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Ju H, Cheng L, Li M, Mei K, He S, Jia C, Guo X. Single-Molecule Electrical Profiling of Peptides and Proteins. Adv Sci (Weinh) 2024:e2401877. [PMID: 38639403 DOI: 10.1002/advs.202401877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/03/2024] [Indexed: 04/20/2024]
Abstract
In recent decades, there has been a significant increase in the application of single-molecule electrical analysis platforms in studying proteins and peptides. These advanced analysis methods have the potential for deep investigation of enzymatic working mechanisms and accurate monitoring of dynamic changes in protein configurations, which are often challenging to achieve in ensemble measurements. In this work, the prominent research progress in peptide and protein-related studies are surveyed using electronic devices with single-molecule/single-event sensitivity, including single-molecule junctions, single-molecule field-effect transistors, and nanopores. In particular, the successful commercial application of nanopores in DNA sequencing has made it one of the most promising techniques in protein sequencing at the single-molecule level. From single peptides to protein complexes, the correlation between their electrical characteristics, structures, and biological functions is gradually being established. This enables to distinguish different molecular configurations of these biomacromolecules through real-time electrical monitoring of their life activities, significantly improving the understanding of the mechanisms underlying various life processes.
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Affiliation(s)
- Hongyu Ju
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Li Cheng
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Mengmeng Li
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Kunrong Mei
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Suhang He
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Chuancheng Jia
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Xuefeng Guo
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
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Eisenhauer K, Weber W, Kemp P, Gebhardt C, Kaufmann M, Tewes N, Zhdanova H, Tietze A, Rauh O, Stein V. Scaling the Functional Nanopore (FuN) Screen: Systematic Evaluation of Self-Assembling Membrane Peptides and Extension with a K +-Responsive Fluorescent Protein Sensor. ACS Synth Biol 2024; 13:1382-1392. [PMID: 38598783 DOI: 10.1021/acssynbio.3c00671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
The functional analysis of protein nanopores is typically conducted in planar lipid bilayers or liposomes exploiting high-resolution but low-throughput electrical and optical read-outs. Yet, the reconstitution of protein nanopores in vitro still constitutes an empiric and low-throughput process. Addressing these limitations, nanopores can now be analyzed using the functional nanopore (FuN) screen exploiting genetically encoded fluorescent protein sensors that resolve distinct nanopore-dependent Ca2+ in- and efflux patterns across the inner membrane of Escherichia coli. With a primary proof-of-concept established for the S2168 holin, and thereof based recombinant nanopore assemblies, the question arises to what extent alternative nanopores can be analyzed with the FuN screen and to what extent alternative fluorescent protein sensors can be adapted. Focusing on self-assembling membrane peptides, three sets of 13 different nanopores are assessed for their capacity to form nanopores in the context of the FuN screen. Nanopores tested comprise both natural and computationally designed nanopores. Further, the FuN screen is extended to K+-specific fluorescent protein sensors and now provides a capacity to assess the specificity of a nanopore or ion channel. Finally, a comparison to high-resolution biophysical and electrophysiological studies in planar lipid bilayers provides an experimental benchmark for future studies.
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Affiliation(s)
- Klara Eisenhauer
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany
| | - Wadim Weber
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany
| | - Philipp Kemp
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany
| | - Carolin Gebhardt
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany
| | - Marwan Kaufmann
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany
| | - Noel Tewes
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany
| | - Hanna Zhdanova
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 412 96 Göteborg, Sweden
| | - Alesia Tietze
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 412 96 Göteborg, Sweden
| | - Oliver Rauh
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany
| | - Viktor Stein
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany
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Xu S, Wang G, Feng Y, Zheng J, Huang L, Wang Y, Liu N. Silica Nanowires-Filled Glass Microporous Sensor for the Ultrasensitive Detection of Deoxyribonucleic Acid. ACS Sens 2024. [PMID: 38632929 DOI: 10.1021/acssensors.4c00072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
DNA carries genetic information and can serve as an important biomarker for the early diagnosis and assessment of the disease prognosis. Here, we propose a bottom-up assembly method for a silica nanowire-filled glass microporous (SiNWs@GMP) sensor and develop a universal sensing platform for the ultrasensitive and specific detection of DNA. The three-dimensional network structure formed by SiNWs provides them with highly abundant and accessible binding sites, allowing for the immobilization of a large amount of capture probe DNA, thereby enabling more target DNA to hybridize with the capture probe DNA to improve detection performance. Therefore, the SiNWs@GMP sensor achieves ultrasensitive detection of target DNA. In the detection range of 1 aM to 100 fM, there is a good linear relationship between the decrease rate of current signal and the concentration of target DNA, and the detection limit is as low as 1 aM. The developed SiNWs@GMP sensor can distinguish target DNA sequences that are 1-, 3-, and 5-mismatched, and specifically recognize target DNA from complex mixed solution. Furthermore, based on this excellent selectivity and specificity, we validate the universality of this sensing strategy by detecting DNA (H1N1 and H5N1) sequences associated with the avian influenza virus. By replacing the types of nucleic acid aptamers, it is expected to achieve a wide range and low detection limit sensitive detection of various biological molecules. The results indicate that the developed universal sensing platform has ultrahigh sensitivity, excellent selectivity, stability, and acceptable reproducibility, demonstrating its potential application in DNA bioanalysis.
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Affiliation(s)
- Shiwei Xu
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Guofeng Wang
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Yueyue Feng
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Juanjuan Zheng
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Liying Huang
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Yajun Wang
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Nannan Liu
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
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Rabolli CP, Naarmann-de Vries IS, Makarewich CA, Baskin KK, Dieterich C, Accornero F. Nanopore Detection of METTL3-Dependent m6A-Modified mRNA Reveals a New Mechanism Regulating Cardiomyocyte Mitochondrial Metabolism. Circulation 2024; 149:1319-1322. [PMID: 38620081 DOI: 10.1161/circulationaha.123.066473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Affiliation(s)
- Charles P Rabolli
- Departments of Physiology and Cell Biology (C.P.R., K.K.B., F.A.), The Ohio State University, Columbus
- Biomedical Engineering (C.P.R.), The Ohio State University, Columbus
- Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University Wexner Medical Center, Columbus (C.P.R., K.K.B., F.A.)
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI (C.P.R., F.A.)
| | - Isabel S Naarmann-de Vries
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology (I.S.N.-d.V., C.D.), University Hospital Heidelberg, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology; I.S.N.-d.V., C.D.), University Hospital Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany (I.S.N.-d.V., C.D.)
| | - Catherine A Makarewich
- The Heart Institute, Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, OH (C.A.M.)
- Department of Pediatrics, University of Cincinnati College of Medicine, OH (C.A.M.)
| | - Kedryn K Baskin
- Departments of Physiology and Cell Biology (C.P.R., K.K.B., F.A.), The Ohio State University, Columbus
- Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University Wexner Medical Center, Columbus (C.P.R., K.K.B., F.A.)
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology (I.S.N.-d.V., C.D.), University Hospital Heidelberg, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology; I.S.N.-d.V., C.D.), University Hospital Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany (I.S.N.-d.V., C.D.)
| | - Federica Accornero
- Departments of Physiology and Cell Biology (C.P.R., K.K.B., F.A.), The Ohio State University, Columbus
- Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University Wexner Medical Center, Columbus (C.P.R., K.K.B., F.A.)
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI (C.P.R., F.A.)
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Zhang M, Tang C, Wang Z, Chen S, Zhang D, Li K, Sun K, Zhao C, Wang Y, Xu M, Dai L, Lu G, Shi H, Ren H, Chen L, Geng J. Real-time detection of 20 amino acids and discrimination of pathologically relevant peptides with functionalized nanopore. Nat Methods 2024; 21:609-618. [PMID: 38443507 PMCID: PMC11009107 DOI: 10.1038/s41592-024-02208-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/12/2024] [Indexed: 03/07/2024]
Abstract
Precise identification and quantification of amino acids is crucial for many biological applications. Here we report a copper(II)-functionalized Mycobacterium smegmatis porin A (MspA) nanopore with the N91H substitution, which enables direct identification of all 20 proteinogenic amino acids when combined with a machine-learning algorithm. The validation accuracy reaches 99.1%, with 30.9% signal recovery. The feasibility of ultrasensitive quantification of amino acids was also demonstrated at the nanomolar range. Furthermore, the capability of this system for real-time analyses of two representative post-translational modifications (PTMs), one unnatural amino acid and ten synthetic peptides using exopeptidases, including clinically relevant peptides associated with Alzheimer's disease and cancer neoantigens, was demonstrated. Notably, our strategy successfully distinguishes peptides with only one amino acid difference from the hydrolysate and provides the possibility to infer the peptide sequence.
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Affiliation(s)
- Ming Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Chao Tang
- Biosafety Laboratory of West China Hospital, West China Hospital, Sichuan University, Chengdu, China
| | - Zichun Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Shanchuan Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Dan Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Kaiju Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ke Sun
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Changjian Zhao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Mengying Xu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Guangwen Lu
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Hubing Shi
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Haiyan Ren
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China
| | - Lu Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China.
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China.
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu, China.
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Sarasa-Buisan C, Nieves-Morión M, Arévalo S, Helm RF, Sevilla E, Luque I, Fillat MF. FurC (PerR) contributes to the regulation of peptidoglycan remodeling and intercellular molecular transfer in the cyanobacterium Anabaena sp. strain PCC 7120. mBio 2024; 15:e0323123. [PMID: 38334377 PMCID: PMC10936207 DOI: 10.1128/mbio.03231-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/09/2024] [Indexed: 02/10/2024] Open
Abstract
Microbial extracellular proteins and metabolites provide valuable information concerning how microbes adapt to changing environments. In cyanobacteria, dynamic acclimation strategies involve a variety of regulatory mechanisms, being ferric uptake regulator proteins as key players in this process. In the nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120, FurC (PerR) is a global regulator that modulates the peroxide response and several genes involved in photosynthesis and nitrogen metabolism. To investigate the possible role of FurC in shaping the extracellular environment of Anabaena, the analysis of the extracellular metabolites and proteins of a furC-overexpressing variant was compared to that of the wild-type strain. There were 96 differentially abundant proteins, 78 of which were found for the first time in the extracellular fraction of Anabaena. While these proteins belong to different functional categories, most of them are predicted to be secreted or have a peripheral location. Several stress-related proteins, including PrxA, flavodoxin, and the Dps homolog All1173, accumulated in the exoproteome of furC-overexpressing cells, while decreased levels of FurA and a subset of membrane proteins, including several export proteins and amiC gene products, responsible for nanopore formation, were detected. Direct repression by FurC of some of those genes, including amiC1 and amiC2, could account for odd septal nanopore formation and impaired intercellular molecular transfer observed in the furC-overexpressing variant. Assessment of the exometabolome from both strains revealed the release of two peptidoglycan fragments in furC-overexpressing cells, namely 1,6-anhydro-N-acetyl-β-D-muramic acid (anhydroMurNAc) and its associated disaccharide (β-D-GlcNAc-(1-4)-anhydroMurNAc), suggesting alterations in peptidoglycan breakdown and recycling.IMPORTANCECyanobacteria are ubiquitous photosynthetic prokaryotes that can adapt to environmental stresses by modulating their extracellular contents. Measurements of the organization and composition of the extracellular milieu provide useful information about cyanobacterial adaptive processes, which can potentially lead to biomimetic approaches to stabilizing biological systems to adverse conditions. Anabaena sp. strain PCC 7120 is a multicellular, nitrogen-fixing cyanobacterium whose intercellular molecular exchange is mediated by septal junctions that traverse the septal peptidoglycan through nanopores. FurC (PerR) is an essential transcriptional regulator in Anabaena, which modulates the response to several stresses. Here, we show that furC-overexpressing cells result in a modified exoproteome and the release of peptidoglycan fragments. Phenotypically, important alterations in nanopore formation and cell-to-cell communication were observed. Our results expand the roles of FurC to the modulation of cell-wall biogenesis and recycling, as well as in intercellular molecular transfer.
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Affiliation(s)
- Cristina Sarasa-Buisan
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias e Instituto de Biocomputación y Física de Sistemas Complejos. Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Sevilla, Spain
| | - Mercedes Nieves-Morión
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Sevilla, Spain
| | - Sergio Arévalo
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Sevilla, Spain
| | - Richard F. Helm
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Emma Sevilla
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias e Instituto de Biocomputación y Física de Sistemas Complejos. Universidad de Zaragoza, Zaragoza, Spain
| | - Ignacio Luque
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Sevilla, Spain
| | - María F. Fillat
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias e Instituto de Biocomputación y Física de Sistemas Complejos. Universidad de Zaragoza, Zaragoza, Spain
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Qian R, Wu M, Yang Z, Wu Y, Guo W, Zhou Z, Wang X, Li D, Lu Y. Rectifying artificial nanochannels with multiple interconvertible permeability states. Nat Commun 2024; 15:2051. [PMID: 38448408 PMCID: PMC10918189 DOI: 10.1038/s41467-024-46312-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Transmembrane channels play a vital role in regulating the permeation process, and have inspired recent development of biomimetic channels. Herein, we report a class of artificial biomimetic nanochannels based on DNAzyme-functionalized glass nanopipettes to realize delicate control of channel permeability, whereby the surface wettability and charge can be tuned by metal ions and DNAzyme-substrates, allowing reversible conversion between different permeability states. We demonstrate that the nanochannels can be reversibly switched between four different permeability states showing distinct permeability to various functional molecules. By embedding the artificial nanochannels into the plasma membrane of single living cells, we achieve selective transport of dye molecules across the cell membrane. Finally, we report on the advanced functions including gene silencing of miR-21 in single cancer cells and selective transport of Ca2+ into single PC-12 cells. In this work, we provide a versatile tool for the design of rectifying artificial nanochannels with on-demand functions.
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Affiliation(s)
- Ruocan Qian
- Key Laboratory for Advanced Materials, East China University of Science and Technology, Shanghai, 200237, P. R. China.
- Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China.
- Frontiers Science Center for Materiobiology & Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China.
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China.
| | - Mansha Wu
- Key Laboratory for Advanced Materials, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Frontiers Science Center for Materiobiology & Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Zhenglin Yang
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Yuting Wu
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Weijie Guo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Zerui Zhou
- Key Laboratory for Advanced Materials, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Frontiers Science Center for Materiobiology & Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Xiaoyuan Wang
- Key Laboratory for Advanced Materials, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Frontiers Science Center for Materiobiology & Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Dawei Li
- Key Laboratory for Advanced Materials, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Frontiers Science Center for Materiobiology & Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA.
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
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8
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Lv Y, Dai Z, Chen Y, Lu Y, Zhang X, Yu J, Zhai W, Yu Y, Wen Z, Cui Y, Liu W. Two-Dimensional Sulfonate-Functionalized Metal-Organic Framework Membranes for Efficient Lithium-Ion Sieving. Nano Lett 2024; 24:2782-2788. [PMID: 38411082 DOI: 10.1021/acs.nanolett.3c04773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Two-dimensional (2D) membranes have shown promising potential for ion-selective separation but often suffer from the trade-off between permeability and selectivity. Herein, we report an ultrathin 2D sulfonate-functionalized metal-organic framework (MOF) membrane for efficient lithium-ion sieving. The narrow pores with angstrom precision in the MOF assist hydrated ions to partially remove the hydration shell, according to different hydration energies. The abundant sulfonate groups in the MOF channels serve as hopping sites for fast lithium-ion transport, contributing to a high Li-ion permeability. Then, the difference in affinity of the Li+, Na+, K+, and Mg2+ ions to the terminal sulfonate groups further enhances the Li-ion selectivity. The reported ultrathin MOF membrane overcomes the trade-off between permeability and selectivity and opens up a new avenue for highly permselective membranes.
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Affiliation(s)
- Yinjie Lv
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, China
| | - Zhongqin Dai
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- The State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050, China
| | - Yu Chen
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, China
| | - Yuan Lu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, China
| | - Xinshui Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, China
| | - Jiameng Yu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, China
| | - Wenbo Zhai
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, China
| | - Yi Yu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, China
| | - Zhaoyin Wen
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- The State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050, China
| | - Yuanyuan Cui
- School of Materials Science and Engineering, Shanghai University, Shanghai 200444, China
| | - Wei Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Key Laboratory of High-resolution Electron Microscopy, ShanghaiTech University, Shanghai 201210, China
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9
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Fan P, Zhang S, Wang Y, Li T, Zhang H, Zhang P, Huang S. Nanopore analysis of salvianolic acids in herbal medicines. Nat Commun 2024; 15:1970. [PMID: 38443335 PMCID: PMC10915175 DOI: 10.1038/s41467-024-45543-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 01/24/2024] [Indexed: 03/07/2024] Open
Abstract
Natural herbs, which contain pharmacologically active compounds, have been used historically as medicines. Conventionally, the analysis of chemical components in herbal medicines requires time-consuming sample separation and state-of-the-art analytical instruments. Nanopore, a versatile single molecule sensor, might be suitable to identify bioactive compounds in natural herbs. Here, a phenylboronic acid appended Mycobacterium smegmatis porin A (MspA) nanopore is used as a sensor for herbal medicines. A variety of bioactive compounds based on salvianolic acids, including caffeic acid, protocatechuic acid, protocatechualdehyde, salvianic acid A, rosmarinic acid, lithospermic acid, salvianolic acid A and salvianolic acid B are identified. Using a custom machine learning algorithm, analyte identification is performed with an accuracy of 99.0%. This sensing principle is further used with natural herbs such as Salvia miltiorrhiza, Rosemary and Prunella vulgaris. No complex sample separation or purification is required and the sensing device is highly portable.
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Affiliation(s)
- Pingping Fan
- 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
| | - 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
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 210023, Nanjing, China
- Institute for the Environment and Health, Nanjing University Suzhou Campus, 215163, Suzhou, China
| | - Tian Li
- 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
| | - Hanhan 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
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, 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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10
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Fan P, Cao Z, Zhang S, Wang Y, Xiao Y, Jia W, Zhang P, Huang S. Nanopore analysis of cis-diols in fruits. Nat Commun 2024; 15:1969. [PMID: 38443434 PMCID: PMC10915164 DOI: 10.1038/s41467-024-46303-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
Natural fruits contain a large variety of cis-diols. However, due to the lack of a high-resolution sensor that can simultaneously identify all cis-diols without a need of complex sample pretreatment, direct and rapid analysis of fruits in a hand-held device has never been previously reported. Nanopore, a versatile single molecule sensor, can be specially engineered to perform this task. A hetero-octameric Mycobacterium smegmatis porin A (MspA) nanopore modified with a sole phenylboronic acid (PBA) adapter is prepared. This engineered MspA accurately recognizes 1,2-diphenols, alditols, α-hydroxy acids and saccharides in prune, grape, lemon, different varieties of kiwifruits and commercial juice products. Assisted with a custom machine learning program, an accuracy of 99.3% is reported and the sample pretreatment is significantly simplified. Enantiomers such as DL-malic acids can also be directly identified, enabling sensing of synthetic food additives. Though demonstrated with fruits, these results suggest wide applications of nanopore in food and drug administration uses.
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Affiliation(s)
- Pingping Fan
- 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
| | - Zhenyuan Cao
- 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
| | - 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
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 210023, Nanjing, China
- Institute for the Environment and Health, Nanjing University Suzhou Campus, 215163, Suzhou, China
| | - Yunqi Xiao
- 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
| | - 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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11
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Shah A, Pathak S, Li K, Garaj S, Bazant MZ, Gupta A, Doyle PS. A Universal Approximation for Conductance Blockade in Thin Nanopore Membranes. Nano Lett 2024. [PMID: 38437028 DOI: 10.1021/acs.nanolett.3c04997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Nanopore-based sensing platforms have transformed single-molecule detection and analysis. The foundation of nanopore translocation experiments lies in conductance measurements, yet existing models, which are largely phenomenological, are inaccurate in critical experimental conditions such as thin and tightly fitting pores. Of the two components of the conductance blockade, channel and access resistance, the access resistance is poorly modeled. We present a comprehensive investigation of the access resistance and associated conductance blockade in thin nanopore membranes. By combining a first-principles approach, multiscale modeling, and experimental validation, we propose a unified theoretical modeling framework. The analytical model derived as a result surpasses current approaches across a broad parameter range. Beyond advancing our theoretical understanding, our framework's versatility enables analyte size inference and predictive insights into conductance blockade behavior. Our results will facilitate the design and optimization of nanopore devices for diverse applications, including nanopore base calling and data storage.
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Affiliation(s)
- Arjav Shah
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602
| | - Shakul Pathak
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Kun Li
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602
| | - Slaven Garaj
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602
- Department of Physics, National University of Singapore, Singapore 119077
| | - Martin Z Bazant
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Ankur Gupta
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Patrick S Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602
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12
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Shi X, Pumm AK, Maffeo C, Kohler F, Feigl E, Zhao W, Verschueren D, Golestanian R, Aksimentiev A, Dietz H, Dekker C. A DNA turbine powered by a transmembrane potential across a nanopore. Nat Nanotechnol 2024; 19:338-344. [PMID: 37884658 PMCID: PMC10950783 DOI: 10.1038/s41565-023-01527-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/12/2023] [Indexed: 10/28/2023]
Abstract
Rotary motors play key roles in energy transduction, from macroscale windmills to nanoscale turbines such as ATP synthase in cells. Despite our abilities to construct engines at many scales, developing functional synthetic turbines at the nanoscale has remained challenging. Here, we experimentally demonstrate rationally designed nanoscale DNA origami turbines with three chiral blades. These DNA nanoturbines are 24-27 nm in height and diameter and can utilize transmembrane electrochemical potentials across nanopores to drive DNA bundles into sustained unidirectional rotations of up to 10 revolutions s-1. The rotation direction is set by the designed chirality of the turbine. All-atom molecular dynamics simulations show how hydrodynamic flows drive this turbine. At high salt concentrations, the rotation direction of turbines with the same chirality is reversed, which is explained by a change in the anisotropy of the electrophoretic mobility. Our artificial turbines operate autonomously in physiological conditions, converting energy from naturally abundant electrochemical potentials into mechanical work. The results open new possibilities for engineering active robotics at the nanoscale.
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Affiliation(s)
- Xin Shi
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
- Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Anna-Katharina Pumm
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
- Munich Institute of Biomedical Engineering, Technical University of Munich, Garching, Germany
| | - Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Fabian Kohler
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Elija Feigl
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Wenxuan Zhao
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
| | - Daniel Verschueren
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
- The SW7 Group, London, UK
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, UK
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Hendrik Dietz
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands.
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13
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Liu J, Aksimentiev A. Molecular Determinants of Current Blockade Produced by Peptide Transport Through a Nanopore. ACS Nanosci Au 2024; 4:21-29. [PMID: 38406313 PMCID: PMC10885333 DOI: 10.1021/acsnanoscienceau.3c00046] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/28/2023] [Accepted: 11/03/2023] [Indexed: 02/27/2024]
Abstract
The nanopore sensing method holds the promise of delivering a single molecule technology for identification of biological proteins, direct detection of post-translational modifications, and perhaps de novo determination of a protein's amino acid sequence. The key quantity measured in such nanopore sensing experiments is the magnitude of the ionic current passing through a nanopore blocked by a polypeptide chain. Establishing a relationship between the amino acid sequence of a peptide fragment confined within a nanopore and the blockade current flowing through the nanopore remains a major challenge for realizing the nanopore protein sequencing. Using the results of all-atom molecular dynamics simulations, here we compare nanopore sequencing of DNA with nanopore sequencing of proteins. We then delineate the factors affecting the blockade current modulation by the peptide sequence, showing that the current can be determined by (i) the steric footprint of an amino acid, (ii) its interactions with the pore wall, (iii) the local stretching of a polypeptide chain, and (iv) the local enhancement of the ion concentration at the nanopore constriction. We conclude with a brief discussion of the prospects for purely computational prediction of the blockade currents.
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Affiliation(s)
- Jingqian Liu
- Center
for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Center
for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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15
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Vögele M, Köfinger J, Hummer G. Nanoporous Membranes of Densely Packed Carbon Nanotubes Formed by Lipid-Mediated Self-Assembly. ACS Appl Bio Mater 2024; 7:528-534. [PMID: 36070609 PMCID: PMC10880049 DOI: 10.1021/acsabm.2c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/29/2022] [Indexed: 11/29/2022]
Abstract
Nanofiltration technology faces the competing challenges of achieving high fluid flux through uniformly narrow pores of a mechanically and chemically stable filter. Supported dense-packed 2D-crystals of single-walled carbon nanotube (CNT) porins with ∼1 nm wide pores could, in principle, meet these challenges. However, such CNT membranes cannot currently be synthesized at high pore density. Here, we use computer simulations to explore lipid-mediated self-assembly as a route toward densely packed CNT membranes, motivated by the analogy to membrane-protein 2D crystallization. In large-scale coarse-grained molecular dynamics (MD) simulations, we find that CNTs in lipid membranes readily self-assemble into large clusters. Lipids trapped between the CNTs lubricate CNT repacking upon collisions of diffusing clusters, thereby facilitating the formation of large ordered structures. Cluster diffusion follows the Saffman-Delbrück law and its generalization by Hughes, Pailthorpe, and White. On longer time scales, we expect the formation of close-packed CNT structures by depletion of the intervening shared annular lipid shell, depending on the relative strength of CNT-CNT and CNT-lipid interactions. Our simulations identify CNT length, diameter, and end functionalization as major factors for the self-assembly of CNT membranes.
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Affiliation(s)
- Martin Vögele
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Jürgen Köfinger
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
- Institute
for Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany
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16
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K NA, Kumar S. Ion Selectivity in Multilayered Stacked Nanoporous Graphene. ACS Appl Mater Interfaces 2024; 16:5294-5301. [PMID: 38236663 DOI: 10.1021/acsami.3c15044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Nanoporous graphene is an ideal candidate for molecular filtration as it can potentially combine high permeability with high selectivity at molecular levels. To make use of graphene in filtration setups, the defects formed during its growth and during the transfer of graphene to the carrier support pose a challenge. These uncontrolled pores can be avoided by stacking graphene layers, and then, controlled pores can be initiated with oxygen plasma. Here, we show that two-layer stacks provide the best balance of defect coverage and high selectivity compared with other stacks. Using the electrical characterization of ionic solutions in the standard diffusion cell, we compare the ionic transport and ionic selectivity of up to three-layered stacks of graphene that have been plasma-treated. We find that there is a decrease in the ionic selectivity of a two-layered stack as one more layer of graphene is added. We provide a model for this occurrence. Our results will be helpful for making practical and high-performance filtration systems from two-dimensional materials.
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Affiliation(s)
- Niketa A K
- Department of Electrical Engineering, Indian Institute of Technology Hyderabad, Hyderabad 502284, Telangana, India
| | - Shishir Kumar
- Department of Electrical Engineering, Indian Institute of Technology Hyderabad, Hyderabad 502284, Telangana, India
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17
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Shoemaker BA, Khalifa O, Haji-Akbari A. Correlations in Charged Multipore Systems: Implications for Enhancing Selectivity and Permeability in Nanoporous Membranes. ACS Nano 2024; 18:1420-1431. [PMID: 38176076 DOI: 10.1021/acsnano.3c07489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Nanoporous membranes have emerged as powerful tools for diverse applications, including gas separation and water desalination. Achieving high permeability for desired molecules alongside exceptional rejection of other species presents a significant design challenge. One potential strategy involves optimizing the chemistry and geometry of isolated nanopores to enhance permeability and selectivity while maximizing their density within a membrane. However, the impact of the pore proximity on membrane performance remains an open question. Through path sampling simulations of model graphitic membranes with multiple subnanometer pores, we reveal that nanoscale proximity between pores detrimentally affects water permeability and salt rejection. Specifically, counterion transport is decelerated, while co-ion transport is accelerated, due to direct interactions among water molecules, salt ions, and the dipoles within neighboring pores. Notably, the observed ionic transport time scales significantly deviate from established theories such as the access resistance model but are well explained using the simple phenomenological model that we develop in this work. We use this model to prescreen and optimize pore arrangements that elicit minimal correlations at a target pore density. These findings deepen our understanding of multipore systems, informing the rational design of nanoporous membranes for enhanced separation processes such as water desalination. They also shed light on the physiology of biological cells that employ ion channel proteins to modulate ion transport and reversal potentials.
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Affiliation(s)
- Brian A Shoemaker
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06511, United States
| | - Omar Khalifa
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06511, United States
| | - Amir Haji-Akbari
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06511, United States
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18
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Wang B, Xu YT, Zhang TY, Wang HY, Zhang X, Wu ZQ, Zhao WW, Chen HY, Xu JJ. An Ultrasensitive and Efficient microRNA Nanosensor Empowered by the CRISPR/Cas Confined in a Nanopore. Nano Lett 2024; 24:202-208. [PMID: 38126308 DOI: 10.1021/acs.nanolett.3c03723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
This work presents a clustered regularly interspaced short palindromic repeat (CRISPR)/Cas-nanopipette nano-electrochemistry (Cas = CRISPR-associated proteins) capable of ultrasensitive microRNA detection. Nanoconfinement of the CRISPR/Cas13a within a nanopipette leads to a high catalytic efficacy of ca. 169 times higher than that in bulk electrolyte, contributing to the amplified electrochemical responses. CRISPR/Cas13a-enabled detection of representative microRNA-25 achieves a low limit of detection down to 10 aM. Practical application of this method is further demonstrated for single-cell and real human serum detection. Its general applicability is validated by addressing microRNA-141 and the SARS-CoV-2 RNA gene fragment. This work introduces a new CRISPR/Cas-empowered nanotechnology for ultrasensitive nano-electrochemistry and bioanalysis.
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Affiliation(s)
- Bing Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yi-Tong Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Tian-Yang Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hai-Yan Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xian Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zeng-Qiang Wu
- School of Public Health, Institute of Analytical Chemistry for Life Science, Nantong University, Nantong 226019, China
| | - Wei-Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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19
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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 2024; 20:e2305186. [PMID: 37649152 DOI: 10.1002/smll.202305186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Berkovich AK, Pyshkina OA, Zorina AA, Rodin VA, Panova TV, Sergeev VG, Zvereva ME. Direct Determination of the Structure of Single Biopolymer Molecules Using Nanopore Sequencing. Biochemistry (Mosc) 2024; 89:S234-S248. [PMID: 38621753 DOI: 10.1134/s000629792414013x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/21/2023] [Accepted: 09/01/2023] [Indexed: 04/17/2024]
Abstract
This review highlights operational principles, features, and modern aspects of the development of third-generation sequencing technology of biopolymers focusing on the nucleic acids analysis, namely the nanopore sequencing system. Basics of the method and technical solutions used for its realization are considered, from the first works showing the possibility of creation of these systems to the easy-to-handle procedure developed by Oxford Nanopore Technologies company. Moreover, this review focuses on applications, which were developed and realized using equipment developed by the Oxford Nanopore Technologies, including assembly of whole genomes, methagenomics, direct analysis of the presence of modified bases.
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Affiliation(s)
- Anna K Berkovich
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Olga A Pyshkina
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Anna A Zorina
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vladimir A Rodin
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Tatyana V Panova
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vladimir G Sergeev
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Maria E Zvereva
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
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21
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Paulo G, Sun K, Di Muccio G, Gubbiotti A, Morozzo Della Rocca B, Geng J, Maglia G, Chinappi M, Giacomello A. Hydrophobically gated memristive nanopores for neuromorphic applications. Nat Commun 2023; 14:8390. [PMID: 38110352 PMCID: PMC10728163 DOI: 10.1038/s41467-023-44019-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/27/2023] [Indexed: 12/20/2023] Open
Abstract
Signal transmission in the brain relies on voltage-gated ion channels, which exhibit the electrical behaviour of memristors, resistors with memory. State-of-the-art technologies currently employ semiconductor-based neuromorphic approaches, which have already demonstrated their efficacy in machine learning systems. However, these approaches still cannot match performance achieved by biological neurons in terms of energy efficiency and size. In this study, we utilise molecular dynamics simulations, continuum models, and electrophysiological experiments to propose and realise a bioinspired hydrophobically gated memristive nanopore. Our findings indicate that hydrophobic gating enables memory through an electrowetting mechanism, and we establish simple design rules accordingly. Through the engineering of a biological nanopore, we successfully replicate the characteristic hysteresis cycles of a memristor and construct a synaptic device capable of learning and forgetting. This advancement offers a promising pathway for the realization of nanoscale, cost- and energy-effective, and adaptable bioinspired memristors.
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Affiliation(s)
- Gonçalo Paulo
- Department of Mechanics and Aerospace Engineering, Sapienza University of Rome, Rome, 00184, Italy
| | - Ke Sun
- Chemical Biology Department, Groningen Biomolecular Sciences & Biotechnology Institute, Groningen, 9700 CC, The Netherlands
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Giovanni Di Muccio
- Department of Mechanics and Aerospace Engineering, Sapienza University of Rome, Rome, 00184, Italy
| | - Alberto Gubbiotti
- Department of Mechanics and Aerospace Engineering, Sapienza University of Rome, Rome, 00184, Italy
| | | | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Giovanni Maglia
- Chemical Biology Department, Groningen Biomolecular Sciences & Biotechnology Institute, Groningen, 9700 CC, The Netherlands
| | - Mauro Chinappi
- Department of Industrial Engineering, Tor Vergata University of Rome, Rome, 00133, Italy
| | - Alberto Giacomello
- Department of Mechanics and Aerospace Engineering, Sapienza University of Rome, Rome, 00184, Italy.
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22
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Koch C, Reilly-O'Donnell B, Gutierrez R, Lucarelli C, Ng FS, Gorelik J, Ivanov AP, Edel JB. Nanopore sequencing of DNA-barcoded probes for highly multiplexed detection of microRNA, proteins and small biomarkers. Nat Nanotechnol 2023; 18:1483-1491. [PMID: 37749222 PMCID: PMC10716039 DOI: 10.1038/s41565-023-01479-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/28/2023] [Indexed: 09/27/2023]
Abstract
There is an unmet need to develop low-cost, rapid and highly multiplexed diagnostic technology platforms for quantitatively detecting blood biomarkers to advance clinical diagnostics beyond the single biomarker model. Here we perform nanopore sequencing of DNA-barcoded molecular probes engineered to recognize a panel of analytes. This allows for highly multiplexed and simultaneous quantitative detection of at least 40 targets, such as microRNAs, proteins and neurotransmitters, on the basis of the translocation dynamics of each probe as it passes through a nanopore. Our workflow is built around a commercially available MinION sequencing device, offering a one-hour turnaround time from sample preparation to results. We also demonstrate that the strategy can directly detect cardiovascular disease-associated microRNA from human serum without extraction or amplification. Due to the modularity of barcoded probes, the number and type of targets detected can be significantly expanded.
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Affiliation(s)
- Caroline Koch
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
| | - Benedict Reilly-O'Donnell
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
- National Heart and Lung Institute, ICTEM, Imperial College London, London, UK
| | | | - Carla Lucarelli
- National Heart and Lung Institute, ICTEM, Imperial College London, London, UK
| | - Fu Siong Ng
- National Heart and Lung Institute, ICTEM, Imperial College London, London, UK
| | - Julia Gorelik
- National Heart and Lung Institute, ICTEM, Imperial College London, London, UK
| | - Aleksandar P Ivanov
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK.
| | - Joshua B Edel
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK.
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23
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Ren R, Cai S, Fang X, Wang X, Zhang Z, Damiani M, Hudlerova C, Rosa A, Hope J, Cook NJ, Gorelkin P, Erofeev A, Novak P, Badhan A, Crone M, Freemont P, Taylor GP, Tang L, Edwards C, Shevchuk A, Cherepanov P, Luo Z, Tan W, Korchev Y, Ivanov AP, Edel JB. Multiplexed detection of viral antigen and RNA using nanopore sensing and encoded molecular probes. Nat Commun 2023; 14:7362. [PMID: 37963924 PMCID: PMC10646045 DOI: 10.1038/s41467-023-43004-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023] Open
Abstract
We report on single-molecule nanopore sensing combined with position-encoded DNA molecular probes, with chemistry tuned to simultaneously identify various antigen proteins and multiple RNA gene fragments of SARS-CoV-2 with high sensitivity and selectivity. We show that this sensing strategy can directly detect spike (S) and nucleocapsid (N) proteins in unprocessed human saliva. Moreover, our approach enables the identification of RNA fragments from patient samples using nasal/throat swabs, enabling the identification of critical mutations such as D614G, G446S, or Y144del among viral variants. In particular, it can detect and discriminate between SARS-CoV-2 lineages of wild-type B.1.1.7 (Alpha), B.1.617.2 (Delta), and B.1.1.539 (Omicron) within a single measurement without the need for nucleic acid sequencing. The sensing strategy of the molecular probes is easily adaptable to other viral targets and diseases and can be expanded depending on the application required.
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Affiliation(s)
- Ren Ren
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
| | - Shenglin Cai
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK.
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Xiaona Fang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
| | - Xiaoyi Wang
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Zheng Zhang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
| | - Micol Damiani
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Charlotte Hudlerova
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Annachiara Rosa
- The Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
- Wolfson Education Centre, Faculty of Medicine, Imperial College London, London, UK
| | - Joshua Hope
- The Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Nicola J Cook
- The Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Peter Gorelkin
- National University of Science and Technology "MISIS", Leninskiy Prospect 4, 119991, Moscow, Russian Federation
| | - Alexander Erofeev
- National University of Science and Technology "MISIS", Leninskiy Prospect 4, 119991, Moscow, Russian Federation
| | - Pavel Novak
- ICAPPIC Limited, The Fisheries, Mentmore Terrace, London, E8 3PN, UK
| | - Anjna Badhan
- Molecular Diagnostic Unit, Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Michael Crone
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Paul Freemont
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Graham P Taylor
- Molecular Diagnostic Unit, Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Longhua Tang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, International Research Center for Advanced Photonics, Zhejiang University, 310027, Hangzhou, China
| | - Christopher Edwards
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
- ICAPPIC Limited, The Fisheries, Mentmore Terrace, London, E8 3PN, UK
| | - Andrew Shevchuk
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
| | - Peter Cherepanov
- The Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
- Molecular Diagnostic Unit, Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Zhaofeng Luo
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
| | - Weihong Tan
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China.
| | - Yuri Korchev
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK.
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK.
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24
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Noh Y, Aluru NR. Scaling of ionic conductance in a fluctuating single-layer nanoporous membrane. Sci Rep 2023; 13:19813. [PMID: 37957224 PMCID: PMC10643653 DOI: 10.1038/s41598-023-46962-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 11/07/2023] [Indexed: 11/15/2023] Open
Abstract
Single-layer membranes have emerged as promising candidates for applications requiring high transport rates due to their low resistance to molecular transport. Owing to their atomically thin structure, these membranes experience significant microscopic fluctuations, emphasizing the need to explore their impact on ion transport processes. In this study, we investigate the effects of membrane fluctuations on the elementary scaling behavior of ion conductance [Formula: see text] as a function of ion concentration [Formula: see text], represented as [Formula: see text], using molecular dynamics simulations. Our findings reveal that membrane fluctuations not only alter the conductance coefficient [Formula: see text] but also the power-law exponent [Formula: see text]. We identify two distinct frequency regimes of membrane fluctuations, GHz-scale and THz-scale fluctuations, and examine their roles in conductance scaling. Furthermore, we demonstrate that the alteration of conductance scaling arises from the non-linearity between ion conductance and membrane shape. This work provides a fundamental understanding of ion transport in fluctuating membranes.
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Affiliation(s)
- Yechan Noh
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - N R Aluru
- Walker Department of Mechanical Engineering, Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, 78712, USA.
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25
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Dutt S, Shao H, Karawdeniya B, Bandara YMNDY, Daskalaki E, Suominen H, Kluth P. High Accuracy Protein Identification: Fusion of Solid-State Nanopore Sensing and Machine Learning. Small Methods 2023; 7:e2300676. [PMID: 37718979 DOI: 10.1002/smtd.202300676] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/25/2023] [Indexed: 09/19/2023]
Abstract
Proteins are arguably one of the most important class of biomarkers for health diagnostic purposes. Label-free solid-state nanopore sensing is a versatile technique for sensing and analyzing biomolecules such as proteins at single-molecule level. While molecular-level information on size, shape, and charge of proteins can be assessed by nanopores, the identification of proteins with comparable sizes remains a challenge. Here, solid-state nanopore sensing is combined with machine learning to address this challenge. The translocations of four similarly sized proteins is assessed using amplifiers with bandwidths (BWs) of 100 kHz and 10 MHz, the highest bandwidth reported for protein sensing, using nanopores fabricated in <10 nm thick silicon nitride membranes. F-values of up to 65.9% and 83.2% (without clustering of the protein signals) are achieved with 100 kHz and 10 MHz BW measurements, respectively, for identification of the four proteins. The accuracy of protein identification is further enhanced by classifying the signals into different clusters based on signal attributes, with F-value and specificity of up to 88.7% and 96.4%, respectively, for combinations of four proteins. The combined use of high bandwidth instruments, advanced clustering and machine learning methods allows label-free identification of proteins with high accuracy.
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Affiliation(s)
- Shankar Dutt
- Department of Materials Physics, Research School of Physics, Australian National University, Canberra, ACT, 2601, Australia
| | - Hancheng Shao
- Department of Materials Physics, Research School of Physics, Australian National University, Canberra, ACT, 2601, Australia
| | - Buddini Karawdeniya
- Department of Electronic Materials Engineering, Research School of Physics, Australian National University, Canberra, ACT, 2601, Australia
| | - Y M Nuwan D Y Bandara
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Elena Daskalaki
- School of Computing, College of Engineering, Computing and Cybernetics, Australian National University, Canberra, ACT, 2601, Australia
| | - Hanna Suominen
- School of Computing, College of Engineering, Computing and Cybernetics, Australian National University, Canberra, ACT, 2601, Australia
- Eccles Institute of Neuroscience, College of Health and Medicine, Australian National University, Canberra, ACT, 2601, Australia
| | - Patrick Kluth
- Department of Materials Physics, Research School of Physics, Australian National University, Canberra, ACT, 2601, Australia
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26
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Liu Q, Miao Y, Villalobos LF, Li S, Chi HY, Chen C, Vahdat MT, Song S, Babu DJ, Hao J, Han Y, Tsapatsis M, Agrawal KV. Unit-cell-thick zeolitic imidazolate framework films for membrane application. Nat Mater 2023; 22:1387-1393. [PMID: 37735526 PMCID: PMC10627807 DOI: 10.1038/s41563-023-01669-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 08/21/2023] [Indexed: 09/23/2023]
Abstract
Zeolitic imidazolate frameworks (ZIFs) are a subset of metal-organic frameworks with more than 200 characterized crystalline and amorphous networks made of divalent transition metal centres (for example, Zn2+ and Co2+) linked by imidazolate linkers. ZIF thin films have been intensively pursued, motivated by the desire to prepare membranes for selective gas and liquid separations. To achieve membranes with high throughput, as in ångström-scale biological channels with nanometre-scale path lengths, ZIF films with the minimum possible thickness-down to just one unit cell-are highly desired. However, the state-of-the-art methods yield membranes where ZIF films have thickness exceeding 50 nm. Here we report a crystallization method from ultradilute precursor mixtures, which exploits registry with the underlying crystalline substrate, yielding (within minutes) crystalline ZIF films with thickness down to that of a single structural building unit (2 nm). The film crystallized on graphene has a rigid aperture made of a six-membered zinc imidazolate coordination ring, enabling high-permselective H2 separation performance. The method reported here will probably accelerate the development of two-dimensional metal-organic framework films for efficient membrane separation.
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Affiliation(s)
- Qi Liu
- Laboratory of Advanced Separations, École Polytechnique Fédérale de Lausanne (EPFL), Sion, Switzerland
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, China
| | - Yurun Miao
- Department of Chemical and Biomolecular Engineering & Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA
| | - Luis Francisco Villalobos
- Laboratory of Advanced Separations, École Polytechnique Fédérale de Lausanne (EPFL), Sion, Switzerland
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California, USA
| | - Shaoxian Li
- Laboratory of Advanced Separations, École Polytechnique Fédérale de Lausanne (EPFL), Sion, Switzerland
| | - Heng-Yu Chi
- Laboratory of Advanced Separations, École Polytechnique Fédérale de Lausanne (EPFL), Sion, Switzerland
| | - Cailing Chen
- Advanced Membranes and Porous Materials Center, Physical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mohammad Tohidi Vahdat
- Laboratory of Advanced Separations, École Polytechnique Fédérale de Lausanne (EPFL), Sion, Switzerland
| | - Shuqing Song
- Laboratory of Advanced Separations, École Polytechnique Fédérale de Lausanne (EPFL), Sion, Switzerland
| | - Deepu J Babu
- Laboratory of Advanced Separations, École Polytechnique Fédérale de Lausanne (EPFL), Sion, Switzerland
- Materials Science and Metallurgical Engineering, Indian Institute of Technology, Hyderabad, India
| | - Jian Hao
- Laboratory of Advanced Separations, École Polytechnique Fédérale de Lausanne (EPFL), Sion, Switzerland
| | - Yu Han
- Advanced Membranes and Porous Materials Center, Physical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Michael Tsapatsis
- Department of Chemical and Biomolecular Engineering & Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD, USA
| | - Kumar Varoon Agrawal
- Laboratory of Advanced Separations, École Polytechnique Fédérale de Lausanne (EPFL), Sion, Switzerland.
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27
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Martin-Baniandres P, Lan WH, Board S, Romero-Ruiz M, Garcia-Manyes S, Qing Y, Bayley H. Enzyme-less nanopore detection of post-translational modifications within long polypeptides. Nat Nanotechnol 2023; 18:1335-1340. [PMID: 37500774 PMCID: PMC10656283 DOI: 10.1038/s41565-023-01462-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/15/2023] [Indexed: 07/29/2023]
Abstract
Means to analyse cellular proteins and their millions of variants at the single-molecule level would uncover substantial information previously unknown to biology. Nanopore technology, which underpins long-read DNA and RNA sequencing, holds potential for full-length proteoform identification. We use electro-osmosis in an engineered charge-selective nanopore for the non-enzymatic capture, unfolding and translocation of individual polypeptides of more than 1,200 residues. Unlabelled thioredoxin polyproteins undergo transport through the nanopore, with directional co-translocational unfolding occurring unit by unit from either the C or N terminus. Chaotropic reagents at non-denaturing concentrations accelerate the analysis. By monitoring the ionic current flowing through the nanopore, we locate post-translational modifications deep within the polypeptide chains, laying the groundwork for compiling inventories of the proteoforms in cells and tissues.
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Affiliation(s)
| | - Wei-Hsuan Lan
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Stephanie Board
- Department of Physics, Randall Centre for Cell and Molecular Biophysics and London Centre for Nanotechnology, King's College London, London, UK
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
| | | | - Sergi Garcia-Manyes
- Department of Physics, Randall Centre for Cell and Molecular Biophysics and London Centre for Nanotechnology, King's College London, London, UK
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
| | - Yujia Qing
- Department of Chemistry, University of Oxford, Oxford, UK.
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford, UK.
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28
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Kawabe H, Thomas CA, Hoshika S, Kim MJ, Kim MS, Miessner L, Kaplan N, Craig JM, Gundlach JH, Laszlo AH, Benner SA, Marchand JA. Enzymatic synthesis and nanopore sequencing of 12-letter supernumerary DNA. Nat Commun 2023; 14:6820. [PMID: 37884513 PMCID: PMC10603101 DOI: 10.1038/s41467-023-42406-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
The 4-letter DNA alphabet (A, T, G, C) as found in Nature is an elegant, yet non-exhaustive solution to the problem of storage, transfer, and evolution of biological information. Here, we report on strategies for both writing and reading DNA with expanded alphabets composed of up to 12 letters (A, T, G, C, B, S, P, Z, X, K, J, V). For writing, we devise an enzymatic strategy for inserting a singular, orthogonal xenonucleic acid (XNA) base pair into standard DNA sequences using 2'-deoxy-xenonucleoside triphosphates as substrates. Integrating this strategy with combinatorial oligos generated on a chip, we construct libraries containing single XNA bases for parameterizing kmer basecalling models for commercially available nanopore sequencing. These elementary steps are combined to synthesize and sequence DNA containing 12 letters - the upper limit of what is accessible within the electroneutral, canonical base pairing framework. By introducing low-barrier synthesis and sequencing strategies, this work overcomes previous obstacles paving the way for making expanded alphabets widely accessible.
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Affiliation(s)
- Hinako Kawabe
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
| | | | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, Alachua, FL, 32615, USA
- Firebird Biomolecular Sciences LLC, Alachua, FL, 32615, USA
| | - Myong-Jung Kim
- Foundation for Applied Molecular Evolution, Alachua, FL, 32615, USA
- Firebird Biomolecular Sciences LLC, Alachua, FL, 32615, USA
| | - Myong-Sang Kim
- Firebird Biomolecular Sciences LLC, Alachua, FL, 32615, USA
| | - Logan Miessner
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Nicholas Kaplan
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Jonathan M Craig
- Department of Physics, University of Washington, Seattle, WA, 98195, USA
| | - Jens H Gundlach
- Department of Physics, University of Washington, Seattle, WA, 98195, USA
| | - Andrew H Laszlo
- Department of Physics, University of Washington, Seattle, WA, 98195, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, FL, 32615, USA
- Firebird Biomolecular Sciences LLC, Alachua, FL, 32615, USA
| | - Jorge A Marchand
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA.
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, USA.
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29
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Liu C, Henning-Knechtel A, Österlund N, Wu J, Wang G, Gräslund RAO, Kirmizialtin S, Luo J. Oligomer Dynamics of LL-37 Truncated Fragments Probed by α-Hemolysin Pore and Molecular Simulations. Small 2023; 19:e2206232. [PMID: 37170734 DOI: 10.1002/smll.202206232] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/01/2023] [Indexed: 05/13/2023]
Abstract
Oligomerization of antimicrobial peptides (AMPs) is critical in their effects on pathogens. LL-37 and its truncated fragments are widely investigated regarding their structures, antimicrobial activities, and application, such as developing new antibiotics. Due to the small size and weak intermolecular interactions of LL-37 fragments, it is still elusive to establish the relationship between oligomeric states and antimicrobial activities. Here, an α-hemolysin nanopore, mass spectrometry (MS), and molecular dynamic (MD) simulations are used to characterize the oligomeric states of two LL-37 fragments. Nanopore studies provide evidence of trapping events related to the oligomer formation and provide further details on their stabilities, which are confirmed by MS and MD simulations. Furthermore, simulation results reveal the molecular basis of oligomer dynamics and states of LL-37 fragments. This work provides unique insights into the relationship between the oligomer dynamics of AMPs and their antimicrobial activities at the single-molecule level. The study demonstrates how integrating methods allows deciphering single molecule level understanding from nanopore sensing approaches.
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Affiliation(s)
- Chang Liu
- Department of Biology and Chemistry, Paul Scherrer Institute, Villigen, 5232, Switzerland
| | - Anja Henning-Knechtel
- Science Division, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, 129188, UAE
| | - Nicklas Österlund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, 106 91, Sweden
| | - Jinming Wu
- Department of Biology and Chemistry, Paul Scherrer Institute, Villigen, 5232, Switzerland
| | - Guangshun Wang
- Department of Pathology and Microbiology, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, NE, 68198-5900, USA
| | | | - Serdal Kirmizialtin
- Science Division, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, 129188, UAE
| | - Jinghui Luo
- Department of Biology and Chemistry, Paul Scherrer Institute, Villigen, 5232, Switzerland
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30
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Affiliation(s)
- Jacob S Koruth
- Helmsely Electrophysiology Center, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Iwanari Kawamura
- Helmsely Electrophysiology Center, Icahn School of Medicine at Mount Sinai, New York, NY
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31
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Kim EJ, Chen C, Gologorsky R, Santandreu A, Torres A, Wright N, Goodin MS, Moyer J, Chui BW, Blaha C, Brakeman P, Vartanian S, Tang Q, David Humes H, Fissell WH, Roy S. Feasibility of an implantable bioreactor for renal cell therapy using silicon nanopore membranes. Nat Commun 2023; 14:4890. [PMID: 37644033 PMCID: PMC10465514 DOI: 10.1038/s41467-023-39888-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 07/03/2023] [Indexed: 08/31/2023] Open
Abstract
The definitive treatment for end-stage renal disease is kidney transplantation, which remains limited by organ availability and post-transplant complications. Alternatively, an implantable bioartificial kidney could address both problems while enhancing the quality and length of patient life. An implantable bioartificial kidney requires a bioreactor containing renal cells to replicate key native cell functions, such as water and solute reabsorption, and metabolic and endocrinologic functions. Here, we report a proof-of-concept implantable bioreactor containing silicon nanopore membranes to offer a level of immunoprotection to human renal epithelial cells. After implantation into pigs without systemic anticoagulation or immunosuppression therapy for 7 days, we show that cells maintain >90% viability and functionality, with normal or elevated transporter gene expression and vitamin D activation. Despite implantation into a xenograft model, we find that cells exhibit minimal damage, and recipient cytokine levels are not suggestive of hyperacute rejection. These initial data confirm the potential feasibility of an implantable bioreactor for renal cell therapy utilizing silicon nanopore membranes.
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Affiliation(s)
- Eun Jung Kim
- University of California, San Francisco, CA, USA
| | - Caressa Chen
- University of California, San Francisco, CA, USA
| | | | | | | | - Nathan Wright
- University of California, San Francisco, CA, USA
- Silicon Kidney LLC, San Ramon, CA, USA
| | | | | | | | - Charles Blaha
- University of California, San Francisco, CA, USA
- Silicon Kidney LLC, San Ramon, CA, USA
| | | | | | - Qizhi Tang
- University of California, San Francisco, CA, USA
| | - H David Humes
- University of Michigan, Ann Arbor, MI, USA
- Innovative Biotherapies Inc, Ann Arbor, MI, USA
| | - William H Fissell
- Silicon Kidney LLC, San Ramon, CA, USA
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shuvo Roy
- University of California, San Francisco, CA, USA.
- Silicon Kidney LLC, San Ramon, CA, USA.
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32
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Tong Y, Liu H, Dai S, Jiang DE. Monolayer Fullerene Membranes for Hydrogen Separation. Nano Lett 2023; 23:7470-7476. [PMID: 37540493 DOI: 10.1021/acs.nanolett.3c01946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Hydrogen separation membranes are a critical component in the emerging hydrogen economy, offering an energy-efficient solution for the purification and production of hydrogen gas. Inspired by the recent discovery of monolayer covalent fullerene networks, here we show from concentration-gradient-driven molecular dynamics that quasi-square-latticed monolayer fullerene membranes provide the best pore size match, a unique funnel-shaped pore, and entropic selectivity. The integration of these attributes renders these membranes promising for separating H2 from larger gases such as CO2 and O2. The ultrathin membranes exhibit excellent hydrogen permeance as well as high selectivity for H2/CO2 and H2/O2 separations, surpassing the 2008 Robeson upper bounds by a large margin. The present work points toward a promising direction of using monolayer fullerene networks as membranes for high-permeance, selective hydrogen separation for processes such as water splitting.
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Affiliation(s)
- Yujing Tong
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Hongjun Liu
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Sheng Dai
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - De-En Jiang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
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33
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Svirelis J, Adali Z, Emilsson G, Medin J, Andersson J, Vattikunta R, Hulander M, Järlebark J, Kolman K, Olsson O, Sakiyama Y, Lim RYH, Dahlin A. Stable trapping of multiple proteins at physiological conditions using nanoscale chambers with macromolecular gates. Nat Commun 2023; 14:5131. [PMID: 37612271 PMCID: PMC10447545 DOI: 10.1038/s41467-023-40889-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023] Open
Abstract
The possibility to detect and analyze single or few biological molecules is very important for understanding interactions and reaction mechanisms. Ideally, the molecules should be confined to a nanoscale volume so that the observation time by optical methods can be extended. However, it has proven difficult to develop reliable, non-invasive trapping techniques for biomolecules under physiological conditions. Here we present a platform for long-term tether-free (solution phase) trapping of proteins without exposing them to any field gradient forces. We show that a responsive polymer brush can make solid state nanopores switch between a fully open and a fully closed state with respect to proteins, while always allowing the passage of solvent, ions and small molecules. This makes it possible to trap a very high number of proteins (500-1000) inside nanoscale chambers as small as one attoliter, reaching concentrations up to 60 gL-1. Our method is fully compatible with parallelization by imaging arrays of nanochambers. Additionally, we show that enzymatic cascade reactions can be performed with multiple native enzymes under full nanoscale confinement and steady supply of reactants. This platform will greatly extend the possibilities to optically analyze interactions involving multiple proteins, such as the dynamics of oligomerization events.
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Affiliation(s)
- Justas Svirelis
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Zeynep Adali
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Gustav Emilsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Jesper Medin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - John Andersson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Radhika Vattikunta
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Mats Hulander
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Julia Järlebark
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Krzysztof Kolman
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Oliver Olsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Yusuke Sakiyama
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, 4056, Basel, Switzerland
| | - Roderick Y H Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, 4056, Basel, Switzerland
| | - Andreas Dahlin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden.
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34
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Qiu X, Cao M, Li Y. Metal-Organic Framework Sub-Nanochannels Formed inside Solid-State Nanopore with Proton Ultra-High Selectivity. Chemistry 2023; 29:e202300976. [PMID: 37221145 DOI: 10.1002/chem.202300976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 05/25/2023]
Abstract
Metal-Organic frameworks (MOFs) have the advantages of high porosity, angstrom-scale pore size, and unique structure. In this work, a kind of MOFs, UiO-66 and its derivatives (including aminated UiO-66-(NH2 )2 and sulfonated UiO-66-(NH-SAG)2 ), were constructed on the inner surface of solid-state nanopores for ultra-selective proton transport. UiO-66 and UiO-66-(NH2 )2 nanocrystal particles were in-situ grown at the orifice of glass nanopores firstly, which were used to investigate the ionic current responses in LiCl and HCl solutions when the monovalent anions (Cl- ) were unchanged. Compared with UiO-66-modifed nanopores, the aminated MOFs modification (UiO-66-(NH2 )2 ) can improve the proton selectivity obviously. However, when the UiO-66-(NH-SAG)2 nanopore is prepared by further post-modification with sulfo-acetic acid, lithium ions can hardly pass through the channel, and the interaction between protons and sulfonic acid groups can promote the transport of protons, thus achieving ultra-high selectivity to protons. This work provides a new way to achieve sub-nanochannels with high selectivity, which can widely be used in ion separation, sensing and energy conversion.
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Affiliation(s)
- Xia Qiu
- Key Laboratory of Functional Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, P.R. China
| | - Mengya Cao
- Key Laboratory of Functional Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, P.R. China
| | - Yongxin Li
- Key Laboratory of Functional Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, P.R. China
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35
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Roelen Z, Briggs K, Tabard-Cossa V. Analysis of Nanopore Data: Classification Strategies for an Unbiased Curation of Single-Molecule Events from DNA Nanostructures. ACS Sens 2023; 8:2809-2823. [PMID: 37436112 PMCID: PMC10913896 DOI: 10.1021/acssensors.3c00751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Nanopores are versatile single-molecule sensors that are being used to sense increasingly complex mixtures of structured molecules with applications in molecular data storage and disease biomarker detection. However, increased molecular complexity presents additional challenges to the analysis of nanopore data, including more translocation events being rejected for not matching an expected signal structure and a greater risk of selection bias entering this event curation process. To highlight these challenges, here, we present the analysis of a model molecular system consisting of a nanostructured DNA molecule attached to a linear DNA carrier. We make use of recent advances in the event segmentation capabilities of Nanolyzer, a graphical analysis tool provided for nanopore event fitting, and describe approaches to the event substructure analysis. In the process, we identify and discuss important sources of selection bias that emerge in the analysis of this molecular system and consider the complicating effects of molecular conformation and variable experimental conditions (e.g., pore diameter). We then present additional refinements to existing analysis techniques, allowing for improved separation of multiplexed samples, fewer translocation events rejected as false negatives, and a wider range of experimental conditions for which accurate molecular information can be extracted. Increasing the coverage of analyzed events within nanopore data is not only important for characterizing complex molecular samples with high fidelity but is also becoming essential to the generation of accurate, unbiased training data as machine-learning approaches to data analysis and event identification continue to increase in prevalence.
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Affiliation(s)
- Zachary Roelen
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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36
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Straathof S, Di Muccio G, Yelleswarapu M, Alzate Banguero M, Wloka C, van der Heide NJ, Chinappi M, Maglia G. Protein Sizing with 15 nm Conical Biological Nanopore YaxAB. ACS Nano 2023; 17:13685-13699. [PMID: 37458334 PMCID: PMC10373527 DOI: 10.1021/acsnano.3c02847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Nanopores are promising single-molecule tools for the electrical identification and sequencing of biomolecules. However, the characterization of proteins, especially in real-time and in complex biological samples, is complicated by the sheer variety of sizes and shapes in the proteome. Here, we introduce a large biological nanopore, YaxAB for folded protein analysis. The 15 nm cis-opening and a 3.5 nm trans-constriction describe a conical shape that allows the characterization of a wide range of proteins. Molecular dynamics showed proteins are captured by the electroosmotic flow, and the overall resistance is largely dominated by the narrow trans constriction region of the nanopore. Conveniently, proteins in the 35-125 kDa range remain trapped within the conical lumen of the nanopore for a time that can be tuned by the external bias. Contrary to cylindrical nanopores, in YaxAB, the current blockade decreases with the size of the trapped protein, as smaller proteins penetrate deeper into the constriction region than larger proteins do. These characteristics are especially useful for characterizing large proteins, as shown for pentameric C-reactive protein (125 kDa), a widely used health indicator, which showed a signal that could be identified in the background of other serum proteins.
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Affiliation(s)
- Sabine Straathof
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Giovanni Di Muccio
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Maaruthy Yelleswarapu
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Melissa Alzate Banguero
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Carsten Wloka
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
- Experimental Ophthalmology, Department of Ophthalmology, Charité - Universitätsmedizin Berlin, A Corporate Member of Freie Universität, Humboldt-University, The Berlin Institute of Health, Berlin 10178, Germany
| | - Nieck Jordy van der Heide
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Mauro Chinappi
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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37
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Miao L, Huang B, Fang H, Chai J, Liu Z, Zhai Y. Single-Nanoparticle-Based Nanomachining for Fabrication of a Uniform Nanochannel Sensor. Adv Mater 2023:e2305159. [PMID: 37486796 DOI: 10.1002/adma.202305159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/07/2023] [Indexed: 07/26/2023]
Abstract
The structure of nanomaterials and nanodevices determines their functionality and applications. A single uniform nanochannel with a high aspect ratio is an attractive structure due to its unique rigid structures, easy preparation, and diverse pore structures and it holds significant promising importance in fields such as nanopore sensing and nanomanufacturing. Although the metal-nanoparticle-assistant silicon etching technique can produce uniform nanochannels, however, the fabrication of single through nanochannels remains a challenge thus far. A simple and versatile strategy is developed that allows for the retention of individual gold nanoparticle on a substrate, enabling single-nanoparticle nanomachining. This method involves three steps: the formation of a carbon protective layer on individual nanoparticles via electron-beam irradiation, selective removal of unprotected nanoparticles using a corrosive agent, and subsequent elimination of the carbon layer. This enables the fabrication of a single submillimeter-long uniform through nanochannel in the silicon wafer, which can be employed for nanopore sensing and shape-based nanoparticle distinguishing. The developed method can also facilitate single-nanoparticle studies and nanomachining for a broad application in materials science, electronics, micro/nano-optics, and catalysis.
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Affiliation(s)
- Longfei Miao
- 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
| | - Hui Fang
- 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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38
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Saharia J, Bandara YMNDY, Karawdeniya BI, Dwyer JR, Kim MJ. Over One Million DNA and Protein Events Through Ultra-Stable Chemically-Tuned Solid-State Nanopores. Small 2023; 19:e2300198. [PMID: 37026669 PMCID: PMC10524034 DOI: 10.1002/smll.202300198] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Stability, long lifetime, resilience against clogging, low noise, and low cost are five critical cornerstones of solid-state nanopore technology. Here, a fabrication protocol is described wherein >1 million events are obtained from a single solid-state nanopore with both DNA and protein at the highest available lowpass filter (LPF, 100 kHz) of the Axopatch 200B-the highest event count mentioned in literature. Moreover, a total of ≈8.1 million events are reported in this work encompassing the two analyte classes. With the 100 kHz LPF, the temporally attenuated population is negligible while with the more ubiquitous 10 kHz, ≈91% of the events are attenuated. With DNA experiments, the pores are operational for hours (typically >7 h) while the average pore growth is merely ≈0.16 ± 0.1 nm h-1 . The current noise is exceptionally stable with traces typically showing <10 pA h-1 increase in noise. Furthermore, a real-time method to clean and revive pores clogged with analyte with the added benefit of minimal pore growth during cleaning (< 5% of the original diameter) is showcased. The enormity of the data collected herein presents a significant advancement to solid-state pore performance and will be useful for future ventures such as machine learning where large amounts of pristine data are a prerequisite.
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Affiliation(s)
- Jugal Saharia
- Department of Mechanical Engineering, Southern Methodist University, TX 75275, USA
- Department of Mechanical Engineering, The University of Texas Permian Basin, Odessa, TX 79762, USA
| | | | - Buddini I. Karawdeniya
- Department of Electronic Materials Engineering, Research School of Physics, The Australian National University, Canberra, ACT 2601 Australia
| | - Jason R. Dwyer
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, RI 02881, USA
| | - Min Jun Kim
- Department of Mechanical Engineering, Southern Methodist University, TX 75275, USA
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39
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Afshar Bakshloo M, Yahiaoui S, Bourderioux M, Daniel R, Pastoriza-Gallego M, Kasianowicz JJ, Oukhaled A. Discrimination between Alpha-Synuclein Protein Variants with a Single Nanometer-Scale Pore. ACS Chem Neurosci 2023. [PMID: 37382504 DOI: 10.1021/acschemneuro.3c00164] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023] Open
Abstract
Alpha-synuclein is one of several key factors in the regulation of nerve activity. It is striking that single- or multiple-point mutations in the 140-amino-acid-long protein can change its structure, which leads to the protein's aggregation and fibril formation (which is associated with several neurodegenerative diseases, e.g., Parkinson's disease). We recently demonstrated that a single nanometer-scale pore can identify proteins based on its ability to discriminate between protease-generated polypeptide fragments. We show here that a variation of this method can readily discriminate between the wild-type alpha synuclein, a known deleterious point mutation of the glutamic acid at position 46 replaced with a lysine (E46K), and post-translational modifications (i.e., tyrosine Y39 nitration and serine 129 phosphorylation).
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Affiliation(s)
| | - Safia Yahiaoui
- CY Cergy Paris Université, CNRS, LAMBE, Cergy 95000, France
| | - Matthieu Bourderioux
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes 91025, France
| | - Regis Daniel
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes 91025, France
| | | | - John J Kasianowicz
- Dept. of Physics, University of South Florida, 4202 E. Fowler Avenue, ISA Building, Tampa, Florida 33620, United States
- Dept. of Applied Physics & Applied Mathematics, Columbia University, New York, New York 10027, United States
- Freiburg Institute for Advanced Studies, Albert-Ludwigs Universität Freiburg, Albertstraße 19, Freiburg 79104, Germany
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40
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Liu M, Li J, Tan CS. Unlocking the Power of Nanopores: Recent Advances in Biosensing Applications and Analog Front-End. Biosensors (Basel) 2023; 13:598. [PMID: 37366963 DOI: 10.3390/bios13060598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023]
Abstract
The biomedical field has always fostered innovation and the development of various new technologies. Beginning in the last century, demand for picoampere-level current detection in biomedicine has increased, leading to continuous breakthroughs in biosensor technology. Among emerging biomedical sensing technologies, nanopore sensing has shown great potential. This paper reviews nanopore sensing applications, such as chiral molecules, DNA sequencing, and protein sequencing. However, the ionic current for different molecules differs significantly, and the detection bandwidths vary as well. Therefore, this article focuses on current sensing circuits, and introduces the latest design schemes and circuit structures of different feedback components of transimpedance amplifiers mainly used in nanopore DNA sequencing.
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Affiliation(s)
- Miao Liu
- Medical College, Tianjin University, Tianjin 300072, China
| | - Junyang Li
- Medical College, Tianjin University, Tianjin 300072, China
| | - Cherie S Tan
- Medical College, Tianjin University, Tianjin 300072, China
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41
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Wu R, Wang Y, Yu J, Li H, Yu C, Wang H, Wang M, Li B. Duplex Polymerization Strategy for General, Programmable and High-Resolution Nanopore Detection. Angew Chem Int Ed Engl 2023:e202304891. [PMID: 37230934 DOI: 10.1002/anie.202304891] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 05/27/2023]
Abstract
Nanopore sensing is highly promising in single molecular analysis but their broad applications have been challenged by the limited strategies that can transduce a target-of-interest into a specific and anti-false/inference signal, especially for solid-state nanopores with relatively lower resolution and higher noise. Here we report a high-resolution signal-production concept named target-induced duplex polymerization strategy (DPS). Through linking the same or different duplex substrates (DSs) with a special linker (L) and an optional structure tag (ST), the DPS can generate target-specific DS polymers with highly controllable duration times, duration intervals and even distinguished secondary tagging currents. Experimentally, DPS mono-polymerization of single DS and co-polymerization of multiple DSs has verified the duration time of a DPS product is the sum of those for each DS monomer. Tetrahedron-DNA structures with different sizes are used as the STs to provide needle-like secondary peaks for further resolution enhancement and multiplex assay. With these examples DPS represents a general, programmable and advanced strategy that may simultaneously provide size-amplification, concentration amplification, and signal-specificity for molecular recognition. It is also promisingly in various applications regarding to single molecular investigation, such as polymerization degree, structure/side chain conformation, programmable multiplex decoding and information index.
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Affiliation(s)
- Ruiping Wu
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences, State Key Lab of Electroanalytical Chemistry, 5625 Remin Street, Changchun, 130022, Changchun, CHINA
| | - Yesheng Wang
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences, State Key Lab of Electroanalytical Chemistry, CHINA
| | - Jin Yu
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences, State Key Lab of Electroanalytical Chemistry, CHINA
| | - Huan Li
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences, State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, 130022, Changchun, CHINA
| | - Chunmiao Yu
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences, State Key Lab of Electroanalytical Chemistry, CHINA
| | - Huaning Wang
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences, State Key Lab of Electroanalytical Chemistry, 5625 Remin Street, Changchun, 130022, Changchun, CHINA
| | - Ming Wang
- Jilin University, State Key Laboratory of Supramolecular Structure and Materials, Changchun, CHINA
| | - Bingling Li
- Changchun Institute of Applied Chemistry, Chinese Academy of Science, State Key Lab of Electroanalytical Chemistry, 5625 Renmin Street, 130022, Changchun, CHINA
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Hu S, Zhang H, Yang Y, Wang W, Zhou W, Shen X, Liu C. Reductive Sequestration of Cr(VI) and Immobilization of C during the Microbially Mediated Transformation of Ferrihydrite-Cr(VI)-Fulvic Acid Coprecipitates. Environ Sci Technol 2023. [PMID: 37216216 DOI: 10.1021/acs.est.2c09803] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cr(VI) detoxification and organic matter (OM) stabilization are usually influenced by the biological transformation of iron (Fe) minerals; however, the underlying mechanisms of metal-reducing bacteria on the coupled kinetics of Fe minerals, Cr, and OM remain unclear. Here, the reductive sequestration of Cr(VI) and immobilization of fulvic acid (FA) during the microbially mediated phase transformation of ferrihydrite with varying Cr/Fe ratios were investigated. No phase transformation occurred until Cr(VI) was completely reduced, and the ferrihydrite transformation rate decreased as the Cr/Fe ratio increased. Microscopic analysis was uncovered, which revealed that the resulting Cr(III) was incorporated into the lattice structure of magnetite and goethite, whereas OM was mainly adsorbed on goethite and magnetite surfaces and located within pore spaces. Fine line scan profiles showed that OM adsorbed on the Fe mineral surface had a lower oxidation state than that within nanopores, and C adsorbed on the magnetite surface had the highest oxidation state. During reductive transformation, the immobilization of FA by Fe minerals was predominantly via surface complexation, and OM with highly aromatic and unsaturated structures and low H/C ratios was easily adsorbed by Fe minerals or decomposed by bacteria, whereas Cr/Fe ratios had little effect on the binding of Fe minerals and OM and the variations in OM components. Owing to the inhibition of crystalline Fe minerals and nanopore formation in the presence of Cr, Cr sequestration and C immobilization can be synchronously favored at low Cr/Fe ratios. These findings provide a profound theoretical basis for Cr detoxification and synchronous sequestration of Cr and C in anoxic soils and sediments.
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Affiliation(s)
- Shiwen Hu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, People's Republic of China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of the Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China
| | - Hanyue Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Yang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, People's Republic of China
| | - Weiqi Wang
- Institute of Geography, Key Laboratory of Humid Sub-tropical Eco-geographical Process of Ministry of Education, Fujian Normal University, Fuzhou 350007, People's Republic of China
| | - Wenjing Zhou
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of the Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China
| | - Xinyue Shen
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of the Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China
| | - Chongxuan Liu
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of the Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China
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Hu T, Zhao L, Wang Y, Lin H, Xie S, Hu Y, Liu C, Zhu W, Wei Z, Liu J, Wang K. High-Sensitivity and Fast-Speed UV Photodetectors Based on Asymmetric Nanoporous-GaN/Graphene Vertical Junction. ACS Nano 2023; 17:8411-8419. [PMID: 37115108 DOI: 10.1021/acsnano.3c00263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
GaN-based photodetectors are strongly desirable in many advanced fields, such as space communication, environmental monitoring, etc. However, the slow photo-response speed in currently reported high-sensitivity GaN-based photodetectors still hinders their applications. Here, we demonstrate a high-sensitivity and fast-speed UV photodetector based on asymmetric Au/nanoporous-GaN/graphene vertical junctions. The nanoporous GaN-based vertical photodetector shows an excellent rectification ratio up to ∼105 at +4 V/-4 V. The photo-responsivity and specific detectivity of the device is up to 1.01 × 104 A/W and 7.84 × 1014 Jones, respectively, more than three orders of magnitude higher than the control planar photodetector. With switching light on and off, the repeatable on/off current ratio of the nanoporous GaN-based vertical photodetector is ∼4.32 × 103, which is about 1.51 × 103 times to that of the control planar device. The measured rise/decay time is 12.2 μs/14.6 μs, which is the fastest value for the high-sensitivity GaN-based photodetectors to date. These results suggest that the asymmetric Au/nanoporous-GaN/graphene structure can improve the sensitivity and the photo-response speed of GaN-based PDs simultaneously.
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Affiliation(s)
- Tiangui Hu
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lixia Zhao
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China
- School of Electrical Engineering, Tiangong University, No. 399, Binshuixi Road, Xiqing District, Tianjin 300387, China
| | - Yujing Wang
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hailong Lin
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shihong Xie
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China
- School of Physics and Astronomy, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Yin Hu
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chang Liu
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China
| | - Wenkai Zhu
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China
| | - Zhongming Wei
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Liu
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaiyou Wang
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
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44
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Zhang X, Galenkamp NS, van der Heide NJ, Moreno J, Maglia G, Kjems J. Specific Detection of Proteins by a Nanobody-Functionalized Nanopore Sensor. ACS Nano 2023; 17:9167-9177. [PMID: 37127291 PMCID: PMC10184537 DOI: 10.1021/acsnano.2c12733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Nanopores are label-free single-molecule analytical tools that show great potential for stochastic sensing of proteins. Here, we described a ClyA nanopore functionalized with different nanobodies through a 5-6 nm DNA linker at its periphery. Ty1, 2Rs15d, 2Rb17c, and nb22 nanobodies were employed to specifically recognize the large protein SARS-CoV-2 Spike, a medium-sized HER2 receptor, and the small protein murine urokinase-type plasminogen activator (muPA), respectively. The pores modified with Ty1, 2Rs15d, and 2Rb17c were capable of stochastic sensing of Spike protein and HER2 receptor, respectively, following a model where unbound nanobodies, facilitated by a DNA linker, move inside the nanopore and provoke reversible blockade events, whereas engagement with the large- and medium-sized proteins outside of the pore leads to a reduced dynamic movement of the nanobodies and an increased current through the open pore. Exploiting the multivalent interaction between trimeric Spike protein and multimerized Ty1 nanobodies enabled the detection of picomolar concentrations of Spike protein. In comparison, detection of the smaller muPA proteins follows a different model where muPA, complexing with the nb22, moves into the pore, generating larger blockage signals. Importantly, the components in blood did not affect the sensing performance of the nanobody-functionalized nanopore, which endows the pore with great potential for clinical detection of protein biomarkers.
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Affiliation(s)
- Xialin Zhang
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
| | | | | | - Julián Moreno
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
| | | | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark
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Wang X, Pettes MT, Wang Y, Zhu JX, Dhall R, Song C, Jones AC, Ciston J, Yoo J. Enhanced Exciton-to-Trion Conversion by Proton Irradiation of Atomically Thin WS 2. Nano Lett 2023; 23:3754-3761. [PMID: 37094221 DOI: 10.1021/acs.nanolett.2c04987] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Defect engineering of van der Waals semiconductors has been demonstrated as an effective approach to manipulate the structural and functional characteristics toward dynamic device controls, yet correlations between physical properties with defect evolution remain underexplored. Using proton irradiation, we observe an enhanced exciton-to-trion conversion of the atomically thin WS2. The altered excitonic states are closely correlated with nanopore induced atomic displacement, W nanoclusters, and zigzag edge terminations, verified by scanning transmission electron microscopy, photoluminescence, and Raman spectroscopy. Density functional theory calculation suggests that nanopores facilitate formation of in-gap states that act as sinks for free electrons to couple with excitons. The ion energy loss simulation predicts a dominating electron ionization effect upon proton irradiation, providing further evidence on band perturbations and nanopore formation without destroying the overall crystallinity. This study provides a route in tuning the excitonic properties of van der Waals semiconductors using an irradiation-based defect engineering approach.
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Affiliation(s)
- Xuejing Wang
- Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Michael Thompson Pettes
- Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Yongqiang Wang
- Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Materials Science in Radiation and Dynamics Extremes (MST-8), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Jian-Xin Zhu
- Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Physics of Condensed Matter and Complex Systems (T-4), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Rohan Dhall
- National Center for Electron Microscopy (NCEM), Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Chengyu Song
- National Center for Electron Microscopy (NCEM), Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Andrew C Jones
- Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Jim Ciston
- National Center for Electron Microscopy (NCEM), Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jinkyoung Yoo
- Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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46
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Tosaka T, Kamiya K. Function Investigations and Applications of Membrane Proteins on Artificial Lipid Membranes. Int J Mol Sci 2023; 24:ijms24087231. [PMID: 37108393 PMCID: PMC10138308 DOI: 10.3390/ijms24087231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Membrane proteins play an important role in key cellular functions, such as signal transduction, apoptosis, and metabolism. Therefore, structural and functional studies of these proteins are essential in fields such as fundamental biology, medical science, pharmacology, biotechnology, and bioengineering. However, observing the precise elemental reactions and structures of membrane proteins is difficult, despite their functioning through interactions with various biomolecules in living cells. To investigate these properties, methodologies have been developed to study the functions of membrane proteins that have been purified from biological cells. In this paper, we introduce various methods for creating liposomes or lipid vesicles, from conventional to recent approaches, as well as techniques for reconstituting membrane proteins into artificial membranes. We also cover the different types of artificial membranes that can be used to observe the functions of reconstituted membrane proteins, including their structure, number of transmembrane domains, and functional type. Finally, we discuss the reconstitution of membrane proteins using a cell-free synthesis system and the reconstitution and function of multiple membrane proteins.
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Affiliation(s)
- Toshiyuki Tosaka
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Gunma 376-8515, Japan
| | - Koki Kamiya
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Gunma 376-8515, Japan
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47
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Xing Y, Dorey A, Howorka S. Multi-Stimuli-Responsive and Mechano-Actuated Biomimetic Membrane Nanopores Self-Assembled from DNA. Adv Mater 2023:e2300589. [PMID: 37029712 DOI: 10.1002/adma.202300589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/31/2023] [Indexed: 06/04/2023]
Abstract
In bioinspired design, biological templates are mimicked in structure and function by highly controllable synthetic means. Of interest are static barrel-like nanopores that enable molecular transport across membranes for use in biosensing, sequencing, and biotechnology. However, biological ion channels offer additional functions such as dynamic changes of the entire pore shape between open and closed states, and triggering of dynamic processes with biochemical and physical stimuli. To better capture this complexity, this report presents multi-stimuli and mechano-responsive biomimetic nanopores which are created with DNA nanotechnology. The nanopores switch between open and closed states, whereby specific binding of DNA and protein molecules as stimuli locks the pores in the open state. Furthermore, the physical stimulus of high transmembrane voltage switches the pores into a closed state. In addition, the pore diameters are larger and more tunable than those of natural templates. These multi-stimuli-responsive and mechanically actuated nanopores mimic several aspects of complex biological channels yet offer easier control over pore size, shape and stimulus response. The designer pores are expected to be applied in biosensing and synthetic biology.
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Affiliation(s)
- Yongzheng Xing
- Department of Chemistry & Institute of Structural and Molecular Biology, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Adam Dorey
- Department of Chemistry & Institute of Structural and Molecular Biology, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Stefan Howorka
- Department of Chemistry & Institute of Structural and Molecular Biology, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
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48
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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. Adv Mater 2023; 35:e2210342. [PMID: 36823450 DOI: 10.1002/adma.202210342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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49
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Singh SL, Chauhan K, Bharadwaj AS, Kishore V, Laux P, Luch A, Singh AV. Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges. Int J Mol Sci 2023; 24:6153. [PMID: 37047125 PMCID: PMC10094227 DOI: 10.3390/ijms24076153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/01/2023] [Accepted: 02/28/2023] [Indexed: 03/31/2023] Open
Abstract
Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.
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Affiliation(s)
- Swarn Lata Singh
- Department of Physics, Mahila Mahavidyalaya (MMV), Banaras Hindu University, Varanasi 221005, UP, India
| | - Keerti Chauhan
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India
| | - Atul S. Bharadwaj
- Department of Physics, CMP Degree College, University of Allahabad, Prayagraj 211002, UP, India
| | - Vimal Kishore
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India
| | - Peter Laux
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Andreas Luch
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Ajay Vikram Singh
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
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Liu HL, Ahmed SA, Jiang QC, Shen Q, Zhan K, Wang K. Gold Nanotriangle-Assembled Nanoporous Structures for Electric Field-Assisted Surface-Enhanced Raman Scattering Detection of Adenosine Triphosphate. ACS Sens 2023; 8:1280-1286. [PMID: 36920780 DOI: 10.1021/acssensors.2c02759] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
A reliable, rapid, cost-effective, and simple method for the detection of biomolecules would greatly promote the research of analytical detection of single molecules. A nanopore-based analytical technique is promising for detecting biomolecules. Conventional electrochemical nanopores cannot distinguish biomolecules precisely because of their fast translocation speed and limited electrochemical information. Therefore, it is highly desirable to develop electrochemical surface-enhanced Raman scattering (SERS) nanopores to obtain multidimensional information. Herein, we designed and fabricated gold nanotriangle (AuNT)-assembled porous structures at the tip of a glass capillary using dithiol adenosine triphosphate (ATP) aptamers as cross-linking molecules. The AuNTs exhibited an edge length of 57.3 ± 6.2 nm and thickness of about 15 nm. The gold nanoporous structure (GPS) showed a strong ion rectification even at a high concentration of electrolyte (2 M) and a high SERS activity. Based on these designed structures, SERS and electrochemistry techniques were combined to control the rapid movement of ATP to the vicinity of the GPS by an applied potential of +1 V, where ATP was concentrated by ATP aptamers and the molecular signals were amplified by SERS. As a result, the GPS successfully detected ATP at a concentration as low as 10-7 M.
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Affiliation(s)
- Hai-Ling Liu
- School of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing 312000, China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Saud Asif Ahmed
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Qiu-Cen Jiang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Qi Shen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Kan Zhan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Kang Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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