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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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2
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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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3
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Guo B, Sheng Y, Zhou K, Liu Q, Liu L, Wu HC. Analyte-Triggered DNA-Probe Release from a Triplex Molecular Beacon for Nanopore Sensing. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711690] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Bingyuan Guo
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center; Institute of High Energy Physics; Chinese Academy of Sciences; Beijing 100049 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Yingying Sheng
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
| | - Ke Zhou
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center; Institute of High Energy Physics; Chinese Academy of Sciences; Beijing 100049 China
| | - Quansheng Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center; Institute of High Energy Physics; Chinese Academy of Sciences; Beijing 100049 China
| | - Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center; Institute of High Energy Physics; Chinese Academy of Sciences; Beijing 100049 China
| | - Hai-Chen Wu
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
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4
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Guo B, Sheng Y, Zhou K, Liu Q, Liu L, Wu HC. Analyte-Triggered DNA-Probe Release from a Triplex Molecular Beacon for Nanopore Sensing. Angew Chem Int Ed Engl 2018; 57:3602-3606. [PMID: 29488675 DOI: 10.1002/anie.201711690] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/14/2018] [Indexed: 12/26/2022]
Abstract
A new nanopore sensing strategy based on triplex molecular beacon was developed for the detection of specific DNA or multivalent proteins. The sensor is composed of a triplex-forming molecular beacon and a stem-forming DNA component that is modified with a host-guest complex. Upon target DNA hybridizing with the molecular beacon loop or multivalent proteins binding to the recognition elements on the stem, the DNA probe is released and produces highly characteristic current signals when translocated through α-hemolysin. The frequency of current signatures can be used to quantify the concentrations of the target molecules. This sensing approach provides a simple, quick, and modular tool for the detection of specific macromolecules with high sensitivity and excellent selectivity. It may find useful applications in point-of-care diagnostics with a portable nanopore kit in the future.
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Affiliation(s)
- Bingyuan Guo
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingying Sheng
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Ke Zhou
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Quansheng Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Hai-Chen Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
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5
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Liu L, Wu HC. DNA-Based Nanopore Sensing. Angew Chem Int Ed Engl 2016; 55:15216-15222. [DOI: 10.1002/anie.201604405] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/13/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics; Chinese Academy of Sciences; Beijing 100049 China
| | - Hai-Chen Wu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics; Chinese Academy of Sciences; Beijing 100049 China
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
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6
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Affiliation(s)
- Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety; Institute of High Energy Physics; Chinese Academy of Sciences; Peking 100049 China
| | - Hai-Chen Wu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety; Institute of High Energy Physics; Chinese Academy of Sciences; Peking 100049 China
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Peking 100190 China
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7
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Single-molecule study of proteins by biological nanopore sensors. SENSORS 2014; 14:18211-22. [PMID: 25268917 PMCID: PMC4239869 DOI: 10.3390/s141018211] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 08/31/2014] [Accepted: 09/19/2014] [Indexed: 01/27/2023]
Abstract
Nanopore technology has been developed for detecting properties of proteins through monitoring of ionic current modulations as protein passes via a nanosize pore. As a real-time, sensitive, selective and stable technology, biological nanopores are of widespread concern. Here, we introduce the background of nanopore researches in the area of α-hemolysin (α-HL) nanopores in protein conformation detections and protein-ligand interactions. Moreover, several original biological nanopores are also introduced with various features and functions.
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8
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Affiliation(s)
- Shengwen Shen
- Department
of Laboratory Medicine
and Pathology, 10-102 Clinical Sciences Building, University
of Alberta, Edmonton, Alberta, Canada, T6G 2G3
| | - Xing-Fang Li
- Department
of Laboratory Medicine
and Pathology, 10-102 Clinical Sciences Building, University
of Alberta, Edmonton, Alberta, Canada, T6G 2G3
| | - William R. Cullen
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver,
British Columbia, Canada, V6T 1Z1
| | - Michael Weinfeld
- Department of Oncology, Cross
Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, Alberta, Canada, T6G 1Z2
| | - X. Chris Le
- Department
of Laboratory Medicine
and Pathology, 10-102 Clinical Sciences Building, University
of Alberta, Edmonton, Alberta, Canada, T6G 2G3
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9
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Hammerstein AF, Shin SH, Bayley H. Single-molecule kinetics of two-step divalent cation chelation. Angew Chem Int Ed Engl 2010; 49:5085-90. [PMID: 20572213 DOI: 10.1002/anie.200906601] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anne F Hammerstein
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA UK
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10
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Hammerstein A, Shin SH, Bayley H. Single-Molecule Kinetics of Two-Step Divalent Cation Chelation. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906601] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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11
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Shin SH, Steffensen MB, Claridge TDW, Bayley H. Formation of a Chiral Center and Pyrimidal Inversion at the Single-Molecule Level. Angew Chem Int Ed Engl 2007; 46:7412-6. [PMID: 17702080 DOI: 10.1002/anie.200700736] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Seong-Ho Shin
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
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12
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Shin SH, Steffensen M, Claridge T, Bayley H. Formation of a Chiral Center and Pyrimidal Inversion at the Single-Molecule Level. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200700736] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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13
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Blake S, Mayer T, Mayer M, Yang J. Monitoring Chemical Reactions by Using Ion-Channel-Forming Peptides. Chembiochem 2006; 7:433-5. [PMID: 16444770 DOI: 10.1002/cbic.200500532] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Steven Blake
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, CA 92093-0358, USA
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14
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Guan X, Gu LQ, Cheley S, Braha O, Bayley H. Stochastic Sensing of TNT with a Genetically Engineered Pore. Chembiochem 2005; 6:1875-81. [PMID: 16118820 DOI: 10.1002/cbic.200500064] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Engineered versions of the transmembrane protein pore alpha-hemolysin (alphaHL) can be used as stochastic sensing elements for the identification and quantification of a wide variety of analytes at the single-molecule level. Until now, nitroaromatic analytes have eluded detection by this approach. We now report that binding sites for nitroaromatics can be built within the lumen of the alphaHL pore from simple rings of seven aromatic amino acid side chains (Phe, Tyr or Trp). By monitoring the ionic current that passes through a single pore at a fixed applied potential, various nitroaromatics can be distinguished from TNT on the basis of the amplitude and duration of individual current-blocking events. Rings of less than seven aromatics bind the analytes more weakly; this suggests that direct aromatic-aromatic interactions are involved. The engineered pores should be useful for the detection of explosives and, in combination with computational approaches and structural analysis, they could further our understanding of noncovalent interactions between aromatic molecules.
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Affiliation(s)
- Xiyun Guan
- Department of Medical Biochemistry & Genetics, The Texas A&M University System Health Science Center, College Station, Texas 77843-1114, USA
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15
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Kang XF, Gu LQ, Cheley S, Bayley H. Single Protein Pores Containing Molecular Adapters at High Temperatures. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200461885] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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16
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Kang XF, Gu LQ, Cheley S, Bayley H. Single Protein Pores Containing Molecular Adapters at High Temperatures. Angew Chem Int Ed Engl 2005; 44:1495-9. [PMID: 15678432 DOI: 10.1002/anie.200461885] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Xiao-Feng Kang
- Department of Medical Biochemistry and Genetics, Texas A&M University System Health Science Center, College Station, TX 77843-1114, USA
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