101
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Ho CW, Van Meervelt V, Tsai KC, De Temmerman PJ, Mast J, Maglia G. Engineering a nanopore with co-chaperonin function. SCIENCE ADVANCES 2015; 1:e1500905. [PMID: 26824063 PMCID: PMC4730846 DOI: 10.1126/sciadv.1500905] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 09/25/2015] [Indexed: 05/20/2023]
Abstract
The emergence of an enzymatic function can reveal functional insights and allows the engineering of biological systems with enhanced properties. We engineered an alpha hemolysin nanopore to function as GroES, a protein that, in complex with GroEL, forms a two-stroke protein-folding nanomachine. The transmembrane co-chaperonin was prepared by recombination of GroES functional elements with the nanopore, suggesting that emergent functions in molecular machines can be added bottom-up by incorporating modular elements into preexisting protein scaffolds. The binding of a single-ring version of GroEL to individual GroES nanopores prompted large changes to the unitary nanopore current, most likely reflecting the allosteric transitions of the chaperonin apical domains. One of the GroEL-induced current levels showed fast fluctuations (<1 ms), a characteristic that might be instrumental for efficient substrate encapsulation or folding. In the presence of unfolded proteins, the pattern of current transitions changed, suggesting a possible mechanism in which the free energy of adenosine triphosphate binding and hydrolysis is expended only when substrate proteins are occupied.
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Affiliation(s)
- Ching-Wen Ho
- Department of Chemistry, University of Leuven, Leuven 3001, Belgium
| | | | - Keng-Chang Tsai
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei 11221, Taiwan
| | - Pieter-Jan De Temmerman
- Electron Microscopy Unit, Veterinary and Agrochemical Research Centre (CODA-CERVA), Brussels 1180, Belgium
| | - Jan Mast
- Electron Microscopy Unit, Veterinary and Agrochemical Research Centre (CODA-CERVA), Brussels 1180, Belgium
| | - Giovanni Maglia
- Groningen Biotechnology Institute, University of Groningen, Groningen 9747AG, Netherlands
- Corresponding author. E-mail:
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102
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Biesemans A, Soskine M, Maglia G. A Protein Rotaxane Controls the Translocation of Proteins Across a ClyA Nanopore. NANO LETTERS 2015; 15:6076-6081. [PMID: 26243210 PMCID: PMC4606981 DOI: 10.1021/acs.nanolett.5b02309] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Rotaxanes, pseudorotaxanes, and catenanes are supramolecular complexes with potential use in nanomachinery, molecular computing, and single-molecule studies. Here we constructed a protein rotaxane in which a polypeptide thread is encircled by a Cytolysin A (ClyA) nanopore and capped by two protein stoppers. The rotaxane could be switched between two states. At low negative applied potentials (<-50 mV) one of the protein stoppers resided inside the nanopore indefinitely. Under this configuration the rotaxane prevents the diffusion of protein molecules across the lipid bilayer and provides a useful platform for single-molecule analysis. High negative applied potentials (-100 mV) dismantled the interlocked rotaxane system by the forceful translocation of the protein stopper, allowing new proteins to be trapped inside or transported across the nanopore. The observed voltage threshold for the translocation of the protein stopper through the nanopore related well to the biphasic voltage dependence of the residence time measured for the freely diffusing protein stopper. We propose a model in which molecules translocate through a nanopore when the average dwell time decreases with the applied potential.
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Affiliation(s)
- Annemie Biesemans
- Department of Chemistry, University of Leuven, Leuven, 3001, Belgium
| | - Misha Soskine
- Groningen Biomolecular Sciences & Biotechnology (GBB) Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology (GBB) Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
- Department of Chemistry, University of Leuven, Leuven, 3001, Belgium
- Corresponding author:
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103
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Liu N, Yang Z, Ou X, Wei B, Zhang J, Jia Y, Xia F. Nanopore-based analysis of biochemical species. Mikrochim Acta 2015; 183:955-963. [PMID: 27013767 PMCID: PMC4778144 DOI: 10.1007/s00604-015-1560-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 06/30/2015] [Indexed: 12/11/2022]
Abstract
Biological nanochannels or nanopores play a crucial role in basic biochemical processes in cells. Artificial nanopores possessing dimensions comparable to the size of biological molecules and mimicking the function of biological ion channels are of particular interest with respect to the design of biosensors with a sensitivity that can go down to the fM level and even to single molecule detection. Nanopore-based analysis (NPA) is currently a new research field with fascinating prospects. This review (with 118 refs.) summarizes the progress made in this field in the recent 10 years. Following an introduction into the fundamentals of NPA, we demonstrate its potential by describing selected methods for sensing (a) proteins such as streptavidin, certain antibodies, or thrombin via aptamers; (b) oligomers, larger nucleic acids, or micro-RNA; (c) small molecules, (d) ions such as K(I) which is vital to the maintenance of life, or Hg(II) which is dangerous to health. We summarize the results and discuss the merits and limitations of the various methods at last. Graphical abstractSchematic of a signal-off system and a signal-on system in nanopore analysis. The effective diameter of nanopores decreases when targets undergo certain interactions with receptors attached on the inner surface of the nanopore. Correspondingly, the current will drop on appearance of the analyte. This is referred to as a "signal-off" system. Conversely, it is called a "signal-on" system.
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Affiliation(s)
- Nannan Liu
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Zekun Yang
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Xiaowen Ou
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Benmei Wei
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Juntao Zhang
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Yongmei Jia
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Fan Xia
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
- />National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan, 430074 China
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104
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Zeng T, Liu L, Li T, Li Y, Gao J, Zhao Y, Wu HC. Detection of 5-methylcytosine and 5-hydroxymethylcytosine in DNA via host-guest interactions inside α-hemolysin nanopores. Chem Sci 2015; 6:5628-5634. [PMID: 28757950 PMCID: PMC5510575 DOI: 10.1039/c5sc01436k] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/24/2015] [Indexed: 01/17/2023] Open
Abstract
After selective modification with a host–guest complex, 5-methylcytosine and 5-hydroxymethylcytosine in ssDNA can be unambiguously detected by the generation of characteristic current events during the translocation of the modified DNA through α-hemolysin nanopores.
Cytosine methylation and hydroxymethylation are both important epigenetic modifications of DNA in mammalian cells. Therefore, profiling DNA (hydroxy)methylation across the genome is vital for understanding their roles in gene regulation. Here, we report a nanopore-based approach for quick and reliable detection of 5-methylcytosine and 5-hydroxymethylcytosine in DNA at the single-molecule level. The single-stranded DNA containing 5-methylcytosine or 5-hydroxymethylcytosine was first selectively modified on the epigenetic base to attach a host–guest complex. Threading of the modified DNA molecules through α-hemolysin nanopores causes unbinding of the host–guest complex and generates highly characteristic current signatures. Statistical analysis of the signature events affords quantitative information about 5-methylcytosine and 5-hydroxymethylcytosine in DNA. Our results suggest that other DNA modifications could also be detected with the developed method. Furthermore, we anticipate our nanopore sensing strategy to be generally useful in biochemical analysis and to find applications in the early diagnosis of diseases.
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Affiliation(s)
- Tao Zeng
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety , Institute of High Energy Physics , Chinese Academy of Sciences , Beijing 100049 , China . ; ; Tel: +86-10-88235745.,National Center for Nanoscience and Technology of China , Beijing 100190 , China .
| | - Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety , Institute of High Energy Physics , Chinese Academy of Sciences , Beijing 100049 , China . ; ; Tel: +86-10-88235745
| | - Ting Li
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety , Institute of High Energy Physics , Chinese Academy of Sciences , Beijing 100049 , China . ; ; Tel: +86-10-88235745
| | - Yuru Li
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety , Institute of High Energy Physics , Chinese Academy of Sciences , Beijing 100049 , China . ; ; Tel: +86-10-88235745
| | - Juan Gao
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety , Institute of High Energy Physics , Chinese Academy of Sciences , Beijing 100049 , China . ; ; Tel: +86-10-88235745
| | - Yuliang Zhao
- National Center for Nanoscience and Technology of China , Beijing 100190 , China .
| | - Hai-Chen Wu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety , Institute of High Energy Physics , Chinese Academy of Sciences , Beijing 100049 , China . ; ; Tel: +86-10-88235745
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105
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Soskine M, Biesemans A, Maglia G. Single-Molecule Analyte Recognition with ClyA Nanopores Equipped with Internal Protein Adaptors. J Am Chem Soc 2015; 137:5793-5797. [PMID: 25871548 PMCID: PMC4424005 DOI: 10.1021/jacs.5b01520] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nanopores have been used to detect molecules, to sequence DNA, or to investigate chemical reactions at the single-molecule level. Because they approach the absolute limit of sensor miniaturization, nanopores are amenable to parallelization and could be used in single-cell measurements. Here we show that single enzymes can be functionally and reversibly trapped inside the confined space of a ClyA nanopore. Remarkably, the binding of ligands to the internalized proteins is mirrored by specific changes to the nanopore conductance. Conveniently, the manipulation of the charge of the protein allowed increasing of the residence time of the protein inside the nanopore. Nanopores with internalized protein adaptors can be used to study proteins in real time or can be incorporated into inexpensive portable devices for the detection of analytes with high selectivity.
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Affiliation(s)
- Misha Soskine
- Groningen Biomolecular Sciences & Biotechnology (GBB) Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
- Department of Chemistry, University of Leuven, Leuven, 3001, Belgium
| | - Annemie Biesemans
- Department of Chemistry, University of Leuven, Leuven, 3001, Belgium
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology (GBB) Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
- Department of Chemistry, University of Leuven, Leuven, 3001, Belgium
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106
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Benke S, Roderer D, Wunderlich B, Nettels D, Glockshuber R, Schuler B. The assembly dynamics of the cytolytic pore toxin ClyA. Nat Commun 2015; 6:6198. [PMID: 25652783 PMCID: PMC4347018 DOI: 10.1038/ncomms7198] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 01/05/2015] [Indexed: 12/15/2022] Open
Abstract
Pore-forming toxins are protein assemblies used by many organisms to disrupt the membranes of target cells. They are expressed as soluble monomers that assemble spontaneously into multimeric pores. However, owing to their complexity, the assembly processes have not been resolved in detail for any pore-forming toxin. To determine the assembly mechanism for the ring-shaped, homododecameric pore of the bacterial cytolytic toxin ClyA, we collected a diverse set of kinetic data using single-molecule spectroscopy and complementary techniques on timescales from milliseconds to hours, and from picomolar to micromolar ClyA concentrations. The entire range of experimental results can be explained quantitatively by a surprisingly simple mechanism. First, addition of the detergent n-dodecyl-β-D-maltopyranoside to the soluble monomers triggers the formation of assembly-competent toxin subunits, accompanied by the transient formation of a molten-globule-like intermediate. Then, all sterically compatible oligomers contribute to assembly, which greatly enhances the efficiency of pore formation compared with simple monomer addition.
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Affiliation(s)
- Stephan Benke
- University of Zurich, Department of Biochemistry, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Daniel Roderer
- ETH Zurich, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Bengt Wunderlich
- University of Zurich, Department of Biochemistry, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Daniel Nettels
- University of Zurich, Department of Biochemistry, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Rudi Glockshuber
- ETH Zurich, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Benjamin Schuler
- University of Zurich, Department of Biochemistry, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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107
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108
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Van Meervelt V, Soskine M, Maglia G. Detection of two isomeric binding configurations in a protein-aptamer complex with a biological nanopore. ACS NANO 2014; 8:12826-35. [PMID: 25493908 PMCID: PMC4410316 DOI: 10.1021/nn506077e] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Protein-DNA interactions play critical roles in biological systems, and they often involve complex mechanisms and dynamics that are not easily measured by ensemble experiments. Recently, we showed that folded proteins can be internalized inside ClyA nanopores and studied by ionic current recordings at the single-molecule level. Here, we use ClyA nanopores to sample the interaction between the G-quadruplex fold of the thrombin binding aptamer (TBA) and human thrombin (HT). Surprisingly, the internalization of the HT:TBA complex inside the nanopore induced two types of current blockades with distinguished residual current and lifetime. Using single nucleobase substitutions to TBA we showed that these two types of blockades originate from TBA binding to thrombin with two isomeric orientations. Voltage dependencies and the use of ClyA nanopores with two different diameters allowed assessing the effect of the applied potential and confinement and revealed that the two binding configurations of TBA to HT display different lifetimes. These results show that the ClyA nanopores can be used to probe conformational heterogeneity in protein:DNA interactions.
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Affiliation(s)
| | - Misha Soskine
- Department of Chemistry, KU Leuven, Leuven, B-3001, Belgium
| | - Giovanni Maglia
- Department of Chemistry, KU Leuven, Leuven, B-3001, Belgium
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, the Netherlands
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109
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Freedman KJ, Haq SR, Fletcher MR, Foley JP, Jemth P, Edel JB, Kim MJ. Nonequilibrium capture rates induce protein accumulation and enhanced adsorption to solid-state nanopores. ACS NANO 2014; 8:12238-49. [PMID: 25426798 DOI: 10.1021/nn5062645] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Single molecule capturing of analytes using an electrically biased nanopore is the fundamental mechanism in which nearly all nanopore experiments are conducted. With pore dimensions being on the order of a single molecule, the spatial zone of sensing only contains approximately a zeptoliter of volume. As a result, nanopores offer high precision sensing within the pore but provide little to no information about the analytes outside the pore. In this study, we use capture frequency and rate balance theory to predict and study the accumulation of proteins at the entrance to the pore. Protein accumulation is found to have positive attributes such as capture rate enhancement over time but can additionally lead to negative effects such as long-term blockages typically attributed to protein adsorption on the surface of the pore. Working with the folded and unfolded states of the protein domain PDZ2 from SAP97, we show that applying short (e.g., 3-25 s in duration) positive voltage pulses, rather than a constant voltage, can prevent long-term current blockades (i.e., adsorption events). By showing that the concentration of proteins around the pore can be controlled in real time using modified voltage protocols, new experiments can be explored which study the role of concentration on single molecular kinetics including protein aggregation, folding, and protein binding.
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Affiliation(s)
- Kevin J Freedman
- Department of Chemistry, Imperial College London , South Kensington, SW7 2AZ London, United Kingdom
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110
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Pastoriza-Gallego M, Breton MF, Discala F, Auvray L, Betton JM, Pelta J. Evidence of unfolded protein translocation through a protein nanopore. ACS NANO 2014; 8:11350-11360. [PMID: 25380310 DOI: 10.1021/nn5042398] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protein nanopores are mainly used to study transport, unfolding, intrinsically disordered proteins, protein-pore interactions, and protein-ligand complexes. This single-molecule sensor for biomedical and biotechnological applications is promising but until now direct proof of protein translocation through a narrow channel is lacking. Here, we report the translocation of a chimera molecule through the aerolysin nanopore in the presence of a denaturing agent, guanidium chloride (1.5 M) and KCl (1 M). The chimera molecule is composed of the recombinant MalE protein with a unique cysteine residue at the C-terminal position covalently linked to a single-stranded DNA oligonucleotide. Real-time polymerase chain reaction (PCR) was used to detect the presence of chimera molecules that have been effectively translocated from the cis to trans chamber of the set up. Comparing the electrical signature of the chimera related to the protein or oligonucleotide alone demonstrates that each type of molecule displays different dynamics in term of transport time, event frequency, and current blockade. This original approach provides the possibility to study protein translocation through different biological, artificial, and biomimetic nanopores or nanotubes. New future applications are now conceivable such as protein refolding at the nanopore exit, peptides and protein sequencing, and peptide characterization for diagnostics.
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Affiliation(s)
- Manuela Pastoriza-Gallego
- CNRS-UMR 8587, LAMBE, Université de Cergy-Pontoise , 2 avenue A. Chauvin, 95302 Cergy-Pontoise Cedex France
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111
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Ying YL, Cao C, Long YT. Single molecule analysis by biological nanopore sensors. Analyst 2014; 139:3826-35. [PMID: 24991734 DOI: 10.1039/c4an00706a] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nanopore sensors provide a highly innovative technique for a rapid and label-free single molecule analysis, which holds a great potential in routing applications. Biological nanopores have been used as ultra-sensitive sensors over a wide range of single molecule analysis including DNA sequencing, disease diagnosis, drug screening, environment monitoring and the construction of molecule machines. This mini review will focus on the current strategies for the identification and characterization of an individual analyte, especially based on our recent achievements in biological nanopore biosensors.
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Affiliation(s)
- Yi-Lun Ying
- Key Laboratory for Advanced Materials & Department of Chemistry, East China University of Science and Technology, P. R. China.
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