1
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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] [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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2
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Kong N, He J, Yang W. Formation of Molecular Junctions by Single-Entity Collision Electrochemistry. J Phys Chem Lett 2023; 14:8513-8524. [PMID: 37722010 DOI: 10.1021/acs.jpclett.3c01955] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
Controlling and understanding the chemistry of molecular junctions is one of the major themes in various fields ranging from chemistry and nanotechnology to biotechnology and biology. Stochastic single-entity collision electrochemistry (SECE) provides powerful tools to study a single entity, such as single cells, single particles, and even single molecules, in a nanoconfined space. Molecular junctions formed by SECE collision show various potential applications in monitoring molecular dynamics with high spatial resolution and high temporal resolution and in feasible combination with hybrid techniques. This Perspective highlights the new breakthroughs, seminal studies, and trends in the area that have been most recently reported. In addition, future challenges for the study of molecular junction dynamics with SECE are discussed.
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Affiliation(s)
- Na Kong
- School of Life and Environmental Science, Centre for Sustainable Bioproducts, Deakin University, Geelong, Victoria 3216, Australia
| | - Jin He
- Physics Department, Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Wenrong Yang
- School of Life and Environmental Science, Centre for Sustainable Bioproducts, Deakin University, Geelong, Victoria 3216, Australia
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3
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Das A, K V, S SD, Mahendran KR. Synthetic α-Helical Nanopore Reactor for Chemical Sensing. JACS AU 2023; 3:2467-2477. [PMID: 37772177 PMCID: PMC10523496 DOI: 10.1021/jacsau.3c00221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 09/30/2023]
Abstract
The use of nanopores for the single-molecule sensing of folded proteins and biomacromolecules has recently gained attention. Here, we introduce a simplified synthetic α-helical transmembrane pore, pPorA, as a nanoreactor and sensor that exhibits functional versatility comparable to that of engineered protein and DNA nanopores. The pore, built from the assembly of synthetic 40-amino-acid-long peptides, is designed to contain cysteine residues within the lumen and at the pore terminus for site-specific chemical modification probed using single-channel electrical recordings. The reaction of the pore with differently charged activated thiol reagents was studied, wherein positively charged reagents electrophoretically driven into the pore resulted in pore blocking in discrete steps upon covalent bond formation. The asymmetric blockage patterns resulting from cis and trans-side addition of reagents reveal the pore orientation in the lipid membrane. Furthermore, activated PEG thiols covalently blocked the pores over a longer duration in a charge-independent manner, establishing the large diameter and orientation of the formed pores. While the covalent binding of thiol reagents caused a drop in the pore conductance, cationic cyclic octasaccharides produced time-resolved translocation events, confirming the structural flexibility and tunability of the pores. The ability of the pore to accommodate large analytes and the considerable current amplitude variation following bond formation events are promising for developing platforms to resolve multistep chemical reactions at the single-molecule level for applications in synthetic nanobiotechnology.
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Affiliation(s)
- Anjali
Devi Das
- Membrane Biology Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India 695014
| | - Vidhu K
- Membrane Biology Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India 695014
| | - Smitha Devi S
- Membrane Biology Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India 695014
| | - Kozhinjampara R Mahendran
- Membrane Biology Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India 695014
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4
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Du X, Zhang S, Wang L, Wang Y, Fan P, Jia W, Zhang P, Huang S. Single-Molecule Interconversion between Chiral Configurations of Boronate Esters Observed in a Nanoreactor. ACS NANO 2023; 17:2881-2892. [PMID: 36655995 DOI: 10.1021/acsnano.2c11286] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Isomers of some chemical compounds may be dynamically interconvertible. Due to a lack of sensing methods with a sufficient resolution, however, direct monitoring of such processes can be difficult. Engineered Mycobacterium smegmatis porin A (MspA) nanopores can be applied as nanoreactors so that chemical reactions can be directly monitored. Here, an MspA modified with a phenylboronic acid (PBA) adapter was prepared and was used to observe dynamic interconversion between chiral configurations of boronate esters, which appears as telegraphic switching on top of nanopore events. The mechanism of this behavior was further confirmed by trials with different halogenated catechols, dopamine, adenosine, 1,2-propanediol, and (2R,3R)-2,3-butanediol, and its generality has been demonstrated. These results suggest that an engineered MspA possesses an exceptional resolution in its monitoring of chemical reaction processes and may inspire the future design of nanopore small-molecule sensors.
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Affiliation(s)
- Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023Nanjing, China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023Nanjing, China
| | - Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023Nanjing, China
| | - Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023Nanjing, China
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5
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Ying YL, Hu ZL, Zhang S, Qing Y, Fragasso A, Maglia G, Meller A, Bayley H, Dekker C, Long YT. Nanopore-based technologies beyond DNA sequencing. NATURE NANOTECHNOLOGY 2022; 17:1136-1146. [PMID: 36163504 DOI: 10.1038/s41565-022-01193-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 06/02/2022] [Indexed: 06/16/2023]
Abstract
Inspired by the biological processes of molecular recognition and transportation across membranes, nanopore techniques have evolved in recent decades as ultrasensitive analytical tools for individual molecules. In particular, nanopore-based single-molecule DNA/RNA sequencing has advanced genomic and transcriptomic research due to the portability, lower costs and long reads of these methods. Nanopore applications, however, extend far beyond nucleic acid sequencing. In this Review, we present an overview of the broad applications of nanopores in molecular sensing and sequencing, chemical catalysis and biophysical characterization. We highlight the prospects of applying nanopores for single-protein analysis and sequencing, single-molecule covalent chemistry, clinical sensing applications for single-molecule liquid biopsy, and the use of synthetic biomimetic nanopores as experimental models for natural systems. We suggest that nanopore technologies will continue to be explored to address a number of scientific challenges as control over pore design improves.
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Affiliation(s)
- Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China
| | - Zheng-Li Hu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China
| | - Shengli Zhang
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Yujia Qing
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Alessio Fragasso
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
| | - Amit Meller
- Faculty of Biomedical Engineering, Technion-IIT, Haifa, Israel.
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford, UK.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China.
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6
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Krishnan R S, Jana K, Shaji AH, Nair KS, Das AD, Vikraman D, Bajaj H, Kleinekathöfer U, Mahendran KR. Assembly of transmembrane pores from mirror-image peptides. Nat Commun 2022; 13:5377. [PMID: 36104348 PMCID: PMC9474448 DOI: 10.1038/s41467-022-33155-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 09/05/2022] [Indexed: 11/18/2022] Open
Abstract
Tailored transmembrane alpha-helical pores with desired structural and functional versatility have promising applications in nanobiotechnology. Herein, we present a transmembrane pore DpPorA, based on the natural pore PorACj, built from D-amino acid α-helical peptides. Using single-channel current recordings, we show that DpPorA peptides self-assemble into uniform cation-selective pores in lipid membranes and exhibit properties distinct from their L-amino acid counterparts. DpPorA shows resistance to protease and acts as a functional nanopore sensor to detect cyclic sugars, polypeptides, and polymers. Fluorescence imaging reveals that DpPorA forms well-defined pores in giant unilamellar vesicles facilitating the transport of hydrophilic molecules. A second D-amino acid peptide based on the polysaccharide transporter Wza forms transient pores confirming sequence specificity in stable, functional pore formation. Finally, molecular dynamics simulations reveal the specific alpha-helical packing and surface charge conformation of the D-pores consistent with experimental observations. Our findings will aid the design of sophisticated pores for single-molecule sensing related technologies. Alpha-helix nanopores have a range of potential applications and the inclusion of non-natural amino acids allows for modification. Here, the authors report on the creation of alpha-helix pores using D-amino acids and show the pores formed, have different properties to the L-counterparts and were resistant to proteases.
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7
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Zhang LL, Zhong CB, Li JG, Niu HY, Ying YL, Long YT. A two-step calibration method for evaluation high bandwidth electrochemical instrument. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Wang L, Wang H, Chen X, Zhou S, Wang Y, Guan X. Chemistry solutions to facilitate nanopore detection and analysis. Biosens Bioelectron 2022; 213:114448. [PMID: 35716643 DOI: 10.1016/j.bios.2022.114448] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/24/2022] [Accepted: 05/30/2022] [Indexed: 11/29/2022]
Abstract
Characteristic ionic current modulations will be produced in a single molecule manner during the communication of individual molecules with a nanopore. Hence, the information regarding the length, composition, and structure of a molecule can be extracted from deciphering the electrical message. However, until now, achieving a satisfactory resolution for observation and quantification of a target analyte in a complex system remains a nontrivial task. In this review, we summarize the progress and especially the recent advance in utilizing chemistry solutions to facilitate nanopore detection and analysis. The discussed chemistry solutions are classified into several major categories, including covalent/non-covalent chemistry, redox chemistry, displacement chemistry, back titration chemistry, chelation chemistry, hydrolysis-chemistry, and click chemistry. Considering the significant success of using chemical reaction-assisted nanopore sensing strategies to improve sensor sensitivity & selectivity and to study various topics, other non-chemistry based methodologies can undoubtedly be employed by nanopore sensors to explore new applications in the interdisciplinary area of chemistry, biology, materials, and nanotechnology.
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Affiliation(s)
- Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Han Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Xiaohan Chen
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Shuo Zhou
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Yunjiao Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China.
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA.
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9
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Hwang HJ, Kim JS, Lee J, Min JS, Jeong KB, Kim E, Lee MK, Chi SW. Single-Molecule Sensing of an Anticancer Therapeutic Protein-Protein Interaction Using the Chemically Modified OmpG Nanopore. Anal Chem 2022; 94:7449-7454. [PMID: 35583342 DOI: 10.1021/acs.analchem.1c04840] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nanopore sensors are a highly attractive platform for single-molecule sensing for sequencing, disease diagnostics, and drug screening. Outer membrane protein G (OmpG) nanopores have advantages for single-molecule sensing owing to their rigid monomeric structure, which comprises seven flexible loops, providing distinct gating patterns upon analyte binding. Blocking of the protein-protein interaction between B-cell lymphoma-extra-large (Bcl-xL) and the BH3 domain of Bcl-2 homologous antagonist/killer (Bak-BH3) has been reported as a promising strategy for anticancer therapy. Here, we characterized the interaction between Bcl-xL and Bak-BH3 as well as its inhibition by a small-molecule inhibitor using click chemistry-based Bak-BH3 peptide-conjugated OmpG nanopores. The binding of Bcl-xL to Bak-BH3 generated characteristic gating signals involving significant changes in the amplitudes of noise and gating parameters such as gating frequency, open probability, and durations of open and closed states. Notably, specific inhibition of Bcl-xL by the small-molecule antagonist, ABT-737, led to the recovery of the noise and gating parameters. Collectively, these results revealed that the chemically modified OmpG nanopore can serve as a valuable sensor platform for ultrasensitive, rapid, and single-molecule-based drug screening against protein-protein interactions, which are therapeutic targets for various diseases.
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Affiliation(s)
- Hye-Jin Hwang
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon 34141, Republic of Korea.,Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Jin-Sik Kim
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon 34141, Republic of Korea
| | - Jeonghyun Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Jun Sik Min
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Ki-Baek Jeong
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon 34141, Republic of Korea
| | - Eunha Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Mi-Kyung Lee
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon 34141, Republic of Korea.,Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Seung-Wook Chi
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon 34141, Republic of Korea.,Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
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10
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Liu W, Yang ZL, Yang CN, Ying YL, Long YT. Profiling single-molecule reaction kinetics under nanopore confinement. Chem Sci 2022; 13:4109-4114. [PMID: 35440975 PMCID: PMC8985585 DOI: 10.1039/d1sc06837g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/13/2022] [Indexed: 02/02/2023] Open
Abstract
The study of a single-molecule reaction under nanoconfinement is beneficial for understanding the reactive intermediates and reaction pathways. However, the kinetics model of the single-molecule reaction under confinement remains elusive. Herein we engineered an aerolysin nanopore reactor to elaborate the single-molecule reaction kinetics under nanoconfinement. By identifying the bond-forming and non-bond-forming events directly, a four-state kinetics model is proposed for the first time. Our results demonstrated that the single-molecule reaction kinetics inside a nanopore depends on the frequency of individual reactants captured and the fraction of effective collision inside the nanopore confined space. This insight will guide the design of confined nanopore reactors for resolving the single-molecule chemistry, and shed light on the mechanistic understanding of dynamic covalent chemistry inside confined systems such as supramolecular cages, coordination cages, and micelles. A four-state kinetics model is proposed to reveal the kinetics of a single-molecule reaction under nanopore confinement.![]()
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Zhong-Lin Yang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Chao-Nan Yang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China .,Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing 210023 P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
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11
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Cairns-Gibson DF, Cockroft SL. Functionalised nanopores: chemical and biological modifications. Chem Sci 2022; 13:1869-1882. [PMID: 35308845 PMCID: PMC8848921 DOI: 10.1039/d1sc05766a] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/22/2021] [Indexed: 12/11/2022] Open
Abstract
Nanopore technology has established itself as a powerful tool for single-molecule studies. By analysing changes in the ion current flowing through a single transmembrane channel, a wealth of molecular information can be elucidated. Early studies utilised nanopore technology for sensing applications, and subsequent developments have diversified its remit. Nanopores can be synthetic, solid-state, or biological in origin, but recent work has seen these boundaries blurred as hybrid functionalised pores emerge. The modification of existing pores and the construction of novel synthetic pores has been an enticing goal for creating systems with tailored properties and functionality. Here, we explore chemically functionalised biological pores and the bio-inspired functionalisation of solid-state pores, highlighting how the convergence of these domains provides enhanced functionality. The convergence of chemistry, biology, and solid-state approaches enables the construction hybrid nanopores with enhanced single-molecule applications.![]()
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Affiliation(s)
- Dominic F. Cairns-Gibson
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
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12
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Abstract
Chemical reactions of single molecules, caused by rapid formation or breaking of chemical bonds, are difficult to observe even with state-of-the-art instruments. A biological nanopore can be engineered into a single molecule reactor, capable of detecting the binding of a monatomic ion or the transient appearance of chemical intermediates. Pore engineering of this type is however technically challenging, which has significantly restricted further development of this technique. We propose a versatile strategy, "programmable nano-reactors for stochastic sensing" (PNRSS), by which a variety of single molecule reactions of hydrogen peroxide, metal ions, ethylene glycol, glycerol, lactic acid, vitamins, catecholamines or nucleoside analogues can be observed directly. PNRSS presents a refined sensing resolution which can be further enhanced by an artificial intelligence algorithm. Remdesivir, a nucleoside analogue and an investigational anti-viral drug used to treat COVID-19, can be distinguished from its active triphosphate form by PNRSS, suggesting applications in pharmacokinetics or drug screening.
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13
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Yan S, Wang L, Du X, Zhang S, Wang S, Cao J, Zhang J, Jia W, Wang Y, Zhang P, Chen HY, Huang S. Rapid and multiplex preparation of engineered Mycobacterium smegmatis porin A (MspA) nanopores for single molecule sensing and sequencing. Chem Sci 2021; 12:9339-9346. [PMID: 34349904 PMCID: PMC8278974 DOI: 10.1039/d1sc01399h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/06/2021] [Indexed: 11/21/2022] Open
Abstract
Acknowledging its unique conical lumen structure, Mycobacterium smegmatis porin A (MspA) was the first type of nanopore that has successfully sequenced DNA. Recent developments of nanopore single molecule chemistry have also suggested MspA to be an optimum single molecule reactor. However, further investigations with this approach require heavy mutagenesis which is labor intensive and requires high end instruments for purifications. We here demonstrate an efficient and economic protocol which performs rapid and multiplex preparation of a variety of MspA mutants. The prepared MspA mutants were demonstrated in operations such as nanopore insertion, sequencing, optical single channel recording (oSCR), nanopore single molecule chemistry and nanopore rectification. The performance is no different from that of pores however prepared by other means. The time of all human operations and the cost for a single batch of preparation have been minimized to 40 min and 0.4$, respectively. This method is extremely useful in the screening of new MspA mutants, which has an urgent requirement in further investigations of new MspA nanoreactors. Its low cost and simplicity also enable efficient preparations of MspA nanopores for both industrial manufacturing and academic research.
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Affiliation(s)
- Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University210023NanjingChina
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University210023NanjingChina
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University210023NanjingChina
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University210023NanjingChina
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University210023NanjingChina
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University210023NanjingChina
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University210023NanjingChina
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University210023NanjingChina
| | - Sha Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University210023NanjingChina
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University210023NanjingChina
| | - Jiao Cao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University210023NanjingChina
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University210023NanjingChina
| | - Jinyue Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University210023NanjingChina
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University210023NanjingChina
| | - Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University210023NanjingChina
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University210023NanjingChina
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University210023NanjingChina
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University210023NanjingChina
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University210023NanjingChina
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University210023NanjingChina
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University210023NanjingChina
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University210023NanjingChina
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University210023NanjingChina
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University210023NanjingChina
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14
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Liang S, Zhang W, Xiang F. The effect of laser irradiation on reducing the noise of solid-state nanopore. NANOTECHNOLOGY 2021; 32:345301. [PMID: 33979783 DOI: 10.1088/1361-6528/ac007f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 05/12/2021] [Indexed: 06/12/2023]
Abstract
The performance of solid-state nanopore is affected by the noise level. This study aimed to investigate the effect of laser irradiation on the noise performance of solid-state nanoporein situ. Laser irradiation is applied to fresh and contaminated nanopores. The measurement results show that the noise of fresh and contaminated nanopores decreases with the laser power and there is a threshold of laser power in reducing the noise of contaminated nanopores. The possible reasons for reducing noise in the laser irradiation process are discussed. The laser treatment is proven to provide a convenient method for reducing the noise of solid-state nanopore.
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Affiliation(s)
- Shengfa Liang
- Key Lab of Microelectronic Devices & Integrated Technology, Institute of Microelectronics, Chinese Academy of Sciences, Beijing 100029, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Wenchang Zhang
- Key Lab of Microelectronic Devices & Integrated Technology, Institute of Microelectronics, Chinese Academy of Sciences, Beijing 100029, People's Republic of China
| | - Feibin Xiang
- Key Lab of Microelectronic Devices & Integrated Technology, Institute of Microelectronics, Chinese Academy of Sciences, Beijing 100029, People's Republic of China
- School of Electronic Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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15
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Yin YD, Zhang L, Leng XZ, Gu ZY. Harnessing biological nanopore technology to track chemical changes. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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Pham B, Chisholm CM, Foster J, Friis E, Fahie MA, Chen M. A pH-independent quiet OmpG pore with enhanced electrostatic repulsion among the extracellular loops. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183485. [PMID: 33058855 DOI: 10.1016/j.bbamem.2020.183485] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 09/22/2020] [Indexed: 11/16/2022]
Abstract
Membrane protein pores have emerged as powerful nanopore sensors for single-molecule detection. OmpG, a monomeric nanopore, is comprised of fourteen β-strands connected by seven flexible extracellular loops. The OmpG nanopore exhibits pH-dependent gating as revealed by planar lipid bilayer studies. Current evidence strongly suggests that the dynamic movement of loop 6 is responsible for the gating mechanism. In this work, we have shown that enhancing the electrostatic repulsion forces between extracellular loops suppressed the pH-dependent gating. Our mutant containing additional negative charges in loop 6 and loop 1 exhibited minimal spontaneous gating and reduced sensitivity to pH changes compared to the wild type OmpG. These results provide new evidence to support the mechanism of OmpG gating controlled by the complex electrostatic network around the gating loop 6. The pH-independent quiet OmpG pores could potentially be used as a sensing platform that operates at a broad range of pH conditions.
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Affiliation(s)
- Bach Pham
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, United States
| | - Christina M Chisholm
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, United States
| | - Joshua Foster
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, United States
| | - Emily Friis
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, United States
| | - Monifa A Fahie
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, United States
| | - Min Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, United States; Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, United States.
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17
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Qing Y, Liu MD, Hartmann D, Zhou L, Ramsay WJ, Bayley H. Single-Molecule Observation of Intermediates in Bioorthogonal 2-Cyanobenzothiazole Chemistry. Angew Chem Int Ed Engl 2020; 59:15711-15716. [PMID: 32589803 PMCID: PMC7496719 DOI: 10.1002/anie.202005729] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Indexed: 11/17/2022]
Abstract
We report a single-molecule mechanistic investigation into 2-cyanobenzothiazole (CBT) chemistry within a protein nanoreactor. When simple thiols reacted reversibly with CBT, the thioimidate monoadduct was approximately 80-fold longer-lived than the tetrahedral bisadduct, with important implications for the design of molecular walkers. Irreversible condensation between CBT derivatives and N-terminal cysteine residues has been established as a biocompatible reaction for site-selective biomolecular labeling and imaging. During the reaction between CBT and aminothiols, we resolved two transient intermediates, the thioimidate and the cyclic precursor of the thiazoline product, and determined the rate constants associated with the stepwise condensation, thereby providing critical information for a variety of applications, including the covalent inhibition of protein targets and dynamic combinatorial chemistry.
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Affiliation(s)
- Yujia Qing
- Department of ChemistryUniversity of OxfordOxfordOX1 3TAUK
| | - Mira D. Liu
- Department of ChemistryUniversity of OxfordOxfordOX1 3TAUK
- W. M. Keck Science DepartmentClaremont McKenna CollegeClaremontCA91711USA
- Present address: Department of ChemistryUniversity of CaliforniaBerkeleyCA94720-1460USA
| | - Denis Hartmann
- Department of ChemistryUniversity of OxfordOxfordOX1 3TAUK
| | - Linna Zhou
- Department of ChemistryUniversity of OxfordOxfordOX1 3TAUK
| | | | - Hagan Bayley
- Department of ChemistryUniversity of OxfordOxfordOX1 3TAUK
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18
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Qing Y, Liu MD, Hartmann D, Zhou L, Ramsay WJ, Bayley H. Single‐Molecule Observation of Intermediates in Bioorthogonal 2‐Cyanobenzothiazole Chemistry. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yujia Qing
- Department of Chemistry University of Oxford Oxford OX1 3TA UK
| | - Mira D. Liu
- Department of Chemistry University of Oxford Oxford OX1 3TA UK
- W. M. Keck Science Department Claremont McKenna College Claremont CA 91711 USA
- Present address: Department of Chemistry University of California Berkeley CA 94720-1460 USA
| | - Denis Hartmann
- Department of Chemistry University of Oxford Oxford OX1 3TA UK
| | - Linna Zhou
- Department of Chemistry University of Oxford Oxford OX1 3TA UK
| | | | - Hagan Bayley
- Department of Chemistry University of Oxford Oxford OX1 3TA UK
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19
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Liu X, Zeng Q, Liu C, Wang L. A Fourier Transform-Induced Data Process for Label-Free Selective Nanopore Analysis under Sinusoidal Voltage Excitations. Anal Chem 2020; 92:11635-11643. [PMID: 32786474 DOI: 10.1021/acs.analchem.0c01339] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Nanopore analysis based on a resistive-pulse technique is an attractive tool for single-molecule detection in different fields, but it suffers a great drawback in selectivity. A common solution to this challenge is to add extra sensing aptamers and labels to analytes by improving the sensitivity of their pulses for distinguishing. Compared to the labeling methods, we alternatively develop and demonstrate a novel data process for label-free nanopore analysis that enables the conversion of resistive current signals to more specific frequency domain phase angle features with the contribution from both sinusoidal voltage excitation and Fourier transform. In particular, we find that the transmural capacitance induced by nanoparticle translocations under a sinusoidal voltage plays an important role in this process, making phase angle features more pronounced. In practical applications, the method is successfully applied to directly distinguish the translocation events through a nanopipette by their unique phase angles for similarly sized SiO2, Ag, and Au nanoparticles and soft living organisms of HeLa and LoVo and even in a more complicated case of a SiO2, Ag, and Au nanoparticle mixture.
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Affiliation(s)
- Xuye Liu
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Qiang Zeng
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Cheng Liu
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Lishi Wang
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
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20
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Evaluating the sensing performance of nanopore blockade sensors: A case study of prostate-specific antigen assay. Biosens Bioelectron 2020; 165:112434. [PMID: 32729547 DOI: 10.1016/j.bios.2020.112434] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 02/07/2023]
Abstract
The detection principle of nanopore sensors relies on measuring changes in electrical signal as analyte molecules translocate through a nanoscale pore. There are two challenges with this experimental construct when using nanopores for quantitative sensing with low detection limits in complex samples. The first is getting the analyte to the nanopore in a reasonable time frame and the second is other species in the sample also translocating through the nanopore and generating erroneous signals. We have developed a nanopore blockade sensor that alleviates the limitations of diffusion-limited mass transport and non-specific signals. Antibody-modified magnetic nanoparticles are utilized to deliver analytes of interest extracted from sample to an array of antibody-modified nanopores under a controlled electromagnet, resulting in long-term nanopore blocking events due to the formation of sandwiched immunocomplexes. Herein, this study reports on understanding some of important parameters in determining the performance of nanopore blockade sensing system, where prostate-specific antigen (PSA) is used as a model analyte. We describe the characterization of nanopore blockade sensing of PSA by (1) tuning on/off the electromagnet, (2) varying nanopore number in a nanopore chip, and (3) deploying the sensor in human plasma. Results show that magnetophoresis effectively facilitates active delivery and selective sensing of PSA to the nanopore. Nanopore chips with a larger number of nanopores are shown to receive more nanopore blockades for a given concentration of analyte. Furthermore, identifiable blockade events accounted for successful detection of PSA in plasma, indicate the high specificity of the sensing system.
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21
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Lee S, Housden NG, Ionescu SA, Zimmer MH, Kaminska R, Kleanthous C, Bayley H. Transmembrane Epitope Delivery by Passive Protein Threading through the Pores of the OmpF Porin Trimer. J Am Chem Soc 2020; 142:12157-12166. [PMID: 32614588 PMCID: PMC7366379 DOI: 10.1021/jacs.0c02362] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Trimeric porins in the outer membrane (OM) of Gram-negative bacteria are the conduits by which nutrients and antibiotics diffuse passively into cells. The narrow gateways that porins form in the OM are also exploited by bacteriocins to translocate into cells by a poorly understood process. Here, using single-channel electrical recording in planar lipid bilayers in conjunction with protein engineering, we explicate the mechanism by which the intrinsically unstructured N-terminal translocation domain (IUTD) of the endonuclease bacteriocin ColE9 is imported passively across the Escherichia coli OM through OmpF. We show that the import is dominated by weak interactions of OmpF pores with binding epitopes within the IUTD that are orientationally biased and result in the threading of over 60 amino acids through 2 subunits of OmpF. Single-molecule kinetic analysis demonstrates that the IUTD enters from the extracellular side of OmpF and translocates to the periplasm where the polypeptide chain does an about turn in order to enter a neighboring subunit, only for some of these molecules to pop out of this second subunit before finally re-entering to form a stable complex. These intimately linked transport/binding processes generate an essentially irreversible, hook-like assembly that constrains an import activating peptide epitope between two subunits of the OmpF trimer.
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Affiliation(s)
- Sejeong Lee
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | | | - Sandra A Ionescu
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Matthew H Zimmer
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
| | - Hagan Bayley
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
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22
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Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
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Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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23
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Affiliation(s)
- Si-Min Lu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yue-Yi Peng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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24
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Wang S, Cao J, Jia W, Guo W, Yan S, Wang Y, Zhang P, Chen HY, Huang S. Single molecule observation of hard-soft-acid-base (HSAB) interaction in engineered Mycobacterium smegmatis porin A (MspA) nanopores. Chem Sci 2019; 11:879-887. [PMID: 34123066 PMCID: PMC8146584 DOI: 10.1039/c9sc05260g] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In the formation of coordination interactions between metal ions and amino acids in natural metalloproteins, the bound metal ion is critical either for the stabilization of the protein structure or as an enzyme co-factor. Though extremely small in size, metal ions, when bound to the restricted environment of an engineered biological nanopore, result in detectable perturbations during single channel recordings. All reported work of this kind was performed with engineered α-hemolysin nanopores and the observed events appear to be extremely small in amplitude (∼1–3 pA). We speculate that the cylindrical pore restriction of α-hemolysin may not be optimal for probing extremely small analytes. Mycobacterium smegmatis porin A (MspA), a conical shaped nanopore, was engineered to interact with Ca2+, Mn2+, Co2+, Ni2+, Zn2+, Pb2+ and Cd2+ and a systematically larger event amplitude (up to 10 pA) was observed. The measured rate constant suggests that the coordination of a single ion with an amino acid follows hard–soft-acid–base theory, which has never been systematically validated in the case of a single molecule. By adjusting the measurement pH from 6.8 to 8.0, the duration of a single ion binding event could be modified with a ∼46-fold time extension. The phenomena reported suggest MspA to be a superior engineering template for probing a variety of extremely small analytes, such as monatomic and polyatomic ions, small molecules or chemical intermediates, and the principle of hard–soft-acid–base interaction may be instructive in the pore design. The principle of hard–soft-acid–base (HSAB) theory was first validated in single molecule by measurements with engineered Mycobacterium smegmatis porin A (MspA) nanopore reactors.![]()
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Affiliation(s)
- Sha 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
| | - Jiao 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
| | - 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
| | - Weiming Guo
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University 210023 Nanjing China .,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University 210023 Nanjing China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University 210023 Nanjing China .,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University 210023 Nanjing China
| | - 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
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University 210023 Nanjing China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University 210023 Nanjing China
| | - 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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25
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Houghtaling J, Ying C, Eggenberger OM, Fennouri A, Nandivada S, Acharjee M, Li J, Hall AR, Mayer M. Estimation of Shape, Volume, and Dipole Moment of Individual Proteins Freely Transiting a Synthetic Nanopore. ACS NANO 2019; 13:5231-5242. [PMID: 30995394 DOI: 10.1021/acsnano.8b09555] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
This paper demonstrates that high-bandwidth current recordings in combination with low-noise silicon nitride nanopores make it possible to determine the molecular volume, approximate shape, and dipole moment of single native proteins in solution without the need for labeling, tethering, or other chemical modifications of these proteins. The analysis is based on current modulations caused by the translation and rotation of single proteins through a uniform electric field inside of a nanopore. We applied this technique to nine proteins and show that the measured protein parameters agree well with reference values but only if the nanopore walls were coated with a nonstick fluid lipid bilayer. One potential challenge with this approach is that an untethered protein is able to diffuse laterally while transiting a nanopore, which generates increasingly asymmetric disruptions in the electric field as it approaches the nanopore walls. These "off-axis" effects add an additional noise-like element to the electrical recordings, which can be exacerbated by nonspecific interactions with pore walls that are not coated by a fluid lipid bilayer. We performed finite element simulations to quantify the influence of these effects on subsequent analyses. Examining the size, approximate shape, and dipole moment of unperturbed, native proteins in aqueous solution on a single-molecule level in real time while they translocate through a nanopore may enable applications such as identifying or characterizing proteins in a mixture, or monitoring the assembly or disassembly of transient protein complexes based on their shape, volume, or dipole moment.
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Affiliation(s)
- Jared Houghtaling
- Department of Biomedical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Adolphe Merkle Insitute, University of Fribourg , CH-1700 Fribourg , Switzerland
| | - Cuifeng Ying
- Adolphe Merkle Insitute, University of Fribourg , CH-1700 Fribourg , Switzerland
| | - Olivia M Eggenberger
- Adolphe Merkle Insitute, University of Fribourg , CH-1700 Fribourg , Switzerland
| | - Aziz Fennouri
- Adolphe Merkle Insitute, University of Fribourg , CH-1700 Fribourg , Switzerland
| | - Santoshi Nandivada
- Department of Physics , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Mitu Acharjee
- Department of Physics , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Jiali Li
- Department of Physics , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Adam R Hall
- Wake Forest University School of Medicine , Winston Salem , North Carolina 27157 , United States
| | - Michael Mayer
- Adolphe Merkle Insitute, University of Fribourg , CH-1700 Fribourg , Switzerland
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26
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Haugland MM, Borsley S, Cairns-Gibson DF, Elmi A, Cockroft SL. Synthetically Diversified Protein Nanopores: Resolving Click Reaction Mechanisms. ACS NANO 2019; 13:4101-4110. [PMID: 30864781 DOI: 10.1021/acsnano.8b08691] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nanopores are emerging as a powerful tool for the investigation of nanoscale processes at the single-molecule level. Here, we demonstrate the methionine-selective synthetic diversification of α-hemolysin (α-HL) protein nanopores and their exploitation as a platform for investigating reaction mechanisms. A wide range of functionalities, including azides, alkynes, nucleotides, and single-stranded DNA, were incorporated into individual pores in a divergent fashion. The ion currents flowing through the modified pores were used to observe the trajectory of a range of azide-alkyne click reactions and revealed several short-lived intermediates in Cu(I)-catalyzed azide-alkyne [3 + 2] cycloadditions (CuAAC) at the single-molecule level. Analysis of ion-current fluctuations enabled the populations of species involved in rapidly exchanging equilibria to be determined, facilitating the resolution of several transient intermediates in the CuAAC reaction mechanism. The versatile pore-modification chemistry offers a useful approach for enabling future physical organic investigations of reaction mechanisms at the single-molecule level.
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Affiliation(s)
- Marius M Haugland
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
| | - Stefan Borsley
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
| | - Dominic F Cairns-Gibson
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
| | - Alex Elmi
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
| | - Scott L Cockroft
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
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27
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Pulcu GS, Galenkamp NS, Qing Y, Gasparini G, Mikhailova E, Matile S, Bayley H. Single-Molecule Kinetics of Growth and Degradation of Cell-Penetrating Poly(disulfide)s. J Am Chem Soc 2019; 141:12444-12447. [DOI: 10.1021/jacs.9b00387] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Gökçe Su Pulcu
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | | | - Yujia Qing
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Giulio Gasparini
- Department of Chemistry, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Ellina Mikhailova
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Stefan Matile
- Department of Chemistry, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
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28
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Nguyen TK, Negishi H, Abe S, Ueno T. Construction of supramolecular nanotubes from protein crystals. Chem Sci 2019; 10:1046-1051. [PMID: 30774900 PMCID: PMC6346403 DOI: 10.1039/c8sc04167a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 10/26/2018] [Indexed: 01/26/2023] Open
Abstract
Investigations involving the design of protein assemblies for the development of biomaterials are receiving significant attention. In nature, proteins can be driven into assemblies frequently by various non-covalent interactions. Assembly of proteins into supramolecules can be conducted under limited conditions in solution. These factors force the assembly process into an equilibrium state with low stability. Here, we report a new method for preparing assemblies using protein crystals as non-equilibrium molecular scaffolds. Protein crystals provide an ideal environment with a highly ordered packing of subunits in which the supramolecular assembled structures are formed in the crystalline matrix. Based on this feature, we demonstrate the self-assembly of supramolecular nanotubes constructed from protein crystals triggered by co-oxidation with cross-linkers. The assembly of tubes is driven by the formation of disulfide bonds to retain the intermolecular interactions within each assembly in the crystalline matrix after dissolution of the crystals.
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Affiliation(s)
- Tien Khanh Nguyen
- School of Life Science and Technology , Tokyo Institute of Technology , Nagatsuta-cho , Midori-ku , Yokohama 226-8501 , Japan .
| | - Hashiru Negishi
- School of Life Science and Technology , Tokyo Institute of Technology , Nagatsuta-cho , Midori-ku , Yokohama 226-8501 , Japan .
| | - Satoshi Abe
- School of Life Science and Technology , Tokyo Institute of Technology , Nagatsuta-cho , Midori-ku , Yokohama 226-8501 , Japan .
| | - Takafumi Ueno
- School of Life Science and Technology , Tokyo Institute of Technology , Nagatsuta-cho , Midori-ku , Yokohama 226-8501 , Japan .
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29
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Ramsay WJ, Bell NAW, Qing Y, Bayley H. Single-Molecule Observation of the Intermediates in a Catalytic Cycle. J Am Chem Soc 2018; 140:17538-17546. [DOI: 10.1021/jacs.8b09282] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- William J. Ramsay
- University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, United Kingdom
| | - Nicholas A. W. Bell
- University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, United Kingdom
| | - Yujia Qing
- University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, United Kingdom
| | - Hagan Bayley
- University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, United Kingdom
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30
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Ying YL, Li YJ, Mei J, Gao R, Hu YX, Long YT, Tian H. Manipulating and visualizing the dynamic aggregation-induced emission within a confined quartz nanopore. Nat Commun 2018; 9:3657. [PMID: 30194303 PMCID: PMC6128826 DOI: 10.1038/s41467-018-05832-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 07/26/2018] [Indexed: 11/18/2022] Open
Abstract
Aggregation-induced emission (AIE) as a unique photophysical process has been intensively explored for their features in fields from optical sensing, bioimaging to optoelectronic devices. However, all AIE luminogens (AIEgens) hardly recover into the initial dispersed state after illuminating at the ultimate aggregated state, which limits AIEgens to achieve reversible sensing and reproducible devices. To real-time manipulate the emission of AIEgen, here we take the advantage of confined space in the quartz nanopore to achieve a nanopore-size-dependent restriction of AIEgens for reversible conversions of “on-to-off” and “off-to-on” emission. By electrochemically manipulating 26 fL AIEgen solution inside nanopore confinement, AIE illuminates while moves along nanopore from the constricted tip to inside cavity at a velocity of 1.4–2.2 μm s−1, and vice versa. We further apply this dynamic manipulation for a target delivery of AIEgen into single cells, which opens up new possibility to design powerful and practical AIE applications. The difficulty in recovering the aggregation-induced emission fluorogens (AIEgens) to the initial dispersed state upon illuminating has limited their applications. Here, the authors employ the confined space in the quartz nanopore to achieve a nanopore-size dependent restriction of AIEgens.
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Affiliation(s)
- Yi-Lun Ying
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P. R. China.
| | - Yuan-Jie Li
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P. R. China
| | - Ju Mei
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P. R. China
| | - Rui Gao
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P. R. China
| | - Yong-Xu Hu
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P. R. China
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31
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Satheesan R, R SK, Mahendran KR. Controlling Interactions of Cyclic Oligosaccharides with Hetero-Oligomeric Nanopores: Kinetics of Binding and Release at the Single-Molecule Level. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1801192. [PMID: 30009552 DOI: 10.1002/smll.201801192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/14/2018] [Indexed: 06/08/2023]
Abstract
Controlling the molecular interactions through protein nanopores is crucial for effectively detecting single molecules. Here, the development of a hetero-oligomeric nanopore derived from Nocardia farcinica porin AB (NfpAB) is discussed for single-molecule sensing of biopolymers. Using single-channel recording, the interaction of cyclic oligosaccharides such as cationic cyclodextrins (CDs) of different symmetries and charges with NfpAB is measured. Studies of the transport kinetics of CDs reveal asymmetric geometry and charge distribution of NfpAB. The applied potential promotes the attachment of the cationic CDs to the negatively charged pore surface due to electrostatic interaction. Further, the attached CDs are released from the pore by reversing the applied potential in time-resolved blockages. Release of CDs from the pore depends on its charge, size, and magnitude of the applied potential. The kinetics of CD attachment and release is controlled by fine-tuning the applied potential demonstrating the successful molecular transport across these nanopores. It is suggested that such controlled molecular interactions with protein nanopores using organic templates can be useful for several applications in nanopore technology and single-molecule chemistry.
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Affiliation(s)
- Remya Satheesan
- Membrane Biology Laboratory, Interdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Smrithi Krishnan R
- Membrane Biology Laboratory, Interdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Kozhinjampara R Mahendran
- Membrane Biology Laboratory, Interdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
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32
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Guo Y, Niu A, Jian F, Wang Y, Yao F, Wei Y, Tian L, Kang X. Metal-organic complex-functionalized protein nanopore sensor for aromatic amino acids chiral recognition. Analyst 2018; 142:1048-1053. [PMID: 28280809 DOI: 10.1039/c7an00097a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chiral recognition at single-molecule level for small active molecules is important, as exhibited by many nanostructures and molecular assemblies in biological systems, but it presents a significant challenge. We report a simple and rapid sensing strategy to discriminate all enantiomers of natural aromatic amino acids (AAA) using a metal-organic complex-functionalized protein nanopore, in which a chiral recognition element and a chiral recognition valve were equipped. A trifunctional molecule, heptakis-(6-deoxy-6-amino)-β-cyclodextrin (am7βCD), was non-covalently lodged within the nanopore of an α-hemolysin (αHL) mutant, (M113R)7-αHL. Copper(ii) ion reversibly bonds to the amino group of am7βCD to form an am7βCD-CuII complex, which allowed chiral recognition for each enantiomer in the mixture of AAA by distinct current signals. The CuII plugging valve plays a crucial rule that holds chiral molecules in the nanocavity for a sufficient registering time. Importantly, six enantiomers of all nature AAA could be simultaneously recognized at one time. Enantiomeric excess (ee) could also be accurately detected by this approach. It should be possible to generalize this approach for sensing of other chiral molecules.
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Affiliation(s)
- Yanli Guo
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Aihua Niu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Feifei Jian
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Ying Wang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Fujun Yao
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Yongfeng Wei
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Lei Tian
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Xiaofeng Kang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
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33
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Lin Y, Ying YL, Gao R, Long YT. Single-Molecule Sensing with Nanopore Confinement: From Chemical Reactions to Biological Interactions. Chemistry 2018; 24:13064-13071. [DOI: 10.1002/chem.201800669] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Yao Lin
- Key Laboratory for Advanced Materials & School of, Chemistry and Molecular Engineering; East China University of Science and Technology; Shanghai 200237 P.R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials & School of, Chemistry and Molecular Engineering; East China University of Science and Technology; Shanghai 200237 P.R. China
| | - Rui Gao
- Key Laboratory for Advanced Materials & School of, Chemistry and Molecular Engineering; East China University of Science and Technology; Shanghai 200237 P.R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials & School of, Chemistry and Molecular Engineering; East China University of Science and Technology; Shanghai 200237 P.R. China
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34
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Ren H, Cheyne CG, Fleming AM, Burrows CJ, White HS. Single-Molecule Titration in a Protein Nanoreactor Reveals the Protonation/Deprotonation Mechanism of a C:C Mismatch in DNA. J Am Chem Soc 2018; 140:5153-5160. [PMID: 29562130 DOI: 10.1021/jacs.8b00593] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Measurement of single-molecule reactions can elucidate microscopic mechanisms that are often hidden from ensemble analysis. Herein, we report the acid-base titration of a single DNA duplex confined within the wild-type α-hemolysin (α-HL) nanopore for up to 3 h, while monitoring the ionic current through the nanopore. Modulation between two states in the current-time trace for duplexes containing the C:C mismatch in proximity to the latch constriction of α-HL is attributed to the base flipping of the C:C mismatch. As the pH is lowered, the rate for the C:C mismatch to flip from the intra-helical state to the extra-helical state ( kintra-extra) decreases, while the rate for base flipping from the extra-helical state to the intra-helical state ( kextra-intra) remains unchanged. Both kintra-extra and kextra-intra are on the order of 1 × 10-2 s-1 to 1 × 10-1 s-1 and remain stable over the time scale of the measurement (several hours). Analysis of the pH-dependent kinetics of base flipping using a hidden Markov kinetic model demonstrates that protonation/deprotonation occurs while the base pair is in the intra-helical state. We also demonstrate that the rate of protonation is limited by transport of H+ into the α-HL nanopore. Single-molecule kinetic isotope experiments exhibit a large kinetic isotope effect (KIE) for kintra-extra ( kH/ kD ≈ 5) but a limited KIE for kextra-intra ( kH/ kD ≈ 1.3), supporting our model. Our experiments correspond to the longest single-molecule measurements performed using a nanopore, and demonstrate its application in interrogating mechanisms of single-molecule reactions in confined geometries.
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Affiliation(s)
- Hang Ren
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Cameron G Cheyne
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Aaron M Fleming
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Cynthia J Burrows
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Henry S White
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
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35
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Zeng T, Fleming AM, Ding Y, Ren H, White HS, Burrows CJ. Nanopore Analysis of the 5-Guanidinohydantoin to Iminoallantoin Isomerization in Duplex DNA. J Org Chem 2018; 83:3973-3978. [PMID: 29490132 DOI: 10.1021/acs.joc.8b00317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In DNA, guanine oxidation yields diastereomers of 5-guanidinohydantoin (Gh) as one of the major products. In nucleosides and single-stranded DNA, Gh is in a pH-dependent equilibrium with its constitutional isomer iminoallantoin (Ia). Herein, the isomerization reaction between Gh and Ia was monitored in duplex DNA using a protein nanopore by measuring the ionic current when duplex DNA interacts with the pore under an electrophoretic force. Monitoring current levels in this single-molecule method proved to be superior for analysis of population distributions in an equilibrating mixture of four isomers in duplex DNA as a function of pH. The results identified Gh as a major isomer observed when base paired with A, C, or G at pH 6.4-8.4, and Ia was a minor isomer of the reaction mixture that was only observed when the pH was >7.4 in the duplex DNA context. The present results suggest that Gh will be the dominant isomer in duplex DNA under physiological conditions regardless of the base-pairing partner in the duplex.
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Affiliation(s)
- Tao Zeng
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Aaron M Fleming
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Yun Ding
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Hang Ren
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Henry S White
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Cynthia J Burrows
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
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36
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Borsley S, Cockroft SL. In Situ Synthetic Functionalization of a Transmembrane Protein Nanopore. ACS NANO 2018; 12:786-794. [PMID: 29244946 DOI: 10.1021/acsnano.7b08105] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Monitoring current flow through a single nanopore has proved to be a powerful technique for the in situ detection of molecular structure, binding, and reactivity. Transmembrane proteins, such as α-hemolysin, provide particularly attractive platforms for nanopore sensing applications due to their atomically precise structures. However, many nanopore applications require the introduction of functional groups to tune selectivity. To date, such modifications have required genetic modification of the protein prior to functionalization. Here we demonstrate the in situ synthetic modification of a wild-type α-hemolysin nanopore embedded in a membrane. We show that reversible dynamic covalent iminoboronate formation and the resulting changes in the ion current flowing through an individual nanopore can be used to map the reactive behavior of lysine residues within the nanopore channel. Crucially, the modification of lysine residues located outside the nanopore channel was found not to affect the stability or utility of the nanopore. Finally, knowledge of the reactivity patterns enabled the irreversible functionalization of a single, assignable lysine residue within the nanopore channel. The approach constitutes a simple, generic tool for the rapid, in situ synthetic modification of protein nanopores that circumvents the need for prior genetic modification.
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Affiliation(s)
- Stefan Borsley
- EaStCHEM School of Chemistry, University of Edinburgh , Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
| | - Scott L Cockroft
- EaStCHEM School of Chemistry, University of Edinburgh , Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
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37
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Qing Y, Pulcu GS, Bell NAW, Bayley H. Bioorthogonal Cycloadditions with Sub-Millisecond Intermediates. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201710262] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yujia Qing
- Department of Chemistry; University of Oxford; Chemistry Research Laboratory; 12 Mansfield Road Oxford OX1 3TA UK
| | - Gökçe Su Pulcu
- Department of Chemistry; University of Oxford; Chemistry Research Laboratory; 12 Mansfield Road Oxford OX1 3TA UK
| | - Nicholas A. W. Bell
- Department of Chemistry; University of Oxford; Chemistry Research Laboratory; 12 Mansfield Road Oxford OX1 3TA UK
| | - Hagan Bayley
- Department of Chemistry; University of Oxford; Chemistry Research Laboratory; 12 Mansfield Road Oxford OX1 3TA UK
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38
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Qing Y, Pulcu GS, Bell NAW, Bayley H. Bioorthogonal Cycloadditions with Sub-Millisecond Intermediates. Angew Chem Int Ed Engl 2018; 57:1218-1221. [DOI: 10.1002/anie.201710262] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Indexed: 01/20/2023]
Affiliation(s)
- Yujia Qing
- Department of Chemistry; University of Oxford; Chemistry Research Laboratory; 12 Mansfield Road Oxford OX1 3TA UK
| | - Gökçe Su Pulcu
- Department of Chemistry; University of Oxford; Chemistry Research Laboratory; 12 Mansfield Road Oxford OX1 3TA UK
| | - Nicholas A. W. Bell
- Department of Chemistry; University of Oxford; Chemistry Research Laboratory; 12 Mansfield Road Oxford OX1 3TA UK
| | - Hagan Bayley
- Department of Chemistry; University of Oxford; Chemistry Research Laboratory; 12 Mansfield Road Oxford OX1 3TA UK
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39
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YANG J, LI S, WU XY, LONG YT. Development of Biological Nanopore Technique in Non-gene Sequencing Application. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1016/s1872-2040(17)61053-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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40
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Construction of an aerolysin nanopore in a lipid bilayer for single-oligonucleotide analysis. Nat Protoc 2017; 12:1901-1911. [PMID: 28837133 DOI: 10.1038/nprot.2017.077] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nanopore techniques offer the possibility to study biomolecules at the single-molecule level in a low-cost, label-free and high-throughput manner. By analyzing the level, duration and frequency of ionic current blockades, information regarding the structural conformation, mass, length and concentration of single molecules can be obtained in physiological conditions. Aerolysin monomers assemble into small pores that provide a confined space for effective electrochemical control of a single molecule interacting with the pore, which significantly improves the temporal resolution of this technique. In comparison with other reported protein nanopores, aerolysin maintains its functional stability in a wide range of pH conditions, which allows for the direct discrimination of oligonucleotides between 2 and 10 nt in length and the monitoring of the stepwise cleavage of oligonucleotides by exonuclease I (Exo I) in real time. This protocol describes the process of activating proaerolysin using immobilized trypsin to obtain the aerolysin monomer, the construction of a lipid membrane and the insertion of an individual aerolysin nanopore into this membrane. A step-by-step description is provided of how to perform single-oligonucleotide analyses and how to process the acquired data. The total time required for this protocol is ∼3 d.
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41
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Gao R, Ying YL, Hu YX, Li YJ, Long YT. Wireless Bipolar Nanopore Electrode for Single Small Molecule Detection. Anal Chem 2017; 89:7382-7387. [DOI: 10.1021/acs.analchem.7b00729] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Rui Gao
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Yong-Xu Hu
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Yuan-Jie Li
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
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42
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Howorka S. Building membrane nanopores. NATURE NANOTECHNOLOGY 2017; 12:619-630. [PMID: 28681859 DOI: 10.1038/nnano.2017.99] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 04/19/2017] [Indexed: 05/28/2023]
Abstract
Membrane nanopores-hollow nanoscale barrels that puncture biological or synthetic membranes-have become powerful tools in chemical- and biosensing, and have achieved notable success in portable DNA sequencing. The pores can be self-assembled from a variety of materials, including proteins, peptides, synthetic organic compounds and, more recently, DNA. But which building material is best for which application, and what is the relationship between pore structure and function? In this Review, I critically compare the characteristics of the different building materials, and explore the influence of the building material on pore structure, dynamics and function. I also discuss the future challenges of developing nanopore technology, and consider what the next-generation of nanopore structures could be and where further practical applications might emerge.
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Affiliation(s)
- Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, UK
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43
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Waduge P, Hu R, Bandarkar P, Yamazaki H, Cressiot B, Zhao Q, Whitford PC, Wanunu M. Nanopore-Based Measurements of Protein Size, Fluctuations, and Conformational Changes. ACS NANO 2017; 11:5706-5716. [PMID: 28471644 DOI: 10.1021/acsnano.7b01212] [Citation(s) in RCA: 171] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Proteins are structurally dynamic macromolecules, and it is challenging to quantify the conformational properties of their native state in solution. Nanopores can be efficient tools to study proteins in a solution environment. In this method, an electric field induces electrophoretic and/or electro-osmotic transport of protein molecules through a nanopore slightly larger than the protein molecule. High-bandwidth ion current measurement is used to detect the transit of each protein molecule. First, our measurements reveal a correlation between the mean current blockade amplitude and the radius of gyration for each protein. Next, we find a correlation between the shape of the current signal amplitude distributions and the protein fluctuation as obtained from molecular dynamics simulations. Further, the magnitude of the structural fluctuations, as probed by experiments and simulations, correlates with the ratio of α-helix to β-sheet content. We highlight the resolution of our measurements by resolving two states of calmodulin, a canonical protein that undergoes a conformational change in response to calcium binding.
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Affiliation(s)
| | - Rui Hu
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University , Beijing 100871, People's Republic of China
| | | | - Hirohito Yamazaki
- Graduate School of Science and Technology, Keio University , 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | | | - Qing Zhao
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University , Beijing 100871, People's Republic of China
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44
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Affiliation(s)
- Wenqing Shi
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Alicia K. Friedman
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Lane A. Baker
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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45
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Mahendran KR, Niitsu A, Kong L, Thomson AR, Sessions RB, Woolfson DN, Bayley H. A monodisperse transmembrane α-helical peptide barrel. Nat Chem 2016; 9:411-419. [PMID: 28430192 DOI: 10.1038/nchem.2647] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 09/13/2016] [Indexed: 12/13/2022]
Abstract
The fabrication of monodisperse transmembrane barrels formed from short synthetic peptides has not been demonstrated previously. This is in part because of the complexity of the interactions between peptides and lipids within the hydrophobic environment of a membrane. Here we report the formation of a transmembrane pore through the self-assembly of 35 amino acid α-helical peptides. The design of the peptides is based on the C-terminal D4 domain of the Escherichia coli polysaccharide transporter Wza. By using single-channel current recording, we define discrete assembly intermediates and show that the pore is most probably a helix barrel that contains eight D4 peptides arranged in parallel. We also show that the peptide pore is functional and capable of conducting ions and binding blockers. Such α-helix barrels engineered from peptides could find applications in nanopore technologies such as single-molecule sensing and nucleic-acid sequencing.
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Affiliation(s)
- Kozhinjampara R Mahendran
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA UK
| | - Ai Niitsu
- School of Chemistry, Cantock's Close, University of Bristol, Bristol BS8 1TS, UK
| | - Lingbing Kong
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA UK
| | - Andrew R Thomson
- School of Chemistry, Cantock's Close, University of Bristol, Bristol BS8 1TS, UK
| | - Richard B Sessions
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK.,BrisSynBio, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, UK
| | - Derek N Woolfson
- School of Chemistry, Cantock's Close, University of Bristol, Bristol BS8 1TS, UK.,School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK.,BrisSynBio, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, UK
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA UK
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46
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Lee J, Boersma A, Boudreau MA, Cheley S, Daltrop O, Li J, Tamagaki H, Bayley H. Semisynthetic Nanoreactor for Reversible Single-Molecule Covalent Chemistry. ACS NANO 2016; 10:8843-50. [PMID: 27537396 PMCID: PMC5043417 DOI: 10.1021/acsnano.6b04663] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 08/18/2016] [Indexed: 05/27/2023]
Abstract
Protein engineering has been used to remodel pores for applications in biotechnology. For example, the heptameric α-hemolysin pore (αHL) has been engineered to form a nanoreactor to study covalent chemistry at the single-molecule level. Previous work has been confined largely to the chemistry of cysteine side chains or, in one instance, to an irreversible reaction of an unnatural amino acid side chain bearing a terminal alkyne. Here, we present four different αHL pores obtained by coupling either two or three fragments by native chemical ligation (NCL). The synthetic αHL monomers were folded and incorporated into heptameric pores. The functionality of the pores was validated by hemolysis assays and by single-channel current recording. By using NCL to introduce a ketone amino acid, the nanoreactor approach was extended to an investigation of reversible covalent chemistry on an unnatural side chain at the single-molecule level.
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Affiliation(s)
- Joongoo Lee
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, U.K.
| | - Arnold
J. Boersma
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Marc A. Boudreau
- Department
of Chemistry, University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Stephen Cheley
- Department
of Pharmacology, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Oliver Daltrop
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, U.K.
| | - Jianwei Li
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, U.K.
| | - Hiroko Tamagaki
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, U.K.
| | - Hagan Bayley
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, U.K.
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47
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Ayub M, Bayley H. Engineered transmembrane pores. Curr Opin Chem Biol 2016; 34:117-126. [PMID: 27658267 DOI: 10.1016/j.cbpa.2016.08.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 08/09/2016] [Accepted: 08/10/2016] [Indexed: 12/15/2022]
Abstract
Today, hundreds of researchers are working on nanopores, making an impact in both basic science and biotechnology. Proteins remain the most versatile sources of nanopores, based on our ability to engineer them with sub-nanometer precision. Recent work aimed at the construction and discovery of novel pores has included unnatural amino acid mutagenesis and the application of selection techniques. The diversity of structures has now been increased through the development of helix-based pores as well as the better-known β barrels. New developments also include truncated pores, which pierce bilayers through lipid rearrangement, and hybrid pores, which do away with bilayers altogether. Pore dimers, which span two lipid bilayers, have been constructed and pores based on DNA nanostructures are gaining in importance. While nanopore DNA sequencing has received enthusiastic attention, protein pores have a wider range of potential applications, requiring specifications that will require engineering efforts to continue for years to come.
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Affiliation(s)
- Mariam Ayub
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom.
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