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Bo Z, Lim ZH, Duarte F, Bayley H, Qing Y. Mobile Molecules: Reactivity Profiling Guides Faster Movement on a Cysteine Track. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202300890. [PMID: 38529338 PMCID: PMC10962685 DOI: 10.1002/ange.202300890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Indexed: 03/19/2023]
Abstract
We previously reported a molecular hopper, which makes sub-nanometer steps by thiol-disulfide interchange along a track with cysteine footholds within a protein nanopore. Here we optimize the hopping rate (ca. 0.1 s-1 in the previous work) with a view towards rapid enzymeless biopolymer characterization during translocation within nanopores. We first took a single-molecule approach to obtain the reactivity profiles of individual footholds. The pK a values of cysteine thiols within a pore ranged from 9.17 to 9.85, and the pH-independent rate constants of the thiolates with a small-molecule disulfide varied by up to 20-fold. Through site-specific mutagenesis and a pH increase from 8.5 to 9.5, the overall hopping rate of a DNA cargo along a five-cysteine track was accelerated 4-fold, and the rate-limiting step 21-fold.
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Affiliation(s)
- Zonghua Bo
- Department of ChemistryUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
| | - Zhong Hui Lim
- Department of ChemistryUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
| | - Fernanda Duarte
- Department of ChemistryUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
| | - Hagan Bayley
- Department of ChemistryUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
| | - Yujia Qing
- Department of ChemistryUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
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2
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Bo Z, Lim ZH, Duarte F, Bayley H, Qing Y. Mobile Molecules: Reactivity Profiling Guides Faster Movement on a Cysteine Track. Angew Chem Int Ed Engl 2023; 62:e202300890. [PMID: 36930533 PMCID: PMC10962549 DOI: 10.1002/anie.202300890] [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: 01/17/2023] [Revised: 03/03/2023] [Accepted: 03/17/2023] [Indexed: 03/18/2023]
Abstract
We previously reported a molecular hopper, which makes sub-nanometer steps by thiol-disulfide interchange along a track with cysteine footholds within a protein nanopore. Here we optimize the hopping rate (ca. 0.1 s-1 in the previous work) with a view towards rapid enzymeless biopolymer characterization during translocation within nanopores. We first took a single-molecule approach to obtain the reactivity profiles of individual footholds. The pKa values of cysteine thiols within a pore ranged from 9.17 to 9.85, and the pH-independent rate constants of the thiolates with a small-molecule disulfide varied by up to 20-fold. Through site-specific mutagenesis and a pH increase from 8.5 to 9.5, the overall hopping rate of a DNA cargo along a five-cysteine track was accelerated 4-fold, and the rate-limiting step 21-fold.
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Affiliation(s)
- Zonghua Bo
- Department of ChemistryUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
| | - Zhong Hui Lim
- Department of ChemistryUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
| | - Fernanda Duarte
- Department of ChemistryUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
| | - Hagan Bayley
- Department of ChemistryUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
| | - Yujia Qing
- Department of ChemistryUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
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3
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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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4
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Domke KF, Aragonès AC. Playing catch and release with single molecules: mechanistic insights into plasmon-controlled nanogaps. NANOSCALE 2023; 15:497-506. [PMID: 36394540 DOI: 10.1039/d2nr05448e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Single-molecule (SM) detection is essential for investigating processes at the molecular level. Nanogap-based detection approaches have proven to be highly accurate SM capture and detection platforms in the last decade. Unfortunately, these approaches face several inherent drawbacks, such as short detection times and the effects of Brownian motion, that can hinder molecular capture. Nanogap-based SM detection approaches have been successfully coupled to optical-based setups to exploit nearfield-assisted trapping to overcome these drawbacks and thus improve SM capture and detection. Here we present the first mechanistic study of nearfield effects on SM capture and release in nanogaps, using unsupervised machine learning methods based on hidden Markov models. We show that the nearfield strength can manipulate the kinetics of the SM capture and release processes. With increasing field strength, the rate constant of the capture kinetics increase while the release kinetics decrease, favouring the former over the latter. As a result, the SM capture state is more likely and more stable than the release state above a specific threshold nearfild strength. We have also estimated the decrease in the capture free-energy profile and the increase in the release profiles to be around 5 kJ mol-1 for the laser powers employed, ranging from laser-OFF conditions to 11 mW μm-2. We envisage that our findings can be combined with the electrocatalytic capabilities of the (nearfield) nanogap to develop next-generation molecular nanoreactors. This approach will open the door to highly efficient SM catalysis with precise extended monitoring timescales facilitated through the longer residence times of the reactant trapped inside the nanogap.
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Affiliation(s)
- Katrin F Domke
- University of Duisburg-Essen, Faculty of Chemistry, Universitätsstr. 5, 45141 Essen, Germany
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Albert C Aragonès
- Departament de Ciència de Materials i Química Física, Universitat de Barcelona, Marti i Franquès 1, 08028, Barcelona, Spain
- Institut de Química Teòrica i Computacional (IQTC), Universitat de Barcelona, Diagonal 645, 08028, Barcelona, Spain.
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5
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Wu Y, Gooding JJ. The application of single molecule nanopore sensing for quantitative analysis. Chem Soc Rev 2022; 51:3862-3885. [PMID: 35506519 DOI: 10.1039/d1cs00988e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Nanopore-based sensors typically work by monitoring transient pulses in conductance via current-time traces as molecules translocate through the nanopore. The unique property of being able to monitor single molecules gives nanopore sensors the potential as quantitative sensors based on the counting of single molecules. This review provides an overview of the concepts and fabrication of nanopore sensors as well as nanopore sensing with a view toward using nanopore sensors for quantitative analysis. We first introduce the classification of nanopores and highlight their applications in molecular identification with some pioneering studies. The review then shifts focus to recent strategies to extend nanopore sensors to devices that can rapidly and accurately quantify the amount of an analyte of interest. Finally, future prospects are provided and briefly discussed. The aim of this review is to aid in understanding recent advances, challenges, and prospects for nanopore sensors for quantitative analysis.
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Affiliation(s)
- Yanfang Wu
- School of Chemistry and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia.
| | - J Justin Gooding
- School of Chemistry and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia.
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6
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Cairns-Gibson DF, Cockroft SL. Functionalised nanopores: chemical and biological modifications. Chem Sci 2022; 13:1869-1882. [PMID: 35308845 PMCID: PMC8848921 DOI: 10.1039/d1sc05766a] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/22/2021] [Indexed: 12/11/2022] Open
Abstract
Nanopore technology has established itself as a powerful tool for single-molecule studies. By analysing changes in the ion current flowing through a single transmembrane channel, a wealth of molecular information can be elucidated. Early studies utilised nanopore technology for sensing applications, and subsequent developments have diversified its remit. Nanopores can be synthetic, solid-state, or biological in origin, but recent work has seen these boundaries blurred as hybrid functionalised pores emerge. The modification of existing pores and the construction of novel synthetic pores has been an enticing goal for creating systems with tailored properties and functionality. Here, we explore chemically functionalised biological pores and the bio-inspired functionalisation of solid-state pores, highlighting how the convergence of these domains provides enhanced functionality. The convergence of chemistry, biology, and solid-state approaches enables the construction hybrid nanopores with enhanced single-molecule applications.![]()
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Affiliation(s)
- Dominic F. Cairns-Gibson
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
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7
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Zhang J, Cao J, Jia W, Zhang S, Yan S, Wang Y, Zhang P, Chen HY, Li W, Huang S. Mapping Potential Engineering Sites of Mycobacterium smegmatis porin A (MspA) to Form a Nanoreactor. ACS Sens 2021; 6:2449-2456. [PMID: 34107684 DOI: 10.1021/acssensors.1c00792] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein nanopores can be engineered as nanoreactors to investigate single-molecule chemical reactions. Recent studies have demonstrated that Mycobacterium smegmatis porin A (MspA) nanopore is a superior engineering template acknowledging its geometrical advantages. However, reported engineering of MspA to form a nanoreactor has focused only on site 91 and mapping of other engineering sites have never been performed before. By taking tetrachloraurate(III) ([AuCl4]-) as a model reactant, potential engineering sites within the pore constriction of MspA have been thoroughly investigated. It is discovered that the produced event amplitude is inversely correlated to the cross-sectional diameter of the pore constriction size at the engineering site, providing evidence that site 91 is actually already the optimum place to introduce the chemical reactivity. Other unavailable engineering sites, which either significantly interfere with the pore assembly or produce reactive sites facing to the pore's exterior instead of to the pore lumen, were also spotted and discussed. All results demonstrated above have provided a complete map of engineering sites within the constriction area of MspA and may be beneficial as a reference in future engineering of corresponding nanoreactors.
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Affiliation(s)
- Jinyue Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Jiao Cao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wenfei Li
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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8
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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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9
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Zhao D, Tang H, Wang H, Yang C, Li Y. Analytes Triggered Conformational Switch of i-Motif DNA inside Gold-Decorated Solid-State Nanopores. ACS Sens 2020; 5:2177-2183. [PMID: 32588619 DOI: 10.1021/acssensors.0c00798] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The nanopore-based technique is a useful tool for single-molecule sensing and characterization. In this work, we have developed a new DNA-functionalized gold-modified nanopore, and analytes can induce the conformational switch of i-motif DNA formed on the inner surface of the nanopore. i-Motif DNA structure can be formed in the presence of silver ions (Ag+), which will result in the change in surface charge and structure of the nanopore tip and ion current rectification (ICR) ratio. The i-motif DNA structure on nanopore surface will be destroyed after the addition of glutathione (GSH) due to the strong interaction of Ag-S bond, which results in the recovery of surface charge, steric hindrance, and ICR ratio. This analyte-triggered conformational switch of i-motif DNA can help us deeply understand the DNA technology inside single nanopore and will benefit the possible applications in an ultrasensitive detection and biological/chemical analysis.
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Affiliation(s)
- Dandan Zhao
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
| | - Haoran Tang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
| | - Hao Wang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
| | - Cheng Yang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
| | - Yongxin Li
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
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10
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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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11
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Sheng Y, Zhang S, Liu L, Wu H. Measuring Enzymatic Activities with Nanopores. Chembiochem 2020; 21:2089-2097. [DOI: 10.1002/cbic.202000079] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/21/2020] [Indexed: 12/20/2022]
Affiliation(s)
- 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
| | - Shouwen Zhang
- Neurophysiology Department Beijing ChaoYang Emergency Medical Center Beijing 100122 China
| | - 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
- 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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12
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Directional conformer exchange in dihydrofolate reductase revealed by single-molecule nanopore recordings. Nat Chem 2020; 12:481-488. [DOI: 10.1038/s41557-020-0437-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/10/2020] [Indexed: 12/18/2022]
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13
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Sheng Y, Zhou K, Liu Q, Liu L, Wu HC. Probing Conformational Polymorphism of DNA Assemblies with Nanopores. Anal Chem 2020; 92:7485-7492. [DOI: 10.1021/acs.analchem.9b05650] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- 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
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, 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
- University of Chinese Academy of Sciences, Beijing 100049, China
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14
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You Y, Zhou K, Guo B, Liu Q, Cao Z, Liu L, Wu HC. Measuring Binding Constants of Cucurbituril-Based Host-Guest Interactions at the Single-Molecule Level with Nanopores. ACS Sens 2019; 4:774-779. [PMID: 30865423 DOI: 10.1021/acssensors.9b00408] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cucurbiturils are one type of widely used macrocyclic host compound in supramolecular chemistry. Their peculiar properties have led to applications in a wide variety of research areas such as fluorescence spectroscopy, drug delivery, catalysis, and nanotechnology. However, the solubilities of cucurbiturils are rather poor in water and many organic solvents, which may cause accuracy problems when measuring binding constants with traditional methods. In this report, we aim to develop an approach to measure the binding constants of cucurbituril-based host-guest interactions at the single-molecule level. First, we covalently attach different guest compounds to the side-chain of DNA molecules. Then, excess cucurbiturils are incubated with DNA probes to form the host-guest complexes. Next, the modified DNA hybrids are threaded through α-hemolysin nanopore to generate highly characteristic current events. Finally, statistical analyses of the obtained events afford the binding constants of cucurbiturils with various molecules. This new approach provides a simple and straightforward method to compare binding strength of different host-guest complexes and may find applications for quantifying other macrocycle-based host-guest interactions.
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Affiliation(s)
- Yi You
- Collaborative Innovation Center of Micro/nano Bio-sensing and Food Safety Inspection, Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, China
| | - Ke Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - 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
| | - Quansheng Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Zhong Cao
- Collaborative Innovation Center of Micro/nano Bio-sensing and Food Safety Inspection, Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, 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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15
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Zhang Z, Li T, Sheng Y, Liu L, Wu HC. Enhanced Sensitivity in Nanopore Sensing of Cancer Biomarkers in Human Blood via Click Chemistry. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1804078. [PMID: 30398696 DOI: 10.1002/smll.201804078] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 10/22/2018] [Indexed: 06/08/2023]
Abstract
Cancer biomarkers are expected to be indicative of the occurrence of certain cancer diseases before the tumors form and metastasize. However, many biomarkers can only be acquired in extremely low concentrations, which are often beyond the limit of detection (LOD) of current instruments and technologies. A practical strategy for nanopore sensing of cancer biomarkers in raw human blood down to the femtomolar level is developed here. This strategy first converts the detection of cancer biomarkers to the quantification of copper ions by conducting a sandwich assay involving copper oxide nanoparticles. The released Cu2+ is then taken to catalyze the "click" reaction which ligates a host-guest modified DNA probe. Finally, this DNA probe is subjected to single-channel recordings to afford the translocation events that can be used to derive the concentrations of the original biomarkers. Due to the amplification effects of nanoparticle loadings and the "click" reaction, the LOD of this strategy can be as low as the subfemtomolar level. Further, the acid treatment step could effectively eliminate the interferences from plasma proteins in raw human blood and make the strategy highly suitable for the detection of cancer biomarkers in clinical samples.
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Affiliation(s)
- Zehui Zhang
- Institute for Advanced Study, Chengdu University, Chengdu, 610052, 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
| | - Ting Li
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center, Institute of High Energy Physics, 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
| | - Lei Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, 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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16
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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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17
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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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18
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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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19
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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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20
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Wu X, Guo B, Sheng Y, Zhang Y, Wang J, Peng S, Liu L, Wu HC. Multiplexed discrimination of microRNA single nucleotide variants through triplex molecular beacon sensors. Chem Commun (Camb) 2018; 54:7673-7676. [DOI: 10.1039/c8cc03574a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Herein, we develop a new nanopore sensing strategy for the selective detection of microRNAs and single nucleotide variants (SNVs) based on triplex molecular beacon sensors.
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Affiliation(s)
- Xiaoyuan Wu
- School of Resource and Environmental Engineering
- Hefei University of Technology
- Hefei 230009
- China
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center
| | - Bingyuan Guo
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center
- Institute of High Energy Physics
- 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
| | - Yun Zhang
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry, Chinese Academy of Sciences
- Beijing 100190
- China
| | - Jin Wang
- School of Resource and Environmental Engineering
- Hefei University of Technology
- Hefei 230009
- China
| | - Shuchuan Peng
- School of Resource and Environmental Engineering
- Hefei University of Technology
- Hefei 230009
- 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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21
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Sheng Y, You Y, Cao Z, Liu L, Wu HC. Rapid and selective DNA-based detection of melamine using α-hemolysin nanopores. Analyst 2018; 143:2411-2415. [DOI: 10.1039/c8an00580j] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We have developed a rapid and selective approach for the detection of melamine based on simple DNA probes and α-hemolysin nanopores.
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Affiliation(s)
- Yingying Sheng
- Collaborative Innovation Center of Micro/nano Bio-sensing and Food Safety Inspection
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation
- School of Chemistry and Biological Engineering
- Changsha University of Science and Technology
- Changsha 410114
| | - Yi You
- Collaborative Innovation Center of Micro/nano Bio-sensing and Food Safety Inspection
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation
- School of Chemistry and Biological Engineering
- Changsha University of Science and Technology
- Changsha 410114
| | - Zhong Cao
- Collaborative Innovation Center of Micro/nano Bio-sensing and Food Safety Inspection
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation
- School of Chemistry and Biological Engineering
- Changsha University of Science and Technology
- Changsha 410114
| | - 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
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22
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Van Meervelt V, Soskine M, Singh S, Schuurman-Wolters GK, Wijma HJ, Poolman B, Maglia G. Real-Time Conformational Changes and Controlled Orientation of Native Proteins Inside a Protein Nanoreactor. J Am Chem Soc 2017; 139:18640-18646. [PMID: 29206456 PMCID: PMC6150693 DOI: 10.1021/jacs.7b10106] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Protein conformations play crucial
roles in most, if not all, biological
processes. Here we show that the current carried through a nanopore
by ions allows monitoring conformational changes of single and native
substrate-binding domains (SBD) of an ATP-Binding Cassette importer
in real-time. Comparison with single-molecule Förster Resonance
Energy Transfer and ensemble measurements revealed that proteins trapped
inside the nanopore have bulk-like properties. Two ligand-free and
two ligand-bound conformations of SBD proteins were inferred and their
kinetic constants were determined. Remarkably, internalized proteins
aligned with the applied voltage bias, and their orientation could
be controlled by the addition of a single charge to the protein surface.
Nanopores can thus be used to immobilize proteins on a surface with
a specific orientation, and will be employed as nanoreactors for single-molecule
studies of native proteins. Moreover, nanopores with internal protein
adaptors might find further practical applications in multianalyte
sensing devices.
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Affiliation(s)
- Veerle Van Meervelt
- Department of Chemistry, University of Leuven , Leuven B-3001, Belgium.,Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen 9747 AG, The Netherlands
| | - Misha Soskine
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen 9747 AG, The Netherlands
| | - Shubham Singh
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen 9747 AG, The Netherlands
| | - Gea K Schuurman-Wolters
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen 9747 AG, The Netherlands
| | - Hein J Wijma
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen 9747 AG, The Netherlands
| | - Bert Poolman
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen 9747 AG, The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen 9747 AG, The Netherlands
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23
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Engineered Protein Nanopore for Real-time Monitoring Single-molecule Reaction Between Cadmium Ion and Glutathione. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1016/s1872-2040(17)61032-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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24
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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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25
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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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26
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Franceschini L, Brouns T, Willems K, Carlon E, Maglia G. DNA Translocation through Nanopores at Physiological Ionic Strengths Requires Precise Nanoscale Engineering. ACS NANO 2016; 10:8394-402. [PMID: 27513592 PMCID: PMC5221729 DOI: 10.1021/acsnano.6b03159] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Many important processes in biology involve the translocation of a biopolymer through a nanometer-scale pore. Moreover, the electrophoretic transport of DNA across nanopores is under intense investigation for single-molecule DNA sequencing and analysis. Here, we show that the precise patterning of the ClyA biological nanopore with positive charges is crucial to observe the electrophoretic translocation of DNA at physiological ionic strength. Surprisingly, the strongly electronegative 3.3 nm internal constriction of the nanopore did not require modifications. Further, DNA translocation could only be observed from the wide entry of the nanopore. Our results suggest that the engineered positive charges are important to align the DNA in order to overcome the entropic and electrostatic barriers for DNA translocation through the narrow constriction. Finally, the dependencies of nucleic acid translocations on the Debye length of the solution are consistent with a physical model where the capture of double-stranded DNA is diffusion-limited while the capture of single-stranded DNA is reaction-limited.
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27
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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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28
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Semisynthetic protein nanoreactor for single-molecule chemistry. Proc Natl Acad Sci U S A 2015; 112:13768-73. [PMID: 26504203 DOI: 10.1073/pnas.1510565112] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The covalent chemistry of individual reactants bound within a protein pore can be monitored by observing the ionic current flow through the pore, which acts as a nanoreactor responding to bond-making and bond-breaking events. In the present work, we incorporated an unnatural amino acid into the α-hemolysin (αHL) pore by using solid-phase peptide synthesis to make the central segment of the polypeptide chain, which forms the transmembrane β-barrel of the assembled heptamer. The full-length αHL monomer was obtained by native chemical ligation of the central synthetic peptide to flanking recombinant polypeptides. αHL pores with one semisynthetic subunit were then used as nanoreactors for single-molecule chemistry. By introducing an amino acid with a terminal alkyne group, we were able to visualize click chemistry at the single-molecule level, which revealed a long-lived (4.5-s) reaction intermediate. Additional side chains might be introduced in a similar fashion, thereby greatly expanding the range of single-molecule covalent chemistry that can be investigated by the nanoreactor approach.
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29
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Fabrication of nanopores with ultrashort single-walled carbon nanotubes inserted in a lipid bilayer. Nat Protoc 2015; 10:1670-8. [PMID: 26426500 DOI: 10.1038/nprot.2015.112] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We describe a protocol for the insertion of ultrashort single-walled carbon nanotubes (SWCNTs) to form nanopores in a Montal-Mueller lipid bilayer. The SWCNTs are designed to bind to a specific analyte of interest; binding will result in the reduction of current in single-channel recording experiments. The first stage of the PROCEDURE is to cut and separate the SWCNTs. We cut long, purified SWCNTs with sonication in concentrated sulfuric acid/nitric acid (3/1). Isolation of ultrashort SWCNTs is carried out by size-exclusion HPLC separation. The second stage is to insert these short SWCNTs into the lipid bilayer. This step requires a microinjection probe made from a glass capillary. The setup for protein nanopore research can be adopted for the single-channel recording experiments without any special treatment. The obtained current traces are of very high quality, showing stable baselines and little background noise. Example procedures are shown for investigating ion transport and DNA translocation through these SWCNT nanopores. This nanopore has potential applications in molecular sensing, nanopore DNA sequencing and early disease diagnosis. For example, we have selectively detected modified 5-hydroxymethylcytosine in single-stranded DNA (ssDNA), which may have implications in screening specific genomic DNA sequences. The protocol takes ∼15 d, including SWCNT purification, cutting and separation, as well as the formation of SWCNT nanopores for DNA analyses.
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30
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Watson MA, Cockroft SL. DNA modulates solvent isotope effects in a nanopore. Chem Commun (Camb) 2015; 51:12243-6. [PMID: 26135014 DOI: 10.1039/c5cc01563d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we investigate the modulation of solvent isotope effects by the entry of DNA molecules into individual α-haemolysin nanopores. Solvent isotope effects in D2O versus H2O were enhanced (kH/kD ≈ 1.6) compared to the bulk (kH/kD ≈ 1.2), except when the pore was most blocked (kH/kD ≤ 1.1).
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Affiliation(s)
- Matthew A Watson
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK.
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31
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Asandei A, Chinappi M, Kang HK, Seo CH, Mereuta L, Park Y, Luchian T. Acidity-Mediated, Electrostatic Tuning of Asymmetrically Charged Peptides Interactions with Protein Nanopores. ACS APPLIED MATERIALS & INTERFACES 2015; 7:16706-16714. [PMID: 26144534 DOI: 10.1021/acsami.5b04406] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Despite success in probing chemical reactions and dynamics of macromolecules on submillisecond time and nanometer length scales, a major impasse faced by nanopore technology is the need to cheaply and controllably modulate macromolecule capture and trafficking across the nanopore. We demonstrate herein that tunable charge separation engineered at the both ends of a macromolecule very efficiently modulates the dynamics of macromolecules capture and traffic through a nanometer-size pore. In the proof-of-principle approach, we employed a 36 amino acids long peptide containing at the N- and C-termini uniform patches of glutamic acids and arginines, flanking a central segment of asparagines, and we studied its capture by the α-hemolysin (α-HL) and the mean residence time inside the pore in the presence of a pH gradient across the protein. We propose a solution to effectively control the dynamics of peptide interaction with the nanopore, with both association and dissociation reaction rates of peptide-α-HL interactions spanning orders of magnitude depending upon solution acidity on the peptide addition side and the transmembrane electric potential, while preserving the amplitude of the blockade current signature.
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Affiliation(s)
- Alina Asandei
- †Department of Interdisciplinary Research, Alexandru I. Cuza University, Iasi, Romania
| | - Mauro Chinappi
- ‡Center for Life Nano Science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Hee-Kyoung Kang
- §Department of Biomedical Science and Research Center for Proteineous Materials, Chosun University, Gwangju, South Korea
| | - Chang Ho Seo
- ∥Department of Bioinformatics, Kongju National University, Kongju, South Korea
| | - Loredana Mereuta
- ⊥Department of Physics, Alexandru I. Cuza University, Iasi, Romania
| | - Yoonkyung Park
- §Department of Biomedical Science and Research Center for Proteineous Materials, Chosun University, Gwangju, South Korea
| | - Tudor Luchian
- ⊥Department of Physics, Alexandru I. Cuza University, Iasi, Romania
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32
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Placement of oppositely charged aminoacids at a polypeptide termini determines the voltage-controlled braking of polymer transport through nanometer-scale pores. Sci Rep 2015; 5:10419. [PMID: 26029865 PMCID: PMC4450769 DOI: 10.1038/srep10419] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 04/13/2015] [Indexed: 11/09/2022] Open
Abstract
Protein and solid-state nanometer-scale pores are being developed for the detection, analysis, and manipulation of single molecules. In the simplest embodiment, the entry of a molecule into a nanopore causes a reduction in the latter's ionic conductance. The ionic current blockade depth and residence time have been shown to provide detailed information on the size, adsorbed charge, and other properties of molecules. Here we describe the use of the nanopore formed by Staphylococcus aureus α-hemolysin and polypeptides with oppositely charged segments at the N- and C-termini to increase both the polypeptide capture rate and mean residence time of them in the pore, regardless of the polarity of the applied electrostatic potential. The technique provides the means to improve the signal to noise of single molecule nanopore-based measurements.
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33
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Fahie M, Chisholm C, Chen M. Resolved single-molecule detection of individual species within a mixture of anti-biotin antibodies using an engineered monomeric nanopore. ACS NANO 2015; 9:1089-98. [PMID: 25575121 PMCID: PMC4958048 DOI: 10.1021/nn506606e] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Oligomeric protein nanopores with rigid structures have been engineered for the purpose of sensing a wide range of analytes including small molecules and biological species such as proteins and DNA. We chose a monomeric β-barrel porin, OmpG, as the platform from which to derive the nanopore sensor. OmpG is decorated with seven flexible loops that move dynamically to create a distinct gating pattern when ionic current passes through the pore. Biotin was chemically tethered to the most flexible one of these loops. The gating characteristic of the loop's movement in and out of the porin was substantially altered by analyte protein binding. The gating characteristics of the pore with bound targets were remarkably sensitive to molecular identity, even providing the ability to distinguish between homologues within an antibody mixture. A total of five gating parameters were analyzed for each analyte to create a unique fingerprint for each biotin-binding protein. Our exploitation of gating noise as a molecular identifier may allow more sophisticated sensor design, while OmpG's monomeric structure greatly simplifies nanopore production.
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Affiliation(s)
- Monifa Fahie
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003
| | - Christina Chisholm
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003
| | - Min Chen
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003
- Address correspondence to:
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Pulcu GS, Mikhailova E, Choi LS, Bayley H. Continuous observation of the stochastic motion of an individual small-molecule walker. NATURE NANOTECHNOLOGY 2015; 10:76-83. [PMID: 25486119 PMCID: PMC5011421 DOI: 10.1038/nnano.2014.264] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 10/15/2014] [Indexed: 05/23/2023]
Abstract
Motion--whether it the ability to change shape, rotate or translate--is an important potential asset for functional nanostructures. For translational motion, a variety of DNA-based and small-molecule walkers have been created, but observing the translational motion of individual molecules in real time remains a significant challenge. Here, we show that the movement of a small-molecule walker along a five-foothold track can be monitored continuously within a protein nanoreactor. The walker is an organoarsenic(III) molecule with exchangeable thiol ligands, and the track a line of cysteine residues 6 Å apart within an α-haemolysin protein pore that acts as the nanoreactor. Changes in the flow of ionic current through the pore reflect the individual steps of a single walker, which require the making and breaking of As-S bonds, and occur in aqueous solution at neutral pH and room temperature. The walker moves considerably faster (∼0.7 s per step) than previous walkers based on covalent chemistry and is weakly processive (6 ± 1 steps per outing). It shows weak net directional movement, which can be described by a thermodynamic sink arising from the different environments of the cysteines that constitute the track.
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Affiliation(s)
- Gökçe Su Pulcu
- Correspondence and requests for materials should be addressed to G.S.P () or H.B ()
| | | | | | - Hagan Bayley
- Correspondence and requests for materials should be addressed to G.S.P () or H.B ()
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35
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Schiopu I, Iftemi S, Luchian T. Nanopore investigation of the stereoselective interactions between Cu(2+) and D,L-histidine amino acids engineered into an amyloidic fragment analogue. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 31:387-396. [PMID: 25479713 DOI: 10.1021/la504243r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Stereochemistry is an essential theme for a number of industries and applications, constructed around discriminating various chiral enantiomers, including amino acids, chiral metal complexes, and drugs. In this work, we designed a set of peptide mutants of the human amyloidic Aβ1-16 sequence, known to display an effective Cu(2+) coordinating pocket provided mainly by the intramolecular His-6, His-13, and His-14 residues, that were engineered to contain L- and D-His enantiomers in positions 6 and 13 and provide a local coordination environment with distinct Cu(2+) binding geometries and affinities. We examined the mechanism of selective chiral recognition of Cu(2+) by such mutant peptides, by quantifying their stochastic sensing in real time with a single α-hemolysin (α-HL) protein immobilized in a planar lipid membrane, while incubated in various concentrations of Cu(2+). Our data reveal that the Cu(2+)-binding affinity lies within the micromolar range, and decreases by orders of magnitude as L-His is replaced with its Denantiomer, with the effect being prevalent when such changes were inflicted on the His-6 residue. The presented results demonstrate the feasibility of tuning the metal selectivity in a relatively simple peptide substrate by enantiomeric replacement of key metal binding residues and illustrates the potential of the protein nanopores as a promising approach to quantify the chiral recognition of l/d amino acids by metals.
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Affiliation(s)
- Irina Schiopu
- Department of Interdisciplinary Research, Alexandru Ioan Cuza University , Blvd. Carol I, No. 11, Iasi 700506, Romania
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36
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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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37
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Mereuta L, Asandei A, Seo CH, Park Y, Luchian T. Quantitative understanding of pH- and salt-mediated conformational folding of histidine-containing, β-hairpin-like peptides, through single-molecule probing with protein nanopores. ACS APPLIED MATERIALS & INTERFACES 2014; 6:13242-13256. [PMID: 25069106 DOI: 10.1021/am5031177] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Inter-amino acid residues electrostatic interactions contribute to the conformational stability of peptides and proteins, influence their folding pathways, and are critically important to a multitude of problems in biology including the onset of misfolding diseases. By varying the pH and ionic strength, the inter-amino acid residues electrostatic interactions of histidine-containing, β-hairpin-like peptides alter their folding behavior, and we studied this through quantifying, at the unimolecular level, the frequency, dwell-times of translocation events, and amplitude of blockades associated with interactions between such peptides and the α-hemolysin (α-HL) protein. Acidic buffers were shown to dramatically decrease the rate of peptide capture by the α-HL protein, through the interplay of enthalpic and entropic contributions brought about on the free energy barrier, which controls the peptides-α-HL association rate. We found that in acidic buffers, the amplitude of the blockage induced by an α-HL, β-barrel-residing peptide is smaller than the value seen at neutral pH, and this supports our interpretation of the pH-induced change in the conformation of the peptide, which behaves as a less-stable hairpin at acidic pH values that obstructs, to a lesser extent, the protein pore. This is also confirmed by the fact that the dissociation rate of such model peptide from the α-HL's β-barrel is higher at acidic, as compared to neutral, pH values. Experiments performed in low-salt buffers revealed the dramatic decrease of the peptide capture rate by the α-HL protein, most likely caused by the increase in the radius of counterions cloud around the peptide that hinders peptide partition into the α-barrel, and histidines protonation at low pH bolsters this effect. Reduced electrostatic screening in low-salt buffers, at neutral pH, leads to a decrease in peptides effective cross-sectional areas and an increase of their mobility inside the α-HL pore, due most likely to the chain stretching augmentation, via increased inter-residues electrostatic interactions.
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Affiliation(s)
- Loredana Mereuta
- Department of Physics, Alexandru I. Cuza University , Iasi 700506, Romania
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38
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Zeng T, Li T, Li Y, Liu L, Wang X, Liu Q, Zhao Y, Wu HC. DNA-based detection of mercury(II) ions through characteristic current signals in nanopores with high sensitivity and selectivity. NANOSCALE 2014; 6:8579-8584. [PMID: 24975417 DOI: 10.1039/c4nr02062f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We report single-molecule detection of Hg(2+) by threading an Hg(2+)-mediated DNA duplex through α-hemolysin nanopores, which generates characteristic three-level current patterns and enables the unambiguous detection of Hg(2+). This strategy precludes any background interference and features high sensitivity and selectivity. Moreover, the platform could be readily integrated with aptamers and molecular beacons, offering extended possibilities for the construction of a new DNA-based nanopore sensing system.
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Affiliation(s)
- Tao Zeng
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety
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39
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Single-molecule analysis of chirality in a multicomponent reaction network. Nat Chem 2014; 6:603-7. [DOI: 10.1038/nchem.1949] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 04/09/2014] [Indexed: 11/08/2022]
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40
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Choi LS, Mach T, Bayley H. Rates and stoichiometries of metal ion probes of cysteine residues within ion channels. Biophys J 2014; 105:356-64. [PMID: 23870257 DOI: 10.1016/j.bpj.2013.04.046] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 04/22/2013] [Accepted: 04/25/2013] [Indexed: 10/26/2022] Open
Abstract
Metal ion probes are used to assess the accessibility of cysteine side chains in polypeptides lining the conductive pathways of ion channels and thereby determine the conformations of channel states. Despite the widespread use of this approach, the chemistry of metal ion-thiol interactions has not been fully elucidated. Here, we investigate the modification of cysteine residues within a protein pore by the commonly used Ag(+) and Cd(2+) probes at the single-molecule level, and provide rates and stoichiometries that will be useful for the design and interpretation of accessibility experiments.
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Affiliation(s)
- Lai-Sheung Choi
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
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41
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Asandei A, Schiopu I, Iftemi S, Mereuta L, Luchian T. Investigation of Cu2+ binding to human and rat amyloid fragments Aβ (1-16) with a protein nanopore. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:15634-15642. [PMID: 24274576 DOI: 10.1021/la403915t] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Recent evidence shows that metal coordination by amyloid beta peptides (Aβ) determines structural alterations of peptides, and His-13 from Aβ is crucial for Cu(2+) binding. This study used the truncated, more soluble Aβ1-16 isoforms derived from human and rat amyloid peptides to explore their interaction with Cu(2+) by employing the membrane-immobilized α-hemolysin (α-HL) protein as a nanoscopic probe in conjunction with single-molecule electrophysiology techniques. Unexpectedly, the experimental data suggest that unlike the case of the human Aβ1-16 peptide, Cu(2+) complexation by its rat counterpart leads to an augmented association and dissociation kinetics of the peptide reversible interaction with the protein pore, as compared to the Cu(2+)-free peptide. Single-molecule electrophysiology data reveal that both human and rat Cu(2+)-complexed Aβ peptides induce a higher degree of current flow obstruction through the α-HL pore, as compared to the Cu(2+)-free peptides. It is suggested that morphology changes brought by Cu(2+) binding to such amyloidic fragments depend crucially upon the presence of the His-13 residue on the primary sequence of such peptide fragments, and the α-HL protein-based approach provides unique opportunities and challenges to probing metal-induced folding of peptides.
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Affiliation(s)
- Alina Asandei
- Department of Interdisciplinary Research and ‡Department of Physics, Laboratory of Molecular Biophysics and Medical Physics, Alexandru Ioan Cuza University , Boulevard Carol I, No. 11, Iasi 700506, Romania
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42
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Stochastic detection of Pim protein kinases reveals electrostatically enhanced association of a peptide substrate. Proc Natl Acad Sci U S A 2013; 110:E4417-26. [PMID: 24194548 DOI: 10.1073/pnas.1312739110] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In stochastic sensing, the association and dissociation of analyte molecules is observed as the modulation of an ionic current flowing through a single engineered protein pore, enabling the label-free determination of rate and equilibrium constants with respect to a specific binding site. We engineered sensors based on the staphylococcal α-hemolysin pore to allow the single-molecule detection and characterization of protein kinase-peptide interactions. We enhanced this approach by using site-specific proteolysis to generate pores bearing a single peptide sensor element attached by an N-terminal peptide bond to the trans mouth of the pore. Kinetics and affinities for the Pim protein kinases (Pim-1, Pim-2, and Pim-3) and cAMP-dependent protein kinase were measured and found to be independent of membrane potential and in good agreement with previously reported data. Kinase binding exhibited a distinct current noise behavior that forms a basis for analyte discrimination. Finally, we observed unusually high association rate constants for the interaction of Pim kinases with their consensus substrate Pimtide (~10(7) to 10(8) M(-1) · s(-1)), the result of electrostatic enhancement, and propose a cellular role for this phenomenon.
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43
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Haque F, Li J, Wu HC, Liang XJ, Guo P. Solid-State and Biological Nanopore for Real-Time Sensing of Single Chemical and Sequencing of DNA. NANO TODAY 2013; 8:56-74. [PMID: 23504223 PMCID: PMC3596169 DOI: 10.1016/j.nantod.2012.12.008] [Citation(s) in RCA: 227] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Sensitivity and specificity are two most important factors to take into account for molecule sensing, chemical detection and disease diagnosis. A perfect sensitivity is to reach the level where a single molecule can be detected. An ideal specificity is to reach the level where the substance can be detected in the presence of many contaminants. The rapidly progressing nanopore technology is approaching this threshold. A wide assortment of biomotors and cellular pores in living organisms perform diverse biological functions. The elegant design of these transportation machineries has inspired the development of single molecule detection based on modulations of the individual current blockage events. The dynamic growth of nanotechnology and nanobiotechnology has stimulated rapid advances in the study of nanopore based instrumentation over the last decade, and inspired great interest in sensing of single molecules including ions, nucleotides, enantiomers, drugs, and polymers such as PEG, RNA, DNA, and polypeptides. This sensing technology has been extended to medical diagnostics and third generation high throughput DNA sequencing. This review covers current nanopore detection platforms including both biological pores and solid state counterparts. Several biological nanopores have been studied over the years, but this review will focus on the three best characterized systems including α-hemolysin and MspA, both containing a smaller channel for the detection of single-strand DNA, as well as bacteriophage phi29 DNA packaging motor connector that contains a larger channel for the passing of double stranded DNA. The advantage and disadvantage of each system are compared; their current and potential applications in nanomedicine, biotechnology, and nanotechnology are discussed.
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Affiliation(s)
- Farzin Haque
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Jinghong Li
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Beijing 100084, China
| | - Hai-Chen Wu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Xing-Jie Liang
- Laboratory of Nanomedicine and Nanosafety, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Peixuan Guo
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
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44
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Mereuta L, Schiopu I, Asandei A, Park Y, Hahm KS, Luchian T. Protein nanopore-based, single-molecule exploration of copper binding to an antimicrobial-derived, histidine-containing chimera peptide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:17079-17091. [PMID: 23140333 DOI: 10.1021/la303782d] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Metal ions binding exert a crucial influence upon the aggregation properties and stability of peptides, and the propensity of folding in various substates. Herein, we demonstrate the use of the α-HL protein as a powerful nanoscopic tool to probe Cu(2+)-triggered physicochemical changes of a 20 aminoacids long, antimicrobial-derived chimera peptide with a His residue as metal-binding site, and simultaneously dissect the kinetics of the free- and Cu(2+)-bound peptide interaction to the α-HL pore. Combining single-molecule electrophysiology on reconstituted lipid membranes and fluorescence spectroscopy, we show that the association rate constant between the α-HL pore and a Cu(2+)-free peptide is higher than that of a Cu(2+)-complexed peptide. We posit that mainly due to conformational changes induced by the bound Cu(2+) on the peptide, the resulting complex encounters a higher energy barrier toward its association with the protein pore, stemming most likely from an extra entropy cost needed to fit the Cu(2+)-complexed peptide within the α-HL lumen region. The lower dissociation rate constant of the Cu(2+)-complexed peptide from α-HL pore, as compared to that of Cu(2+)-free peptide, supports the existence of a deeper free energy well for the protein interaction with a Cu(2+)-complexed peptide, which may be indicative of specific Cu(2+)-mediated contributions to the binding of the Cu(2+)-complexed peptide within the pore lumen.
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Affiliation(s)
- Loredana Mereuta
- Department of Physics, Laboratory of Molecular Biophysics and Medical Physics, Alexandru I. Cuza University, Blvd. Carol I, No. 11, Iasi 700506, Romania
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45
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Boersma AJ, Brain KL, Bayley H. Real-time stochastic detection of multiple neurotransmitters with a protein nanopore. ACS NANO 2012; 6:5304-8. [PMID: 22616662 DOI: 10.1021/nn301125y] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The detection of several different neurotransmitters with the same sensor in real-time would be a powerful asset to the field of neurochemistry. We have developed a detector for a broad range of neurotransmitters including amino acids, catecholamines, and nucleotides, which relies on the reversible binding of the analytes to a copper(II) complex within an engineered protein nanopore.
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Affiliation(s)
- Arnold J Boersma
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
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46
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Mohammad MM, Iyer R, Howard KR, McPike MP, Borer PN, Movileanu L. Engineering a rigid protein tunnel for biomolecular detection. J Am Chem Soc 2012; 134:9521-31. [PMID: 22577864 DOI: 10.1021/ja3043646] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
One intimidating challenge in protein nanopore-based technologies is designing robust protein scaffolds that remain functionally intact under a broad spectrum of detection conditions. Here, we show that an extensively engineered bacterial ferric hydroxamate uptake component A (FhuA), a β-barrel membrane protein, functions as a robust protein tunnel for the sampling of biomolecular events. The key implementation in this work was the coupling of direct genetic engineering with a refolding approach to produce an unusually stable protein nanopore. More importantly, this nanostructure maintained its stability under many experimental circumstances, some of which, including low ion concentration and highly acidic aqueous phase, are normally employed to gate, destabilize, or unfold β-barrel membrane proteins. To demonstrate these advantageous traits, we show that the engineered FhuA-based protein nanopore functioned as a sensing element for examining the proteolytic activity of an enzyme at highly acidic pH and for determining the kinetics of protein-DNA aptamer interactions at physiological salt concentration.
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Affiliation(s)
- Mohammad M Mohammad
- Department of Physics, Syracuse University, New York 13244-1130, United States
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47
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48
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Rotem D, Jayasinghe L, Salichou M, Bayley H. Protein detection by nanopores equipped with aptamers. J Am Chem Soc 2012; 134:2781-7. [PMID: 22229655 PMCID: PMC3278221 DOI: 10.1021/ja2105653] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
Protein nanopores have been used as stochastic sensors
for the
detection of analytes that range from small molecules to proteins.
In this approach, individual analyte molecules modulate the ionic
current flowing through a single nanopore. Here, a new type of stochastic
sensor based on an αHL pore modified with an aptamer is described.
The aptamer is bound to the pore by hybridization to an oligonucleotide
that is attached covalently through a disulfide bond to a single cysteine
residue near a mouth of the pore. We show that the binding of thrombin
to a 15-mer DNA aptamer, which forms a cation-stabilized quadruplex,
alters the ionic current through the pore. The approach allows the
quantification of nanomolar concentrations of thrombin, and provides
association and dissociation rate constants and equilibrium dissociation
constants for thrombin·aptamer interactions. Aptamer-based nanopores
have the potential to be integrated into arrays for the parallel detection
of multiple analytes.
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Affiliation(s)
- Dvir Rotem
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
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49
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Jayawardhana DA, Sengupta MK, Krishantha DM, Gupta J, Armstrong DW, Guan X. Chemical-induced pH-mediated molecular switch. Anal Chem 2011; 83:7692-7. [PMID: 21919492 PMCID: PMC3214665 DOI: 10.1021/ac2019393] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The transmembrane protein α-hemolysin pore has been used to develop ultrasensitive biosensors, study biomolecular folding and unfolding, investigate covalent and noncovalent bonding interactions, and probe enzyme kinetics. Here, we report that, by addition of ionic liquid tetrakis(hydroxymethyl)phosphonium chloride solution to the α-hemolysin pore, the α-hemolysin channel can be controlled open or closed by adjusting the pH of the solution. This approach can be employed to develop a novel molecular switch to regulate molecular transport and should find potential applications as a "smart" drug delivery method.
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Affiliation(s)
- Dilani A. Jayawardhana
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, 700 Planetarium Place, Arlington, Texas 76019-0065, USA
| | - Mrinal K. Sengupta
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, 700 Planetarium Place, Arlington, Texas 76019-0065, USA
| | - D.M. Milan Krishantha
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, 700 Planetarium Place, Arlington, Texas 76019-0065, USA
| | - Jyoti Gupta
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, 700 Planetarium Place, Arlington, Texas 76019-0065, USA
| | - Daniel W. Armstrong
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, 700 Planetarium Place, Arlington, Texas 76019-0065, USA
| | - Xiyun Guan
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, 700 Planetarium Place, Arlington, Texas 76019-0065, USA
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50
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de Zoysa RSS, Krishantha DMM, Zhao Q, Gupta J, Guan X. Translocation of single-stranded DNA through the α-hemolysin protein nanopore in acidic solutions. Electrophoresis 2011; 32:3034-41. [PMID: 21997574 DOI: 10.1002/elps.201100216] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 06/02/2011] [Accepted: 06/09/2011] [Indexed: 11/12/2022]
Abstract
The effect of acidic pH on the translocation of single-stranded DNA through the α-hemolysin pore is investigated. Two significantly different types of events, i.e. deep blockades and shallow blockades, are observed at low pH. The residence times of the shallow blockades are not significantly different from those of the DNA translocation events obtained at or near physiological pH, whereas the deep blockades have much larger residence times and blockage amplitudes. With a decrease in the pH of the electrolyte solution, the percentage of the deep blockades in the total events increases. Furthermore, the mean residence time of these long-lived events is dependent on the length of DNA, and also varies with the nucleotide base, suggesting that they are appropriate for use in DNA analysis. In addition to being used as an effective approach to affect DNA translocation in the nanopore, manipulation of the pH of the electrolyte solution provides a potential means to greatly enhance the sensitivity of nanopore stochastic sensing.
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Affiliation(s)
- Ranulu S S de Zoysa
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019-0065, USA
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