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Kawaguchi T, Tsutsui M, Murayama S, Leong IW, Yokota K, Komoto Y, Taniguchi M. Enhanced Nanoparticle Sensing in a Highly Viscous Nanopore. SMALL METHODS 2024; 8:e2301523. [PMID: 38725330 DOI: 10.1002/smtd.202301523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 04/26/2024] [Indexed: 08/18/2024]
Abstract
Slowing down translocation dynamics is a crucial challenge in nanopore sensing of small molecules and particles. Here, it is reported on nanoparticle motion-mediated local viscosity enhancement of water-organic mixtures in a nanofluidic channel that enables slow translocation speed, enhanced capture efficiency, and improved signal-to-noise ratio by transmembrane voltage control. It is found that higher detection rates of nanoparticles under larger electrophoretic voltage in the highly viscous solvents. Meanwhile, the strongly pulled particles distort the liquid in the pore at high shear rates over 103 s-1 which leads to a counterintuitive phenomenon of slower translocation speed under higher voltage via the induced dilatant viscosity behavior. This mechanism is demonstrated as feasible with a variety of organic molecules, including glycerol, xanthan gum, and polyethylene glycol. The present findings can be useful in resistive pulse analyses of nanoscale objects such as viruses and proteins by allowing a simple and effective way for translocation slowdown, improved detection throughput, and enhanced signal-to-noise ratio.
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Affiliation(s)
- Taiga Kawaguchi
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Sanae Murayama
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Iat Wai Leong
- 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
| | - Yuki Komoto
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
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2
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Tsutsui M, Wada M, Arima A, Tsunekawa Y, Sasaki T, Sakamoto K, Yokota K, Baba Y, Kawai T, Okada T. Identifying Viral Vector Characteristics by Nanopore Sensing. ACS NANO 2024; 18:15695-15704. [PMID: 38836590 DOI: 10.1021/acsnano.4c01888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Using viral vectors as gene delivery vehicles for gene therapy necessitates their quality control. Here, we report on nanopore sensing for nondestructively inspecting genomes inside the nanoscale cargoes at the single-molecule level. Using ionic current measurements, we motion-tracked the adeno-associated virus (AAV) vectors as they translocated through a solid-state nanopore. Considering the varying contributions of the electrophoretic forces from the negatively charged internal polynucleotides of different lengths, the nanocargoes carrying longer DNA moved more slowly in the nanochannel. Moreover, ion blockage characteristics revealed their larger volume by up to approximately 3600 nm3 in proportion to the length of single-stranded DNA packaged inside, thereby allowing electrical discriminations of AAV vectors by the gene-derived physical features. The present findings can be a promising tool for the enhanced quality control of AAV products by enabling the screening of empty and intermediate vectors at the single-particle level.
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Affiliation(s)
- Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Osaka 567-0047, Japan
| | - Mikako Wada
- Division of Molecular and Medical Genetics, Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Akihide Arima
- Institute of Nano-Life-Systems Institutes of Innovation for Future Society, Nagoya University, Nagoya 464-8603, Japan
| | - Yuji Tsunekawa
- Division of Molecular and Medical Genetics, Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Takako Sasaki
- Division of Molecular and Medical Genetics, Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kenji Sakamoto
- Division of Molecular and Medical Genetics, Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kazumichi Yokota
- National Institute of Advanced Industrial Science and Technology, Kagawa 761-0395, Japan
| | - Yoshinobu Baba
- Institute of Nano-Life-Systems Institutes of Innovation for Future Society, Nagoya University, Nagoya 464-8603, Japan
- Department of Biomolecular Engineering Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
- Institute of Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Osaka 567-0047, Japan
| | - Takashi Okada
- Division of Molecular and Medical Genetics, Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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3
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Zhu L, Wu H, Xu Z, Guo L, Zhao J. Analysis of the effect of cations on protein conformational stability using solid-state nanopores. Analyst 2024; 149:3186-3194. [PMID: 38639484 DOI: 10.1039/d4an00248b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
The conformation of proteins is closely related to their biological functions, and it is affected by many factors, including the type of cations in solution. However, it is difficult to detect the conformational changes of a protein in situ. As a single-molecule sensing technology, nanopores can convert molecular structural information into analyzable current signals within a reasonable time range. Herein, we detect and analyze the effects of two different types of monovalent cations (Na+ and Li+) on a model protein bovine serum albumin (BSA) conformation using SiNx nanopores with different diameters. The quantitative analysis results show that the excluded volume of BSA in LiCl salt solutions is larger than the value in NaCl solution, indicating that Li+ is more prone to unfolding the proteins and making them unstable. This study demonstrated that nanopores enable the in situ detection of the structure of proteins at the single-molecule level and provide a new approach for the quantitative analysis of proteins.
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Affiliation(s)
- Libo Zhu
- School of Medical Imaging, Wannan Medical College, Wuhu, 241002, China.
| | - Hongwen Wu
- Jiangxi Institute of Respiratory Disease, the First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Zhengyuan Xu
- School of Medical Imaging, Wannan Medical College, Wuhu, 241002, China.
| | - Lanying Guo
- School of Medical Imaging, Wannan Medical College, Wuhu, 241002, China.
| | - Jinsong Zhao
- School of Medical Imaging, Wannan Medical College, Wuhu, 241002, China.
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4
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Tao C, Bai Y, Chen J, Lu J, Bi Y, Li J. Detection of Glutamate Decarboxylase Antibodies and Simultaneous Multi-Molecular Translocation Exploration by Glass Nanopores. BIOSENSORS 2024; 14:255. [PMID: 38785729 PMCID: PMC11118187 DOI: 10.3390/bios14050255] [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: 03/21/2024] [Revised: 05/09/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Glutamic acid decarboxylase antibody (GADAb) has emerged as a significant biomarker for clinical diagnosis and prognosis in type 1 diabetes (T1D). In this study, we investigated the potential utilization of glass capillary solid-state nanopores as a cost-effective and easily preparable platform for the detection of individual antigens, antibodies, and antigen-antibody complexes without necessitating any modifications to the nanopores. Our findings revealed notable characteristic variations in the translocation events of glutamic acid decarboxylase (GAD65) through nanopores under different voltage conditions, discovered that anomalous phenomenon of protein translocation events increasing with voltage may potentially be caused by the crowding of multiple proteins in the nanopores, and demonstrated that there are multiple components in the polyclonal antibodies (GADAb-poly). Furthermore, we achieved successful differentiation between GAD65, GADAb, and GADAb-GAD65 complexes. These results offer promising prospects for the development of a rapid and reliable GADAb detection method, which holds the potential to be applied in patient serum samples, thereby facilitating a label-free, cost-effective, and early diagnosis of type I diabetes.
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Affiliation(s)
- Chongxin Tao
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Yun Bai
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Jiang Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Jing Lu
- Department of Endocrinology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Yan Bi
- Department of Endocrinology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Jian Li
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing 210096, China
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5
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Meyer N, Torrent J, Balme S. Characterizing Prion-Like Protein Aggregation: Emerging Nanopore-Based Approaches. SMALL METHODS 2024:e2400058. [PMID: 38644684 DOI: 10.1002/smtd.202400058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/10/2024] [Indexed: 04/23/2024]
Abstract
Prion-like protein aggregation is characteristic of numerous neurodegenerative diseases, such as Alzheimer's and Parkinson's diseases. This process involves the formation of aggregates ranging from small and potentially neurotoxic oligomers to highly structured self-propagating amyloid fibrils. Various approaches are used to study protein aggregation, but they do not always provide continuous information on the polymorphic, transient, and heterogeneous species formed. This review provides an updated state-of-the-art approach to the detection and characterization of a wide range of protein aggregates using nanopore technology. For each type of nanopore, biological, solid-state polymer, and nanopipette, discuss the main achievements for the detection of protein aggregates as well as the significant contributions to the understanding of protein aggregation and diagnostics.
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Affiliation(s)
- Nathan Meyer
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, Cedex 5, Montpellier, 34095, France
- INM, University of Montpellier, INSERM, Montpellier, 34095, France
| | - Joan Torrent
- INM, University of Montpellier, INSERM, Montpellier, 34095, France
| | - Sébastien Balme
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, Cedex 5, Montpellier, 34095, France
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Gonzalez Solveyra E, Perez Sirkin YA, Tagliazucchi M, Szleifer I. Orientational Pathways during Protein Translocation through Polymer-Modified Nanopores. ACS NANO 2024; 18:10427-10438. [PMID: 38556978 DOI: 10.1021/acsnano.3c11318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Protein translocation through nanopores holds significant promise for applications in biotechnology, biomolecular analysis, and medicine. However, the interpretation of signals generated by the translocation of the protein remains challenging. In this way, it is crucial to gain a comprehensive understanding on how macromolecules translocate through a nanopore and to identify what are the critical parameters that govern the process. In this study, we investigate the interplay between protein charge regulation, orientation, and nanopore surface modifications using a theoretical framework that allows us to explicitly take into account the acid-base reactions of the titrable amino acids in the proteins and in the polyelectrolytes grafted to the nanopore surface. Our goal is to thoroughly characterize the translocation process of different proteins (GFP, β-lactoglobulin, lysozyme, and RNase) through nanopores modified with weak polyacids. Our calculations show that the charge regulation mechanism exerts a profound effect on the translocation process. The pH-dependent interactions between proteins and charged polymers within the nanopore lead to diverse free energy landscapes with barriers, wells, and flat regions dictating translocation efficiency. Comparison of different proteins allows us to identify the significance of protein isoelectric point, size, and morphology in the translocation behavior. Taking advantage of these insights, we propose pH-responsive nanopores that can load proteins at one pH and release them at another, offering opportunities for controlled protein delivery, separation, and sensing applications.
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Affiliation(s)
- Estefania Gonzalez Solveyra
- Instituto de Nanosistemas, Universidad Nacional de San Martín-CONICET, San Martín, Buenos Aires B1650, Argentina
| | - Yamila A Perez Sirkin
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica Analítica y Química Física y CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Instituto de Química de los Materiales, Ambiente y Energía (INQUIMAE). Pabellón 2, Ciudad Universitaria, C1428 Ciudad Autónoma de Buenos Aires, Argentina
| | - Mario Tagliazucchi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica Analítica y Química Física y CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Instituto de Química de los Materiales, Ambiente y Energía (INQUIMAE). Pabellón 2, Ciudad Universitaria, C1428 Ciudad Autónoma de Buenos Aires, Argentina
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
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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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8
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Zhang X, Dai Y, Sun J, Shen J, Lin M, Xia F. Solid-State Nanopore/Nanochannel Sensors with Enhanced Selectivity through Pore-in Modification. Anal Chem 2024; 96:2277-2285. [PMID: 38285919 DOI: 10.1021/acs.analchem.3c05228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Nanopore sensing technology, as an emerging analytical method, has the advantages of simple operation, fast output, and label-free and has been widely used in fields such as protein analysis, gene sequencing, and biomarker detection. Inspired by biological ion channels, scientists have prepared various artificial solid-state nanopores/nanochannels. Biological ion channels have extremely high ion transport selectivity, while solid-state nanopores/nanochannels have poor selectivity. The selectivity of solid-state nanopores and nanochannels can be enhanced by modifying channel charge, varying pore size, incorporating specific chemical functionality, and adjusting operating (or solution) conditions. This Perspective highlights pore-in modification strategies for enhancing the selectivity of solid-state nanopore/nanochannel sensors by summarizing the articles published in the last 10 years. The future development prospects and challenges of pore-in modification in solid-state nanopore and nanochannel sensors are discussed. This Perspective helps readers better understand nanopore sensing technology, especially the importance of detection selectivity. We believe that solid-state nanopore/nanochannel sensors will soon enter our homes after various challenges.
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Affiliation(s)
- Xiaojin Zhang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Yu Dai
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Jielin Sun
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Meihua Lin
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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9
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Jodeyri Z, Taghipoor M. Multivariate analysis of nanoparticle translocation through a nanopore to improve the accuracy of resistive pulse sensing. Phys Chem Chem Phys 2024; 26:5097-5105. [PMID: 38259043 DOI: 10.1039/d3cp05565e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The advent of nanopore-based sensors based on resistive pulse sensing gave rise to a remarkable breakthrough in the detection and characterization of nanoscale species. Some strong correlations have been reported between the resistive pulse characteristics and the particle's geometrical and physical properties. These correlations are commonly used to obtain information about the particles in commercial devices and research setups. The correlations, however, do not consider the simultaneous effect of influential factors such as particle shape and off-axis translocation, which complicates the extraction of accurate information from the resistive pulses. In this paper, we numerically studied the impact of the shape and position of particles on pulse characteristics in order to estimate the errors that arise from neglecting the influence of multiple factors on resistive pulses. We considered the sphere, oblate, and prolate particles to investigate the nanoparticle shape effect. Moreover, the trajectory dependency was examined by considering the translocation of nanoparticles away from the nanopore axis. Meanwhile, the shape effect was studied for different trajectories. We observed that the simultaneous effects of influential parameters could lead to significant errors in estimating particle properties if the coupled effects are neglected. Based on the results, we introduce the "pulse waveshape" as a novel characteristic of the resistive pulse that can be utilized as a decoupling parameter in the analysis of resistive pulses.
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Affiliation(s)
- Zohre Jodeyri
- Micro Nano Systems Laboratory (MNSL), Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran.
| | - Mojtaba Taghipoor
- Micro Nano Systems Laboratory (MNSL), Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran.
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Confederat S, Lee S, Vang D, Soulias D, Marcuccio F, Peace TI, Edwards MA, Strobbia P, Samanta D, Wälti C, Actis P. Next-Generation Nanopore Sensors Based on Conductive Pulse Sensing for Enhanced Detection of Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2305186. [PMID: 37649152 DOI: 10.1002/smll.202305186] [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: 06/23/2023] [Revised: 07/28/2023] [Indexed: 09/01/2023]
Abstract
Nanopore sensing has been successfully used to characterize biological molecules with single-molecule resolution based on the resistive pulse sensing approach. However, its use in nanoparticle characterization has been constrained by the need to tailor the nanopore aperture size to the size of the analyte, precluding the analysis of heterogeneous samples. Additionally, nanopore sensors often require the use of high salt concentrations to improve the signal-to-noise ratio, which further limits their ability to study a wide range of nanoparticles that are unstable at high ionic strength. Here, a new paradigm in nanopore research that takes advantage of a polymer electrolyte system to comprise a conductive pulse sensing approach is presented. A finite element model is developed to explain the conductive pulse signals observed and compare these results with experiments. This system enables the analytical characterization of heterogeneous nanoparticle mixtures at low ionic strength . Furthermore, the wide applicability of the method is demonstrated by characterizing metallic nanospheres of varied sizes, plasmonic nanostars with various degrees of branching, and protein-based spherical nucleic acids with different oligonucleotide loadings. This system will complement the toolbox of nanomaterials characterization techniques to enable real-time optimization workflow for engineering a wide range of nanomaterials.
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Affiliation(s)
- Samuel Confederat
- Bragg Centre for Materials Research, University of Leeds, LS2 9JT, Leeds, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, LS2 9JT, Leeds, UK
| | - Seungheon Lee
- Department of Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Der Vang
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Dimitrios Soulias
- Bragg Centre for Materials Research, University of Leeds, LS2 9JT, Leeds, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, LS2 9JT, Leeds, UK
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, OX1 3QZ, Oxford, UK
| | - Fabio Marcuccio
- Bragg Centre for Materials Research, University of Leeds, LS2 9JT, Leeds, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, LS2 9JT, Leeds, UK
- Faculty of Medicine, Imperial College London, SW7 2AZ, London, UK
| | - Timotheus I Peace
- Bragg Centre for Materials Research, University of Leeds, LS2 9JT, Leeds, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, LS2 9JT, Leeds, UK
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK
| | - Martin Andrew Edwards
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Pietro Strobbia
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Devleena Samanta
- Department of Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Christoph Wälti
- Bragg Centre for Materials Research, University of Leeds, LS2 9JT, Leeds, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, LS2 9JT, Leeds, UK
| | - Paolo Actis
- Bragg Centre for Materials Research, University of Leeds, LS2 9JT, Leeds, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, LS2 9JT, Leeds, UK
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11
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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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12
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Wang J, Chen C, Yao G, Ding J, Wang L, Jiang H. Intelligent Protein Design and Molecular Characterization Techniques: A Comprehensive Review. Molecules 2023; 28:7865. [PMID: 38067593 PMCID: PMC10707872 DOI: 10.3390/molecules28237865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/13/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
In recent years, the widespread application of artificial intelligence algorithms in protein structure, function prediction, and de novo protein design has significantly accelerated the process of intelligent protein design and led to many noteworthy achievements. This advancement in protein intelligent design holds great potential to accelerate the development of new drugs, enhance the efficiency of biocatalysts, and even create entirely new biomaterials. Protein characterization is the key to the performance of intelligent protein design. However, there is no consensus on the most suitable characterization method for intelligent protein design tasks. This review describes the methods, characteristics, and representative applications of traditional descriptors, sequence-based and structure-based protein characterization. It discusses their advantages, disadvantages, and scope of application. It is hoped that this could help researchers to better understand the limitations and application scenarios of these methods, and provide valuable references for choosing appropriate protein characterization techniques for related research in the field, so as to better carry out protein research.
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Affiliation(s)
| | | | | | - Junjie Ding
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China; (J.W.); (C.C.); (G.Y.)
| | - Liangliang Wang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China; (J.W.); (C.C.); (G.Y.)
| | - Hui Jiang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China; (J.W.); (C.C.); (G.Y.)
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13
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Lucas FLR, Finol-Urdaneta RK, Van Thillo T, McArthur JR, van der Heide NJ, Maglia G, Dedecker P, Strauss O, Wloka C. Evidence of Cytolysin A nanopore incorporation in mammalian cells assessed by a graphical user interface. NANOSCALE 2023; 15:16914-16923. [PMID: 37853831 DOI: 10.1039/d3nr01977b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Technologies capable of assessing cellular metabolites with high precision and temporal resolution are currently limited. Recent developments in the field of nanopore sensors allow the non-stochastic quantification of metabolites, where a nanopore is acting as an electrical transducer for selective substrate binding proteins (SBPs). Here we show that incorporation of the pore-forming toxin Cytolysin A (ClyA) into the plasma membrane of Chinese hamster ovary cells (CHO-K1) results in the appearance of single-channel conductance amenable to multiplexed automated patch-clamp (APC) electrophysiology. In CHO-K1 cells, SBPs modify the ionic current flowing though ClyA nanopores, thus demonstrating its potential for metabolite sensing of living cells. Moreover, we developed a graphical user interface for the analysis of the complex signals resulting from multiplexed APC recordings. This system lays the foundation to bridge the gap between recent advances in the nanopore field (e.g., proteomic and transcriptomic) and potential cellular applications.
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Affiliation(s)
| | - Rocio K Finol-Urdaneta
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
- Electrophysiology Facility for Cell Phenotyping and Drug Discovery, Wollongong, NSW 2522, Australia
- Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Toon Van Thillo
- Lab for Nanobiology, Department of Chemistry, KU Leuven, Belgium.
| | - Jeffrey R McArthur
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
- Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Nieck Jordy van der Heide
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747 AG, Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747 AG, Groningen, The Netherlands
| | - Peter Dedecker
- Lab for Nanobiology, Department of Chemistry, KU Leuven, Belgium.
| | - Olaf Strauss
- Experimental Ophthalmology, Department of Ophthalmology, Charité - Universitätsmedizin Berlin, A Corporate Member of Freie Universität, Humboldt-University, The Berlin Institute of Health, Berlin, Germany.
| | - Carsten Wloka
- Experimental Ophthalmology, Department of Ophthalmology, Charité - Universitätsmedizin Berlin, A Corporate Member of Freie Universität, Humboldt-University, The Berlin Institute of Health, Berlin, Germany.
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14
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Moderne M, Abrao-Nemeir I, Meyer N, Du J, Charles-Achille S, Janot JM, Torrent J, Lepoitevin M, Balme S. Combining iontronic, chromatography and nanopipette for Aβ42 aggregates detection and separation. Anal Chim Acta 2023; 1275:341587. [PMID: 37524475 DOI: 10.1016/j.aca.2023.341587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/13/2023] [Accepted: 07/04/2023] [Indexed: 08/02/2023]
Abstract
In this work, we aim to capture, detect and analysis at single molecule level Aβ42 aggregates. To this end, two strategies of track-etched nanopore membranes functionalization were investigated. The first one uses an aptamer and requires only three steps, whereas the second strategy uses Lecanemab antibodies and requires six steps. Out of the two presented strategies, the second one was found to be the most suitable to detect Aβ42 aggregates using a quick current-voltage readout. The resulting single nanopore was then upscale to multipore membranes to capture the Aβ42 aggregates before analysis through them through a single-molecule approach. By comparing the species present in the retentate and filtrate, we confirmed the membrane's affinity for the larger Aβ42 aggregates present in the sample. We found that chromatographic membranes combined with an ionic diode for binary on/off readout are powerful tools for detecting rare biomarkers before single molecule analysis.
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Affiliation(s)
- Mathilde Moderne
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier, Cedex 5, France
| | - Imad Abrao-Nemeir
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier, Cedex 5, France
| | - Nathan Meyer
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier, Cedex 5, France; INM, University of Montpellier, INSERM, Montpellier, France
| | - Jun Du
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier, Cedex 5, France
| | - Saly Charles-Achille
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier, Cedex 5, France
| | - Jean-Marc Janot
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier, Cedex 5, France
| | - Joan Torrent
- INM, University of Montpellier, INSERM, Montpellier, France
| | - Mathilde Lepoitevin
- Institut des Matériaux Poreux de Paris (IMAP), UMR 8004 CNRS, Ecole Normale Supérieure de Paris, Ecole Supérieure de Physique et de Chimie Industrielles de Paris, PSL Université, 75005, Paris, France
| | - Sebastien Balme
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier, Cedex 5, France.
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15
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Awasthi S, Ying C, Li J, Mayer M. Simultaneous Determination of the Size and Shape of Single α-Synuclein Oligomers in Solution. ACS NANO 2023. [PMID: 37327131 DOI: 10.1021/acsnano.3c01393] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Soluble oligomers of amyloid-forming proteins are implicated as toxic species in the context of several neurodegenerative diseases. Since the size and shape of these oligomers influence their toxicity, their biophysical characterization is essential for a better understanding of the structure-toxicity relationship. Amyloid oligomers are difficult to characterize by conventional approaches due to their heterogeneity in size and shape, their dynamic aggregation process, and their low abundance. This work demonstrates that resistive pulse measurements using polymer-coated solid-state nanopores enable single-particle-level characterization of the size and shape of individual αSyn oligomers in solution within minutes. A comparison of the resulting size distribution with single-particle analysis by transmission electron microscopy and mass photometry reveals good agreement with superior resolution by nanopore-based characterization. Moreover, nanopore-based analysis has the capability to combine rapid size analysis with an approximation of the oligomer shape. Applying this shape approximation to putatively toxic oligomeric species that range in size from 18 ± 7 aggregated monomers (10S) to 29 ± 10 aggregated monomers (15S) and in concentration from picomolar to nanomolar revealed oligomer shapes that agree well with previous estimates by cryo-EM with the added advantage that nanopore-based analysis occurs rapidly, in solution, and has the potential to become a widely accessible technique.
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Affiliation(s)
- Saurabh Awasthi
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
| | - Cuifeng Ying
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
| | - Jiali Li
- University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
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16
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Hong H, Wei J, Lei X, Chen H, Sarro PM, Zhang G, Liu Z. Study on the controllability of the fabrication of single-crystal silicon nanopores/nanoslits with a fast-stop ionic current-monitored TSWE method. MICROSYSTEMS & NANOENGINEERING 2023; 9:63. [PMID: 37206700 PMCID: PMC10188523 DOI: 10.1038/s41378-023-00532-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 03/28/2023] [Indexed: 05/21/2023]
Abstract
The application of single-crystal silicon (SCS) nanopore structures in single-molecule-based analytical devices is an emerging approach for the separation and analysis of nanoparticles. The key challenge is to fabricate individual SCS nanopores with precise sizes in a controllable and reproducible way. This paper introduces a fast-stop ionic current-monitored three-step wet etching (TSWE) method for the controllable fabrication of SCS nanopores. Since the nanopore size has a quantitative relationship with the corresponding ionic current, it can be regulated by controlling the ionic current. Thanks to the precise current-monitored and self-stop system, an array of nanoslits with a feature size of only 3 nm was obtained, which is the smallest size ever reported using the TSWE method. Furthermore, by selecting different current jump ratios, individual nanopores of specific sizes were controllably prepared, and the smallest deviation from the theoretical value was 1.4 nm. DNA translocation measurement results revealed that the prepared SCS nanopores possessed the excellent potential to be applied in DNA sequencing.
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Affiliation(s)
- Hao Hong
- Department of Microelectronics, Delft University of Technology, 2628 CD Delft, The Netherlands
- School of Integrated Circuits, Tsinghua University, 100084 Beijing, China
| | - Jiangtao Wei
- School of Integrated Circuits, Tsinghua University, 100084 Beijing, China
| | - Xin Lei
- School of Chemistry, Beihang University, 100084 Beijing, China
| | - Haiyun Chen
- School of Electronic and Information Engineering, Beijing Jiaotong University, 100084 Beijing, China
| | - Pasqualina M. Sarro
- Department of Microelectronics, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Guoqi Zhang
- Department of Microelectronics, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Zewen Liu
- School of Integrated Circuits, Tsinghua University, 100084 Beijing, China
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17
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Marcuccio F, Soulias D, Chau CCC, Radford SE, Hewitt E, Actis P, Edwards MA. Mechanistic Study of the Conductance and Enhanced Single-Molecule Detection in a Polymer-Electrolyte Nanopore. ACS NANOSCIENCE AU 2023; 3:172-181. [PMID: 37096230 PMCID: PMC10119975 DOI: 10.1021/acsnanoscienceau.2c00050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 04/26/2023]
Abstract
Solid-state nanopores have been widely employed in the detection of biomolecules, but low signal-to-noise ratios still represent a major obstacle in the discrimination of nucleic acid and protein sequences substantially smaller than the nanopore diameter. The addition of 50% poly(ethylene) glycol (PEG) to the external solution is a simple way to enhance the detection of such biomolecules. Here, we demonstrate with finite-element modeling and experiments that the addition of PEG to the external solution introduces a strong imbalance in the transport properties of cations and anions, drastically affecting the current response of the nanopore. We further show that the strong asymmetric current response is due to a polarity-dependent ion distribution and transport at the nanopipette tip region, leading to either ion depletion or enrichment for few tens of nanometers across its aperture. We provide evidence that a combination of the decreased/increased diffusion coefficients of cations/anions in the bath outside the nanopore and the interaction between a translocating molecule and the nanopore-bath interface is responsible for the increase in the translocation signals. We expect this new mechanism to contribute to further developments in nanopore sensing by suggesting that tuning the diffusion coefficients of ions could enhance the sensitivity of the system.
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Affiliation(s)
- Fabio Marcuccio
- School
of Electronic and Electrical Engineering, University of Leeds, LeedsLS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, LeedsLS2 9JT, U.K.
| | - Dimitrios Soulias
- School
of Electronic and Electrical Engineering, University of Leeds, LeedsLS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, LeedsLS2 9JT, U.K.
| | - Chalmers C. C. Chau
- School
of Electronic and Electrical Engineering, University of Leeds, LeedsLS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, LeedsLS2 9JT, U.K.
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, LeedsLS2 9JT, U.K.
| | - Sheena E. Radford
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, LeedsLS2 9JT, U.K.
| | - Eric Hewitt
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, LeedsLS2 9JT, U.K.
| | - Paolo Actis
- School
of Electronic and Electrical Engineering, University of Leeds, LeedsLS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, LeedsLS2 9JT, U.K.
| | - Martin Andrew Edwards
- Department
of Chemistry and Biochemistry, University
of Arkansas, Fayetteville, Arkansas72701, United States
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18
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Li J, Huang B, Wang Y, Li A, Wang Y, Pan Y, Chai J, Liu Z, Zhai Y. Light-Driven Conversion of Silicon Nitride Nanopore to Nanonet for Single-Protein Trapping Analysis. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2210342. [PMID: 36823450 DOI: 10.1002/adma.202210342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/12/2023] [Indexed: 06/18/2023]
Abstract
The single-molecule technique for investigation of an unlabeled protein in solution is very attractive but with great challenges. Nanopore sensing as a label-free tool can be used for collecting the structural information of individual proteins, but currently offers only limited capabilities due to the fast translocation of the target. Here, a reliable and facile method is developed to convert the silicon nitride nanopore to a stable nanonet platform for single-entity sensing by electrophoretic or electroosmotic trapping. A nanonet is fabricated based on a material reorganization process caused by electron-beam and light-irradiation treatment. Using protein molecules as a model, it is revealed that the solid-state nanonet can produce collision and trapping flipping signals of the protein, which provides more structural information than traditional nanopore sensing. More importantly, thanks to the excellent stability of the solid-state silicon nitride nanonet, it is demonstrated that the ultraviolet-light-irradiation-induced structural-change process of an individual protein can be captured. The developed nanonet supplies a robust platform for single-entity studies but is not limited to proteins.
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Affiliation(s)
- Jing Li
- The Institute for Advanced Studies (IAS), Wuhan University, Wuhan, 430072, P. R. China
| | - Bintong Huang
- The Institute for Advanced Studies (IAS), Wuhan University, Wuhan, 430072, P. R. China
| | - Yuanhao Wang
- The Institute for Advanced Studies (IAS), Wuhan University, Wuhan, 430072, P. R. China
| | - Aijia Li
- The Institute for Advanced Studies (IAS), Wuhan University, Wuhan, 430072, P. R. China
| | - Yong Wang
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, 314400, P. R. China
- College of Life Sciences, Shanghai Institute for Advanced Study, Institute of Quantitative Biology, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Yangyang Pan
- Department of Engineering Mechanics, School of Civil Engineering, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Jia Chai
- The Institute for Advanced Studies (IAS), Wuhan University, Wuhan, 430072, P. R. China
| | - Ze Liu
- Department of Engineering Mechanics, School of Civil Engineering, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Yueming Zhai
- The Institute for Advanced Studies (IAS), Wuhan University, Wuhan, 430072, P. R. China
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19
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Chau C, Marcuccio F, Soulias D, Edwards MA, Tuplin A, Radford SE, Hewitt E, Actis P. Probing RNA Conformations Using a Polymer-Electrolyte Solid-State Nanopore. ACS NANO 2022; 16:20075-20085. [PMID: 36279181 PMCID: PMC9798860 DOI: 10.1021/acsnano.2c08312] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nanopore systems have emerged as a leading platform for the analysis of biomolecular complexes with single-molecule resolution. The conformation of biomolecules, such as RNA, is highly dependent on the electrolyte composition, but solid-state nanopore systems often require high salt concentration to operate, precluding analysis of macromolecular conformations under physiologically relevant conditions. Here, we report the implementation of a polymer-electrolyte solid-state nanopore system based on alkali metal halide salts dissolved in 50% w/v poly(ethylene) glycol (PEG) to augment the performance of our system. We show that polymer-electrolyte bath governs the translocation dynamics of the analyte which correlates with the physical properties of the salt used in the bath. This allowed us to identify CsBr as the optimal salt to complement PEG to generate the largest signal enhancement. Harnessing the effects of the polymer-electrolyte, we probed the conformations of the Chikungunya virus (CHIKV) RNA genome fragments under physiologically relevant conditions. Our system was able to fingerprint CHIKV RNA fragments ranging from ∼300 to ∼2000 nt length and subsequently distinguish conformations between the co-transcriptionally folded and the natively refolded ∼2000 nt CHIKV RNA. We envision that the polymer-electrolyte solid-state nanopore system will further enable structural and conformational analyses of individual biomolecules under physiologically relevant conditions.
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Affiliation(s)
- Chalmers Chau
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
- 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.
| | - Dimitrios Soulias
- 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.
| | - Martin Andrew Edwards
- Department
of Chemistry & Biochemistry, University
of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Andrew Tuplin
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Sheena E. Radford
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Eric Hewitt
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - 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.
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20
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Gu C, Yu Z, Li X, Zhu X, Jin C, Cao Z, Dong S, Luo J, Ye Z, Liu Y. Experimental study on single biomolecule sensing using MoS 2-graphene heterostructure nanopores. NANOSCALE 2022; 15:266-274. [PMID: 36477179 DOI: 10.1039/d2nr04485d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Solid-state nanopores play an important role in sensing single-biomolecules such as DNA and proteins. However, an ultra-short translocation time hinders nanopores from acquiring more detailed information about biomolecules, and further applications such as sequencing and molecular structure analysis are limited. Related studies have shown that MoS2 has no obvious impediment to biomolecule translocation while graphene may cause obstacles to this process. By combining these two-dimensional materials, nanopores might slow the biomolecule passage. Herein, we fabricated sub-10 nm ultra-thin MoS2-graphene heterostructure nanopores with high stability and tested both dsDNA and native protein (BSA) at the single-molecule level in experiments for the first time. Some special signals with advanced order are observed, which may reflect the shape change of the BSA molecules during the slow translocation process. The results show that the translocation time of BSA is slowed down up to more than 100 ms and the signal length and form are determined by the extent of interaction between the BSA and the heterostructure nanopore. The weak interaction between the BSA and the MoS2 layer increases the translocation probability, and meanwhile, the strong interaction of the graphene layer to BSA slows down the translocation and changes its structure. Therefore, our findings indicate the possibilities of slowing down the single-biomolecule translocation and the capability of acquiring more detailed information about biomolecules using MoS2-graphene heterostructure nanopores.
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Affiliation(s)
- Chaoming Gu
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Zhoubin Yu
- State Key Laboratory of Silicon Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou 310027, P. R. China
| | - Xiaojie Li
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Xin Zhu
- Chemistry Research Laboratory, Oxford University, Oxford, OX1 3TA, UK
| | - Chuanhong Jin
- State Key Laboratory of Silicon Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou 310027, P. R. China
| | - Zhen Cao
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Shurong Dong
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Jikui Luo
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Zhi Ye
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Yang Liu
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
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21
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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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22
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Ivanova KA, Bashkirov PV. Noise in Ultrashort Elastic Membrane Nanotube. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES A: MEMBRANE AND CELL BIOLOGY 2022. [DOI: 10.1134/s1990747822050063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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23
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Yan H, Xi G, Meng H, Fu J, Hu G, Lu Z, Tu J. The Mechanism of Overflow Amplitude in Nanopore Experiments and Its Application in Molecule Detection. J Phys Chem B 2022; 126:9261-9270. [PMID: 36321852 DOI: 10.1021/acs.jpcb.2c06245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The investigation of abnormal experimental phenomena observed in nanopore research improves our understanding of nanopores. In this article, we report and explore the unusual phenomenon that the amplitude of current blockage decreases beyond zero baseline (overflow amplitudes), which was observed in the translocation behavior of 100 bp double-stranded DNA molecules through SiNx nanopores. In our experiments, the overflow amplitude decreases with the increase of salt concentration and also decreases when the dwell time is shortened as the normalized amplitude of the overflow current showed a reduction with the increase of voltage. Upon analyzing the electric double layer meanwhile, the overflow amplitudes were shown to be positively correlated with the depth of the electric double layer and the duration of interaction between biological molecules. The formation of overflow amplitude can be attributed to the double electric layer ionic perturbation and reconfiguration, which are the results of the interaction between the biomolecule and the electric bilayer. The validation of the assumption using biomolecules containing different charges demonstrated that the overflow amplitude increased with the increase of the charge. It was concluded that proteins that pass through the nanopore with different orientation were differentiated based on their different overflow amplitude patterns. The investigation of overflow amplitude helps to enhance the understanding and the performance of nanopores.
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Affiliation(s)
- Han Yan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing210096, China
| | - Guohao Xi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing210096, China
| | - Hao Meng
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing210096, China
| | - Jiye Fu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing210096, China
| | - Gang Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing210096, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing210096, China
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing210096, China
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24
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Leong IW, Kishimoto S, Tsutsui M, Taniguchi M. Interference of electrochemical ion diffusion in nanopore sensing. iScience 2022; 25:105073. [PMID: 36147952 PMCID: PMC9485904 DOI: 10.1016/j.isci.2022.105073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/06/2022] [Accepted: 08/30/2022] [Indexed: 11/14/2022] Open
Abstract
Stable and fast-responding ionic current is a prerequisite for reliable measurements of small objects with a nanopore. Here, we report on the interference of ion diffusion kinetics at liquid-electrode interfaces in nanopore sensing. Using platinum as electrodes, we observed a slow and large decrease in the ionic current through a nanopore in a salt solution suggestive of the considerable influence of the growing impedance at the liquid-metal interfaces via Cottrell diffusion. When detecting nanoparticles, the resistive pulses became weaker following the steady increase in the resistance at the partially polarizable electrodes. The interfacial impedance was also demonstrated to couple with the nanopore chip capacitance thereby degraded the temporal resolution of the ionic current measurements in a time-varying manner. These findings can be useful for choosing the suitable size and material of electrodes for the single-particle and -molecule analyses by ionic current. Ag/AgCl electrodes enable reliable resistive pulse detections of nanoparticles Pt electrodes induce ionic current decay by time via the Cottrell diffusion Cottrell diffusion deteriorates the nanopore sensor temporal resolution
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Affiliation(s)
- Iat Wai Leong
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Shohei Kishimoto
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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25
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Abrao‐Nemeir I, Bentin J, Meyer N, Janot J, Torrent J, Picaud F, Balme S. Investigation of α-Synuclein and Amyloid-β(42)-E22Δ Oligomers Using SiN Nanopore Functionalized with L-Dopa. Chem Asian J 2022; 17:e202200726. [PMID: 36038502 PMCID: PMC9826174 DOI: 10.1002/asia.202200726] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/25/2022] [Indexed: 01/11/2023]
Abstract
Solid-state nanopores are an emerging technology used as a high-throughput, label-free analytical method for the characterization of protein aggregation in an aqueous solution. In this work, we used Levodopamine to coat a silicon nitride nanopore surface that was fabricated through a dielectric breakdown in order to reduce the unspecific adsorption. The coating of inner nanopore wall by investigation of the translocation of heparin. The functionalized nanopore was used to investigate the aggregation of amyloid-β and α-synuclein, two biomarkers of degenerative diseases. In the first application, we demonstrate that the α-synuclein WT is more prone to form dimers than the variant A53T. In the second one, we show for the Aβ(42)-E22Δ (Osaka mutant) that the addition of Aβ(42)-WT monomers increases the polymorphism of oligomers, while the incubation with Aβ(42)-WT fibrils generates larger aggregates.
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Affiliation(s)
- Imad Abrao‐Nemeir
- European Institute of Membranes, UMR5635University of Montpelier, ENCSM CNRSPlace Eugène Bataillon34095Montpellier cedex 5France
| | - Jeremy Bentin
- Laboratory of Nanomedicin, Imagery and Therapeutics, EA4662University hospital center of BesançonUniversity of Bourgogne-Franche-Comté (UFR Sciences et Techniques)16 route de Gray25030BesançonFrance
| | - Nathan Meyer
- European Institute of Membranes, UMR5635University of Montpelier, ENCSM CNRSPlace Eugène Bataillon34095Montpellier cedex 5France,Neurological institute of MontpellierUniversity of Montpellier, INSERM CNRSPlace Eugène Bataillon34095Montpellier cedex 5France
| | - Jean‐Marc Janot
- European Institute of Membranes, UMR5635University of Montpelier, ENCSM CNRSPlace Eugène Bataillon34095Montpellier cedex 5France
| | - Joan Torrent
- Neurological institute of MontpellierUniversity of Montpellier, INSERM CNRSPlace Eugène Bataillon34095Montpellier cedex 5France
| | - Fabien Picaud
- Laboratory of Nanomedicin, Imagery and Therapeutics, EA4662University hospital center of BesançonUniversity of Bourgogne-Franche-Comté (UFR Sciences et Techniques)16 route de Gray25030BesançonFrance
| | - Sebastien Balme
- European Institute of Membranes, UMR5635University of Montpelier, ENCSM CNRSPlace Eugène Bataillon34095Montpellier cedex 5France
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26
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Ensslen T, Sarthak K, Aksimentiev A, Behrends JC. Resolving Isomeric Posttranslational Modifications Using a Biological Nanopore as a Sensor of Molecular Shape. J Am Chem Soc 2022; 144:16060-16068. [PMID: 36007197 DOI: 10.1021/jacs.2c06211] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The chemical nature and precise position of posttranslational modifications (PTMs) in proteins or peptides are crucial for various severe diseases, such as cancer. State-of-the-art PTM diagnosis is based on elaborate and costly mass-spectrometry or immunoassay-based approaches, which are limited in selectivity and specificity. Here, we demonstrate the use of a protein nanopore to differentiate peptides─derived from human histone H4 protein─of identical mass according to the positions of acetylated and methylated lysine residues. Unlike sequencing by stepwise threading, our method detects PTMs and their positions by sensing the shape of a fully entrapped peptide, thus eliminating the need for controlled translocation. Molecular dynamics simulations show that the sensitivity to molecular shape derives from a highly nonuniform electric field along the pore. This molecular shape-sensing principle offers a path to versatile, label-free, and high-throughput characterizations of protein isoforms.
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Affiliation(s)
- Tobias Ensslen
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Kumar Sarthak
- Center for the Physics of Living Cells, Beckman Institute for Advanced Science and Technology and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Center for the Physics of Living Cells, Beckman Institute for Advanced Science and Technology and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
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27
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Huang G, Voorspoels A, Versloot RCA, van der Heide NJ, Carlon E, Willems K, Maglia G. PlyAB Nanopores Detect Single Amino Acid Differences in Folded Haemoglobin from Blood. Angew Chem Int Ed Engl 2022; 61:e202206227. [PMID: 35759385 PMCID: PMC9541544 DOI: 10.1002/anie.202206227] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Indexed: 01/04/2023]
Abstract
The real‐time identification of protein biomarkers is crucial for the development of point‐of‐care and portable devices. Here, we use a PlyAB biological nanopore to detect haemoglobin (Hb) variants. Adult haemoglobin (HbA) and sickle cell anaemia haemoglobin (HbS), which differ by just one amino acid, were distinguished in a mixture with more than 97 % accuracy based on individual blockades. Foetal Hb, which shows a larger sequence variation, was distinguished with near 100 % accuracy. Continuum and Brownian dynamics simulations revealed that Hb occupies two energy minima, one near the inner constriction and one at the trans entry of the nanopore. Thermal fluctuations, the charge of the protein, and the external bias influence the dynamics of Hb within the nanopore, which in turn generates the unique ionic current signal in the Hb variants. Finally, Hb was counted from blood samples, demonstrating that direct discrimination and quantification of Hb from blood using nanopores, is feasible.
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Affiliation(s)
- Gang Huang
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Aderik Voorspoels
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001, Leuven, Belgium
| | | | - Nieck Jordy van der Heide
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Enrico Carlon
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001, Leuven, Belgium
| | | | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
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28
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Lucas FLR, Willems K, Tadema MJ, Tych KM, Maglia G, Wloka C. Unbiased Data Analysis for the Parameterization of Fast Translocation Events through Nanopores. ACS OMEGA 2022; 7:26040-26046. [PMID: 35936408 PMCID: PMC9352258 DOI: 10.1021/acsomega.2c00871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Single-molecule nanopore electrophysiology is an emerging technique for the detection of analytes in aqueous solutions with high sensitivity. These detectors have proven applicable for the enzyme-assisted sequencing of oligonucleotides. There has recently been an increased interest in the use of nanopores for the fingerprinting of peptides and proteins, referred to as single-molecule nanopore spectrometry. However, the analysis of the resulting electrophysiology traces remains complicated due to the fast unassisted translocation of such analytes, usually in the order of micro- to milliseconds, and the small ion current signal produced (in the picoampere range). Here, we present the application of a generalized normal distribution function (gNDF) for the characterization of short-lived ion current signals (blockades). We show that the gNDF can be used to determine if the observed blockades have adequate time to reach their maximum current plateau while also providing a description of each blockade based on the open pore current (I O), the difference caused by the pore blockade (ΔI B), the position in time (μ), the standard deviation (σ), and a shape parameter (β), leaving only the noise component. In addition, this method allows the estimation of an ideal range of low-pass filter frequencies that contains maximum information with minimal noise. In summary, we show a parameter-free and generalized method for the analysis of short-lived ion current blockades, which facilitates single-molecule nanopore spectrometry with minimal user bias.
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Affiliation(s)
- Florian L. R. Lucas
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9712 CP Groningen, The Netherlands
- Lab
for Nanobiology, Department of Chemistry, KU Leuven, 3001 Leuven, Belgium
| | | | - Matthijs J. Tadema
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9712 CP Groningen, The Netherlands
| | - Katarzyna M. Tych
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9712 CP Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9712 CP Groningen, The Netherlands
| | - Carsten Wloka
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9712 CP Groningen, The Netherlands
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29
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Ying C, Ma T, Xu L, Rahmani M. Localized Nanopore Fabrication via Controlled Breakdown. NANOMATERIALS 2022; 12:nano12142384. [PMID: 35889608 PMCID: PMC9323289 DOI: 10.3390/nano12142384] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 12/03/2022]
Abstract
Nanopore sensors provide a unique platform to detect individual nucleic acids, proteins, and other biomolecules without the need for fluorescent labeling or chemical modifications. Solid-state nanopores offer the potential to integrate nanopore sensing with other technologies such as field-effect transistors (FETs), optics, plasmonics, and microfluidics, thereby attracting attention to the development of commercial instruments for diagnostics and healthcare applications. Stable nanopores with ideal dimensions are particularly critical for nanopore sensors to be integrated into other sensing devices and provide a high signal-to-noise ratio. Nanopore fabrication, although having benefited largely from the development of sophisticated nanofabrication techniques, remains a challenge in terms of cost, time consumption and accessibility. One of the latest developed methods—controlled breakdown (CBD)—has made the nanopore technique broadly accessible, boosting the use of nanopore sensing in both fundamental research and biomedical applications. Many works have been developed to improve the efficiency and robustness of pore formation by CBD. However, nanopores formed by traditional CBD are randomly positioned in the membrane. To expand nanopore sensing to a wider biomedical application, controlling the localization of nanopores formed by CBD is essential. This article reviews the recent strategies to control the location of nanopores formed by CBD. We discuss the fundamental mechanism and the efforts of different approaches to confine the region of nanopore formation.
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Affiliation(s)
- Cuifeng Ying
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
- Correspondence:
| | - Tianji Ma
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation & Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, China;
| | - Lei Xu
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
| | - Mohsen Rahmani
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
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30
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Di Muccio G, Morozzo della Rocca B, Chinappi M. Geometrically Induced Selectivity and Unidirectional Electroosmosis in Uncharged Nanopores. ACS NANO 2022; 16:8716-8728. [PMID: 35587777 PMCID: PMC9245180 DOI: 10.1021/acsnano.1c03017] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Selectivity toward positive and negative ions in nanopores is often associated with electroosmotic flow, the control of which is pivotal in several micro-nanofluidic technologies. Selectivity is traditionally understood to be a consequence of surface charges that alter the ion distribution in the pore lumen. Here we present a purely geometrical mechanism to induce ionic selectivity and electroosmotic flow in uncharged nanopores, and we tested it via molecular dynamics simulations. Our approach exploits the accumulation of charges, driven by an external electric field, in a coaxial cavity that decorates the membrane close to the pore entrance. The selectivity was shown to depend on the applied voltage and becomes completely inverted when reversing the voltage. The simultaneous inversion of ionic selectivity and electric field direction causes a unidirectional electroosmotic flow. We developed a quantitatively accurate theoretical model for designing pore geometry to achieve the desired electroosmotic velocity. Finally, we show that unidirectional electroosmosis also occurs in much more complex scenarios, such as a biological pore whose structure presents a coaxial cavity surrounding the pore constriction as well as a complex surface charge pattern. The capability to induce ion selectivity without altering the pore lumen shape or the surface charge may be useful for a more flexible design of selective membranes.
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Affiliation(s)
- Giovanni Di Muccio
- Dipartimento
di Ingegneria Industriale, Università
di Roma Tor Vergata, Via del Politecnico 1, 00133, Rome, Italy
| | - Blasco Morozzo della Rocca
- Dipartimento
di Biologia, Università di Roma Tor
Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Mauro Chinappi
- Dipartimento
di Ingegneria Industriale, Università
di Roma Tor Vergata, Via del Politecnico 1, 00133, Rome, Italy
- E-mail:
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31
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Huang G, Voorspoels A, Versloot RCA, Van Der Heide NJ, Carlon E, Willems K, Maglia G. PlyAB Nanopores Detect Single Amino Acid Differences in Folded Haemoglobin from Blood. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Gang Huang
- University of Groningen: Rijksuniversiteit Groningen Chemical Biology NETHERLANDS
| | - Aderik Voorspoels
- KU Leuven: Katholieke Universiteit Leuven Soft Matter and Biophysics BELGIUM
| | | | | | - Enrico Carlon
- KU Leuven University: Katholieke Universiteit Leuven Soft Matter and Biophysics NETHERLANDS
| | - Kherim Willems
- Imec Integrated photonics for microscopy and biomedical imaging BELGIUM
| | - Giovanni Maglia
- Rijksuniversiteit Groningen Chemical Biology Nijenborgh 7 9747 AG Groningen NETHERLANDS
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32
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Wei G, Hu R, Li Q, Lu W, Liang H, Nan H, Lu J, Li J, Zhao Q. Oligonucleotide Discrimination Enabled by Tannic Acid-Coordinated Film-Coated Solid-State Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:6443-6453. [PMID: 35544765 DOI: 10.1021/acs.langmuir.2c00638] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Discrimination of nucleotides serves as the basis for DNA sequencing using solid-state nanopores. However, the translocation of DNA is usually too fast to be detected, not to mention nucleotide discrimination. Here, we utilized polyphenolic TA and Fe3+, an attractive metal-organic thin film, and achieved a fast and robust surface coating for silicon nitride nanopores. The hydrophilic coating layer can greatly reduce the low-frequency noise of an original unstable nanopore, and the nanopore size can be finely tuned in situ at the nanoscale by simply adjusting the relative ratio of Fe3+ and TA monomers. Moreover, the hydrogen bonding interaction formed between the hydroxyl groups provided by TA and the phosphate groups of DNAs significantly increases the residence time of a short double-strand (100 bp) DNA. More importantly, we take advantage of the different strengths of hydrogen bonding interactions between the hydroxyl groups provided by TA and the analytes to discriminate between two oligonucleotide samples (oligodeoxycytidine and oligodeoxyadenosine) with similar sizes and lengths, of which the current signal patterns are significantly different using the coated nanopore. The results shed light on expanding the biochemical functionality of surface coatings on solid-state nanopores for future biomedical applications.
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Affiliation(s)
- Guanghao Wei
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-Optoelectronics, School of Physics, Peking University, Beijing 100871, China
| | - Rui Hu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-Optoelectronics, School of Physics, Peking University, Beijing 100871, China
| | - Qiuhui Li
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-Optoelectronics, School of Physics, Peking University, Beijing 100871, China
| | - Wenlong Lu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-Optoelectronics, School of Physics, Peking University, Beijing 100871, China
| | - Hanyu Liang
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Zhejiang, 310022 Hangzhou, China
| | - Hexin Nan
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Zhejiang, 310022 Hangzhou, China
| | - Jing Lu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-Optoelectronics, School of Physics, Peking University, Beijing 100871, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, 226010 Jiangsu, China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, China
| | - Juan Li
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Zhejiang, 310022 Hangzhou, China
| | - Qing Zhao
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-Optoelectronics, School of Physics, Peking University, Beijing 100871, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, 226010 Jiangsu, China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, China
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Abstract
Despite tremendous gains over the past decade, methods for characterizing proteins have generally lagged behind those for nucleic acids, which are characterized by extremely high sensitivity, dynamic range, and throughput. However, the ability to directly characterize proteins at nucleic acid levels would address critical biological challenges such as more sensitive medical diagnostics, deeper protein quantification, large-scale measurement, and discovery of alternate protein isoforms and modifications and would open new paths to single-cell proteomics. In response to this need, there has been a push to radically improve protein sequencing technologies by taking inspiration from high-throughput nucleic acid sequencing, with a particular focus on developing practical methods for single-molecule protein sequencing (SMPS). SMPS technologies fall generally into three categories: sequencing by degradation (e.g., mass spectrometry or fluorosequencing), sequencing by transit (e.g., nanopores or quantum tunneling), and sequencing by affinity (as in DNA hybridization-based approaches). We describe these diverse approaches, which range from those that are already experimentally well-supported to the merely speculative, in this nascent field striving to reformulate proteomics.
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Affiliation(s)
- Brendan M Floyd
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, Texas, USA; ,
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, Texas, USA; ,
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34
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Abrao-Nemeir I, Zaki O, Meyer N, Lepoitevin M, Torrent J, Janot JM, Balme S. Combining ionic diode, resistive pulse and membrane for detection and separation of anti-CD44 antibody. J Memb Sci 2022. [DOI: 10.1016/j.memsci.2022.120391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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35
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Ying C, Houghtaling J, Mayer M. Effects of off-axis translocation through nanopores on the determination of shape and volume estimates for individual particles. NANOTECHNOLOGY 2022; 33:275501. [PMID: 35320779 DOI: 10.1088/1361-6528/ac6087] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Resistive pulses generated by nanoparticles that translocate through a nanopore contain multi-parametric information about the physical properties of those particles. For example, non-spherical particles sample several different orientations during translocation, producing fluctuations in blockade current that relate to their shape. Due to the heterogenous distribution of electric field from the center to the wall of a nanopore while a particle travels through the pore, its radial position influences the blockade current, thereby affecting the quantification of parameters related to the particle's characteristics. Here, we investigate the influence of these off-axis effects on parameters estimated by performing finite element simulations of dielectric particles transiting a cylindrical nanopore. We varied the size, ellipsoidal shape, and radial position of individual particles, as well as the size of the nanopore. As expected, nanoparticles translocating near the nanopore wall produce increase current blockades, resulting in overestimates of particle volume. We demonstrated that off-axis effects also influence estimates of shape determined from resistive pulse analyses, sometimes producing a multiple-fold deviation in ellipsoidal length-to-diameter ratio between estimates and reference values. By using a nanopore with the minimum possible diameter that still allows the particle to rotate while translocating, off-axis effects on the determination of both volume and shape can be minimized. In addition, tethering the nanoparticles to a fluid coating on the nanopore wall makes it possible to determine an accurate particle shape with an overestimated volume. This work provides a framework to select optimal ratios of nanopore to nanoparticle size for experiments targeting free translocations.
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Affiliation(s)
- Cuifeng Ying
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham, United Kingdom
| | - Jared Houghtaling
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
| | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
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36
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Identification of plasmon-driven nanoparticle-coalescence-dominated growth of gold nanoplates through nanopore sensing. Nat Commun 2022; 13:1402. [PMID: 35301326 PMCID: PMC8931024 DOI: 10.1038/s41467-022-29123-9] [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: 09/14/2021] [Accepted: 03/01/2022] [Indexed: 11/09/2022] Open
Abstract
The fascinating phenomenon that plasmon excitation can convert isotropic silver nanospheres to anisotropic nanoprisms has already been developed into a general synthetic technique since the discovery in 2001. However, the mechanism governing the morphology conversion is described with different reaction processes. So far, the mechanism based on redox reactions dominated anisotropic growth by plasmon-produced hot carriers is widely accepted and developed. Here, we successfully achieved plasmon-driven high yield conversion of gold nanospheres into nanoplates with iodine as the inducer. To investigate the mechanism, nanopore sensing technology is established to statistically study the intermediate species at the single-nanoparticle level. Surprisingly, the morphology conversion is proved as a hot hole-controlled coalescence-dominated growth process. This work conclusively elucidates that a controllable plasmon-driven nanoparticle-coalescence mechanism could enable the production of well-defined anisotropic metal nanostructures and suggests that the nanopore sensing could be of general use for studying the growth process of nanomaterials.
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37
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Zhao Y, Iarossi M, De Fazio AF, Huang JA, De Angelis F. Label-Free Optical Analysis of Biomolecules in Solid-State Nanopores: Toward Single-Molecule Protein Sequencing. ACS PHOTONICS 2022; 9:730-742. [PMID: 35308409 PMCID: PMC8931763 DOI: 10.1021/acsphotonics.1c01825] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Sequence identification of peptides and proteins is central to proteomics. Protein sequencing is mainly conducted by insensitive mass spectroscopy because proteins cannot be amplified, which hampers applications such as single-cell proteomics and precision medicine. The commercial success of portable nanopore sequencers for single DNA molecules has inspired extensive research and development of single-molecule techniques for protein sequencing. Among them, three challenges remain: (1) discrimination of the 20 amino acids as building blocks of proteins; (2) unfolding proteins; and (3) controlling the motion of proteins with nonuniformly charged sequences. In this context, the emergence of label-free optical analysis techniques for single amino acids and peptides by solid-state nanopores shows promise for addressing the first challenge. In this Perspective, we first discuss the current challenges of single-molecule fluorescence detection and nanopore resistive pulse sensing in a protein sequencing. Then, label-free optical methods are described to show how they address the single-amino-acid identification within single peptides. They include localized surface plasmon resonance detection and surface-enhanced Raman spectroscopy on plasmonic nanopores. Notably, we report new data to show the ability of plasmon-enhanced Raman scattering to record and discriminate the 20 amino acids at a single-molecule level. In addition, we discuss briefly the manipulation of molecule translocation and liquid flow in plasmonic nanopores for controlling molecule movement to allow high-resolution reading of protein sequences. We envision that a combination of Raman spectroscopy with plasmonic nanopores can succeed in single-molecule protein sequencing in a label-free way.
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Affiliation(s)
- Yingqi Zhao
- Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Marzia Iarossi
- Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | | | - Jian-An Huang
- Faculty
of Medicine, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 5 A, 90220 Oulu, Finland
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38
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Wu J, Liang L, Zhang M, Zhu R, Wang Z, Yin Y, Yin B, Weng T, Fang S, Xie W, Wang L, Wang D. Single-Molecule Identification of the Conformations of Human C-Reactive Protein and Its Aptamer Complex with Solid-State Nanopores. ACS APPLIED MATERIALS & INTERFACES 2022; 14:12077-12088. [PMID: 35234028 DOI: 10.1021/acsami.2c00453] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Human C-reactive protein (CRP) is an established inflammatory biomarker and was proved to be potentially relevant to disease pathology and cancer progression. A large body of methodologies have been reported for CRP analysis, including electrochemical/optical biosensors, aptamer, or antibody-based detection. Although the detection limit is rather low until pg/uL, most of which are time-consuming and relatively expensive, and few of them provided CRP single-molecule information. This work demonstrated the nanopore-based approach for the characterization of CRP conformation under versatile conditions. With an optimized pore of 14 nm in diameter, we achieved the detection limit as low as 0.3 ng/μL, voltage polarity significantly influences the electro-osmotic force and CRP translocation behavior, and the pentameric conformation of CRP may dissociate into pro-inflammatory CRP isoforms and monomeric CRP at bias potential above 300 mV. CRP tends to translocate through nanopores faster along with the increase in pH values, due to more surface charge on both CRP and pore inner wall and stronger electro-osmotic force. The CRP could specifically bind with its aptamer of different concentrations to form complexes, and the complexes exhibited distinguishable nanopore translocation behavior compared with CRP alone. The variation of the molar ratio of aptamer significantly influences the orientation of CRP translocation. The plasma test under physiological conditions displayed the ability of the nanopore system on the CRP identification with a concentration of 3 ng/μL.
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Affiliation(s)
- Ji Wu
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Liyuan Liang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Mingkun Zhang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Rui Zhu
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Zhong Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Yajie Yin
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Bohua Yin
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Ting Weng
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Shaoxi Fang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Wanyi Xie
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Liang Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Deqiang Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
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39
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Rivas F, DeAngelis PL, Rahbar E, Hall AR. Optimizing the sensitivity and resolution of hyaluronan analysis with solid-state nanopores. Sci Rep 2022; 12:4469. [PMID: 35296752 PMCID: PMC8927330 DOI: 10.1038/s41598-022-08533-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/03/2022] [Indexed: 11/09/2022] Open
Abstract
Hyaluronan (HA) is an essential carbohydrate in vertebrates that is a potentially robust bioindicator due to its critical roles in diverse physiological functions in health and disease. The intricate size-dependent function that exists for HA and its low abundance in most biological fluids have highlighted the need for sensitive technologies to provide accurate and quantitative assessments of polysaccharide molecular weight and concentration. We have demonstrated that solid state (SS-) nanopore technology can be exploited for this purpose, given its molecular sensitivity and analytical capacity, but there remains a need to further understand the impacts of experimental variables on the SS-nanopore signal for optimal interpretation of results. Here, we use model quasi-monodisperse HA polymers to determine the dependence of HA signal characteristics on a range of SS-nanopore measurement conditions, including applied voltage, pore diameter, and ionic buffer asymmetry. Our results identify important factors for improving the signal-to-noise ratio, resolution, and sensitivity of HA analysis with SS-nanopores.
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Affiliation(s)
- Felipe Rivas
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, 27101, USA
| | - Paul L DeAngelis
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma, OK, 73104, USA
| | - Elaheh Rahbar
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, 27101, USA
| | - Adam R Hall
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, 27101, USA. .,Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.
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40
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Modifying the pH sensitivity of OmpG nanopore for improved detection at acidic pH. Biophys J 2022; 121:731-741. [PMID: 35131293 PMCID: PMC8943698 DOI: 10.1016/j.bpj.2022.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 01/02/2022] [Accepted: 01/25/2022] [Indexed: 11/22/2022] Open
Abstract
The outer membrane protein G (OmpG) nanopore is a monomeric β-barrel channel consisting of seven flexible extracellular loops. Its most flexible loop, loop 6, can be used to host high-affinity binding ligands for the capture of protein analytes, which induces characteristic current patterns for protein identification. At acidic pH, the ability of OmpG to detect protein analytes is hampered by its tendency toward the closed state, which renders the nanopore unable to reveal current signal changes induced by bound analytes. In this work, critical residues that control the pH-dependent gating of loop 6 were identified, and an OmpG nanopore that can stay predominantly open at a broad range of pHs was created by mutating these pH-sensitive residues. A short single-stranded DNA was chemically tethered to the pH-insensitive OmpG to demonstrate the utility of the OmpG nanopore for sensing complementary DNA and a DNA binding protein at an acidic pH.
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41
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Xia Z, Lin CY, Drndić M. Protein-enabled detection of ibuprofen and sulfamethoxazole using solid-state nanopores. Proteomics 2022; 22:e2100071. [PMID: 34974637 DOI: 10.1002/pmic.202100071] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 02/01/2023]
Abstract
Enabled by proteins, we present an all-electrical method for rapid detection of small pharmaceuticals (ibuprofen and sulfamethoxazole [SMZ]) in aqueous media using silicon nitride pores. Specifically, we use carrier proteins, bovine serum albumin (BSA), and take advantage of their interactions with two small drug molecules to form BSA-drug complexes which can be detected by nm-diameter pores, thereby confirming the presence of small pharmaceuticals. We demonstrate detection of ibuprofen and SMZ at concentrations down to 100 nM (∼21 μg/L) and 48.5 nM (12 μg/L), respectively. We observe changes in electrical signal characteristics (reflected in event durations, rates, current magnitudes, and estimated particle diameters) of BSA-drug complexes compared to BSA-only, and differences between these two small pharmaceuticals, possibly paving a path toward developing selective sensors by identifying "electrical fingerprints" of these molecules in the future. These distinct electrical signals are likely a combined result of diffusion, electrophoretic and electroosmotic effects, interactions between the pore and particles, which depend on pore diameters, pH, and the resulting surface charges. The use of single-molecule-counting nanopores allows sensing of small pharmaceuticals, studies of protein conformational changes, and may aid in efforts to evaluate the impact of small drug molecules on aquatic and human life.
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Affiliation(s)
- Zehui Xia
- Goeppert LLC, Philadelphia, Pennsylvania, USA
| | - Chih-Yuan Lin
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marija Drndić
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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42
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Cairns-Gibson DF, Cockroft SL. Functionalised nanopores: chemical and biological modifications. Chem Sci 2022; 13:1869-1882. [PMID: 35308845 PMCID: PMC8848921 DOI: 10.1039/d1sc05766a] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/22/2021] [Indexed: 12/11/2022] Open
Abstract
Nanopore technology has established itself as a powerful tool for single-molecule studies. By analysing changes in the ion current flowing through a single transmembrane channel, a wealth of molecular information can be elucidated. Early studies utilised nanopore technology for sensing applications, and subsequent developments have diversified its remit. Nanopores can be synthetic, solid-state, or biological in origin, but recent work has seen these boundaries blurred as hybrid functionalised pores emerge. The modification of existing pores and the construction of novel synthetic pores has been an enticing goal for creating systems with tailored properties and functionality. Here, we explore chemically functionalised biological pores and the bio-inspired functionalisation of solid-state pores, highlighting how the convergence of these domains provides enhanced functionality. The convergence of chemistry, biology, and solid-state approaches enables the construction hybrid nanopores with enhanced single-molecule applications.![]()
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Affiliation(s)
- Dominic F. Cairns-Gibson
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
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43
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Fu J, Wu L, Hu G, Li F, Ge Q, Lu Z, Tu J. Solid-state nanopore analysis on the conformation change of DNA polymerase I induced by a DNA substrate. Analyst 2022; 147:3087-3095. [DOI: 10.1039/d2an00567k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We studied the conformational changes between a Klenow fragment and its monomer complex with a DNA substrate using a SiN nanopore and found that the monomer complex has a tighter structure and transports slower.
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Affiliation(s)
- Jiye Fu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Linlin Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Gang Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Fuyao Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
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44
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Leong IW, Tsutsui M, Yokota K, Taniguchi M. Salt Gradient Control of Translocation Dynamics in a Solid-State Nanopore. Anal Chem 2021; 93:16700-16708. [PMID: 34860500 DOI: 10.1021/acs.analchem.1c04342] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tuning capture rates and translocation time of analytes in solid-state nanopores are one of the major challenges for their use in detecting and analyzing individual nanoscale objects via ionic current measurements. Here, we report on the use of salt gradient for the fine control of capture-to-translocation dynamics in 300 nm sized SiNx nanopores. We demonstrated a decrease up to a factor of 3 in the electrophoretic speed of nanoparticles at the pore exit along with an over 3-fold increase in particle detection efficiency by subjecting a 5-fold ion concentration difference across the dielectric membrane. The improvement in the sensor performance was elucidated to be a result of the salt-gradient-mediated electric field and electroosmotic flow asymmetry at nanochannel orifices. The present findings can be used to enhance nanopore sensing capability for detecting biomolecules such as amyloids and proteins.
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Affiliation(s)
- Iat Wai Leong
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Kazumichi Yokota
- National Institute of Advanced Industrial Science and Technology, Takamatsu, Kagawa 761-0395, Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
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45
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Meyer N, Abrao-Nemeir I, Janot JM, Torrent J, Lepoitevin M, Balme S. Solid-state and polymer nanopores for protein sensing: A review. Adv Colloid Interface Sci 2021; 298:102561. [PMID: 34768135 DOI: 10.1016/j.cis.2021.102561] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/29/2021] [Accepted: 10/31/2021] [Indexed: 01/15/2023]
Abstract
In two decades, the solid state and polymer nanopores became attractive method for the protein sensing with high specificity and sensitivity. They also allow the characterization of conformational changes, unfolding, assembly and aggregation as well the following of enzymatic reaction. This review aims to provide an overview of the protein sensing regarding the technique of detection: the resistive pulse and ionic diodes. For each strategy, we report the most significant achievement regarding the detection of peptides and protein as well as the conformational change, protein-protein assembly and aggregation process. We discuss the limitations and the recent strategies to improve the nanopore resolution and accuracy. A focus is done about concomitant problematic such as protein adsorption and nanopore lifetime.
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46
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Carlsen A, Tabard-Cossa V. Mapping shifts in nanopore signal to changes in protein and protein-DNA conformation. Proteomics 2021; 22:e2100068. [PMID: 34845853 DOI: 10.1002/pmic.202100068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/28/2021] [Accepted: 11/12/2021] [Indexed: 11/08/2022]
Abstract
Solid-state nanopores have been used extensively in biomolecular studies involving DNA and proteins. However, the interpretation of signals generated by the translocation of proteins or protein-DNA complexes remains challenging. Here, we investigate the behavior of monovalent streptavidin and the complex it forms with short biotinylated DNA over a range of nanopore sizes, salts, and voltages. We describe a simple geometric model that is broadly applicable and employ it to explain observed variations in conductance blockage and dwell time with experimental conditions. The general approach developed here underscores the value of nanopore-based protein analysis and represents progress toward the interpretation of complex translocation signals.
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Affiliation(s)
- Autumn Carlsen
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
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47
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Yang W, van Dijk M, Primavera C, Dekker C. FIB-milled plasmonic nanoapertures allow for long trapping times of individual proteins. iScience 2021; 24:103237. [PMID: 34746702 PMCID: PMC8551080 DOI: 10.1016/j.isci.2021.103237] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/15/2021] [Accepted: 10/04/2021] [Indexed: 11/18/2022] Open
Abstract
We have developed a fabrication methodology for label-free optical trapping of individual nanobeads and proteins in inverted-bowtie-shaped plasmonic gold nanopores. Arrays of these nanoapertures can be reliably produced using focused ion beam (FIB) milling with gap sizes of 10–20 nm, single-nanometer variation, and with a remarkable stability that allows for repeated use. We employ an optical readout where the presence of the protein entering the trap is marked by an increase in the transmission of light through the nanoaperture from the shift of the plasmonic resonance. In addition, the optical trapping force of the plasmonic nanopores allows 20-nm polystyrene beads and proteins, such as beta-amylase and Heat Shock Protein (HSP90), to be trapped for very long times (approximately minutes). On demand, we can release the trapped molecule for another protein to be interrogated. Our work opens up new routes to acquire information on the conformation and dynamics of individual proteins. We demonstrate fabrication of arrays of inverted-bowtie-shaped plasmonic gold nanopores Arrays (>64) of bowties with 10 to 20-nm size gap and single-nanometer variation can be produced We optically tweeze and detect single 20-nm polystyrene beads and individual proteins Our system allows for long observations (approximately minutes) of protein dynamics
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Affiliation(s)
- Wayne Yang
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Madeleine van Dijk
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Christian Primavera
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Cees Dekker
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
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48
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Liu Y, Pan T, Wang K, Wang Y, Yan S, Wang L, Zhang S, Du X, Jia W, Zhang P, Chen H, Huang S. Allosteric Switching of Calmodulin in a
Mycobacterium smegmatis
porin A (MspA) Nanopore‐Trap. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Tiezheng Pan
- School of Life Sciences Northwestern Polytechnical University 710072 Xi'an China
| | - Kefan Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Hong‐Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
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49
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Liu Y, Pan T, Wang K, Wang Y, Yan S, Wang L, Zhang S, Du X, Jia W, Zhang P, Chen HY, Huang S. Allosteric Switching of Calmodulin in a Mycobacterium smegmatis porin A (MspA) Nanopore-Trap. Angew Chem Int Ed Engl 2021; 60:23863-23870. [PMID: 34449124 DOI: 10.1002/anie.202110545] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/21/2021] [Indexed: 01/23/2023]
Abstract
Recent developments concerning large protein nanopores suggest a new approach to structure profiling of native folded proteins. In this work, the large vestibule of Mycobacterium smegmatis porin A (MspA) and calmodulin (CaM), a Ca2+ -binding protein, were used in the direct observation of the protein structure. Three conformers, including the Ca2+ -free, Ca2+ -bound, and target peptide-bound states of CaM, were unambiguously distinguished. A disease related mutant, CaM D129G was also discriminated by MspA, revealing how a single amino acid replacement can interfere with the Ca2+ -binding capacity of the whole protein. The binding capacity and aggregation effect of CaM induced by different ions (Mg2+ /Sr2+ /Ba2+ /Ca2+ /Pb2+ /Tb3+ ) were also investigated and the stability of MspA in extreme conditions was evaluated. This work demonstrates the most systematic single-molecule investigation of different allosteric conformers of CaM, acknowledging the high sensing resolution offered by the MspA nanopore trap.
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Affiliation(s)
- Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Tiezheng Pan
- School of Life Sciences, Northwestern Polytechnical University, 710072, Xi'an, China
| | - Kefan Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
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de Lannoy C, Lucas FLR, Maglia G, de Ridder D. In silico assessment of a novel single-molecule protein fingerprinting method employing fragmentation and nanopore detection. iScience 2021; 24:103202. [PMID: 34703997 PMCID: PMC8521182 DOI: 10.1016/j.isci.2021.103202] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/10/2021] [Accepted: 09/28/2021] [Indexed: 10/28/2022] Open
Abstract
The identification of proteins at the single-molecule level would open exciting new venues in biological research and disease diagnostics. Previously, we proposed a nanopore-based method for protein identification called chop-n-drop fingerprinting, in which the fragmentation pattern induced and measured by a proteasome-nanopore construct is used to identify single proteins. In the simulation study presented here, we show that 97.1% of human proteome constituents are uniquely identified under close to ideal measuring circumstances, using a simple alignment-based classification method. We show that our method is robust against experimental error, as 69.4% can still be identified if the resolution is twice as low as currently attainable, and 10% of proteasome restriction sites and protein fragments are randomly ignored. Based on these results and our experimental proof of concept, we argue that chop-n-drop fingerprinting has the potential to make cost-effective single-molecule protein identification feasible in the near future.
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Affiliation(s)
- Carlos de Lannoy
- Bioinformatics Group, Wageningen University, 6708PB Wageningen, The Netherlands
| | | | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747AG Groningen, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, 6708PB Wageningen, The Netherlands
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