1
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Xiang Y, Liu J, Chen J, Xiao M, Pei H, Li L. MoS 2-Based Sensor Array for Accurate Identification of Cancer Cells with Ensemble-Modified Aptamers. ACS APPLIED MATERIALS & INTERFACES 2024; 16:15861-15869. [PMID: 38508220 DOI: 10.1021/acsami.3c19159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
In this work, we present an array-based chemical nose sensor that utilizes a set of ensemble-modified aptamer (EMAmer) probes to sense subtle physicochemical changes on the cell surface for cancer cell identification. The EMAmer probes are engineered by domain-selective incorporation of different types and/or copies of positively charged functional groups into DNA scaffolds, and their differential interactions with cancer cells can be transduced through competitive adsorption of fluorophore-labeled EMAmer probes loaded on MoS2 nanosheets. We demonstrate that this MoS2-EMAmer-based sensor array enables rapid and effective discrimination among six types of cancer cells and their mixtures with a concentration of 104 cells within 60 min, achieving a 94.4% accuracy in identifying blinded unknown cell samples. The established MoS2-EMAmer sensing platform is anticipated to show significant promise in the advancement of cancer diagnostics.
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Affiliation(s)
- Ying Xiang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Jingjing Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Jing Chen
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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2
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Zhou J, Yang S, Zhang Y, Ren JC, Liu W. Effective Descriptor for Screening Single-Molecule Conductance Switches. J Am Chem Soc 2024; 146:6962-6973. [PMID: 38426449 DOI: 10.1021/jacs.3c14655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The adsorption-type molecular switch exhibits bistable states with an equivalently long lifetime at the organic/inorganic interface, promising reliable switching behavior and superior assembly ability in the electronic circuits at the molecular scale. However, the number of reported adsorption-type molecular switches is currently less than 10, and exploring these molecular switches poses a formidable challenge due to the intricate interplay occurring at the interface. To address this challenge, we have developed a model enabling the identification of diverse molecular switches on metal surfaces based on easily accessible physical characteristics. These characteristics primarily include the metal valency electron concentration, the work function of metal surfaces, and the electronegativity difference of molecules. Using this model, we identified 56 new molecular switches. Employing the gradient descent algorithm and statistical linear discriminant analysis, we constructed an explicit descriptor that establishes a relationship between the interfacial structure and chemical environment and the stability of molecular switches. The model's accuracy was validated through density functional theory calculations, achieving a 90% accuracy for aromatic molecular switches. The conductive switching behaviors were further confirmed by nonequilibrium Green's function transport calculations.
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Affiliation(s)
- Junjun Zhou
- Nano and Heterogeneous Materials Center, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, Jiangsu, China
| | - Sha Yang
- Nano and Heterogeneous Materials Center, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, Jiangsu, China
| | - Yirong Zhang
- Nano and Heterogeneous Materials Center, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, Jiangsu, China
| | - Ji-Chang Ren
- Nano and Heterogeneous Materials Center, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, Jiangsu, China
| | - Wei Liu
- Nano and Heterogeneous Materials Center, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, Jiangsu, China
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, China
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3
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Song H, Guo Y, Zhang G, Shi L. Tailored Water-Soluble Covalent Organic Cages for Encapsulation of Pyrene and Information Encryption. Int J Mol Sci 2023; 24:17541. [PMID: 38139371 PMCID: PMC10743434 DOI: 10.3390/ijms242417541] [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: 10/29/2023] [Revised: 12/04/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Forming pyridine salts to construct covalent organic cages is an effective strategy for constructing covalent cage compounds. Covalent organic cages based on pyridine salt structures are prone to form water-soluble supramolecular compounds. Herein, we designed and synthesized a triangular prism-shaped hexagonal cage with a larger cavity and relatively flexible conformation. The supramolecular cage structure was also applied to the encapsulation of pyrene and information encryption.
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Affiliation(s)
| | | | - Guorui Zhang
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China; (H.S.); (Y.G.)
| | - Linlin Shi
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China; (H.S.); (Y.G.)
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4
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Wojtuch A, Danel T, Podlewska S, Maziarka Ł. Extended study on atomic featurization in graph neural networks for molecular property prediction. J Cheminform 2023; 15:81. [PMID: 37726841 PMCID: PMC10507875 DOI: 10.1186/s13321-023-00751-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 08/23/2023] [Indexed: 09/21/2023] Open
Abstract
Graph neural networks have recently become a standard method for analyzing chemical compounds. In the field of molecular property prediction, the emphasis is now on designing new model architectures, and the importance of atom featurization is oftentimes belittled. When contrasting two graph neural networks, the use of different representations possibly leads to incorrect attribution of the results solely to the network architecture. To better understand this issue, we compare multiple atom representations by evaluating them on the prediction of free energy, solubility, and metabolic stability using graph convolutional networks. We discover that the choice of atom representation has a significant impact on model performance and that the optimal subset of features is task-specific. Additional experiments involving more sophisticated architectures, including graph transformers, support these findings. Moreover, we demonstrate that some commonly used atom features, such as the number of neighbors or the number of hydrogens, can be easily predicted using only information about bonds and atom type, yet their explicit inclusion in the representation has a positive impact on model performance. Finally, we explain the predictions of the best-performing models to better understand how they utilize the available atomic features.
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Affiliation(s)
- Agnieszka Wojtuch
- Faculty of Mathematics and Computer Science, Jagiellonian University, Łojasiewicza 6, 30-348, Kraków, Poland.
| | - Tomasz Danel
- Faculty of Mathematics and Computer Science, Jagiellonian University, Łojasiewicza 6, 30-348, Kraków, Poland
| | - Sabina Podlewska
- Maj Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, 31-343, Kraków, Poland
| | - Łukasz Maziarka
- Faculty of Mathematics and Computer Science, Jagiellonian University, Łojasiewicza 6, 30-348, Kraków, Poland
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5
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Motiei L, Margulies D. Molecules that Generate Fingerprints: A New Class of Fluorescent Sensors for Chemical Biology, Medical Diagnosis, and Cryptography. Acc Chem Res 2023. [PMID: 37335975 DOI: 10.1021/acs.accounts.3c00162] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
ConspectusFluorescent molecular sensors, often referred to as "turn-on" or "turn-off" fluorescent probes, are synthetic agents that change their fluorescence signal in response to analyte binding. Although these sensors have become powerful analytical tools in a wide range of research fields, they are generally limited to detecting only one or a few analytes. Pattern-generating fluorescent probes, which can generate unique identification (ID) fingerprints for different analytes, have recently emerged as a new class of luminescent sensors that can address this limitation. A unique characteristic of these probes, termed ID-probes, is that they integrate the qualities of conventional small-molecule-based fluorescent sensors and cross-reactive sensor arrays (often referred to as chemical, optical, or electronic noses/tongues). On the one hand, ID-probes can discriminate between various analytes and their combinations, akin to array-based analytical devices. On the other hand, their minute size enables them to analyze small-volume samples, track dynamic changes in a single solution, and operate in the microscopic world, which the macroscopic arrays cannot access.Here, we describe the principles underlying the ID-probe technology, as well as provide an overview of different ID-probes that have been developed to date and the ways they can be applied to a wide range of research fields. We describe, for example, ID-probes that can identify combinations of protein biomarkers in biofluids and in living cells, screen for several protein inhibitors simultaneously, analyze the content of Aβ aggregates, as well as ensure the quality of small-molecule and biological drugs. These examples highlight the relevance of this technology to medical diagnosis, bioassay development, cell and chemical biology, and pharmaceutical quality assurance, among others. ID-probes that can authorize users and protect secret data are also presented and the mechanisms that enable them to hide (steganography), encrypt (cryptography), and prevent access to (password protection) information are discussed.The versatility of this technology is further demonstrated by describing two types of probes: unimolecular ID-probes and self-assembled ID-probes. Probes from the first type can operate inside living cells, be recycled, and their initial patterns can be more easily obtained in a reproducible manner. The second type of probes can be readily modified and optimized, allowing one to prepare various different probes from a much wider range of fluorescent reporters and supramolecular recognition elements. Taken together, these developments indicate that the ID-probe sensing methodology is generally applicable, and that such probes can better characterize analyte mixtures or process chemically encoded information than can the conventional fluorescent molecular sensors. We therefore hope that this review will inspire the development of new types of pattern-generating probes, which would extend the fluorescence molecular toolbox currently used in the analytical sciences.
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Affiliation(s)
- Leila Motiei
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Margulies
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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6
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Han X, Guo C, Xu C, Shi L, Liu B, Zhang Z, Bai Q, Song B, Pan F, Lu S, Zhu X, Wang H, Hao XQ, Song MP, Li X. Water-Soluble Metallo-Supramolecular Nanoreactors for Mediating Visible-Light-Promoted Cross-Dehydrogenative Coupling Reactions. ACS NANO 2023; 17:3723-3736. [PMID: 36757357 DOI: 10.1021/acsnano.2c10856] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Water-soluble metallo-supramolecular cages with well-defined nanosized cavities have a wide range of functions and applications. Herein, we design and synthesize two series of metallo-supramolecular octahedral cages based on the self-assembly of two congeneric truxene-derived tripyridyl ligands modified with two polyethylene glycol (PEG) chains, i.e., monodispersed tetraethylene glycol (TEG) and polydispersed PEG-1000, with four divalent transition metals (i.e., Pd, Cu, Ni, and Zn). The resulting monodispersed cages C1-C4 are fully characterized by electrospray ionization mass spectrometry (ESI-MS), nuclear magnetic resonance (NMR) spectroscopy, and single-crystal X-ray diffraction. The polydispersed cages C5-C8 display good water solubilities and can act as nanoreactors to mediate visible-light-promoted C(sp3)-C(sp2) cross-dehydrogenative coupling reactions in an aqueous phase. In particular, the most robust Pd(II)-linked water-soluble polydispersed nanoreactor C5 is characterized by ESI-MS and capable of mediating the reactions with the highest efficiencies. Detailed host-guest binding studies in conjunction with control studies suggest that these cages could encapsulate the substrates simultaneously inside its hydrophobic cavity while interacting with the photosensitizer (i.e., eosin Y).
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Affiliation(s)
- Xin Han
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450001, China
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518055, China
| | - Chenxing Guo
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518055, China
- School of Biomedical Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Chen Xu
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212003, China
| | - Linlin Shi
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Binghui Liu
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Zhe Zhang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, Guangdong 510006, China
| | - Qixia Bai
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, Guangdong 510006, China
| | - Bo Song
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Fangfang Pan
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan, Hubei 430079, China
| | - Shuai Lu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518055, China
| | - Xinju Zhu
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Heng Wang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518055, China
| | - Xin-Qi Hao
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Mao-Ping Song
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Xiaopeng Li
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518055, China
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7
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Tailored Supramolecular Cage for Efficient Bio-Labeling. Int J Mol Sci 2023; 24:ijms24032147. [PMID: 36768471 PMCID: PMC9916613 DOI: 10.3390/ijms24032147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/10/2022] [Accepted: 12/21/2022] [Indexed: 01/25/2023] Open
Abstract
Fluorescent chemosensors are powerful imaging tools used in a broad range of biomedical fields. However, the application of fluorescent dyes in bioimaging still remains challenging, with small Stokes shifts, interfering signals, background noise, and self-quenching on current microscope configurations. In this work, we reported a supramolecular cage (CA) by coordination-driven self-assembly of benzothiadiazole derivatives and Eu(OTf)3. The CA exhibited high fluorescence with a quantum yield (QY) of 38.57%, good photoluminescence (PL) stability, and a large Stokes shift (153 nm). Furthermore, the CCK-8 assay against U87 glioblastoma cells verified the low cytotoxicity of CA. We revealed that the designed probes could be used as U87 cells targeting bioimaging.
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8
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Jin X, Jiang H, Chen Y, Han X, Sun K, Shi L, Hao XQ, Song MP. A Cavity-Tailored Metal-Organic Tetrahedral Nanocage and Gas Adsorption Property. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:4402. [PMID: 36558254 PMCID: PMC9783787 DOI: 10.3390/nano12244402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Porous organometallic nanomaterials are a new class of materials based on a three-dimensional structure. They have excellent applications in different fields, but their applications in gas storage and separation have not been fully developed. CO2 adsorption storage and hydrocarbon separation has been a challenging industrial problem. Several typical molecular adsorbents have been used to study the separation, but the problems of long-term stability, high selectivity and synthetic complexity of these adsorbents remain to be solved. Here, we have designed and synthesized tetrahedral metal supramolecular nanocage with custom cavities based on the unique rigid structure of triptycene derivatives. Using the unique discrete porous structure of tetrahedral metal nanocages, the gas adsorption and separation performance of the metal supramolecular nanocage was investigated. By analyzing the adsorption and desorption isotherms and the multi-component competitive adsorption curves, we noticed that the tetrahedral supramolecular nanocages had good CO2 storage capacity and good separation capacity for C2H2/CO2 and C2H2/N2. All these indicate that porous organic metal nanomaterials are expected to be a new energy saving separation material.
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Affiliation(s)
- Xin Jin
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Hui Jiang
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Yi Chen
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Xin Han
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Ken Sun
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
- College of Energy and Power Engineering, North China University of Water Resources and Electric Power, Zhengzhou 450045, China
| | - Linlin Shi
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Xin-Qi Hao
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Mao-Ping Song
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
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9
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Lianglu J, Hu W, Zhu X, Zhang HY, Shi L, Hao XQ, Song MP. Synthesis of a Tetrahedral Metal-Organic Supramolecular Cage with Dendritic Carbazole Arms. Int J Mol Sci 2022; 23:15580. [PMID: 36555222 PMCID: PMC9779595 DOI: 10.3390/ijms232415580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
In recent years, incredible endeavors have been devoted to the design and self-assembly of discrete metal-organic cages (MOCs) with expanding intricacy and functionality. The controlled synthesis of metal-organic supramolecular cages with large branched chains remains an interesting and challenging work in supramolecular chemistry. Herein, a tetrahedral metal-organic supramolecular cage (ZnII4L4) containing 12 dendritic carbazole arms is unprecedentedly constructed through coordination-driven subcomponent self-assembly and characterized in different ways. Interestingly, tetrahedral supramolecular Cage-1 exhibited the potential for aggregation-induced emission (AIE) performance and stimulus-responsive luminescence features, and it achieved color-tunable photoluminescence due to the introduction of dendritic carbazole arms. Crucially, owing to the great photophysical properties of Cage-1 in solution, Cage-1 was enabled to act as a fluorescent ink for the vapor-responsive recording and wiping of information.
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Affiliation(s)
- Juanzi Lianglu
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Weinan Hu
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Xinju Zhu
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Hong-Yu Zhang
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
- School of Basic Medical Science, Zhengzhou University, Zhengzhou 450001, China
| | - Linlin Shi
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Xin-Qi Hao
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Mao-Ping Song
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
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10
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Tunable gregation-induced fluorescent and pressure-responsive luminescence supramolecular cages achieved by subcomponent self-assembly. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.107921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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11
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Tian JH, Hu XY, Hu ZY, Tian HW, Li JJ, Pan YC, Li HB, Guo DS. A facile way to construct sensor array library via supramolecular chemistry for discriminating complex systems. Nat Commun 2022; 13:4293. [PMID: 35879312 PMCID: PMC9314354 DOI: 10.1038/s41467-022-31986-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 07/13/2022] [Indexed: 12/15/2022] Open
Abstract
Differential sensing, which discriminates analytes via pattern recognition by sensor arrays, plays an important role in our understanding of many chemical and biological systems. However, it remains challenging to develop new methods to build a sensor unit library without incurring a high workload of synthesis. Herein, we propose a supramolecular approach to construct a sensor unit library by taking full advantage of recognition and assembly. Ten sensor arrays are developed by replacing the building block combinations, adjusting the ratio between system components, and changing the environment. Using proteins as model analytes, we examine the discriminative abilities of these supramolecular sensor arrays. Then the practical applicability for discriminating complex analytes is further demonstrated using honey as an example. This sensor array construction strategy is simple, tunable, and capable of developing many sensor units with as few syntheses as possible.
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Affiliation(s)
- Jia-Hong Tian
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Xin-Yue Hu
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Zong-Ying Hu
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Han-Wen Tian
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Juan-Juan Li
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Yu-Chen Pan
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Hua-Bin Li
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Dong-Sheng Guo
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China.
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12
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Zeng L, Kaoud TS, Zamora-Olivares D, Bohanon AL, Li Y, Pridgen JR, Ekpo YE, Zhuang DL, Nye JR, Telles M, Winkler M, Rivera S, Marini F, Dalby KN, Anslyn EV. Multiplexing the Quantitation of MAP Kinase Activities Using Differential Sensing. J Am Chem Soc 2022; 144:4017-4025. [PMID: 35195411 DOI: 10.1021/jacs.1c12757] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein kinases are therapeutic targets for many human diseases, but the lack of user-friendly quantitative assays limits the ability to follow the activities of numerous kinases at once (multiplexing). To develop such an assay, we report an array of sulfonamido-oxine (SOX)-labeled peptides showing cross-reactivity to different mitogen-activated protein kinases (MAPKs) for use in a differential sensing scheme. We first verified using linear discriminant analysis that the array could differentiate MAPK isoforms. Then, using principal component analysis, the array was optimized based on the discrimination imparted by each SOX-peptide. Next, the activity of individual MAPK families in ternary mixtures was quantified by support vector machine regression. Finally, we multiplexed the quantification of three MAPK families using partial least squares regression in A549 cell lysates, which has possible interference from other kinase classes. Thus, our method simultaneously quantifies the activity of multiple kinases. The technique could be applied to other protein kinase families and the monitoring of diseases.
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Affiliation(s)
- Lingyu Zeng
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Tamer S Kaoud
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Diana Zamora-Olivares
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States.,Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Amanda L Bohanon
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Yiru Li
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jacey R Pridgen
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Yakndara E Ekpo
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Deborah L Zhuang
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jessica R Nye
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Mitchell Telles
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Michelle Winkler
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Sebastian Rivera
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Federico Marini
- Department of Chemistry, University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Eric V Anslyn
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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13
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Sugai H, Tomita S, Kurita R. Pattern-recognition-based Sensor Arrays for Cell Characterization: From Materials and Data Analyses to Biomedical Applications. ANAL SCI 2020; 36:923-934. [PMID: 32249248 DOI: 10.2116/analsci.20r002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
To capture a broader scope of complex biological phenomena, alternatives to conventional sensing based on specificity for cell detection and characterization are needed. Pattern-recognition-based sensing is an analytical method designed to mimic mammalian sensory systems for analyte identification based on the pattern recognition of multivariate data, which are generated using an array of multiple probes that cross-reactively interact with analytes. This sensing approach is significantly different from conventional specific cell sensing based on highly specific probes, including antibodies against biomarkers. Encouraged by the advantages of this technique, such as the simplicity, rapidity, and tunability of the systems without requiring a priori knowledge of biomarkers, numerous sensor arrays have been developed over the past decade and used in a variety of cell sensing applications; these include disease diagnosis, drug discovery, and fundamental research. This review summarizes recent progress in pattern-recognition-based cell sensing, with a particular focus on guidelines for designing materials and arrays, techniques for analyzing response patterns, and applications of sensor systems that are focused primarily for the biomedical field.
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Affiliation(s)
- Hiroka Sugai
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Shunsuke Tomita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).,DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST)
| | - Ryoji Kurita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).,DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST).,Faculty of Pure and Applied Sciences, University of Tsukuba
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14
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Geng Y, Hardie J, Landis RF, Mas-Rosario JA, Chattopadhyay AN, Keshri P, Sun J, Rizzo EM, Gopalakrishnan S, Farkas ME, Rotello VM. High-content and high-throughput identification of macrophage polarization phenotypes. Chem Sci 2020; 11:8231-8239. [PMID: 34123093 PMCID: PMC8163325 DOI: 10.1039/d0sc02792h] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/17/2020] [Indexed: 12/13/2022] Open
Abstract
Macrophages are plastic cells of the innate immune system that perform a wide range of immune- and homeostasis-related functions. Due to their plasticity, macrophages can polarize into a spectrum of activated phenotypes. Rapid identification of macrophage polarization states provides valuable information for drug discovery, toxicological screening, and immunotherapy evaluation. The complexity associated with macrophage activation limits the ability of current biomarker-based methods to rapidly identify unique activation states. In this study, we demonstrate the ability of a 2-element sensor array that provides an information-rich 5-channel output to successfully determine macrophage polarization phenotypes in a matter of minutes. The simple and robust sensor generates a high dimensional data array which enables accurate macrophage evaluations in standard cell lines and primary cells after cytokine treatment, as well as following exposure to a model disease environment.
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Affiliation(s)
- Yingying Geng
- Molecular and Cellular Biology Program, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
- Department of Chemistry, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
| | - Joseph Hardie
- Department of Chemistry, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
| | - Ryan F Landis
- Department of Chemistry, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
| | - Javier A Mas-Rosario
- Molecular and Cellular Biology Program, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
- Department of Chemistry, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
| | - Aritra Nath Chattopadhyay
- Department of Chemistry, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
| | - Puspam Keshri
- Department of Chemistry, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
| | - Jiadi Sun
- Department of Chemistry, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
| | - Erik M Rizzo
- Department of Chemistry, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
| | - Sanjana Gopalakrishnan
- Department of Chemistry, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
| | - Michelle E Farkas
- Molecular and Cellular Biology Program, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
- Department of Chemistry, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
| | - Vincent M Rotello
- Molecular and Cellular Biology Program, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
- Department of Chemistry, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
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15
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Kieffer M, Bilbeisi RA, Thoburn JD, Clegg JK, Nitschke JR. Guest Binding Drives Host Redistribution in Libraries of Co II 4 L 4 Cages. Angew Chem Int Ed Engl 2020; 59:11369-11373. [PMID: 32243707 PMCID: PMC7383889 DOI: 10.1002/anie.202004627] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Indexed: 12/29/2022]
Abstract
Two CoII 4 L4 tetrahedral cages prepared from similar building blocks showed contrasting host-guest properties. One cage did not bind guests, whereas the second encapsulated a series of anions, due to electronic and geometric effects. When the building blocks of both cages were present during self-assembly, a library of five CoII LA x LB 4-x cages was formed in a statistical ratio in the absence of guests. Upon incorporation of anions able to interact preferentially with some library members, the products obtained were redistributed in favor of the best anion binders. To quantify the magnitudes of these templation effects, ESI-MS was used to gauge the effect of each template upon library redistribution.
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Affiliation(s)
- Marion Kieffer
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Rana A. Bilbeisi
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Department of Civil and Environmental EngineeringAmerican University of BeirutBeirutLebanon
| | - John D. Thoburn
- Department of ChemistryRandolph-Macon CollegeAshlandVA23005USA
| | - Jack K. Clegg
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQLD4072Australia
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16
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17
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Zamora-Olivares D, Kaoud TS, Zeng L, Pridgen JR, Zhuang DL, Ekpo YE, Nye JR, Telles M, Anslyn EV, Dalby KN. Quantification of ERK Kinase Activity in Biological Samples Using Differential Sensing. ACS Chem Biol 2020; 15:83-92. [PMID: 31775004 DOI: 10.1021/acschembio.9b00580] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The understanding of complex biological systems requires an ability to evaluate interacting networks of genes, proteins, and cellular reactions. Enabling technologies that support the rapid quantification of these networks will facilitate the development of biological models and help to identify treatment targets and to assess treatment plans. The biochemical process of protein phosphorylation, which underlies almost all aspects of cell signaling, is typically evaluated by immunoblotting procedures (Western blot) or more recently proteomics procedures, which provide qualitative estimates of the concentration of proteins and their modifications in cells. However, protein modifications are difficult to correlate with activity, and while immunoblotting and proteomics approaches have the potential to be quantitative, they require a complex series of steps that diminish reproducibility. Here, a complementary approach is presented that allows for the rapid quantification of a protein kinase activity in cell lysates and tumor samples. Using the activity of cellular ERK (extracellular signal-regulated kinase) as a test case, an array sensing approach that utilizes a library of differential peptide-based biosensors and chemometric tools was used to rapidly quantify nanograms of active ERK in micrograms of unfractionated cell lysates and tumor extracts. This approach has the potential both for high-throughput and for quantifying the activities of multiple protein kinases in a single biological sample. The critical advantages of this differential sensing approach over others are that it removes the need for the addition of exogenous inhibitors to suppress the activities of major off-target kinases and allows us to quantitate the amount of active kinase in tested samples rather than measuring the changes in its activity upon induction or inhibition.
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Affiliation(s)
- Diana Zamora-Olivares
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Tamer S. Kaoud
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
- Medicinal Chemistry Department, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
| | - Lingyu Zeng
- College of Chemistry and Molecular Science, Wuhan University, Wuhan, Hubei 430072, China
| | - Jacey R. Pridgen
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Deborah L. Zhuang
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Yakndara E. Ekpo
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jessica R. Nye
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Mitchell Telles
- Texas Institute for Discovery Education in Science and Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Eric V. Anslyn
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Kevin N. Dalby
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, Texas 78712, United States
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18
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Solà J, Jimeno C, Alfonso I. Exploiting complexity to implement function in chemical systems. Chem Commun (Camb) 2020; 56:13273-13286. [DOI: 10.1039/d0cc04170j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This feature article reflects a personal overview of the importance of complexity as an additional parameter to be considered in chemical research, being illustrated with selected examples in molecular recognition and catalysis.
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Affiliation(s)
- Jordi Solà
- Department of Biological Chemistry
- Institute of Advanced Chemistry of Catalonia
- IQAC-CSIC
- 08034 Barcelona
- Spain
| | - Ciril Jimeno
- Department of Biological Chemistry
- Institute of Advanced Chemistry of Catalonia
- IQAC-CSIC
- 08034 Barcelona
- Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry
- Institute of Advanced Chemistry of Catalonia
- IQAC-CSIC
- 08034 Barcelona
- Spain
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19
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Liu Y, Peng S, Angelova L, Nau WM, Hennig A. Label-Free Fluorescent Kinase and Phosphatase Enzyme Assays with Supramolecular Host-Dye Pairs. ChemistryOpen 2019; 8:1350-1354. [PMID: 31741820 PMCID: PMC6848908 DOI: 10.1002/open.201900299] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Indexed: 12/21/2022] Open
Abstract
The combination of the macrocyclic hosts p-sulfonatocalix[4]arene and cucurbit[7]uril with the fluorescent dyes lucigenin and berberine affords two label-free enzyme assays for the detection of kinase and phosphatase activity by fluorescence monitoring. In contrast to established assays, no substrate labeling is required. Since phosphorylation is one of the most important regulatory mechanisms in biological signal transduction, the assays should be useful for identification of inhibitors and activators in high-throughput screening (HTS) format for drug discovery.
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Affiliation(s)
- Yan‐Cen Liu
- Department of Life Sciences and ChemistryJacobs University Bremen gGmbHCampus Ring 128759BremenGermany
| | - Shu Peng
- Department of Life Sciences and ChemistryJacobs University Bremen gGmbHCampus Ring 128759BremenGermany
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials, Ministry of EducationNankai UniversityTianjin300071 TianjinChina
| | - Lora Angelova
- Department of Life Sciences and ChemistryJacobs University Bremen gGmbHCampus Ring 128759BremenGermany
| | - Werner M. Nau
- Department of Life Sciences and ChemistryJacobs University Bremen gGmbHCampus Ring 128759BremenGermany
| | - Andreas Hennig
- Department of Life Sciences and ChemistryJacobs University Bremen gGmbHCampus Ring 128759BremenGermany
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20
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Beck JR, Cabral F, Rasineni K, Casey CA, Harris EN, Stains CI. A Panel of Protein Kinase Chemosensors Distinguishes Different Types of Fatty Liver Disease. Biochemistry 2019; 58:3911-3917. [PMID: 31433166 DOI: 10.1021/acs.biochem.9b00547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The worldwide incidence of fatty liver disease continues to rise, which may account for concurrent increases in the frequencies of more aggressive liver ailments. Given the existence of histologically identical fatty liver disease subtypes, there is a critical need for the identification of methods that can classify disease and potentially predict progression. Herein, we show that a panel of protein kinase chemosensors can distinguish fatty liver disease subtypes. These direct activity measurements highlight distinct differences between histologically identical fatty liver diseases arising from diets rich in fat versus alcohol and identify a previously unreported decrease in p38α activity associated with a high-fat diet. In addition, we have profiled kinase activities in both benign (diet-induced) and progressive (STAM) disease models. These experiments provide temporal insights into kinase activity during disease development and progression. Altogether, this work provides the basis for the future development of clinical diagnostics and potential treatment strategies.
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Affiliation(s)
- Jon R Beck
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States
| | - Fatima Cabral
- Department of Biochemistry , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States
| | - Karuna Rasineni
- Division of Gastroenterology-Hepatology , University of Nebraska Medical Center , Omaha , Nebraska 68198 , United States.,Research Service, Veterans' Affairs , Nebraska-Western Iowa Health Care System , Omaha , Nebraska 68105 , United States
| | - Carol A Casey
- Division of Gastroenterology-Hepatology , University of Nebraska Medical Center , Omaha , Nebraska 68198 , United States.,Research Service, Veterans' Affairs , Nebraska-Western Iowa Health Care System , Omaha , Nebraska 68105 , United States.,Nebraska Center for Integrated Biomolecular Communication , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States
| | - Edward N Harris
- Department of Biochemistry , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States.,Nebraska Center for Integrated Biomolecular Communication , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States.,Cancer Genes and Molecular Regulation Program, Fred & Pamela Buffet Cancer Center , University of Nebraska Medical Center , Omaha , Nebraska 68198 , United States
| | - Cliff I Stains
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States.,Nebraska Center for Integrated Biomolecular Communication , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States.,Cancer Genes and Molecular Regulation Program, Fred & Pamela Buffet Cancer Center , University of Nebraska Medical Center , Omaha , Nebraska 68198 , United States.,Department of Chemistry , University of Virginia , Charlottesville , Virginia 22904 , United States
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21
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Osypenko A, Dhers S, Lehn JM. Pattern Generation and Information Transfer through a Liquid/Liquid Interface in 3D Constitutional Dynamic Networks of Imine Ligands in Response to Metal Cation Effectors. J Am Chem Soc 2019; 141:12724-12737. [DOI: 10.1021/jacs.9b05438] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Artem Osypenko
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d’Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Sébastien Dhers
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d’Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Jean-Marie Lehn
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d’Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, 8 allée Gaspard Monge, 67000 Strasbourg, France
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22
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Geng Y, Peveler WJ, Rotello VM. Array-based "Chemical Nose" Sensing in Diagnostics and Drug Discovery. Angew Chem Int Ed Engl 2019; 58:5190-5200. [PMID: 30347522 PMCID: PMC6800156 DOI: 10.1002/anie.201809607] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Indexed: 12/29/2022]
Abstract
Array-based sensor "chemical nose/tongue" platforms are inspired by the mammalian olfactory system. Multiple sensor elements in these devices selectively interact with target analytes, producing a distinct pattern of response and enabling analyte identification. This approach offers unique opportunities relative to "traditional" highly specific sensor elements such as antibodies. Array-based sensors excel at distinguishing small changes in complex mixtures, and this capability is being leveraged for chemical biology studies and clinical pathology, enabled by a diverse toolkit of new molecular, bioconjugate and nanomaterial technologies. Innovation in the design and analysis of arrays provides a robust set of tools for advancing biomedical goals, including precision medicine.
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Affiliation(s)
- Yingying Geng
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, 710 N. Pleasant St., Amherst MA 01003, U.S.A
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St., Amherst MA 01003, U.S.A
| | - William J. Peveler
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow G12 8LT, U.K
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Vincent M. Rotello
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St., Amherst MA 01003, U.S.A
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23
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Mullins AG, Pinkin NK, Hardin JA, Waters ML. Achieving High Affinity and Selectivity for Asymmetric Dimethylarginine by Putting a Lid on a Box. Angew Chem Int Ed Engl 2019; 58:5282-5285. [DOI: 10.1002/anie.201814645] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 01/30/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Alexandria G. Mullins
- Department of Chemistry, CB 3290University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599 USA
| | - Nicholas K. Pinkin
- Department of Chemistry, CB 3290University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599 USA
| | - Joshua A. Hardin
- Department of Chemistry, CB 3290University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599 USA
| | - Marcey L. Waters
- Department of Chemistry, CB 3290University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599 USA
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24
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Bravin C, Guidetti A, Licini G, Zonta C. Supramolecular cages as differential sensors for dicarboxylate anions: guest length sensing using principal component analysis of ESI-MS and 1H-NMR raw data. Chem Sci 2019; 10:3523-3528. [PMID: 30996943 PMCID: PMC6432344 DOI: 10.1039/c8sc05527k] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/05/2019] [Indexed: 01/05/2023] Open
Abstract
Dynamic covalent libraries (DCLs) have been widely used in the development of differential sensors. Inspired by recent studies which use supramolecular recognition systems for sensing, we report the use of a tris(-pyridylmethyl)amine (TPMA)-based supramolecular cage as a differential sensor for dicarboxylate anions. In particular, a library of molecular cages constituted by linkers differing in size and flexibility was allowed to equilibrate toward a series of guests differing in molecular size. The differential system was able to discriminate a series of dicarboxylates depending on their chain length. This differentiation was evaluated through the application of the Principal Component Analysis (PCA) method using interpolated and raw data obtained from ESI-MS. Interestingly, while the 1H NMR spectra of the differential system did not allow for the discrimination of the analytes by the naked eye, PCA of the raw data from the spectra revealed information on the chain length of the guest and also on the odd-even character of the carbon chain.
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Affiliation(s)
- Carlo Bravin
- Department of Chemical Sciences , University of Padova , Via Marzolo 1 , 35131 Padova , Italy .
| | - Andrea Guidetti
- Department of Chemical Sciences , University of Padova , Via Marzolo 1 , 35131 Padova , Italy .
| | - Giulia Licini
- Department of Chemical Sciences , University of Padova , Via Marzolo 1 , 35131 Padova , Italy .
| | - Cristiano Zonta
- Department of Chemical Sciences , University of Padova , Via Marzolo 1 , 35131 Padova , Italy .
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25
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Mullins AG, Pinkin NK, Hardin JA, Waters ML. Achieving High Affinity and Selectivity for Asymmetric Dimethylarginine by Putting a Lid on a Box. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814645] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Alexandria G. Mullins
- Department of Chemistry, CB 3290University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599 USA
| | - Nicholas K. Pinkin
- Department of Chemistry, CB 3290University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599 USA
| | - Joshua A. Hardin
- Department of Chemistry, CB 3290University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599 USA
| | - Marcey L. Waters
- Department of Chemistry, CB 3290University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599 USA
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26
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Geng Y, Peveler WJ, Rotello VM. Array‐basierte Sensorik mit der “chemischen Nase” in der Diagnostik und Wirkstoffentdeckung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201809607] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yingying Geng
- Molecular and Cellular Biology ProgramUniversity of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
- Department of ChemistryUniversity of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
| | - William J. Peveler
- Division of Biomedical EngineeringSchool of EngineeringUniversity of Glasgow Glasgow G12 8LT Großbritannien
- Department of ChemistryUniversity of British Columbia 2036 Main Mall Vancouver British Columbia V6T 1Z1 Kanada
| | - Vincent M. Rotello
- Department of ChemistryUniversity of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
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27
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Ashokkumar P, Ashoka AH, Collot M, Das A, Klymchenko AS. A fluorogenic BODIPY molecular rotor as an apoptosis marker. Chem Commun (Camb) 2019; 55:6902-6905. [DOI: 10.1039/c9cc03242h] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Based on a BODIPY molecular rotor, we designed a probe that lights up its green fluorescence in apoptotic cells and distinguishes between early and late apoptosis.
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Affiliation(s)
- Pichandi Ashokkumar
- Laboratoire de Bioimagerie et Pathologies
- UMR 7021 CNRS
- Faculté de Pharmacie
- Université de Strasbourg
- Strasbourg CS 60024
| | - Anila Hoskere Ashoka
- Laboratoire de Bioimagerie et Pathologies
- UMR 7021 CNRS
- Faculté de Pharmacie
- Université de Strasbourg
- Strasbourg CS 60024
| | - Mayeul Collot
- Laboratoire de Bioimagerie et Pathologies
- UMR 7021 CNRS
- Faculté de Pharmacie
- Université de Strasbourg
- Strasbourg CS 60024
| | - Amitava Das
- CSIR-Central Salt & Marine Chemicals Research Institute
- Bhavnagar 364002
- India
| | - Andrey S. Klymchenko
- Laboratoire de Bioimagerie et Pathologies
- UMR 7021 CNRS
- Faculté de Pharmacie
- Université de Strasbourg
- Strasbourg CS 60024
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28
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Liu Y, Gill AD, Duan Y, Perez L, Hooley RJ, Zhong W. A supramolecular sensor array for selective immunoglobulin deficiency analysis. Chem Commun (Camb) 2019; 55:11563-11566. [DOI: 10.1039/c9cc06064b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A host–guest based fluorescence sensor array can fully discriminate five structurally similar Ig protein isotypes, and recognize Ig deficiencies in serum.
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Affiliation(s)
- Yang Liu
- University of California – Riverside
- Environmental Toxicology Program
- Riverside
- USA
| | - Adam D. Gill
- University of California – Riverside
- Department of Biochemistry and Molecular Biology
- Riverside
- USA
| | - Yaokai Duan
- University of California – Riverside
- Department of Chemistry
- Riverside
- USA
| | - Lizeth Perez
- University of California – Riverside
- Department of Chemistry
- Riverside
- USA
| | - Richard J. Hooley
- University of California – Riverside
- Department of Biochemistry and Molecular Biology
- Riverside
- USA
- University of California – Riverside
| | - Wenwan Zhong
- University of California – Riverside
- Environmental Toxicology Program
- Riverside
- USA
- University of California – Riverside
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29
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Liu Y, Lee J, Perez L, Gill AD, Hooley RJ, Zhong W. Selective Sensing of Phosphorylated Peptides and Monitoring Kinase and Phosphatase Activity with a Supramolecular Tandem Assay. J Am Chem Soc 2018; 140:13869-13877. [PMID: 30269482 DOI: 10.1021/jacs.8b08693] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Simple tuning of a host:guest pair allows selective sensing of different peptide modifications, exploiting orthogonal recognition mechanisms. Excellent selectivity for either lysine trimethylations or alcohol phosphorylations is possible by simply varying the fluorophore guest. The phosphorylation sensor can be modulated by the presence of small (μM) concentrations of metal ions, allowing array-based sensing. Phosphorylation at serine, threonine, and tyrosine can be selectively sensed via discriminant analysis. The phosphopeptide sensing is effective in the presence of small-molecule phosphates such as ATP, which in turn enables the sensor to be employed in continuous optical assays of both serine kinase and tyrosine phosphatase activity. The activity of multiple different kinases can be monitored, and the sensor is capable of detecting the phosphorylation of peptides containing multiple different modifications, including lysine methylations and acetylation. A single deep cavitand can be used as a "one size fits all" sensor that can selectively detect multiple different modifications to oligopeptides, as well as monitoring the function of their post-translational modification writer and eraser enzymes in complex systems.
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30
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Li Z, Askim JR, Suslick KS. The Optoelectronic Nose: Colorimetric and Fluorometric Sensor Arrays. Chem Rev 2018; 119:231-292. [DOI: 10.1021/acs.chemrev.8b00226] [Citation(s) in RCA: 476] [Impact Index Per Article: 79.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Zheng Li
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jon R. Askim
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Kenneth S. Suslick
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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31
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Peveler WJ, Algar WR. More Than a Light Switch: Engineering Unconventional Fluorescent Configurations for Biological Sensing. ACS Chem Biol 2018; 13:1752-1766. [PMID: 29461796 DOI: 10.1021/acschembio.7b01022] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence is a powerful and sensitive tool in biological detection, used widely for cellular imaging and in vitro molecular diagnostics. Over time, three prominent conventions have emerged in the design of fluorescent biosensors: a sensor is ideally specific for its target, only one fluorescence signal turns on or off in response to the target, and each target requires its own sensor and signal combination. These are conventions but not requirements, and sensors that break with one or more of these conventions can offer new capabilities and advantages. Here, we review "unconventional" fluorescent sensor configurations based on fluorescent dyes, proteins, and nanomaterials such as quantum dots and metal nanoclusters. These configurations include multifluorophore Förster resonance energy transfer (FRET) networks, temporal multiplexing, photonic logic, and cross-reactive arrays or "noses". The more complex but carefully engineered biorecognition and fluorescence signaling modalities in unconventional designs are richer in information, afford greater multiplexing capacity, and are potentially better suited to the analysis of complex biological samples, interactions, processes, and diseases. We conclude with a short perspective on the future of unconventional fluorescent sensors and encourage researchers to imagine sensing beyond the metaphorical light bulb and light switch combination.
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Affiliation(s)
- William J. Peveler
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow G12 8LT, U.K
| | - W. Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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32
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Tomita S, Nomoto H, Yoshitomi T, Iijima K, Hashizume M, Yoshimoto K. Noninvasive Fingerprinting-Based Tracking of Replicative Cellular Senescence Using a Colorimetric Polyion Complex Array. Anal Chem 2018; 90:6348-6352. [DOI: 10.1021/acs.analchem.8b00795] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Shunsuke Tomita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology and DAILAB, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Hiroki Nomoto
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Toru Yoshitomi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Kazutoshi Iijima
- Department of Industrial Chemistry, Faculty of Engineering, Tokyo University of Science, 12-1 Ichigayafunagawara-machi, Shinjuku, Tokyo 162-0826, Japan
| | - Mineo Hashizume
- Department of Industrial Chemistry, Faculty of Engineering, Tokyo University of Science, 12-1 Ichigayafunagawara-machi, Shinjuku, Tokyo 162-0826, Japan
| | - Keitaro Yoshimoto
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
- JST, PRESTO, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
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33
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Eubanks CS, Hargrove AE. Sensing the impact of environment on small molecule differentiation of RNA sequences. Chem Commun (Camb) 2018; 53:13363-13366. [PMID: 29199743 DOI: 10.1039/c7cc07157d] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Using pattern recognition of RNA with small molecules (PRRSM) with fluorescent RNA chemosensors and aminoglycosides, we reveal the impact of changing environmental conditions on the differentiation of a range of RNA structures as well as the ability to predict different sequence/size compositions of five canonical RNA motifs.
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34
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Sathiyajith C, Shaikh RR, Han Q, Zhang Y, Meguellati K, Yang YW. Biological and related applications of pillar[n]arenes. Chem Commun (Camb) 2018; 53:677-696. [PMID: 27942626 DOI: 10.1039/c6cc08967d] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pillar[n]arenes are a new class of synthetic supramolecular macrocycles streamlined by their particular pillar-shaped architecture which consists of an electron-rich cavity and two fine-tuneable rims. The ease and diversity of the functionalization of the two rims open possibilities for the design of new architectures, topological isomers, and scaffolds. Significantly, this emerging class of macrocyclic receptors offers a unique platform for biological purposes. This review article covers the most recent contributions from the pillar[n]arene field in terms of artificial membrane transport systems, controlled drug delivery systems, biomedical imaging, biosensors, cell adhesion, fluorescent sensing, and pesticide detection based on host-guest interactions. The review also uniquely describes the properties of sub-units that make pillar[n]arenes suitable for biological applications and it provides a detailed outline for the design of new innovative pillar-like structures with specific properties to open up a new avenue for pillar[n]arene chemistry.
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Affiliation(s)
- CuhaWijay Sathiyajith
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC), College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China.
| | - Rafik Rajjak Shaikh
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC), College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China.
| | - Qian Han
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC), College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China.
| | - Yue Zhang
- The First Clinical College, Harbin Medical University, 23 Youzheng Street, Harbin, 150001, P. R. China.
| | - Kamel Meguellati
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC), College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China.
| | - Ying-Wei Yang
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC), College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China.
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35
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Bravin C, Badetti E, Puttreddy R, Pan F, Rissanen K, Licini G, Zonta C. Binding Profiles of Self-Assembled Supramolecular Cages from ESI-MS Based Methodology. Chemistry 2018; 24:2936-2943. [DOI: 10.1002/chem.201704725] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Carlo Bravin
- Department of Chemical Sciences; University of Padova; via Marzolo 1 35131 Padova (PD) Italy
| | - Elena Badetti
- Department of Chemical Sciences; University of Padova; via Marzolo 1 35131 Padova (PD) Italy
| | - Rakesh Puttreddy
- Nanoscience Center; Department of Chemistry; University of Jyvaskyla; P.O. Box 35 40014 Jyvaskyla Finland
| | - Fangfang Pan
- Nanoscience Center; Department of Chemistry; University of Jyvaskyla; P.O. Box 35 40014 Jyvaskyla Finland
| | - Kari Rissanen
- Nanoscience Center; Department of Chemistry; University of Jyvaskyla; P.O. Box 35 40014 Jyvaskyla Finland
| | - Giulia Licini
- Department of Chemical Sciences; University of Padova; via Marzolo 1 35131 Padova (PD) Italy
| | - Cristiano Zonta
- Department of Chemical Sciences; University of Padova; via Marzolo 1 35131 Padova (PD) Italy
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36
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Badetti E, Carmo dos Santos NA, Scaramuzzo FA, Bravin C, Wurst K, Licini G, Zonta C. Diasteroselective multi-component assemblies from dynamic covalent imine condensation and metal-coordination chemistry: mechanism and narcissistic stereochemistry self-sorting. RSC Adv 2018; 8:19494-19498. [PMID: 35540993 PMCID: PMC9080712 DOI: 10.1039/c8ra03989e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 05/21/2018] [Indexed: 12/03/2022] Open
Abstract
Self-assembly of a modified tris(2-pyridylmethyl)amine TPMA ligand, zinc(ii) or cobalt(ii) ions, and amino acids have been used effectively as stereo dynamic optical probes for the determination of the enantiomeric excess of free amino acids either using Electronic or Vibrational Circular Dichroism (CD and VCD). Herein, we report the mechanistic and stereochemical study of the self-assembly process which reveals a complex equilibrium in solution where even small variations in the experimental conditions can profoundly affect the final products of the reaction. In particular, variation on the metal stoichiometry switch give rises to an entirely enantio narcissistic self-assembly of the structure. Enantio narcissistic self-assembly is observed in a multi-metallic structure used as stereodynamic probe for CD measurements.![]()
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Affiliation(s)
- Elena Badetti
- Department of Chemical Sciences
- University of Padova
- Via Marzolo 1
- 35131 Padova (PD)
- Italy
| | | | | | - Carlo Bravin
- Department of Chemical Sciences
- University of Padova
- Via Marzolo 1
- 35131 Padova (PD)
- Italy
| | - Klaus Wurst
- Institute of General
- Inorganic and Theoretical Chemistry
- University of Innsbruck
- 6020 Innsbruck
- Austria
| | - Giulia Licini
- Department of Chemical Sciences
- University of Padova
- Via Marzolo 1
- 35131 Padova (PD)
- Italy
| | - Cristiano Zonta
- Department of Chemical Sciences
- University of Padova
- Via Marzolo 1
- 35131 Padova (PD)
- Italy
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37
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Pode Z, Peri-Naor R, Georgeson JM, Ilani T, Kiss V, Unger T, Markus B, Barr HM, Motiei L, Margulies D. Protein recognition by a pattern-generating fluorescent molecular probe. NATURE NANOTECHNOLOGY 2017; 12:1161-1168. [PMID: 29035400 DOI: 10.1038/nnano.2017.175] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 07/25/2017] [Indexed: 06/07/2023]
Abstract
Fluorescent molecular probes have become valuable tools in protein research; however, the current methods for using these probes are less suitable for analysing specific populations of proteins in their native environment. In this study, we address this gap by developing a unimolecular fluorescent probe that combines the properties of small-molecule-based probes and cross-reactive sensor arrays (the so-called chemical 'noses/tongues'). On the one hand, the probe can detect different proteins by generating unique identification (ID) patterns, akin to cross-reactive arrays. On the other hand, its unimolecular scaffold and selective binding enable this ID-generating probe to identify combinations of specific protein families within complex mixtures and to discriminate among isoforms in living cells, where macroscopic arrays cannot access. The ability to recycle the molecular device and use it to track several binding interactions simultaneously further demonstrates how this approach could expand the fluorescent toolbox currently used to detect and image proteins.
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Affiliation(s)
- Zohar Pode
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ronny Peri-Naor
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Joseph M Georgeson
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tal Ilani
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Vladimir Kiss
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tamar Unger
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Barak Markus
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Haim M Barr
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Leila Motiei
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Margulies
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
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38
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Tomita S, Ishihara S, Kurita R. A Multi-Fluorescent DNA/Graphene Oxide Conjugate Sensor for Signature-Based Protein Discrimination. SENSORS (BASEL, SWITZERLAND) 2017; 17:E2194. [PMID: 28946622 PMCID: PMC5677448 DOI: 10.3390/s17102194] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/15/2017] [Accepted: 09/19/2017] [Indexed: 12/13/2022]
Abstract
Signature-based protein sensing has recently emerged as a promising prospective alternative to conventional lock-and-key methods. However, most of the current examples require the measurement of optical signals from spatially-separated materials for the generation of signatures. Herein, we present a new approach for the construction of multi-fluorescent sensing systems with high accessibility and tunability, which allows generating protein fluorescent signatures from a single microplate well. This approach is based on conjugates between nano-graphene oxide (nGO) and three single-stranded DNAs (ssDNAs) that exhibit different sequences and fluorophores. Initially, the three fluorophore-modified ssDNAs were quenched simultaneously by binding to nGO. Subsequent addition of analyte proteins caused a partial recovery in fluorescent intensity of the individual ssDNAs. Based on this scheme, we have succeeded in acquiring fluorescence signatures unique to (i) ten proteins that differ with respect to pI and molecular weight and (ii) biochemical marker proteins in the presence of interferent human serum. Pattern-recognition methods demonstrated high levels of discrimination for this system. The high discriminatory power and simple format of this sensor system should enable an easy and fast evaluation of proteins and protein mixtures.
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Affiliation(s)
- Shunsuke Tomita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, and DAILAB, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
| | - Sayaka Ishihara
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, and DAILAB, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
| | - Ryoji Kurita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, and DAILAB, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan.
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39
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Valdivielso AM, Puig-Castellví F, Atcher J, Solà J, Tauler R, Alfonso I. Unraveling the Multistimuli Responses of a Complex Dynamic System of Pseudopeptidic Macrocycles. Chemistry 2017; 23:10789-10799. [DOI: 10.1002/chem.201701294] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Angel M. Valdivielso
- Department of Biological Chemistry and Molecular Modeling; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | | | - Joan Atcher
- Department of Biological Chemistry and Molecular Modeling; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Jordi Solà
- Department of Biological Chemistry and Molecular Modeling; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Romà Tauler
- Department of Environmental Chemistry; IDAEA-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry and Molecular Modeling; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
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40
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Eubanks CS, Forte JE, Kapral GJ, Hargrove AE. Small Molecule-Based Pattern Recognition To Classify RNA Structure. J Am Chem Soc 2017; 139:409-416. [PMID: 28004925 PMCID: PMC5465965 DOI: 10.1021/jacs.6b11087] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Three-dimensional RNA structures are notoriously difficult to determine, and the link between secondary structure and RNA conformation is only beginning to be understood. These challenges have hindered the identification of guiding principles for small molecule:RNA recognition. We herein demonstrate that the strong and differential binding ability of aminoglycosides to RNA structures can be used to classify five canonical RNA secondary structure motifs through principal component analysis (PCA). In these analyses, the aminoglycosides act as receptors, while RNA structures labeled with a benzofuranyluridine fluorophore act as analytes. Complete (100%) predictive ability for this RNA training set was achieved by incorporating two exhaustively guanidinylated aminoglycosides into the receptor library. The PCA was then externally validated using biologically relevant RNA constructs. In bulge-stem-loop constructs of HIV-1 transactivation response element (TAR) RNA, we achieved nucleotide-specific classification of two independent secondary structure motifs. Furthermore, examination of cheminformatic parameters and PCA loading factors revealed trends in aminoglycoside:RNA recognition, including the importance of shape-based discrimination, and suggested the potential for size and sequence discrimination within RNA structural motifs. These studies present a new approach to classifying RNA structure and provide direct evidence that RNA topology, in addition to sequence, is critical for the molecular recognition of RNA.
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Affiliation(s)
- Christopher S Eubanks
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
| | - Jordan E Forte
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
| | - Gary J Kapral
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
| | - Amanda E Hargrove
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
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41
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TOMITA S, YOSHIMOTO K, NIWA O, KURITA R. Protein Sensing Based on Cross-reactive Optical Fingerprinting. BUNSEKI KAGAKU 2017. [DOI: 10.2116/bunsekikagaku.66.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Shunsuke TOMITA
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | | | - Osamu NIWA
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
- Advanced Science Research Laboratory, Saitama Institute of Technology
| | - Ryoji KURITA
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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42
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Li X, Zamora-Olivares D, Diehl KL, Tian W, Anslyn EV. Differential sensing of oils by conjugates of serum albumins and 9,10-distyrylanthracene probes: a cautionary tale. Supramol Chem 2016. [DOI: 10.1080/10610278.2016.1228934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Xing Li
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, P.R. China
| | | | - Katharine L. Diehl
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Wenjing Tian
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, P.R. China
| | - Eric V. Anslyn
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
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43
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He H, Li C, Tian Y, Wu P, Hou X. Phosphorescent Differential Sensing of Physiological Phosphates with Lanthanide Ions-Modified Mn-Doped ZnCdS Quantum Dots. Anal Chem 2016; 88:5892-7. [DOI: 10.1021/acs.analchem.6b00780] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hengwei He
- College of Chemistry and ‡Analytical & Testing Center, Sichuan University, Chengdu 610064, China
| | - Chenghui Li
- College of Chemistry and ‡Analytical & Testing Center, Sichuan University, Chengdu 610064, China
| | - Yunfei Tian
- College of Chemistry and ‡Analytical & Testing Center, Sichuan University, Chengdu 610064, China
| | - Peng Wu
- College of Chemistry and ‡Analytical & Testing Center, Sichuan University, Chengdu 610064, China
| | - Xiandeng Hou
- College of Chemistry and ‡Analytical & Testing Center, Sichuan University, Chengdu 610064, China
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44
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Anslyn EV. Art, auto-mechanics, and supramolecular chemistry. A merging of hobbies and career. Beilstein J Org Chem 2016; 12:362-76. [PMID: 26977197 PMCID: PMC4778509 DOI: 10.3762/bjoc.12.40] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/12/2016] [Indexed: 12/24/2022] Open
Abstract
While the strict definition of supramolecular chemistry is "chemistry beyond the molecule", meaning having a focus on non-covalent interactions, the field is primarily associated with the creation of synthetic receptors and self-assembly. For synthetic ease, the receptors and assemblies routinely possess a high degree of symmetry, which lends them an aspect of aesthetic beauty. Pictures of electron orbitals similarly can be seen as akin to works of art. This similarity was an early draw for me to the fields of supramolecular chemistry and molecular orbital theory, because I grew up in a household filled with art. In addition to art, my childhood was filled with repairing and constructing mechanical entities, such as internal combustion motors, where many components work together to achieve a function. Analogously, the field of supramolecular chemistry creates systems of high complexity that achieve functions or perform tasks. Therefore, in retrospect a career in supramolecular chemistry appears to be simply an extension of childhood hobbies involving art and auto-mechanics.
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Affiliation(s)
- Eric V Anslyn
- Department of Chemistry, University of Texas, Austin, TX 78712, USA
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45
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Tomita S, Sakao M, Kurita R, Niwa O, Yoshimoto K. A polyion complex sensor array for markerless and noninvasive identification of differentiated mesenchymal stem cells from human adipose tissue. Chem Sci 2015; 6:5831-5836. [PMID: 28970874 PMCID: PMC5618151 DOI: 10.1039/c5sc01259g] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/29/2015] [Indexed: 12/12/2022] Open
Abstract
Currently available methods for stem cell evaluation require both prior knowledge of specific markers and invasive cell lysis or staining, hampering the development of stem cell products with assured safety and quality. Here, we present a strategy using optical cross-reactive sensor arrays for markerless and noninvasive identification of differentiated stem cell lineages with common laboratory equipment. The sensor array consists of a library of polyion complexes (PICs) between anionic enzymes and synthetic poly(ethylene glycol)-modified polyamines, which can recognize "secretomic signatures" in cell culture supernatants. Due to the reversible nature of PIC formation, the incubation of diluted culture supernatants with PICs caused enzyme release through competitive interactions between the secreted molecules and the PICs, generating unique patterns of recovery in enzyme activity for individual cell types or lineages. Linear discriminant analysis of the patterns allowed not only normal/cancer cell discrimination but also lineage identification of osteogenic and adipogenic differentiation of human mesenchymal stem cells, therefore providing an effective way to characterize cultured cells in the fields of regenerative medicine, tissue engineering and cell biology.
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Affiliation(s)
- Shunsuke Tomita
- Biomedical Research Institute , National Institute of Advanced Industrial Science and Technology , 1-1-1 Higashi , Tsukuba , Ibaraki 305-8566 , Japan .
| | - Miho Sakao
- College of Arts and Sciences , The University of Tokyo , 3-8-1 Komaba , Meguro , Tokyo 153-8902 , Japan .
| | - Ryoji Kurita
- Biomedical Research Institute , National Institute of Advanced Industrial Science and Technology , 1-1-1 Higashi , Tsukuba , Ibaraki 305-8566 , Japan .
| | - Osamu Niwa
- Biomedical Research Institute , National Institute of Advanced Industrial Science and Technology , 1-1-1 Higashi , Tsukuba , Ibaraki 305-8566 , Japan .
| | - Keitaro Yoshimoto
- College of Arts and Sciences , The University of Tokyo , 3-8-1 Komaba , Meguro , Tokyo 153-8902 , Japan .
- Department of Life Sciences , Graduate School of Arts and Sciences , The University of Tokyo , 3-8-1 Komaba , Meguro , Tokyo 153-8902 , Japan
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46
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Nissinkorn Y, Lahav‐Mankovski N, Rabinkov A, Albeck S, Motiei L, Margulies D. Sensing Protein Surfaces with Targeted Fluorescent Receptors. Chemistry 2015; 21:15981-7. [DOI: 10.1002/chem.201502069] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Yael Nissinkorn
- Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - Naama Lahav‐Mankovski
- Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - Aharon Rabinkov
- Department of Biological Services, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - Shira Albeck
- Israel Structural Proteomics Center, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - Leila Motiei
- Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - David Margulies
- Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot (Israel)
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47
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Serio N, Moyano DF, Rotello VM, Levine M. Array-based detection of persistent organic pollutants via cyclodextrin promoted energy transfer. Chem Commun (Camb) 2015; 51:11615-8. [PMID: 26096542 DOI: 10.1039/c5cc04153h] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report herein the selective array-based detection of 30 persistent organic pollutants via cyclodextrin-promoted energy transfer. The use of three fluorophores enabled the development of an array that classified 30 analytes with 100% accuracy and identified unknown analytes with 96% accuracy, as well as identifying 92% of analytes in urine.
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Affiliation(s)
- Nicole Serio
- Department of Chemistry, University of Rhode Island, 51 Lower College Road, Kingston, RI 02881, USA.
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48
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Busschaert N, Caltagirone C, Van Rossom W, Gale PA. Applications of Supramolecular Anion Recognition. Chem Rev 2015; 115:8038-155. [PMID: 25996028 DOI: 10.1021/acs.chemrev.5b00099] [Citation(s) in RCA: 857] [Impact Index Per Article: 95.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - Claudia Caltagirone
- ‡Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, 09042 Monserrato, Cagliari, Italy
| | - Wim Van Rossom
- †Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Philip A Gale
- †Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
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49
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Selvakumar K, Motiei L, Margulies D. Enzyme-Artificial Enzyme Interactions as a Means for Discriminating among Structurally Similar Isozymes. J Am Chem Soc 2015; 137:4892-5. [PMID: 25819325 DOI: 10.1021/jacs.5b02496] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We describe the design and function of an artificial enzyme-linked receptor (ELR) that can bind different members of the glutathione-S-transferase (GST) enzyme family. The artificial enzyme-enzyme interactions distinctly affect the catalytic activity of the natural enzymes, the biomimetic, or both, enabling the system to discriminate among structurally similar GST isozymes.
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Affiliation(s)
| | - Leila Motiei
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel 76100
| | - David Margulies
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel 76100
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50
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You L, Zha D, Anslyn EV. Recent Advances in Supramolecular Analytical Chemistry Using Optical Sensing. Chem Rev 2015; 115:7840-92. [PMID: 25719867 DOI: 10.1021/cr5005524] [Citation(s) in RCA: 624] [Impact Index Per Article: 69.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Lei You
- †State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 35002, People's Republic of China
| | - Daijun Zha
- †State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 35002, People's Republic of China
| | - Eric V Anslyn
- ‡Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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