (Chengdu) Industrial Research Institute, Chengdu610000, People’s Republic of China
| | - Jianjun Ma
- China
Mobile (Chengdu) Industrial Research Institute, Chengdu610000, People’s Republic of China
| | - Jingjie Sha
- Jiangsu
Key Laboratory for Design and Manufacture of Micro-Nano Biomedical
Instruments, School of Mechanical Engineering, Southeast University, Nanjing210096, People’s Republic
of China
| | - Jian Li
- Key
Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing210096, People’s Republic of China
| | - Li-Qun Xu
- China
Mobile (Chengdu) Industrial Research Institute, Chengdu610000, People’s Republic of China
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10
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Jeong KB, Kim JS, Dhanasekar NN, Lee MK, Chi SW. Application of nanopore sensors for biomolecular interactions and drug discovery. Chem Asian J 2022; 17:e202200679. [PMID: 35929410 DOI: 10.1002/asia.202200679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/04/2022] [Indexed: 11/07/2022]
Abstract
Biomolecular interactions, including protein-protein, protein-nucleic acid, and protein/nucleic acid-ligand interactions, play crucial roles in various cellular signaling and biological processes, and offer attractive therapeutic targets in numerous human diseases. Currently, drug discovery is limited by the low efficiency and high cost of conventional ensemble-averaging-based techniques for biomolecular interaction analysis and high-throughput drug screening. Nanopores are an emerging technology for single-molecule sensing of biomolecules. Owing to the robust advantages of single-molecule sensing, nanopore sensors have contributed tremendously to nucleic acid sequencing and disease diagnostics. In this minireview, we summarize the recent developments and outlooks in single-molecule sensing of various biomolecular interactions for drug discovery applications using biological and solid-state nanopore sensors.
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Affiliation(s)
- Ki-Baek Jeong
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, 34141, Daejeon, Republic of Korea
| | - Jin-Sik Kim
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, 34141, Daejeon, Republic of Korea
| | - Naresh Niranjan Dhanasekar
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
| | - Mi-Kyung Lee
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, 34141, Daejeon, Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, 34113, Daejeon, Republic of Korea
| | - Seung-Wook Chi
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, 34113, Daejeon, Republic of Korea
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11
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Promising Assays for Examining a Putative Role of Ribosomal Heterogeneity in COVID-19 Susceptibility and Severity. Life (Basel) 2022; 12:life12020203. [PMID: 35207490 PMCID: PMC8880406 DOI: 10.3390/life12020203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 11/17/2022] Open
Abstract
The heterogeneity of ribosomes, characterized by structural variations, arises from differences in types, numbers, and/or post-translational modifications of participating ribosomal proteins (RPs), ribosomal RNAs (rRNAs) sequence variants plus post-transcriptional modifications, and additional molecules essential for forming a translational machinery. The ribosomal heterogeneity within an individual organism or a single cell leads to preferential translations of selected messenger RNA (mRNA) transcripts over others, especially in response to environmental cues. The role of ribosomal heterogeneity in SARS-CoV-2 coronavirus infection, propagation, related symptoms, or vaccine responses is not known, and a technique to examine these has not yet been developed. Tools to detect ribosomal heterogeneity or to profile translating mRNAs independently cannot identify unique or specialized ribosome(s) along with corresponding mRNA substrate(s). Concurrent characterizations of RPs and/or rRNAs with mRNA substrate from a single ribosome would be critical to decipher the putative role of ribosomal heterogeneity in the COVID-19 disease, caused by the SARS-CoV-2, which hijacks the host ribosome to preferentially translate its RNA genome. Such a protocol should be able to provide a high-throughput screening of clinical samples in a large population that would reach a statistical power for determining the impact of a specialized ribosome to specific characteristics of the disease. These characteristics may include host susceptibility, viral infectivity and transmissibility, severity of symptoms, antiviral treatment responses, and vaccine immunogenicity including its side effect and efficacy. In this study, several state-of-the-art techniques, in particular, chemical probing of ribosomal components or rRNA structures, proximity ligation to generate rRNA-mRNA chimeras for sequencing, nanopore gating of individual ribosomes, nanopore RNA sequencing and/or structural analyses, single-ribosome mass spectrometry, and microfluidic droplets for separating ribosomes or indexing rRNAs/mRNAs, are discussed. The key elements for further improvement and proper integration of the above techniques to potentially arrive at a high-throughput protocol for examining individual ribosomes and their mRNA substrates in a clinical setting are also presented.
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12
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Chen H, Lin Y, Long YT, Minteer SD, Ying YL. Nanopore-based measurement of the interaction of P450cam monooxygenase and putidaredoxin at the single-molecule level. Faraday Discuss 2021; 233:295-302. [PMID: 34889330 DOI: 10.1039/d1fd00042j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein-protein interactions occur in a wide range of biological processes and are of great significance to life function. Characterization of transient protein-protein interactions remains a significant barrier to our understanding of cellular processes. Nanopores provide unique nanoscale environments that accommodate single molecules from the surrounding bulk solution. This method permits label-free sensing at the single-molecule level with extremely high sensitivity. Herein, the interaction between a single P450cam monooxygenase and its redox partner putidaredoxin (Pdx) was monitored via transient ionic current by using functionalized glass nanopores. Results show that the volume of P450cam determines the blockage current while the interactions between the P450cam and Pdx give a long blockage duration. Our glass nanopore sensor with adjustable diameter could be applied for real-time sensing of protein-protein interactions between individual proteins with a wide range of molecular weight.
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Affiliation(s)
- Hui Chen
- Department of Chemistry, University of Utah, USA.
| | - Yao Lin
- Department of Chemistry, University of Utah, USA. .,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
| | | | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China. .,Chemistry and Biomedicine Innovation Center, Nanjing University, China
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13
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Tsutsui M, Yokota K, Arima A, Washio T, Baba Y, Kawai T. Detecting Single Molecule Deoxyribonucleic Acid in a Cell Using a Three-Dimensionally Integrated Nanopore. SMALL METHODS 2021; 5:e2100542. [PMID: 34928053 DOI: 10.1002/smtd.202100542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/11/2021] [Indexed: 06/14/2023]
Abstract
Amplification-free genome analysis can revolutionize biology and medicine by uncovering genetic variations among individuals. Here, the authors report on a 3D-integrated nanopore for electrolysis to in situ detection of single-molecule DNA in a cell by ionic current measurements. It consists of a SiO2 multipore sheet and a SiNx nanopore membrane stacked vertically on a Si wafer. Single cell lysis is demonstrated by 106 V m-1 -level electrostatic field focused at the multinanopore. The intracellular molecules are then directly detected as they move through a sensing zone, wherein the authors find telegraphic current signatures reflecting folding degrees of freedom of the millimeter-long polynucleotides threaded through the SiNx nanopore. The present device concept may enable on-chip single-molecule sequencing to multi-omics analyses at a single-cell level.
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Affiliation(s)
- Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Kazumichi Yokota
- National Institute of Advanced Industrial Science and Technology, Takamatsu, Kagawa, 761-0395, Japan
| | - Akihide Arima
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Institute of Nano-Life-Systems, Nagoya, Aichi, 464-8603, Japan
| | - Takashi Washio
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Yoshinobu Baba
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Institute of Nano-Life-Systems, Nagoya, Aichi, 464-8603, Japan
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Institute of Nano-Life-Systems, Nagoya, Aichi, 464-8603, Japan
- Institute of Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Anagawa 4-9-1, Inage-ku, Chiba, 263-8555, Japan
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
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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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15
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Zheng T, Zhu Y, Zhu A. Boronic Acid‐Containing Stimuli‐Responsive Polymers Modified Nanopores for Label‐Free Dual‐Signal‐Output Detection of Glucose. ELECTROANAL 2021. [DOI: 10.1002/elan.202100268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tingting Zheng
- School of Chemistry and Molecular Engineering Engineering Research Center of Nanophotonics and Advanced Instrument Ministry of Education Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration East China Normal University 500 Dongchuan Road Shanghai 200241 People's Republic of China
| | - Yujie Zhu
- School of Chemistry and Molecular Engineering Engineering Research Center of Nanophotonics and Advanced Instrument Ministry of Education Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration East China Normal University 500 Dongchuan Road Shanghai 200241 People's Republic of China
| | - Anwei Zhu
- School of Chemistry and Molecular Engineering Engineering Research Center of Nanophotonics and Advanced Instrument Ministry of Education Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration East China Normal University 500 Dongchuan Road Shanghai 200241 People's Republic of China
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16
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Xu C, Liu Y, Xiong T, Wu F, Yu P, Wang J, Mao L. Dynamic Behavior of Charged Particles at the Nanopipette Orifice. ACS Sens 2021; 6:2330-2338. [PMID: 34138539 DOI: 10.1021/acssensors.1c00418] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding the dynamic behavior of charged particles driven by flow and electric field in nanochannels/pores is highly important for both fundamental study and practical applications. While a great breakthrough has been made in understanding the translocation dynamics of charged particles within the nanochannels/pores, studies on the dynamics of particles at the orifice of nanochannels/pores are scarcely reported. Here, we study particle motion at a smaller-sized orifice of a nanopipette by combining experimentally observed current transients with simulated force conditions. The theoretical force analysis reveals that dielectrophoretic force plays an equally important role as electrophoretic force and electroosmotic force, although it has often been neglected in understanding the particle translocation dynamics within the nanopipette. Under the combined action of these forces, it thus becomes difficult for particles to physically collide with the orifice of the nanopipette, resulting in a relatively low decrease in the current transients, which coincides with experimental results. We then regulate the dynamic behavior by altering experimental conditions (i.e., bias potential, nanopipette surface charge, and particle size), and the results further validate the presence and influence of forces being considered. This study improves the understanding of the relationship between particle properties and observed current transients, providing more possibilities for accurate single-particle analysis and single-entity regulation.
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Affiliation(s)
- Cong Xu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, The Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, The Chinese Academy of Sciences, Beijing 100190, China
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Tianyi Xiong
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, The Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, The Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Yu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, The Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhua Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Lanqun Mao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, The Chinese Academy of Sciences, Beijing 100190, China
- College of Chemistry, Beijing Normal University, Beijing 100875, China
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17
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Yang H, Saqib M, Hao R. Single-Entity Detection With TEM-Fabricated Nanopores. Front Chem 2021; 9:664820. [PMID: 34026729 PMCID: PMC8138203 DOI: 10.3389/fchem.2021.664820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/13/2021] [Indexed: 12/04/2022] Open
Abstract
Nanopore-based single-entity detection shows immense potential in sensing and sequencing technologies. Solid-state nanopores permit unprecedented detail while preserving mechanical robustness, reusability, adjustable pore size, and stability in different physical and chemical environments. The transmission electron microscope (TEM) has evolved into a powerful tool for fabricating and characterizing nanometer-sized pores within a solid-state ultrathin membrane. By detecting differences in the ionic current signals due to single-entity translocation through the nanopore, solid-state nanopores can enable gene sequencing and single molecule/nanoparticle detection with high sensitivity, improved acquisition speed, and low cost. Here we briefly discuss the recent progress in the modification and characterization of TEM-fabricated nanopores. Moreover, we highlight some key applications of these nanopores in nucleic acids, protein, and nanoparticle detection. Additionally, we discuss the future of computer simulations in DNA and protein sequencing strategies. We also attempt to identify the challenges and discuss the future development of nanopore-detection technology aiming to promote the next-generation sequencing technology.
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Affiliation(s)
| | | | - Rui Hao
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, China
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Huo W, Ling W, Wang Z, Li Y, Zhou M, Ren M, Li X, Li J, Xia Z, Liu X, Huang X. Miniaturized DNA Sequencers for Personal Use: Unreachable Dreams or Achievable Goals. FRONTIERS IN NANOTECHNOLOGY 2021. [DOI: 10.3389/fnano.2021.628861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The appearance of next generation sequencing technology that features short read length with high measurement throughput and low cost has revolutionized the field of life science, medicine, and even computer science. The subsequent development of the third-generation sequencing technologies represented by nanopore and zero-mode waveguide techniques offers even higher speed and long read length with promising applications in portable and rapid genomic tests in field. Especially under the current circumstances, issues such as public health emergencies and global pandemics impose soaring demand on quick identification of origins and species of analytes through DNA sequences. In addition, future development of disease diagnosis, treatment, and tracking techniques may also require frequent DNA testing. As a result, DNA sequencers with miniaturized size and highly integrated components for personal and portable use to tackle increasing needs for disease prevention, personal medicine, and biohazard protection may become future trends. Just like many other biological and medical analytical systems that were originally bulky in sizes, collaborative work from various subjects in engineering and science eventually leads to the miniaturization of these systems. DNA sequencers that involve nanoprobes, detectors, microfluidics, microelectronics, and circuits as well as complex functional materials and structures are extremely complicated but may be miniaturized with technical advancement. This paper reviews the state-of-the-art technology in developing essential components in DNA sequencers and analyzes the feasibility to achieve miniaturized DNA sequencers for personal use. Future perspectives on the opportunities and associated challenges for compact DNA sequencers are also identified.
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