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Xiang FF, Zhang H, Wu YL, Chen YJ, Liu YZ, Chen SY, Guo YZ, Yu XQ, Li K. Machine-Learning-Assisted Rational Design of Si─Rhodamine as Cathepsin-pH-Activated Probe for Accurate Fluorescence Navigation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2404828. [PMID: 38781580 DOI: 10.1002/adma.202404828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/06/2024] [Indexed: 05/25/2024]
Abstract
High-performance fluorescent probes stand as indispensable tools in fluorescence-guided imaging, and are crucial for precise delineation of focal tissue while minimizing unnecessary removal of healthy tissue. Herein, machine-learning-assisted strategy to investigate the current available xanthene dyes is first proposed, and a quantitative prediction model to guide the rational synthesis of novel fluorescent molecules with the desired pH responsivity is constructed. Two novel Si─rhodamine derivatives are successfully achieved and the cathepsin/pH sequentially activated probe Si─rhodamine─cathepsin-pH (SiR─CTS-pH) is constructed. The results reveal that SiR─CTS-pH exhibits higher signal-to-noise ratio of fluorescence imaging, compared to single pH or cathepsin-activated probe. Moreover, SiR─CTS-pH shows strong differentiation abilities for tumor cells and tissues and accurately discriminates the complex hepatocellular carcinoma tissues from normal ones, indicating its significant application potential in clinical practice. Therefore, the continuous development of xanthene dyes and the rational design of superior fluorescent molecules through machine-learning-assisted model broaden the path and provide more advanced methods to researchers.
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Affiliation(s)
- Fei-Fan Xiang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, P. R. China
| | - Hong Zhang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, P. R. China
- Huaxi MR Research Center (HMRRC), Department of Radiology, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Yan-Ling Wu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, P. R. China
| | - Yu-Jin Chen
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, P. R. China
| | - Yan-Zhao Liu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, P. R. China
| | - Shan-Yong Chen
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, P. R. China
| | - Yan-Zhi Guo
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, P. R. China
| | - Xiao-Qi Yu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, P. R. China
- Asymmetric Synthesis and Chiral Technology Key Laboratory of Sichuan Province, Department of Chemistry, Xihua University, Chengdu, 610039, P. R. China
| | - Kun Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, P. R. China
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Nicolau I, Hădade ND, Matache M, Funeriu DP. Synthetic Approaches of Epoxysuccinate Chemical Probes. Chembiochem 2023; 24:e202300157. [PMID: 37096389 DOI: 10.1002/cbic.202300157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 04/26/2023]
Abstract
Synthetic chemical probes are powerful tools for investigating biological processes. They are particularly useful for proteomic studies such as activity-based protein profiling (ABPP). These chemical methods initially used mimics of natural substrates. As the techniques gained prominence, more and more elaborate chemical probes with increased specificity towards given enzyme/protein families and amenability to various reaction conditions were used. Among the chemical probes, peptidyl-epoxysuccinates represent one of the first types of compounds used to investigate the activity of the cysteine protease papain-like family of enzymes. Structurally derived from the natural substrate, a wide body of inhibitors and activity- or affinity-based probes bearing the electrophilic oxirane unit for covalent labeling of active enzymes now exists. Herein, we review the literature regarding the synthetic approaches to epoxysuccinate-based chemical probes together with their reported applications, from biological chemistry and inhibition studies to supramolecular chemistry and the formation of protein arrays.
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Affiliation(s)
- Ioana Nicolau
- University of Bucharest, Faculty of Chemistry, Department of Organic Chemistry, Biochemistry and Catalysis, Research Centre of Applied Organic Chemistry, 90 Panduri Street, 050663, Bucharest, Romania
| | - Niculina D Hădade
- Babes-Bolyai University, Faculty of Chemistry and Chemical Engineering, Supramolecular and Organometallic Chemistry Centre, 11 Arany Janos Street, 400028, Cluj-Napoca, Romania
| | - Mihaela Matache
- University of Bucharest, Faculty of Chemistry, Department of Organic Chemistry, Biochemistry and Catalysis, Research Centre of Applied Organic Chemistry, 90 Panduri Street, 050663, Bucharest, Romania
| | - Daniel P Funeriu
- University of Bucharest, Faculty of Chemistry, Department of Organic Chemistry, Biochemistry and Catalysis, Research Centre of Applied Organic Chemistry, 90 Panduri Street, 050663, Bucharest, Romania
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3
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Li Y, Huang Z, Li Z, Li C, Liu R, Lv Y. Mass Spectrometric Multiplex Detection of MicroRNA and Protein Biomarkers for Liver Cancer. Anal Chem 2022; 94:17248-17254. [PMID: 36448711 DOI: 10.1021/acs.analchem.2c04171] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The occurrence of cancers is often accompanied by the abnormal expression of several sorts of biomarkers (e.g., nucleic acids and proteins). The multiplex assessment of them would substantially aid in the early detection and precise diagnosis, which is often hampered by their different detection schemes, different reaction matrix and reagents, and spectral overlapping. Herein, we propose a simple and sensitive mass spectrometric method for the multiplex detection of nucleic acid and protein, in which liver cancer-related biomarkers miRNA 223 and alpha-fetoprotein (AFP) were selected as model analytes. The self-amplification effect of metal atom-based nanoparticle probes can provide high sensitivity in complex serum samples without any additional amplification procedure. The detection limits for the simultaneous detection of miRNA 223 and AFP were 103 (2.1 pM) and 219 amol (0.15 ng/mL), respectively, with high specificity and selectivity. The proposed method is potentially useful for the rapid screening of cancers.
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Affiliation(s)
- Yan Li
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064 Sichuan, China
| | - Zili Huang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064 Sichuan, China
| | - Ziyan Li
- Analytical & Testing Center, Sichuan University, Chengdu 610064 Sichuan, China
| | - Caixia Li
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064 Sichuan, China
| | - Rui Liu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064 Sichuan, China
| | - Yi Lv
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064 Sichuan, China.,Analytical & Testing Center, Sichuan University, Chengdu 610064 Sichuan, China
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Gao L, Shi Y, Zhang E, You J, Han J, Su X, Han S. Biocapture-Directed Chemical Labeling for Discerning Stressed States of Organelles. Anal Chem 2022; 94:9903-9910. [PMID: 35754322 DOI: 10.1021/acs.analchem.2c01892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lysosomal rupture engaged in diverse diseases remains poorly discerned from lysosomal membrane permeabilization (LMP). We herein reported biocapture-directed chemical labeling (BCCL) for the discern of lysosomal rupture by tracking the release of optically labeled cathepsins from damaged lysosomes into the cytosol. BCCL entails covalent anchoring of an azide-tagged suicide substrate (Epo-LeuTyrAz) to the enzyme active site and bioorthogonal ligation of the introduced azide with DBCORC, a ratiometric sensor featuring an acidity-reporting red emissive X-rhodamine-lactam (ROX), blue emissive coumarin (CM) inert to pH, and DBCO reactive to azide. Aided with fluorescein isocyanate-labeled sialic acid (FITC-Sia), a probe remained in pH-elevated lysosomes but dissipated from LMP+ lysosomes, BCCL enables optical discern of four states of lysosomes: ruptured lysosomes (blue in cytosol), LMP+ lysosomes (blue in lysosomes), pH-elevated lysosomes (blue and green in lysosomes), and physiological lysosomes (blue, green and red in lysosomes). This approach could find applicability to study lysosome rupture over LMP in diseases and to evaluate lysosome rupture-inducing drugs.
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Affiliation(s)
- Lei Gao
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, State Key Laboratory for Physical Chemistry of Solid Surfaces, The Key Laboratory for Chemical Biology of Fujian Province, and The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Xiamen University, Xiamen 361005, China
| | - Yilong Shi
- College of Life Science and State Key Laboratory for Cell Stress, Xiamen University, Xiamen 361005, China
| | - Enkang Zhang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, State Key Laboratory for Physical Chemistry of Solid Surfaces, The Key Laboratory for Chemical Biology of Fujian Province, and The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Xiamen University, Xiamen 361005, China
| | - Jinxuan You
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, State Key Laboratory for Physical Chemistry of Solid Surfaces, The Key Laboratory for Chemical Biology of Fujian Province, and The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Xiamen University, Xiamen 361005, China
| | - Jiahuai Han
- College of Life Science and State Key Laboratory for Cell Stress, Xiamen University, Xiamen 361005, China
| | - Xinhui Su
- PET Center, Department of Nuclear Medicine, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Shoufa Han
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, State Key Laboratory for Physical Chemistry of Solid Surfaces, The Key Laboratory for Chemical Biology of Fujian Province, and The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Xiamen University, Xiamen 361005, China
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Chen X, Song H, Li Z, Liu R, Lv Y. Lanthanide Nanoprobes for the Multiplex Evaluation of Breast Cancer Biomarkers. Anal Chem 2021; 93:13719-13726. [PMID: 34595914 DOI: 10.1021/acs.analchem.1c03445] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Metal stable isotope tagging has demonstrated great and unique success in the multiplex and ratiometry-based accurate detection of biomolecules and single cells, while its sensitivity is regarded as an Achilles' heel. Although lanthanide nanoparticles remain the most promising tags for elemental mass spectrometry, there is no report on the lanthanide nanoparticle-based multiplex immunoassay of disease markers in clinical serum samples because of their tough synthesis and bioconjugation and a complex physiological sample matrix. Herein, to fill this gap, multiple lanthanide nanoparticle tags (NaEuF4, NaTbF4, and NaHoF4) were delicately designed and facilely synthesized with a one-pot solvothermal method for the multiplex evaluation of breast cancer biomarkers carcinoembryonic antigen (CEA), CA153, and CA125 in human serum samples. The proposed method exhibited wide linear ranges and low levels of the detection limit for all biomarkers. The test results were consistent with the routine electrochemiluminescence results in clinical serum samples, which proved the possibility of the early prognosis of breast cancer as well as improving the surgical outcome prediction.
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Affiliation(s)
- Xue Chen
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Hongjie Song
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Ziyan Li
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Rui Liu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yi Lv
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China.,Analytical & Testing Center, Sichuan University, Chengdu 610064, China
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Mystery of methamphetamine-induced autophagosome accumulation in hippocampal neurons: loss of syntaxin 17 in defects of dynein-dynactin driving and autophagosome-late endosome/lysosome fusion. Arch Toxicol 2021; 95:3263-3284. [PMID: 34374793 DOI: 10.1007/s00204-021-03131-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 08/04/2021] [Indexed: 01/07/2023]
Abstract
Methamphetamine (METH), a psychoactive-stimulant facilitates massive accumulation of autophagosomes and causes autophagy-associated neuronal death. However, the underlying mechanisms involving METH-induced auto-phagosome accumulation remain poorly understood. In the current study, autophagic flux was tracked by mRFP-GFP-LC3 adenovirus, 900 μM METH treatment was found to significantly disrupt autophagic flux, which was further validated by remarkable increase of co-localized of LC3 and SQSTM1/p62, enhancement of LC3-II and SQSTM1/p62 protein levels, and massive autophagosome puncta aggregation. With the cycloheximide (CHX) treatment, METH treatment was displayed a significant inhibition of SQSTM1/p62 degradation. Therefore, the mRNAs associated with vesicle degradation were screened, and syntaxin 17 (Stx17) and dynein-dynactin mRNA levels significantly decreased, an effect was proved in protein level as well. Intriguingly, METH induced autophagosome accumulation and autophagic flux disturbance was incredibly retarded by overexpression of Stx17, which was validated by the restoration of the fusion autophagosome-late endosome/lysosome fusion. Moreover, Stx17 overexpression obviously impeded the METH-induced decrease of co-localization of the retrograded motor protein dynein/dynactin and autophagosome-late endosome, though the dynein/dynactin proteins were not involved in autophagosome-late endosome/lysosome fusion. Collectively, our findings unravel the mechanism of METH-induced autophagosome accumulation involving autophagosome-late endosome/lysosome fusion deficiency and that autophagy-enhancing mechanisms such as the overexpression of Stx17 may be therapeutic strategies for the treatment of METH-induced neuronal damage.
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Wang C, Deng Z, Zhang H, Liu R, Lv Y. Old commercialized magnetic particles new trick: Intrinsic internal standard. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.07.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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8
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Wang X, Chen X, Zhou R, Hu P, Huang K, Chen P. Filter-Assisted Separation of Multiple Nanomaterials: Mechanism and Application in Atomic/Mass Spectrometry/Fluorescence Label-Free Multimode Bioassays. Anal Chem 2021; 93:3889-3897. [PMID: 33595278 DOI: 10.1021/acs.analchem.0c04562] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Atomic spectrometry (AS) has been widely used in bioassay, but it requires steps to immobilize or separate the signal molecules. In this work, based on the phenomenon that the filter membrane can selectively separate multiple nanomaterials (nanoparticles (NPs) and quantum dots (QDs)) and its related ions, including poly(thymine)-templated Cu NPs and free Cu2+, Ag NPs and free Ag+, CdTe QDs and Cd2+, we constructed multimode and label-free biosensors by chemical vapor generation-atomic fluorescence spectrometry (CVG-AFS), inductively coupled plasma mass spectrometry (ICP-MS), and fluorescence. In this strategy, terminal deoxynucleotidyl transferase (TdT) and polynucleotide kinase (PNK), H2O2, and mucin 1 can be sensitively detected using Cu2+, Ag+, and Cd2+ as the signal probe, respectively. As a result, TdT and T4 PNK in single cells level can be accurately quantified. In addition, the possible separation mechanism of filter membrane was proposed, both Donnan repulsion by charged functional layer and entrapment effect by nanomaterials size contributed to the outstanding separation performance. Subsequently, on the basis that CdTe QDs can selectively identify Cu NPs/Cu2+, Ag NPs/Ag+, and C-Ag+-C/Ag+, cation-exchange reaction (CER) was introduced in this platform due to its unique advantages, including improving the sensitivity of the above system (an order of magnitude), converting the non-CVG metal elements into CVG elements, and using low-cost AFS to substitute the high-cost ICP-MS. In addition, we performed theoretical calculations of the selective CER using density functional theory (DFT). Therefore, this label-free and simple separation AS/ICP-MS sensing platform shows great potential for biomarker analysis.
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Affiliation(s)
- Xiu Wang
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, Sichuan 610068, China
| | - Xin Chen
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, Sichuan 610068, China
| | - Ronghui Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Pingyue Hu
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, Sichuan 610068, China
| | - Ke Huang
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, Sichuan 610068, China
| | - Piaopiao Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
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Mhlongo NZ, Ebenhan T, Driver CHS, Maguire GEM, Kruger HG, Govender T, Naicker T. Microwave-assisted synthesis of meso-carboxyalkyl-BODIPYs and an application to fluorescence imaging. Org Biomol Chem 2020; 18:7876-7883. [PMID: 32986056 DOI: 10.1039/d0ob01415j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this study, a significantly improved method for the synthesis of modular meso-BODIPY (boron dipyrromethene) derivatives possessing a free carboxylic acid group (which was subsequently coupled to peptides), is disclosed. This method provides a vastly efficient synthetic route with a > threefold higher overall yield than other reports. The resultant meso-BODIPY acid allowed for further easy incorporation into peptides. The meso-BODIPY peptides showed absorption maxima from 495-498 nm and emission maxima from 504-506 nm, molar absorptivity coefficients from 33 383-80 434 M-1 cm-1 and fluorescent quantum yields from 0.508-0.849. The meso-BODIPY-c(RGDyK) peptide was evaluated for plasma stability and (proved to be durable even up to 4 h) was then assessed for its fluorescence imaging applicability in vivo and ex vivo. The optical imaging in vivo was limited due to autofluorescence, however, the ex vivo tissue analysis displayed BODIPY-c(RGDyK) internalization and cancer detection thereby making it a novel tumor-integrin associated fluorescent probe while displaying the lack of interference the dye has on the properties of this ligand to bind the receptor.
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Affiliation(s)
- Neliswa Z Mhlongo
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Durban, South Africa.
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Li Z, Li H, Deng D, Liu R, Lv Y. Mass Spectrometric Assay of Alpha-Fetoprotein Isoforms for Accurate Serological Evaluation. Anal Chem 2020; 92:4807-4813. [DOI: 10.1021/acs.analchem.9b03995] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ziyan Li
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Hongmei Li
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Dongyan Deng
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Rui Liu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yi Lv
- Analytical & Testing Center, Sichuan University, Chengdu 610064, China
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