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Reichstein J, Müssig S, Wintzheimer S, Mandel K. Communicating Supraparticles to Enable Perceptual, Information-Providing Matter. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2306728. [PMID: 37786273 DOI: 10.1002/adma.202306728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/04/2023] [Indexed: 10/04/2023]
Abstract
Materials are the fundament of the physical world, whereas information and its exchange are the centerpieces of the digital world. Their fruitful synergy offers countless opportunities for realizing desired digital transformation processes in the physical world of materials. Yet, to date, a perfect connection between these worlds is missing. From the perspective, this can be achieved by overcoming the paradigm of considering materials as passive objects and turning them into perceptual, information-providing matter. This matter is capable of communicating associated digitally stored information, for example, its origin, fate, and material type as well as its intactness on demand. Herein, the concept of realizing perceptual, information-providing matter by integrating customizable (sub-)micrometer-sized communicating supraparticles (CSPs) is presented. They are assembled from individual nanoparticulate and/or (macro)molecular building blocks with spectrally differentiable signals that are either robust or stimuli-susceptible. Their combination yields functional signal characteristics that provide an identification signature and one or multiple stimuli-recorder features. This enables CSPs to communicate associated digital information on the tagged material and its encountered stimuli histories upon signal readout anywhere across its life cycle. Ultimately, CSPs link the materials and digital worlds with numerous use cases thereof, in particular fostering the transition into an age of sustainability.
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Affiliation(s)
- Jakob Reichstein
- Department of Chemistry and Pharmacy, Inorganic Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Egerlandstraße 1, D-91058, Erlangen, Germany
| | - Stephan Müssig
- Department of Chemistry and Pharmacy, Inorganic Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Egerlandstraße 1, D-91058, Erlangen, Germany
| | - Susanne Wintzheimer
- Department of Chemistry and Pharmacy, Inorganic Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Egerlandstraße 1, D-91058, Erlangen, Germany
- Fraunhofer-Institute for Silicate Research ISC, Neunerplatz 2, D-97082, Würzburg, Germany
| | - Karl Mandel
- Department of Chemistry and Pharmacy, Inorganic Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Egerlandstraße 1, D-91058, Erlangen, Germany
- Fraunhofer-Institute for Silicate Research ISC, Neunerplatz 2, D-97082, Würzburg, Germany
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2
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Dagher M, Ongo G, Robichaud N, Kong J, Rho W, Teahulos I, Tavakoli A, Bovaird S, Merjaneh S, Tan A, Edwardson K, Scheepers C, Ng A, Hajjar A, Sow B, Vrouvides M, Lee A, DeCorwin-Martin P, Rasool S, Huang J, Han Y, Erps T, Coffin S, Chandrasekaran SN, Miller L, Kost-Alimova M, Skepner A, Singh S, Carpenter AE, Munzar J, Juncker D. nELISA: A high-throughput, high-plex platform enables quantitative profiling of the secretome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.535914. [PMID: 37131604 PMCID: PMC10153206 DOI: 10.1101/2023.04.17.535914] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We present the nELISA, a high-throughput, high-fidelity, and high-plex protein profiling platform. DNA oligonucleotides are used to pre-assemble antibody pairs on spectrally encoded microparticles and perform displacement-mediated detection. Spatial separation between non-cognate antibodies prevents the rise of reagent-driven cross-reactivity, while read-out is performed cost-efficiently and at high-throughput using flow cytometry. We assembled an inflammatory panel of 191 targets that were multiplexed without cross-reactivity or impact on performance vs 1-plex signals, with sensitivities as low as 0.1pg/mL and measurements spanning 7 orders of magnitude. We then performed a large-scale secretome perturbation screen of peripheral blood mononuclear cells (PBMCs), with cytokines as both perturbagens and read-outs, measuring 7,392 samples and generating ~1.5M protein datapoints in under a week, a significant advance in throughput compared to other highly multiplexed immunoassays. We uncovered 447 significant cytokine responses, including multiple putatively novel ones, that were conserved across donors and stimulation conditions. We also validated the nELISA's use in phenotypic screening, and propose its application to drug discovery.
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3
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Magnetic quantum dots barcodes using Fe 3O 4/TiO 2 with weak spectral absorption in the visible region for high-sensitivity multiplex detection of tumor markers. Biosens Bioelectron 2023; 227:115153. [PMID: 36805273 DOI: 10.1016/j.bios.2023.115153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/07/2023] [Accepted: 02/12/2023] [Indexed: 02/16/2023]
Abstract
Magnetic quantum dot (QD) barcode holds great potential for automatic suspension array and rapid point-of-care detection since it enables simultaneous target encoding, enrichment and separation. However, a serious obstacle to enhancing the encoding capacity of magnetic QD microbeads (MBs) is the fluorescence quenching of magnetic nanoparticles (MNPs) to quantum dots (QDs) in the visible wavelength range due to the broad and strong optical absorption spectrum of MNPs. Here, we report Fe3O4/TiO2 core/shell MNPs and CdSe/ZnS QDs for the construction of dual-function magnetic QD barcodes. Fe3O4/TiO2 MNPs can significantly inhibit fluorescence quenching because the weak absorption of visible light by the TiO2. The two-dimension barcode library of 30 magnetic QD barcodes was constructed based on Fe3O4/TiO2 MNPs and CdSe/ZnS QDs. Moreover, the magnetic QD barcodes showed high sensitivity for the multiplex detection of four tumor markers, cancer antigen 125 (CA125), cancer antigen 199 (CA199), alpha-fetoprotein (AFP), and neuron specific enolase (NSE) with detection limits of 0.89 KU/L, 0.72 KU/L, 0.05 ng/mL, and 0.15 ng/mL, respectively. This bifunctional magnetic QD barcodes are promising for automatic high-sensitivity multiplex bioassay.
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4
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Ortiz-Perez A, Izquierdo-Lozano C, Meijers R, Grisoni F, Albertazzi L. Identification of fluorescently-barcoded nanoparticles using machine learning. NANOSCALE ADVANCES 2023; 5:2307-2317. [PMID: 37056621 PMCID: PMC10089084 DOI: 10.1039/d2na00648k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Barcoding of nano- and micro-particles allows distinguishing multiple targets at the same time within a complex mixture and is emerging as a powerful tool to increase the throughput of many assays. Fluorescent barcoding is one of the most used strategies, where microparticles are labeled with dyes and classified based on fluorescence color, intensity, or other features. Microparticles are ideal targets due to their relative ease of detection, manufacturing, and higher homogeneity. Barcoding is considerably more challenging in the case of nanoparticles (NPs), where their small size results in a lower signal and greater heterogeneity. This is a significant limitation since many bioassays require the use of nano-sized carriers. In this study, we introduce a machine-learning-assisted workflow to write, read, and classify barcoded PLGA-PEG NPs at a single-particle level. This procedure is based on the encapsulation of fluorescent markers without modifying their physicochemical properties (writing), the optimization of their confocal imaging (reading), and the implementation of a machine learning-based barcode reader (classification). We found nanoparticle heterogeneity as one of the main factors that challenges barcode separation, and that information extracted from the dyes' nanoscale confinement effects (such as Förster Resonance Energy Transfer, FRET) can aid barcode identification. Moreover, we provide a guide to reaching the optimal trade-off between the number of simultaneous barcodes and classification accuracy supporting the use of this workflow for a variety of bioassays.
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Affiliation(s)
- Ana Ortiz-Perez
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology PO Box 513 5600 MB Eindhoven The Netherlands
| | - Cristina Izquierdo-Lozano
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology PO Box 513 5600 MB Eindhoven The Netherlands
| | - Rens Meijers
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology PO Box 513 5600 MB Eindhoven The Netherlands
| | - Francesca Grisoni
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology PO Box 513 5600 MB Eindhoven The Netherlands
| | - Lorenzo Albertazzi
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology PO Box 513 5600 MB Eindhoven The Netherlands
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Jin Q, Zhang X, Zhang L, Li J, Lv Y, Li N, Wang L, Wu R, Li LS. Fabrication of CuInZnS/ZnS Quantum Dot Microbeads by a Two-Step Approach of Emulsification-Solvent Evaporation and Surfactant Substitution and Its Application for Quantitative Detection. Inorg Chem 2023; 62:3474-3484. [PMID: 36789761 DOI: 10.1021/acs.inorgchem.2c03783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
CuInS2 quantum dots (CIS QDs) are considered to be promising alternatives for Cd-based QDs in the fields of biology and medicine. However, high-quality hydrophobic CIS QDs are difficult to be transferred to water due to their 1-dodecylmercaptan (DDT) ligands. Therefore, the fluorescence and stability of the prepared aqueous CIS QDs is not enough to meet the requirement for sensitive detection. Here, as large as 13 nm CuInZnS/ZnS QDs with DDT ligands were first synthesized, and then, CuInZnS/ZnS microbeads (QBs) containing thousands of QDs were successfully fabricated by a two-step approach of emulsion-solvent evaporation and surfactant substitution. Through emulsion-solvent evaporation, the CuInZnS/ZnS QDs formed microbeads in the microemulsion with dodecyl trimethylammonium bromide (DTAB), and the Förster resonance energy transfer (FRET) has been effectively overcome. Then, CO-520 was introduced to substitute DTAB to improve the stability and water solubility. Lastly, the microbeads were coated with a SiO2 shell and carboxylated. Subsequently, the constructed QBs (∼210 nm) were used as labels in a fluorescence immunosorbent assay (FLISA) for quantitative detection of heart type fatty acid binding protein (H-FABP), and the limit of detection was 0.48 ng mL-1, which indicated a greatly improved detection sensitivity compared to that of the Cd-free QDs. The highly fluorescent and stable CuInZnS/ZnS QBs will have great application prospects in many biological fields.
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Affiliation(s)
- Qiaoli Jin
- Key Laboratory for Special Functional Materials of Ministry of Education, School of Materials Science, and National and Local Joint Engineering Research Center for High-Efficiency Display and Lighting Technology, Henan University, Kaifeng 475004, China
| | - Xuhui Zhang
- Key Laboratory for Special Functional Materials of Ministry of Education, School of Materials Science, and National and Local Joint Engineering Research Center for High-Efficiency Display and Lighting Technology, Henan University, Kaifeng 475004, China
| | - Lifang Zhang
- Key Laboratory for Special Functional Materials of Ministry of Education, School of Materials Science, and National and Local Joint Engineering Research Center for High-Efficiency Display and Lighting Technology, Henan University, Kaifeng 475004, China
| | - Jinjie Li
- Key Laboratory for Special Functional Materials of Ministry of Education, School of Materials Science, and National and Local Joint Engineering Research Center for High-Efficiency Display and Lighting Technology, Henan University, Kaifeng 475004, China
| | - Yanbing Lv
- Key Laboratory for Special Functional Materials of Ministry of Education, School of Materials Science, and National and Local Joint Engineering Research Center for High-Efficiency Display and Lighting Technology, Henan University, Kaifeng 475004, China
| | - Ning Li
- Key Laboratory for Special Functional Materials of Ministry of Education, School of Materials Science, and National and Local Joint Engineering Research Center for High-Efficiency Display and Lighting Technology, Henan University, Kaifeng 475004, China
| | - Lei Wang
- Key Laboratory for Special Functional Materials of Ministry of Education, School of Materials Science, and National and Local Joint Engineering Research Center for High-Efficiency Display and Lighting Technology, Henan University, Kaifeng 475004, China
| | - Ruili Wu
- Key Laboratory for Special Functional Materials of Ministry of Education, School of Materials Science, and National and Local Joint Engineering Research Center for High-Efficiency Display and Lighting Technology, Henan University, Kaifeng 475004, China
| | - Lin Song Li
- Key Laboratory for Special Functional Materials of Ministry of Education, School of Materials Science, and National and Local Joint Engineering Research Center for High-Efficiency Display and Lighting Technology, Henan University, Kaifeng 475004, China
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6
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Liu X, Li M, Yu X, Shen L, Li W. Silent region barcode particle arrays for ultrasensitive multiplexed SERS detection. Biosens Bioelectron 2023; 219:114804. [PMID: 36272345 DOI: 10.1016/j.bios.2022.114804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 09/30/2022] [Accepted: 10/10/2022] [Indexed: 11/19/2022]
Abstract
Suspension arrays are a critical components of next generation multiplexed detection technologies. Current fluorescence suspension arrays are limited by a multiplexed coding ceiling and difficulties with ultrasensitive detection. Raman mode is a promising substitute, but the complex spectral peak distributions and extremely weak intrinsic signal intensity severely diminish Raman signal performance in suspension arrays. To address these limitations, we constructed a Raman suspension array system using plasmonic microbeads as barcode substrates and Au nanoflowers as reporter carriers. The well-designed shell morphology and plasmonic microbead composition enabled significant surface enhancement Raman scattering (SERS) such that we were able to adjust silent region Raman-coding intensity levels. Due to synergistic SERS effects from the plasmonic shell and the multi-branched Au nanoflower nanostructure, the reporting signal was greatly improved, enabling ultrasensitive detection of 5-plexed lung cancer markers. Detection in patient serum samples demonstrated good consistency with the standard electrochemiluminescence method. Thus, this silent region SERS barcode-based suspension array is a developmental advance for modern multiplexed biodetection, potentially providing a powerful early disease screening and diagnosis tool.
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Affiliation(s)
- Xinyi Liu
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, PR China
| | - Meng Li
- Zhejiang Orient Gene Biotech Co., Ltd., 3787 East Yangguang Avenue, Anji, 313300, Zhejiang, PR China
| | - Xujiang Yu
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, PR China
| | - Lisong Shen
- Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, 1665 Kongjiang Road, Shanghai, 200092, PR China
| | - Wanwan Li
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, PR China.
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7
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Zhang RM, Tiedemann K, Muthu ML, Dinesh NEH, Komarova S, Ramkhelawon B, Reinhardt DP. Fibrillin-1-regulated miR-122 has a critical role in thoracic aortic aneurysm formation. Cell Mol Life Sci 2022; 79:314. [PMID: 35606547 PMCID: PMC11072253 DOI: 10.1007/s00018-022-04337-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/08/2022] [Accepted: 04/28/2022] [Indexed: 11/30/2022]
Abstract
Thoracic aortic aneurysms (TAA) in Marfan syndrome, caused by fibrillin-1 mutations, are characterized by elevated cytokines and fragmentated elastic laminae in the aortic wall. This study explored whether and how specific fibrillin-1-regulated miRNAs mediate inflammatory cytokine expression and elastic laminae degradation in TAA. miRNA expression profiling at early and late TAA stages using a severe Marfan mouse model (Fbn1mgR/mgR) revealed a spectrum of differentially regulated miRNAs. Bioinformatic analyses predicted the involvement of these miRNAs in inflammatory and extracellular matrix-related pathways. We demonstrate that upregulation of pro-inflammatory cytokines and matrix metalloproteinases is a common characteristic of mouse and human TAA tissues. miR-122, the most downregulated miRNA in the aortae of 10-week-old Fbn1mgR/mgR mice, post-transcriptionally upregulated CCL2, IL-1β and MMP12. Similar data were obtained at 70 weeks of age using Fbn1C1041G/+ mice. Deficient fibrillin-1-smooth muscle cell interaction suppressed miR-122 levels. The marker for tissue hypoxia HIF-1α was upregulated in the aortic wall of Fbn1mgR/mgR mice, and miR-122 was reduced under hypoxic conditions in cell and organ cultures. Reduced miR-122 was partially rescued by HIF-1α inhibitors, digoxin and 2-methoxyestradiol in aortic smooth muscle cells. Digoxin-treated Fbn1mgR/mgR mice demonstrated elevated miR-122 and suppressed CCL2 and MMP12 levels in the ascending aortae, with reduced elastin fragmentation and aortic dilation. In summary, this study demonstrates that miR-122 in the aortic wall inhibits inflammatory responses and matrix remodeling, which is suppressed by deficient fibrillin-1-cell interaction and hypoxia in TAA.
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Affiliation(s)
- Rong-Mo Zhang
- Faculty of Medicine and Health Sciences, McGill University, Montreal, Canada
| | - Kerstin Tiedemann
- Shriners Hospital for Children-Canada, Montreal, Canada
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, Canada
| | - Muthu L Muthu
- Faculty of Medicine and Health Sciences, McGill University, Montreal, Canada
| | - Neha E H Dinesh
- Faculty of Medicine and Health Sciences, McGill University, Montreal, Canada
| | - Svetlana Komarova
- Shriners Hospital for Children-Canada, Montreal, Canada
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, Canada
| | - Bhama Ramkhelawon
- Department of Surgery, New York University School of Medicine, New York, USA
| | - Dieter P Reinhardt
- Faculty of Medicine and Health Sciences, McGill University, Montreal, Canada.
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, Canada.
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, QC, H3A 0C7, Canada.
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8
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Wei W, Dai W, Yang F, Lu H, Zhang K, Xing Y, Meng X, Zhou L, Zhang Y, Yang Q, Cheng Y, Dong H. Spatially Resolved, Error-Robust Multiplexed MicroRNA Profiling in Single Living Cells. Angew Chem Int Ed Engl 2022; 61:e202116909. [PMID: 35194913 DOI: 10.1002/anie.202116909] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Indexed: 12/11/2022]
Abstract
Simultaneous imaging of multiple microRNAs (miRNAs) in individual living cells is challenging due to the lack of spectrally distinct encoded fluorophores and non-cytotoxic methods. We describe a multiplexed error-robust combinatorial fluorescent label-encoding method, termed fluorophores encoded error-corrected labels (FluoELs), enabling multiplexed miRNA imaging in living cells with error-correcting capability. The FluoELs comprise proportional dual fluorophores for encoding and a constant quantitative single fluorophore for error-corrected quantification. Both are embedded in 260 nm core-shell silica nanoparticles modified with molecular beacon detection probes. The FluoELs are low cytotoxic and could accurately quantify and spatially resolve nine breast-cancer-related miRNAs and evaluate their coordination. The FluoELs enabled a single-cell analysis platform to evaluate miRNA expression profiles and the molecular mechanisms underlying miRNA-associated diseases.
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Affiliation(s)
- Wei Wei
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, 100083, Beijing, China
| | - Wenhao Dai
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, 100083, Beijing, China
| | - Fan Yang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, 100083, Beijing, China
| | - Huiting Lu
- Department of Chemistry, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Kai Zhang
- College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yi Xing
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, 100083, Beijing, China
| | - Xiangdan Meng
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, 100083, Beijing, China
| | - Liping Zhou
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, 100083, Beijing, China
| | - Yiyi Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, 100083, Beijing, China
| | - Qiqi Yang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, 100083, Beijing, China
| | - Yaru Cheng
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, 100083, Beijing, China
| | - Haifeng Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, 100083, Beijing, China.,Marshall Laboratory of Biomedical Engineering, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, 3688, Nanhai Road, Shenzhen, 518060, Guangdong, China
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9
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Dual-Signal-Encoded Barcodes with Low Background Signal for High-Sensitivity Analysis of Multiple Tumor Markers. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10040142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The suspension array technology (SAT) is promising for high-sensitivity multiplexed analysis of tumor markers. Barcodes as the core elements of SAT, can generate encoding fluorescence signals (EFS) and detection fluorescence signals (DFS) in the corresponding flow cytometer channel. However, the bleed-through effect of EFS in the DFS channel and the reagent-driven non-specific binding (NSB) lead to background interference for ultrasensitive assay of multiple targets. Here, we report an ingenious method to eliminate background interference between barcode and reporter using low-background dual-signal-encoded barcodes (DSBs) based on microbeads (MBs) and quantum dots (QDs). The low-background DSBs were prepared via combination strategy of two signals containing scatter signals and fluorescence signals. Three types of MBs were distinguished by the scattering channel of flow cytometer (FSC vs. SSC) to obtain the scattered signals. Green quantum dots (GQDs) or red quantum dots (RQDs) were coupled to the surface of MBs by sandwich immune structure to obtain the distinguishable fluorescent signals. Furthermore, the amount of conjugated capture antibody on the MB’s surface was optimized by comparing the change of detection sensitivity with the addition of capture antibody. The combination measurements of specificity and NSB in SAT platform were performed by incubating the capture antibody-conjugated MBs (cAb-MBs) with individual QD-conjugated detection antibody (QDs-dAb). Finally, an SAT platform based on DSBs was successfully established for highly sensitive multiplexed analysis of six tumor markers in one test, which suggests the promising tool for highly sensitive multiplexed bioassay applications.
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10
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Wei W, Dai W, Yang F, Lu H, Zhang K, Xing Y, Meng X, Zhou L, Zhang Y, Yang Q, Cheng Y, Dong H. Spatially Resolved, Error‐Robust Multiplexed MicroRNA Profiling in Single Living Cells. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Wei Wei
- Beijing Key Laboratory for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Wenhao Dai
- Beijing Key Laboratory for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Fan Yang
- Beijing Key Laboratory for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Huiting Lu
- Department of Chemistry School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road Beijing 100083 China
| | - Kai Zhang
- College of Materials Science and Engineering Beijing University of Chemical Technology Beijing 100029 China
| | - Yi Xing
- Beijing Key Laboratory for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Xiangdan Meng
- Beijing Key Laboratory for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Liping Zhou
- Beijing Key Laboratory for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Yiyi Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Qiqi Yang
- Beijing Key Laboratory for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Yaru Cheng
- Beijing Key Laboratory for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Haifeng Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
- Marshall Laboratory of Biomedical Engineering Research Center for Biosensor and Nanotheranostic School of Biomedical Engineering Health Science Center Shenzhen University 3688, Nanhai Road Shenzhen 518060, Guangdong China
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11
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Cheng Y, Borum RM, Clark AE, Jin Z, Moore C, Fajtová P, O'Donoghue AJ, Carlin AF, Jokerst JV. A Dual-Color Fluorescent Probe Allows Simultaneous Imaging of Main and Papain-like Proteases of SARS-CoV-2-Infected Cells for Accurate Detection and Rapid Inhibitor Screening. Angew Chem Int Ed Engl 2022; 61:e202113617. [PMID: 34889013 PMCID: PMC8854376 DOI: 10.1002/anie.202113617] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Indexed: 11/15/2022]
Abstract
The main protease (Mpro ) and papain-like protease (PLpro ) play critical roles in SARS-CoV-2 replication and are promising targets for antiviral inhibitors. The simultaneous visualization of Mpro and PLpro is extremely valuable for SARS-CoV-2 detection and rapid inhibitor screening. However, such a crucial investigation has remained challenging because of the lack of suitable probes. We have now developed a dual-color probe (3MBP5) for the simultaneous detection of Mpro and PLpro by fluorescence (or Förster) resonance energy transfer (FRET). This probe produces fluorescence from both the Cy3 and Cy5 fluorophores that are cleaved by Mpro and PLpro . 3MBP5-activatable specificity was demonstrated with recombinant proteins, inhibitors, plasmid-transfected HEK 293T cells, and SARS-CoV-2-infected TMPRSS2-Vero cells. Results from the dual-color probe first verified the simultaneous detection and intracellular distribution of SARS-CoV-2 Mpro and PLpro . This is a powerful tool for the simultaneous detection of different proteases with value for the rapid screening of inhibitors.
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Affiliation(s)
- Yong Cheng
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Raina M. Borum
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Alex E. Clark
- Department of MedicineUniversity of California, San DiegoLa JollaCA 92093USA
| | - Zhicheng Jin
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Colman Moore
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCA 92093USA
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCA 92093USA
| | - Aaron F. Carlin
- Department of MedicineUniversity of California, San DiegoLa JollaCA 92093USA
| | - Jesse V. Jokerst
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
- Materials Science and Engineering ProgramUniversity of California, San DiegoLa JollaCA 92093USA
- Department of RadiologyUniversity of California, San DiegoLa JollaCA 92093USA
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12
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Cheng Y, Borum RM, Clark AE, Jin Z, Moore C, Fajtová P, O'Donoghue AJ, Carlin AF, Jokerst JV. A Dual‐Color Fluorescent Probe Allows Simultaneous Imaging of Main and Papain‐like Proteases of SARS‐CoV‐2‐Infected Cells for Accurate Detection and Rapid Inhibitor Screening. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yong Cheng
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Raina M. Borum
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Alex E. Clark
- Department of Medicine University of California, San Diego La Jolla CA 92093 USA
| | - Zhicheng Jin
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Colman Moore
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego La Jolla CA 92093 USA
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego La Jolla CA 92093 USA
| | - Aaron F. Carlin
- Department of Medicine University of California, San Diego La Jolla CA 92093 USA
| | - Jesse V. Jokerst
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
- Materials Science and Engineering Program University of California, San Diego La Jolla CA 92093 USA
- Department of Radiology University of California, San Diego La Jolla CA 92093 USA
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13
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Vu T, Vallmitjana A, Gu J, La K, Xu Q, Flores J, Zimak J, Shiu J, Hosohama L, Wu J, Douglas C, Waterman ML, Ganesan A, Hedde PN, Gratton E, Zhao W. Spatial transcriptomics using combinatorial fluorescence spectral and lifetime encoding, imaging and analysis. Nat Commun 2022; 13:169. [PMID: 35013281 PMCID: PMC8748653 DOI: 10.1038/s41467-021-27798-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 12/15/2021] [Indexed: 12/14/2022] Open
Abstract
Multiplexed mRNA profiling in the spatial context provides new information enabling basic research and clinical applications. Unfortunately, existing spatial transcriptomics methods are limited due to either low multiplexing or complexity. Here, we introduce a spatialomics technology, termed Multi Omic Single-scan Assay with Integrated Combinatorial Analysis (MOSAICA), that integrates in situ labeling of mRNA and protein markers in cells or tissues with combinatorial fluorescence spectral and lifetime encoded probes, spectral and time-resolved fluorescence imaging, and machine learning-based decoding. We demonstrate MOSAICA's multiplexing scalability in detecting 10-plex targets in fixed colorectal cancer cells using combinatorial labeling of five fluorophores with facile error-detection and removal of autofluorescence. MOSAICA's analysis is strongly correlated with sequencing data (Pearson's r = 0.96) and was further benchmarked using RNAscopeTM and LGC StellarisTM. We further apply MOSAICA for multiplexed analysis of clinical melanoma Formalin-Fixed Paraffin-Embedded (FFPE) tissues. We finally demonstrate simultaneous co-detection of protein and mRNA in cancer cells.
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Affiliation(s)
- Tam Vu
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA
| | - Alexander Vallmitjana
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, CA, 92697, USA
| | - Joshua Gu
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
| | - Kieu La
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
| | - Qi Xu
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
| | - Jesus Flores
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA
- CIRM Stem Cell Research Biotechnology Training Program at California State University, Long Beach, Long Beach, CA, 90840, USA
| | - Jan Zimak
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Jessica Shiu
- Department of Dermatology, University of California, Irvine, Irvine, CA, 92697, USA
| | - Linzi Hosohama
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, 92697, USA
| | - Jie Wu
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, 92697, USA
| | - Christopher Douglas
- Department of Pathology & Laboratory Medicine, University of California, Irvine, Irvine, CA, 92617, USA
| | - Marian L Waterman
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, 92697, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, 92697, USA
| | - Anand Ganesan
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
- Department of Dermatology, University of California, Irvine, Irvine, CA, 92697, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, 92697, USA
| | - Per Niklas Hedde
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, CA, 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
- Beckman Laser Institute & Medical Clinic, University of California, Irvine, Irvine, CA, 92697, USA
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA.
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, CA, 92697, USA.
- Beckman Laser Institute & Medical Clinic, University of California, Irvine, Irvine, CA, 92697, USA.
| | - Weian Zhao
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA.
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA.
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA.
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, 92697, USA.
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14
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Wu W, Liu X, Li W. Progress and challenges in functional nanomaterial‐based suspension array technology for multiplexed biodetection. VIEW 2022. [DOI: 10.1002/viw.20200140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Weijie Wu
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering Shanghai Jiao Tong University Shanghai P. R. China
| | - Xinyi Liu
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering Shanghai Jiao Tong University Shanghai P. R. China
| | - Wanwan Li
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering Shanghai Jiao Tong University Shanghai P. R. China
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15
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Tang Y, Zhong X, Yan S, Liu X, Cheng L, Wang Y, Liu X. Enantiospecific Detection of D‐Amino Acid through Synergistic Upconversion Energy Transfer. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yongan Tang
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & Technology International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education Institute of Microscale Optoelectronics Shenzhen University Shenzhen 518060 China
- Department of Chemistry National University of Singapore Singapore 117549 Singapore
| | - Xiaoyan Zhong
- Institute of Functional Nano & Soft Materials (FUNSOM) Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices Soochow University Suzhou 215123 China
| | - Shuangqian Yan
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & Technology International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education Institute of Microscale Optoelectronics Shenzhen University Shenzhen 518060 China
- Department of Chemistry National University of Singapore Singapore 117549 Singapore
| | - Xiaowang Liu
- MIIT Key Laboratory of Flexible Electronics (KLoFE) and Xi'an Institute of Flexible Electronics Northwestern Polytechnical University 710072 Xi'an Shaanxi China
| | - Liang Cheng
- Institute of Functional Nano & Soft Materials (FUNSOM) Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices Soochow University Suzhou 215123 China
| | - Yu Wang
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & Technology International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education Institute of Microscale Optoelectronics Shenzhen University Shenzhen 518060 China
| | - Xiaogang Liu
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & Technology International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education Institute of Microscale Optoelectronics Shenzhen University Shenzhen 518060 China
- Department of Chemistry National University of Singapore Singapore 117549 Singapore
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16
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Tang Y, Zhong X, Yan S, Liu X, Cheng L, Wang Y, Liu X. Enantiospecific Detection of D-Amino Acid through Synergistic Upconversion Energy Transfer. Angew Chem Int Ed Engl 2021; 60:19648-19652. [PMID: 34224644 DOI: 10.1002/anie.202105297] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/20/2021] [Indexed: 01/23/2023]
Abstract
D-amino acids (DAAs) are indispensable in regulating diverse metabolic pathways. Selective and sensitive detection of DAAs is crucial for understanding the complexity of metabolic processes and managing associated diseases. However, current DAA detection strategies mainly rely on bulky instrumentation or electrochemical probes, limiting their cellular and animal applications. Here we report an enzyme-coupled nanoprobe that can detect enantiospecific DAAs through synergistic energy transfer. This nanoprobe offers near-infrared upconversion capability, a wide dynamic detection range, and a detection limit of 2.2 μM, providing a versatile platform for in vivo noninvasive detection of DAAs with high enantioselectivity. These results potentially allow real-time monitoring of biomolecular handedness in living animals, as well as developing antipsychotic treatment strategies.
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Affiliation(s)
- Yongan Tang
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & Technology, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China.,Department of Chemistry, National University of Singapore, Singapore, 117549, Singapore
| | - Xiaoyan Zhong
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, 215123, China
| | - Shuangqian Yan
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & Technology, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China.,Department of Chemistry, National University of Singapore, Singapore, 117549, Singapore
| | - Xiaowang Liu
- MIIT Key Laboratory of Flexible Electronics (KLoFE) and Xi'an Institute of Flexible Electronics, Northwestern Polytechnical University, 710072, Xi'an, Shaanxi, China
| | - Liang Cheng
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, 215123, China
| | - Yu Wang
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & Technology, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China
| | - Xiaogang Liu
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & Technology, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China.,Department of Chemistry, National University of Singapore, Singapore, 117549, Singapore
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17
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Zhang B, Tang WS, Ding SN. Rational design of fluorescent barcodes for suspension array through a simple simulation strategy. Analyst 2021; 146:4796-4802. [PMID: 34259241 DOI: 10.1039/d1an01052b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantum dot (QD)-encoded microbeads as optical barcode with high fluorescence intensity and fluorescence uniformity, excellent stability and dispersity are greatly important for suspension array (SA). However, the size distribution of the microbeads mass-produced by the membrane emulsification method usually shows polydispersity, which leads to obstacles, imposing labour-intensive experimental iterations for the application of fluorescence-encoded microbeads as a distinguishable barcode. Herein, a simple simulation strategy based on a multicolor fluorescence model (MFM) was used to predict the influence of the microbeads' size distribution on the barcode signals. The point L and S respectively represent the two end points of the barcode, and the line segment LS can be considered as a cluster of the QD-encoded microbeads (simulated barcode). Experimental clusters of fluorescent microbeads were found to be in good agreement with the simulated barcodes. This simple simulation strategy can effectively simplify the experimental iteration process because the fluorescence-encoded microbeads are not decoded by a flow cytometer. Moreover, when applied for the high-throughput ultrasensitive detection of three tumor markers (CEA, CA125 and CA199) in a single sample, these barcodes exhibit superior detection performance. Detection limits of 0.028 ± 0.001 ng mL-1 for CEA, 1.5 ± 0.02 KU L-1 for CA125 and 0.8 ± 0.1 KU L-1 for CA199 are achieved, which meet the sensitivity criteria of tumor marker analysis. Therefore, this simple simulation strategy helps to overcome technical and economic obstacles for the widespread application of SA.
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Affiliation(s)
- Bo Zhang
- Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Wan-Sheng Tang
- Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Shou-Nian Ding
- Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
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18
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Huang Q, Chen B, Shen J, Liu L, Li J, Shi J, Li Q, Zuo X, Wang L, Fan C, Li J. Encoding Fluorescence Anisotropic Barcodes with DNA Fameworks. J Am Chem Soc 2021; 143:10735-10742. [PMID: 34242004 DOI: 10.1021/jacs.1c04942] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence anisotropy (FA) holds great potential for multiplexed analysis and imaging of biomolecules since it can effectively discriminate fluorophores with overlapping emission spectra. Nevertheless, its susceptibility to environmental variation hampers its widespread applications in biology and biotechnology. In this study, we design FA DNA frameworks (FAFs) by scaffolding fluorophores in a fluorescent protein-like microenvironment. We find that the FA stability of the fluorophores is remarkably improved due to the sequestration effects of FAFs. The FA level of the fluorophores can be finely tuned when placed at different locations on an FAF, analogous to spectral shifts of protein-bound fluorophores. The high programmability of FAFs further enables the design of a spectrum of encoded FA barcodes for multiplexed sensing of nucleic acids and multiplexed labeling of live cells. This FAF system thus establishes a new paradigm for designing multiplexing FA probes for cellular imaging and other biological applications.
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Affiliation(s)
- Qiuling Huang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Chen
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Liu
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jiajun Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lihua Wang
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200127, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiang Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.,The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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19
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Liu X, Wu W, Cui D, Chen X, Li W. Functional Micro-/Nanomaterials for Multiplexed Biodetection. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2004734. [PMID: 34137090 DOI: 10.1002/adma.202004734] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 11/08/2020] [Indexed: 05/24/2023]
Abstract
When analyzing biological phenomena and processes, multiplexed biodetection has many advantages over single-factor biodetection and is highly relevant to both human health issues and advancements in the life sciences. However, many key problems with current multiplexed biodetection strategies remain unresolved. Herein, the main issues are analyzed and summarized: 1) generating sufficient signal to label targets, 2) improving the signal-to-noise ratio to ensure total detection sensitivity, and 3) simplifying the detection process to reduce the time and labor costs of multiple target detection. Then, available solutions made possible by designing and controlling the properties of micro- and nanomaterials are introduced. The aim is to emphasize the role that micro-/nanomaterials can play in the improvement of multiplexed biodetection strategies. Through analyzing existing problems, introducing state-of-the-art developments regarding relevant materials, and discussing future directions of the field, it is hopeful to help promote necessary developments in multiplexed biodetection and associated scientific research.
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Affiliation(s)
- Xinyi Liu
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Weijie Wu
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Daxiang Cui
- Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Engineering Research Center for Intelligent Diagnosis and Treatment Instrument, Key Laboratory of Thin Film and Microfabrication (Ministry of Education), Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Xiaoyuan Chen
- Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 117597, Singapore
| | - Wanwan Li
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
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20
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Luo T, Zhou T, Qu J. Lifetime Division Multiplexing by Multilevel Encryption Algorithm. ACS NANO 2021; 15:6257-6265. [PMID: 33625205 DOI: 10.1021/acsnano.0c09177] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Asymmetric, multilevel, switchable, and reversible encryption is realized by algorithm encryption, which plays an important role in encryption technology. Fluorescence lifetime encryption is currently not executed by an algorithm. It is well-known that the short fluorescence lifetime (τ1), long fluorescence lifetime (τ2), amplitude-weighted average fluorescence lifetime (τm), and intensity-weighted average fluorescence lifetime (τi) can be obtained using a double exponential fitting, and then these four lifetime parameters can be considered as four lifetime algorithms. Therefore, we propose that the acquisition of these four fluorescence lifetimes can be regarded as further dividing the lifetime by different algorithms and optimizing lifetime multiplexing. Moreover, the four lifetime algorithms of τ1, τm, τ2, and τi can be switched between each other and can be used to perform asymmetric, multilevel, and reversible lifetime encryption to effectively increase the difficulties of anticounterfeiting.
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Affiliation(s)
- Teng Luo
- Center for Biomedical Photonics, College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems, Shenzhen University, Shenzhen 518060, P. R. China
| | - Ting Zhou
- Center for Biomedical Photonics, College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems, Shenzhen University, Shenzhen 518060, P. R. China
| | - Junle Qu
- Center for Biomedical Photonics, College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems, Shenzhen University, Shenzhen 518060, P. R. China
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21
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Abstract
Mapping the complex biogeography of microbial communities in situ with high taxonomic and spatial resolution poses a major challenge because of the high density1 and rich diversity2 of species in environmental microbiomes and the limitations of optical imaging technology3–6. Here, we introduce High Phylogenetic Resolution microbiome mapping by Fluorescence in situ Hybridization (HiPR-FISH), a versatile technology that uses binary encoding, spectral imaging, and machine learning based decoding to create micron-scale maps of the locations and identities of hundreds of microbial species in complex communities. We demonstrate the ability of 10-bit HiPR-FISH to distinguish 1023 E. coli isolates, each fluorescently labeled with a unique binary barcode. HiPR-FISH, in conjunction with custom algorithms for automated probe design and single-cell image analysis, reveals the disruption of spatial networks in the mouse gut microbiome in response to antibiotic treatment and the longitudinal stability of spatial architectures in the human oral plaque microbiome. Combined with super-resolution imaging, HiPR-FISH reveals the diverse ribosome organization strategies of human oral microbial taxa. HiPR-FISH provides a framework for analyzing the spatial ecology of environmental microbial communities at single-cell resolution.
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22
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Feng Y, White AK, Hein JB, Appel EA, Fordyce PM. MRBLES 2.0: High-throughput generation of chemically functionalized spectrally and magnetically encoded hydrogel beads using a simple single-layer microfluidic device. MICROSYSTEMS & NANOENGINEERING 2020; 6:109. [PMID: 33299601 PMCID: PMC7704393 DOI: 10.1038/s41378-020-00220-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/09/2020] [Accepted: 09/20/2020] [Indexed: 05/04/2023]
Abstract
The widespread adoption of bead-based multiplexed bioassays requires the ability to easily synthesize encoded microspheres and conjugate analytes of interest to their surface. Here, we present a simple method (MRBLEs 2.0) for the efficient high-throughput generation of microspheres with ratiometric barcode lanthanide encoding (MRBLEs) that bear functional groups for downstream surface bioconjugation. Bead production in MRBLEs 2.0 relies on the manual mixing of lanthanide/polymer mixtures (each of which comprises a unique spectral code) followed by droplet generation using single-layer, parallel flow-focusing devices and the off-chip batch polymerization of droplets into beads. To streamline downstream analyte coupling, MRBLEs 2.0 crosslinks copolymers bearing functional groups on the bead surface during bead generation. Using the MRBLEs 2.0 pipeline, we generate monodisperse MRBLEs containing 48 distinct well-resolved spectral codes with high throughput (>150,000/min and can be boosted to 450,000/min). We further demonstrate the efficient conjugation of oligonucleotides and entire proteins to carboxyl MRBLEs and of biotin to amino MRBLEs. Finally, we show that MRBLEs can also be magnetized via the simultaneous incorporation of magnetic nanoparticles with only a minor decrease in the potential code space. With the advantages of dramatically simplified device fabrication, elimination of the need for custom-made equipment, and the ability to produce spectrally and magnetically encoded beads with direct surface functionalization with high throughput, MRBLEs 2.0 can be directly applied by many labs towards a wide variety of downstream assays, from basic biology to diagnostics and other translational research.
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Affiliation(s)
- Yinnian Feng
- Department of Genetics, Stanford University, Stanford, CA 94305 USA
| | - Adam K. White
- Department of Genetics, Stanford University, Stanford, CA 94305 USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305 USA
| | - Jamin B. Hein
- Department of Biology, Stanford University, Stanford, CA 94305 USA
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
| | - Eric A. Appel
- Department of Materials Science & Engineering, Stanford University, Stanford, CA 94305 USA
| | - Polly M. Fordyce
- Department of Genetics, Stanford University, Stanford, CA 94305 USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305 USA
- Stanford ChEM-H, Stanford University, Stanford, CA 94305 USA
- Chan Zuckerberg Biohub, San Francisco, CA 94110 USA
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23
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Zhao H, Wang M, Xiong X, Liu Y, Chen X. Simultaneous fluorescent detection of multiplexed miRNA of liver cancer based on DNA tetrahedron nanotags. Talanta 2020; 210:120677. [DOI: 10.1016/j.talanta.2019.120677] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/20/2019] [Accepted: 12/24/2019] [Indexed: 02/08/2023]
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24
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25
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Hu J, Li WC, Qiu JG, Jiang B, Zhang CY. A multifunctional DNA nanostructure based on multicolor FRET for nuclease activity assay. Analyst 2020; 145:6054-6060. [DOI: 10.1039/d0an01212b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We develop a four-color fluorescent probe for ratiometric detection of multiple nucleases based on multistep fluorescence resonance energy transfer.
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Affiliation(s)
- Juan Hu
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Wen-can Li
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Jian-Ge Qiu
- Academy of Medical Sciences
- Zhengzhou University
- Zhengzhou
- China
| | - BingHua Jiang
- Academy of Medical Sciences
- Zhengzhou University
- Zhengzhou
- China
| | - Chun-yang Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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26
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Wu Q, Zhang KY, Dai P, Zhu H, Wang Y, Song L, Wang L, Liu S, Zhao Q, Huang W. Bioorthogonal “Labeling after Recognition” Affording an FRET-Based Luminescent Probe for Detecting and Imaging Caspase-3 via Photoluminescence Lifetime Imaging. J Am Chem Soc 2019; 142:1057-1064. [DOI: 10.1021/jacs.9b12191] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Qi Wu
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Kenneth Yin Zhang
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Peiling Dai
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Hengyu Zhu
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Yun Wang
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Linna Song
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Ling Wang
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Shujuan Liu
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Qiang Zhao
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Wei Huang
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
- Xi’an Institute of Flexible Electronics (XIFE), Northwestern Polytechnical University (NPU), 127 West Youyi Road, Xi’an 710072, P. R. China
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27
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Li CC, Liu WX, Hu J, Zhang CY. A single quantum dot-based nanosensor with multilayer of multiple acceptors for ultrasensitive detection of human alkyladenine DNA glycosylase. Chem Sci 2019; 10:8675-8684. [PMID: 31803442 PMCID: PMC6849492 DOI: 10.1039/c9sc02137j] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/05/2019] [Indexed: 12/17/2022] Open
Abstract
Base excision repair (BER) is an important DNA repair pathway involved in the maintenance of genome stability. As the initiator of BER, DNA glycosylase can remove a damaged base from DNA through cleaving the N-glycosidic bond between the sugar moiety and the damaged base. Accurate quantification of DNA glycosylase is essential for the early diagnosis of various human diseases. However, conventional methods for DNA glycosylase assay usually suffer from poor sensitivity and complex probe design. Herein, we develop a single quantum dot-based nanosensor with multilayer of multiple acceptors for ultrasensitive detection of human alkyladenine DNA glycosylase (hAAG) using apurinic/apyrimidinic endonuclease 1 (APE1)-assisted cyclic cleavage-mediated signal amplification in combination with the DNA polymerase-assisted multiple cyanine 5 (Cy5)-mediated fluorescence resonance energy transfer (FRET). The presence of hAAG induces the cleavage of the hairpin substrate, generating a trigger. The resultant trigger can hybridize with a probe modified with an AP site, initiating the APE1-mediated cyclic cleavage to produce a large number of primers. The primers can subsequently initiate the polymerase-mediated signal amplification with a biotin-modified capture probe as the template, generating the biotin-/multiple Cy5-labeled double-stranded DNAs (dsDNAs). The resultant dsDNAs can assemble onto the QD surface to form the QD-dsDNA-Cy5 nanostructure, leading to efficient FRET from the QD to Cy5 under the excitation of 405 nm. In contrast to the typical QD-based FRET approaches, the assembly of multilayer of multiple Cy5 molecules onto a single QD significantly amplifies the FRET signal. We further verify the FRET model with one donor and multilayered acceptors theoretically and experimentally. This single QD-based nanosensor can sensitively detect hAAG with a detection limit of as low as 4.42 × 10-12 U μL-1. Moreover, it can detect hAAG even in a single cancer cell, and distinguish the cancer cells from the normal cells. Importantly, this single QD-based nanosensor can be used for the kinetic study and inhibition assay, and it may become a universal platform for the detection of other DNA repair enzymes by designing appropriate DNA substrates.
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Affiliation(s)
- Chen-Chen Li
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; ; Tel: +86 0531-86186033
| | - Wan-Xin Liu
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; ; Tel: +86 0531-86186033
| | - Juan Hu
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; ; Tel: +86 0531-86186033
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; ; Tel: +86 0531-86186033
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28
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Qiu X, Hildebrandt N. A clinical role for Förster resonance energy transfer in molecular diagnostics of disease. Expert Rev Mol Diagn 2019; 19:767-771. [DOI: 10.1080/14737159.2019.1649144] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Xue Qiu
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, France
| | - Niko Hildebrandt
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, France
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29
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Hu J, Liu MH, Zhang CY. Construction of Tetrahedral DNA-Quantum Dot Nanostructure with the Integration of Multistep Förster Resonance Energy Transfer for Multiplex Enzymes Assay. ACS NANO 2019; 13:7191-7201. [PMID: 31180625 DOI: 10.1021/acsnano.9b02679] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Three-dimensional (3D) DNA scaffolds with well-defined structure and high controllability hold promising potentials for biosensing and drug delivery. However, most of 3D DNA scaffolds can detect only a single type of molecule with the involvement of complex logic operations. Herein, we develop a 3D DNA nanostructure with the capability of multiplexed detection by exploiting a multistep Förster resonance energy transfer (FRET). The tetrahedron-structured DNA is constructed by four oligonucleotide strands and is subsequently conjugated to a streptavidin-coated quantum dot (QD) to obtain a QD-Cy3-Texas Red-Cy5 tetrahedron DNA. This QD-Cy3-Texas Red-Cy5 tetrahedral DNA nanostructure has well-defined dye-to-dye spacing and high controllability for energy transfer between intermediary acceptors and terminal acceptors, enabling the generation of multistep FRET between the QD and three dyes (i.e., Cy3, Texas Red, and Cy5) for simultaneous detection of multiple endonucleases and methyltransferases even in complex biological samples as well as the screening of multiple enzyme inhibitors.
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Affiliation(s)
- Juan Hu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China
| | - Ming-Hao Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China
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30
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Chen C, Corry B, Huang L, Hildebrandt N. FRET-Modulated Multihybrid Nanoparticles for Brightness-Equalized Single-Wavelength Barcoding. J Am Chem Soc 2019; 141:11123-11141. [DOI: 10.1021/jacs.9b03383] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Chi Chen
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay Cedex, France
| | - Ben Corry
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Liang Huang
- College of Chemical Engineering, Zhejiang University of Technology, 310014, Hangzhou, People’s Republic of China
| | - Niko Hildebrandt
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay Cedex, France
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31
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Yang CT, Xu Y, Pourhassan-Moghaddam M, Tran DP, Wu L, Zhou X, Thierry B. Surface Plasmon Enhanced Light Scattering Biosensing: Size Dependence on the Gold Nanoparticle Tag. SENSORS (BASEL, SWITZERLAND) 2019; 19:E323. [PMID: 30650578 PMCID: PMC6359480 DOI: 10.3390/s19020323] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/11/2019] [Accepted: 01/11/2019] [Indexed: 12/31/2022]
Abstract
Surface plasmon enhanced light scattering (SP-LS) is a powerful new sensing SPR modality that yields excellent sensitivity in sandwich immunoassay using spherical gold nanoparticle (AuNP) tags. Towards further improving the performance of SP-LS, we systematically investigated the AuNP size effect. Simulation results indicated an AuNP size-dependent scattered power, and predicted the optimized AuNPs sizes (i.e., 100 and 130 nm) that afford extremely high signal enhancement in SP-LS. The maximum scattered power from a 130 nm AuNP is about 1700-fold higher than that obtained from a 17 nm AuNP. Experimentally, a bio-conjugation protocol was developed by coating the AuNPs with mixture of low and high molecular weight PEG molecules. Optimal IgG antibody bioconjugation conditions were identified using physicochemical characterization and a model dot-blot assay. Aggregation prevented the use of the larger AuNPs in SP-LS experiments. As predicted by simulation, AuNPs with diameters of 50 and 64 nm yielded significantly higher SP-LS signal enhancement in comparison to the smaller particles. Finally, we demonstrated the feasibility of a two-step SP-LS protocol based on a gold enhancement step, aimed at enlarging 36 nm AuNPs tags. This study provides a blue-print for the further development of SP-LS biosensing and its translation in the bioanalytical field.
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Affiliation(s)
- Chih-Tsung Yang
- Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes 5095, Australia.
| | - Yi Xu
- Electronics and Photonics Department, Institute of High Performance Computing, Agency for Science, Technology, and Research (A*STAR), Singapore 138632, Singapore.
- SUTD-MIT International Design Center & Science and Math Cluster, Singapore University of Technology and Design, Singapore 487372, Singapore.
| | - Mohammad Pourhassan-Moghaddam
- School of Biomedical Engineering, University of Technology Sydney, Sydney 2007, Australia.
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia.
| | - Duy Phu Tran
- Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes 5095, Australia.
| | - Lin Wu
- Electronics and Photonics Department, Institute of High Performance Computing, Agency for Science, Technology, and Research (A*STAR), Singapore 138632, Singapore.
| | - Xin Zhou
- Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China.
| | - Benjamin Thierry
- Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes 5095, Australia.
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