51
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Chen H, Yu J, Zhang J, Sun K, Ding Z, Jiang Y, Hu Q, Wu C, Chiu DT. Monitoring Metabolites Using an NAD(P)H‐sensitive Polymer Dot and a Metabolite‐Specific Enzyme. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Haobin Chen
- Department of Chemistry and Bioengineering University of Washington Seattle WA 98195 USA
| | - Jiangbo Yu
- Department of Chemistry and Bioengineering University of Washington Seattle WA 98195 USA
| | - Jicheng Zhang
- Department of Chemistry and Bioengineering University of Washington Seattle WA 98195 USA
| | - Kai Sun
- Department of Chemistry and Bioengineering University of Washington Seattle WA 98195 USA
| | - Zhaoyang Ding
- Department of Chemistry and Bioengineering University of Washington Seattle WA 98195 USA
| | - Yifei Jiang
- Department of Chemistry and Bioengineering University of Washington Seattle WA 98195 USA
| | - Qiongzheng Hu
- Department of Chemistry and Bioengineering University of Washington Seattle WA 98195 USA
| | - Changfeng Wu
- Department of Biomedical Engineering Southern University of Science and Technology Shenzhen Guangdong 510855 China
| | - Daniel T. Chiu
- Department of Chemistry and Bioengineering University of Washington Seattle WA 98195 USA
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52
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Chen H, Yu J, Zhang J, Sun K, Ding Z, Jiang Y, Hu Q, Wu C, Chiu DT. Monitoring Metabolites Using an NAD(P)H-sensitive Polymer Dot and a Metabolite-Specific Enzyme. Angew Chem Int Ed Engl 2021; 60:19331-19336. [PMID: 34146440 DOI: 10.1002/anie.202106156] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/06/2021] [Indexed: 12/24/2022]
Abstract
We introduce an NAD(P)H-sensitive polymer dot (Pdot) biosensor for point-of-care monitoring of metabolites. The Pdot is combined with a metabolite-specific NAD(P)H-dependent enzyme that catalyzes the oxidation of the metabolite, generating NAD(P)H. Upon UV illumination, the NAD(P)H quenches the fluorescence emission of Pdot at 627 nm via electron transfer, and also fluoresces at 458 nm, resulting in a shift from red to blue emission at higher NAD(P)H concentrations. Metabolite concentration is quantified ratiometrically-based on the ratio of blue-to-red channel emission intensities, with a digital camera-with high sensitivity and specificity. We demonstrate phenylalanine biosensing in human plasma for a phenylketonuria screening test, quantifying several other disease-related metabolites (lactate, glucose, glutamate, and β-hydroxybutyrate), and a paper-based assay with smartphore imaging for point-of-care use.
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Affiliation(s)
- Haobin Chen
- Department of Chemistry and Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Jiangbo Yu
- Department of Chemistry and Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Jicheng Zhang
- Department of Chemistry and Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Kai Sun
- Department of Chemistry and Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Zhaoyang Ding
- Department of Chemistry and Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Yifei Jiang
- Department of Chemistry and Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Qiongzheng Hu
- Department of Chemistry and Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Changfeng Wu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 510855, China
| | - Daniel T Chiu
- Department of Chemistry and Bioengineering, University of Washington, Seattle, WA, 98195, USA
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53
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Delamarche E, Temiz Y, Lovchik RD, Christiansen MG, Schuerle S. Capillary Microfluidics for Monitoring Medication Adherence. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Yuksel Temiz
- IBM Research Europe Saeumerstrasse 4 Rueschlikon Switzerland
| | | | - Michael G. Christiansen
- Institute for Translational Medicine Department of Health Sciences and Technology ETH Zurich Vladimir-Prelog-Weg 1–5/10 8092 Zurich Switzerland
| | - Simone Schuerle
- Institute for Translational Medicine Department of Health Sciences and Technology ETH Zurich Vladimir-Prelog-Weg 1–5/10 8092 Zurich Switzerland
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Engineering with NanoLuc: a playground for the development of bioluminescent protein switches and sensors. Biochem Soc Trans 2021; 48:2643-2655. [PMID: 33242085 DOI: 10.1042/bst20200440] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022]
Abstract
The small engineered luciferase NanoLuc has rapidly become a powerful tool in the fields of biochemistry, chemical biology, and cell biology due to its exceptional brightness and stability. The continuously expanding NanoLuc toolbox has been employed in applications ranging from biosensors to molecular and cellular imaging, and currently includes split complementation variants, engineering techniques for spectral tuning, and bioluminescence resonance energy transfer-based concepts. In this review, we provide an overview of state-of-the-art NanoLuc-based sensors and switches with a focus on the underlying protein engineering approaches. We discuss the advantages and disadvantages of various strategies with respect to sensor sensitivity, modularity, and dynamic range of the sensor and provide a perspective on future strategies and applications.
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55
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A plug-and-play platform of ratiometric bioluminescent sensors for homogeneous immunoassays. Nat Commun 2021; 12:4586. [PMID: 34321486 PMCID: PMC8319308 DOI: 10.1038/s41467-021-24874-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 07/08/2021] [Indexed: 01/07/2023] Open
Abstract
Heterogeneous immunoassays such as ELISA have become indispensable in modern bioanalysis, yet translation into point-of-care assays is hindered by their dependence on external calibration and multiple washing and incubation steps. Here, we introduce RAPPID (Ratiometric Plug-and-Play Immunodiagnostics), a mix-and-measure homogeneous immunoassay platform that combines highly specific antibody-based detection with a ratiometric bioluminescent readout. The concept entails analyte-induced complementation of split NanoLuc luciferase fragments, photoconjugated to an antibody sandwich pair via protein G adapters. Introduction of a calibrator luciferase provides a robust ratiometric signal that allows direct in-sample calibration and quantitative measurements in complex media such as blood plasma. We developed RAPPID sensors that allow low-picomolar detection of several protein biomarkers, anti-drug antibodies, therapeutic antibodies, and both SARS-CoV-2 spike protein and anti-SARS-CoV-2 antibodies. With its easy-to-implement standardized workflow, RAPPID provides an attractive, fast, and low-cost alternative to traditional immunoassays, in an academic setting, in clinical laboratories, and for point-of-care applications. Many current immunoassays require multiple washing, incubation and optimization steps. Here the authors present Ratiometric Plug-and-Play Immunodiagnostics (RAPPID), a generic assay platform that uses ratiometric bioluminescent detection to allow sandwich immunoassays to be performed directly in solution.
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56
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Stroppel AS, Lappalainen R, Stafforst T. Controlling Site-Directed RNA Editing by Chemically Induced Dimerization. Chemistry 2021; 27:12300-12304. [PMID: 34169589 PMCID: PMC8456898 DOI: 10.1002/chem.202101985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Indexed: 11/24/2022]
Abstract
Various RNA‐targeting approaches have been engineered to modify specific sites on endogenous transcripts, breaking new ground for a variety of basic research tools and promising clinical applications in the future. Here, we combine site‐directed adenosine‐to‐inosine RNA editing with chemically induced dimerization. Specifically, we achieve tight and dose‐dependent control of the editing reaction with gibberellic acid, and obtain editing yields up to 20 % and 44 % in the endogenous STAT1 and GAPDH transcript in cell culture. Furthermore, the disease‐relevant MECP2 R106Q mutation was repaired with editing yields up to 42 %. The introduced principle will enable new applications where temporal or spatiotemporal control of an RNA‐targeting mechanism is desired.
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Affiliation(s)
- Anna S Stroppel
- Interfaculty Institute of Biochemistry, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Ruth Lappalainen
- Interfaculty Institute of Biochemistry, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Thorsten Stafforst
- Interfaculty Institute of Biochemistry, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
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57
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Establishment of live-cell-based coupled assay system for identification of compounds to modulate metabolic activities of cells. Cell Rep 2021; 36:109311. [PMID: 34233188 DOI: 10.1016/j.celrep.2021.109311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 03/29/2021] [Accepted: 06/04/2021] [Indexed: 12/29/2022] Open
Abstract
In this study, we present a live-cell-based fluorometric coupled assay system to identify the compounds that can regulate the targeted metabolic pathways in live cells. The assay is established through targeting specific metabolic pathways and using "input" and "output" metabolite pairs. The changes in the extracellular output that are generated and released into the extracellular media from the input are assessed as the activity of the pathway. The screening for the glycolytic pathway and amino acid metabolism reveals the activities of the present drugs, 6-BIO and regorafenib, that regulate the metabolic fate of tumor cells.
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58
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Tsai YH, Doura T, Kiyonaka S. Tethering-based chemogenetic approaches for the modulation of protein function in live cells. Chem Soc Rev 2021; 50:7909-7923. [PMID: 34114579 DOI: 10.1039/d1cs00059d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Proteins are the workhorse molecules performing various tasks to sustain life. To investigate the roles of a protein under physiological conditions, the rapid modulation of the protein with high specificity in a living system would be ideal, but achieving this is often challenging. To address this challenge, researchers have developed chemogenetic strategies for the rapid and selective modulation of protein function in live cells. Here, the target protein is modified genetically to become sensitive to a designer molecule that otherwise has no effect on other cellular biomolecules. One powerful chemogenetic strategy is to introduce a tethering point into the target protein, allowing covalent or non-covalent attachment of the designer molecule. In this tutorial review, we focus on tethering-based chemogenetic approaches for modulating protein function in live cells. We first describe genetic, optogenetic and chemical means to study protein function. These means lay the basis for the chemogenetic concept, which is explained in detail. The next section gives an overview, including advantages and limitations, of tethering tactics that have been employed for modulating cellular protein function. The third section provides examples of the modulation of cell-surface proteins using tethering-based chemogenetics through non-covalent tethering and covalent tethering for irreversible modulation or functional switching. The fourth section presents intracellular examples. The last section summarizes key considerations in implementing tethering-based chemogenetics and shows perspectives highlighting future directions and other applications of this burgeoning research field.
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Affiliation(s)
- Yu-Hsuan Tsai
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen 518132, China.
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59
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Delamarche E, Temiz Y, Lovchik RD, Christiansen MG, Schuerle S. Capillary Microfluidics for Monitoring Medication Adherence. Angew Chem Int Ed Engl 2021; 60:17784-17796. [PMID: 33710725 DOI: 10.1002/anie.202101316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/08/2021] [Indexed: 02/06/2023]
Abstract
Medication adherence is a medical and societal issue worldwide, with approximately half of patients failing to adhere to prescribed treatments. The goal of this Minireview is to examine how recent work on microfluidics for point-of-care diagnostics may be used to enhance adherence to medication. It specifically focuses on capillary microfluidics since these devices are self-powered, easy to use, and well established for diagnostics and drug monitoring. Considering that an improvement in medication adherence can have a much larger effect than the development of new medical treatments, it is long overdue for the research communities working in chemistry, biology, pharmacology, and material sciences to consider developing technologies to enhance medication adherence. For these reasons, this Minireview is not meant to be exhaustive but rather to provide a quick starting point for researchers interested in joining this complex but intriguing and exciting field of research.
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Affiliation(s)
| | - Yuksel Temiz
- IBM Research Europe, Saeumerstrasse 4, Rueschlikon, Switzerland
| | | | - Michael G Christiansen
- Institute for Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8092, Zurich, Switzerland
| | - Simone Schuerle
- Institute for Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8092, Zurich, Switzerland
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60
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Selection of fluorescent biosensors against galectin-3 from an NBD-modified phage library displaying designed α-helical peptides. Bioorg Med Chem Lett 2021; 37:127835. [PMID: 33556574 DOI: 10.1016/j.bmcl.2021.127835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 10/22/2022]
Abstract
Fluorescent biosensors are indispensable tools for molecular imaging, detection, and drug screening. Conventionally, fluorescent biosensors were constructed by incorporating fluorophores into ligands. Here, to develop ligand-independent biosensors, we demonstrated biosensor selection from a fluorophore-modified peptide phage library. In this library, the peptides were designed to form α-helical structures, and one cysteine, the probe modification site, was located at the center of four randomized residues on the same face of the helix. By conjugation with 4-nitrobenzoxadiazole (NBD), we constructed an NBD-modified phage library. We conducted selection against galectin-3 (Gal-3), a galactose-specific lectin associated with various biological events such as tumor metastasis and insulin resistance. After biopanning, we obtained NBD-modified peptides that selectively bind to Gal-3 from the library. The fluorescence intensity of the hit biosensors increased with the concentration of Gal-3, and this fluorescent response was visually observed.
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61
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Abstract
The field of single nanoparticle plasmonics has grown enormously. There is no doubt that a wide diversity of the nanoplasmonic techniques and nanostructures represents a tremendous opportunity for fundamental biomedical studies as well as sensing and imaging applications. Single nanoparticle plasmonic biosensors are efficient in label-free single-molecule detection, as well as in monitoring real-time binding events of even several biomolecules. In the present review, we have discussed the prominent advantages and advances in single particle characterization and synthesis as well as new insight into and information on biomedical diagnosis uniquely obtained using single particle approaches. The approaches include the fundamental studies of nanoplasmonic behavior, two typical methods based on refractive index change and characteristic light intensity change, exciting innovations of synthetic strategies for new plasmonic nanostructures, and practical applications using single particle sensing, imaging, and tracking. The basic sphere and rod nanostructures are the focus of extensive investigations in biomedicine, while they can be programmed into algorithmic assemblies for novel plasmonic diagnosis. Design of single nanoparticles for the detection of single biomolecules will have far-reaching consequences in biomedical diagnosis.
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Affiliation(s)
- Xingyi Ma
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Korea.
| | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Korea.
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62
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Hall MP, Kincaid VA, Jost EA, Smith TP, Hurst R, Forsyth SK, Fitzgerald C, Ressler VT, Zimmermann K, Lazar D, Wood MG, Wood KV, Kirkland TA, Encell LP, Machleidt T, Dart ML. Toward a Point-of-Need Bioluminescence-Based Immunoassay Utilizing a Complete Shelf-Stable Reagent. Anal Chem 2021; 93:5177-5184. [PMID: 33730483 DOI: 10.1021/acs.analchem.0c05074] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enzyme-linked immunosorbent assays (ELISAs) are used extensively for the detection and quantification of biomolecules in clinical diagnostics as well as in basic research. Although broadly used, the inherent complexities of ELISAs preclude their utility for straightforward point-of-need testing, where speed and simplicity are essential. With this in mind, we developed a bioluminescence-based immunoassay format that provides a sensitive and simple method for detecting biomolecules in clinical samples. We utilized a ternary, split-NanoLuc luciferase complementation reporter consisting of two small peptides (11mer, 13mer) and a 17 kDa polypeptide combined with a luminogenic substrate to create a complete, shelf-stable add-and-read assay detection reagent. Directed evolution was used to optimize reporter constituent sequences to impart chemical and thermal stability, as well as solubility, while formulation optimization was applied to stabilize an all-in-one reagent that can be reconstituted in aqueous buffers or sample matrices. The result of these efforts is a robust, first-generation bioluminescence-based homogenous immunoassay reporter platform where all assay components can be configured into a stable lyophilized cake, supporting homogeneous, rapid, and sensitive one-step biomolecule quantification in complex human samples. This technology represents a promising alternative immunoassay format with significant potential to bring critical diagnostic molecular detection testing closer to the point-of-need.
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Affiliation(s)
- Mary P Hall
- Promega Corporation, Madison, Wisconsin 53711, United States
| | | | - Emily A Jost
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Thomas P Smith
- Promega Biosciences LLC, San Luis Obispo, California 93401, United States
| | - Robin Hurst
- Promega Corporation, Madison, Wisconsin 53711, United States
| | | | - Connor Fitzgerald
- Promega Biosciences LLC, San Luis Obispo, California 93401, United States
| | | | - Kris Zimmermann
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Dan Lazar
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Monika G Wood
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Keith V Wood
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Thomas A Kirkland
- Promega Biosciences LLC, San Luis Obispo, California 93401, United States
| | - Lance P Encell
- Promega Corporation, Madison, Wisconsin 53711, United States
| | | | - Melanie L Dart
- Promega Corporation, Madison, Wisconsin 53711, United States
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63
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Quijano-Rubio A, Yeh HW, Park J, Lee H, Langan RA, Boyken SE, Lajoie MJ, Cao L, Chow CM, Miranda MC, Wi J, Hong HJ, Stewart L, Oh BH, Baker D. De novo design of modular and tunable protein biosensors. Nature 2021; 591:482-487. [PMID: 33503651 PMCID: PMC8074680 DOI: 10.1038/s41586-021-03258-z] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 01/19/2021] [Indexed: 01/30/2023]
Abstract
Naturally occurring protein switches have been repurposed for the development of biosensors and reporters for cellular and clinical applications1. However, the number of such switches is limited, and reengineering them is challenging. Here we show that a general class of protein-based biosensors can be created by inverting the flow of information through de novo designed protein switches in which the binding of a peptide key triggers biological outputs of interest2. The designed sensors are modular molecular devices with a closed dark state and an open luminescent state; analyte binding drives the switch from the closed to the open state. Because the sensor is based on the thermodynamic coupling of analyte binding to sensor activation, only one target binding domain is required, which simplifies sensor design and allows direct readout in solution. We create biosensors that can sensitively detect the anti-apoptosis protein BCL-2, the IgG1 Fc domain, the HER2 receptor, and Botulinum neurotoxin B, as well as biosensors for cardiac troponin I and an anti-hepatitis B virus antibody with the high sensitivity required to detect these molecules clinically. Given the need for diagnostic tools to track the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)3, we used the approach to design sensors for the SARS-CoV-2 spike protein and antibodies against the membrane and nucleocapsid proteins. The former, which incorporates a de novo designed spike receptor binding domain (RBD) binder4, has a limit of detection of 15 pM and a luminescence signal 50-fold higher than the background level. The modularity and sensitivity of the platform should enable the rapid construction of sensors for a wide range of analytes, and highlights the power of de novo protein design to create multi-state protein systems with new and useful functions.
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Affiliation(s)
- Alfredo Quijano-Rubio
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA,Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA
| | - Hsien-Wei Yeh
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Jooyoung Park
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Hansol Lee
- Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Robert A. Langan
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Scott E. Boyken
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Marc J. Lajoie
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Longxing Cao
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Cameron M. Chow
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Marcos C. Miranda
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Jimin Wi
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Hyo Jeong Hong
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Lance Stewart
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Byung-Ha Oh
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA,Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea,Correspondence and requests for materials should be addressed to D.B. or B.-H.O
| | - David Baker
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA,Correspondence and requests for materials should be addressed to D.B. or B.-H.O
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64
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Liu F, Chen R, Song W, Li L, Lei C, Nie Z. Modular Combination of Proteolysis-Responsive Transcription and Spherical Nucleic Acids for Smartphone-Based Colorimetric Detection of Protease Biomarkers. Anal Chem 2021; 93:3517-3525. [DOI: 10.1021/acs.analchem.0c04894] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Fang Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Ru Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Wenlu Song
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Liangwen Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
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65
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Weihs F, Anderson A, Trowell S, Caron K. Resonance Energy Transfer-Based Biosensors for Point-of-Need Diagnosis-Progress and Perspectives. SENSORS (BASEL, SWITZERLAND) 2021; 21:660. [PMID: 33477883 PMCID: PMC7833371 DOI: 10.3390/s21020660] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/08/2021] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
The demand for point-of-need (PON) diagnostics for clinical and other applications is continuing to grow. Much of this demand is currently serviced by biosensors, which combine a bioanalytical sensing element with a transducing device that reports results to the user. Ideally, such devices are easy to use and do not require special skills of the end user. Application-dependent, PON devices may need to be capable of measuring low levels of analytes very rapidly, and it is often helpful if they are also portable. To date, only two transduction modalities, colorimetric lateral flow immunoassays (LFIs) and electrochemical assays, fully meet these requirements and have been widely adopted at the point-of-need. These modalities are either non-quantitative (LFIs) or highly analyte-specific (electrochemical glucose meters), therefore requiring considerable modification if they are to be co-opted for measuring other biomarkers. Förster Resonance Energy Transfer (RET)-based biosensors incorporate a quantitative and highly versatile transduction modality that has been extensively used in biomedical research laboratories. RET-biosensors have not yet been applied at the point-of-need despite its advantages over other established techniques. In this review, we explore and discuss recent developments in the translation of RET-biosensors for PON diagnoses, including their potential benefits and drawbacks.
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Affiliation(s)
- Felix Weihs
- CSIRO Health & Biosecurity, Parkville, 343 Royal Parade, Melbourne, VIC 3030, Australia;
| | - Alisha Anderson
- CSIRO Health & Biosecurity, Black Mountain, Canberra, ACT 2600, Australia;
| | - Stephen Trowell
- PPB Technology Pty Ltd., Centre for Entrepreneurial Agri-Technology, Australian National University, Canberra, ACT 2601, Australia;
| | - Karine Caron
- CSIRO Health & Biosecurity, Black Mountain, Canberra, ACT 2600, Australia;
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66
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Pan MM, Wang YF, Wang L, Yu X, Xu L. Recent advances in visual detection for cancer biomarkers and infectious pathogens. J Mater Chem B 2021; 9:35-52. [PMID: 33225338 DOI: 10.1039/d0tb01883j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
It is an urgency to detect infectious pathogens or cancer biomarkers using rapid, simple, convenient and cost-effective methods in complex biological samples. Many existing approaches (traditional virus culture, ELISA or PCR) for the pathogen and biomarker assays face several challenges in the clinical applications that require lengthy time, sophisticated sample pre-treatment and expensive instruments. Due to the simple and rapid detection manner as well as no requirement of expensive equipment, many visual detection methods have been considered to resolve the aforementioned problems. Meanwhile, various new materials and colorimetric/fluorescent methods have been tried to construct new biosensors for infectious pathogens and biomarkers. However, the recent progress of these aspects is rarely reviewed, especially in terms of integration of new materials, microdevice and detection mechanism into the visual detection systems. Herein, we provide a broad field of view to discuss the recent progress in the visual detection of infectious pathogens and cancer biomarkers along with the detection mechanism, new materials, novel detection methods, special targets as well as multi-functional microdevices and systems. The novel visual approaches for the infectious pathogens and biomarkers, such as bioluminescence resonance energy transfer (BRET), metal-induced metallization and clustered regularly interspaced short palindromic repeats (CRISPR)-based biosensors, are discussed. Additionally, recent advancements in visual assays utilizing various new materials for proteins, nucleic acids, viruses, exosomes and small molecules are comprehensively reviewed. Future perspectives on the visual sensing systems for infectious pathogens and cancers are also proposed.
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Affiliation(s)
- Meng-Meng Pan
- Tongji School of Pharmacy, HuaZhong University of Science and Technology, Wuhan 430030, China.
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67
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Gräwe A, Stein V. Linker Engineering in the Context of Synthetic Protein Switches and Sensors. Trends Biotechnol 2020; 39:731-744. [PMID: 33293101 DOI: 10.1016/j.tibtech.2020.11.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 12/17/2022]
Abstract
Linkers play critical roles in the construction of synthetic protein switches and sensors as they functionally couple a receptor with an actuator. With an increasing number of molecular toolboxes and experimental strategies becoming available that can be applied to engineer protein switches and sensors with tailored response functions, optimising the connecting linkers remains an idiosyncratic and empiric process. This review aims to provide an in-depth analysis of linker motifs, the biophysical properties they confer, and how they impact the performance of synthetic protein switches and sensors while identifying trends, mechanisms, and strategies that underlie the most potent switches and sensors.
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Affiliation(s)
- Alexander Gräwe
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany; Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany
| | - Viktor Stein
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany; Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany.
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68
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Abstract
Biological signaling pathways are underpinned by protein switches that sense and respond to molecular inputs. Inspired by nature, engineered protein switches have been designed to directly transduce analyte binding into a quantitative signal in a simple, wash-free, homogeneous assay format. As such, they offer great potential to underpin point-of-need diagnostics that are needed across broad sectors to improve access, costs, and speed compared to laboratory assays. Despite this, protein switch assays are not yet in routine diagnostic use, and a number of barriers to uptake must be overcome to realize this potential. Here, we review the opportunities and challenges in engineering protein switches for rapid diagnostic tests. We evaluate how their design, comprising a recognition element, reporter, and switching mechanism, relates to performance and identify areas for improvement to guide further optimization. Recent modular switches that enable new analytes to be targeted without redesign are crucial to ensure robust and efficient development processes. The importance of translational steps toward practical implementation, including integration into a user-friendly device and thorough assay validation, is also discussed.
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Affiliation(s)
- Hope Adamson
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Lars J. C. Jeuken
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
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69
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Zhou X, Mehta S, Zhang J. Genetically Encodable Fluorescent and Bioluminescent Biosensors Light Up Signaling Networks. Trends Biochem Sci 2020; 45:889-905. [PMID: 32660810 PMCID: PMC7502535 DOI: 10.1016/j.tibs.2020.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 12/12/2022]
Abstract
Cell signaling networks are intricately regulated in time and space to determine the responses and fates of cells to different cues. Genetically encodable fluorescent and bioluminescent biosensors enable the direct visualization of these spatiotemporal signaling dynamics within the native biological context, and have therefore become powerful molecular tools whose unique benefits are being used to address challenging biological questions. We first review the basis of biosensor design and remark on recent technologies that are accelerating biosensor development. We then discuss a few of the latest advances in the development and application of genetically encodable fluorescent and bioluminescent biosensors that have led to scientific or technological breakthroughs.
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Affiliation(s)
- Xin Zhou
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
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70
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Tiedt S, Brandmaier S, Kollmeier H, Duering M, Artati A, Adamski J, Klein M, Liebig T, Holdt LM, Teupser D, Wang-Sattler R, Schwedhelm E, Gieger C, Dichgans M. Circulating Metabolites Differentiate Acute Ischemic Stroke from Stroke Mimics. Ann Neurol 2020; 88:736-746. [PMID: 32748431 DOI: 10.1002/ana.25859] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Early discrimination of patients with ischemic stroke (IS) from stroke mimics (SMs) poses a diagnostic challenge. The circulating metabolome might reflect pathophysiological events related to acute IS. Here, we investigated the utility of early metabolic changes for differentiating IS from SM. METHODS We performed untargeted metabolomics on serum samples obtained from patients with IS (N = 508) and SM (N = 349; defined by absence of a diffusion weighted imaging [DWI] positive lesion on magnetic resonance imaging [MRI]) who presented to the hospital within 24 hours after symptom onset (median time from symptom onset to blood sampling = 3.3 hours; interquartile range [IQR] = 1.6-6.7 hours) and from neurologically normal controls (NCs; N = 112). We compared diagnostic groups in a discovery-validation approach by applying multivariable linear regression models, machine learning techniques, and propensity score matching. We further performed a targeted look-up of published metabolite sets. RESULTS Levels of 41 metabolites were significantly associated with IS compared to NCs. The top metabolites showing the highest value in separating IS from SMs were asymmetrical and symmetrical dimethylarginine, pregnenolone sulfate, and adenosine. Together, these 4 metabolites differentiated patients with IS from SMs with an area under the curve (AUC) of 0.90 in the replication sample, which was superior to multimodal cranial computed tomography (CT; AUC = 0.80) obtained for routine diagnostics. They were further superior to previously published metabolite sets detected in our samples. All 4 metabolites returned to control levels by day 90. INTERPRETATION A set of 4 metabolites with known biological effects relevant to stroke pathophysiology shows unprecedented utility to identify patients with IS upon hospital arrival, thus encouraging further investigation, including multicenter studies. ANN NEUROL 2020;88:736-746.
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Affiliation(s)
- Steffen Tiedt
- Institute for Stroke and Dementia Research, University Hospital, LMU Munich, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Stefan Brandmaier
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Hanna Kollmeier
- Institute for Stroke and Dementia Research, University Hospital, LMU Munich, Munich, Germany
| | - Marco Duering
- Institute for Stroke and Dementia Research, University Hospital, LMU Munich, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Anna Artati
- Research Unit Molecular Endocrinology and Metabolism, Genome Analysis Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jerzy Adamski
- Research Unit Molecular Endocrinology and Metabolism, Genome Analysis Center, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Experimental Genetics, Technical University of Munich, Freising, Germany.,German Center for Diabetes Research (DZD), Munich, Germany.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Matthias Klein
- Department of Neurology, University Hospital, LMU Munich, Munich, Germany
| | - Thomas Liebig
- Institute of Neuroradiology, University Hospital, LMU Munich, Munich, Germany
| | - Lesca M Holdt
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Daniel Teupser
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Rui Wang-Sattler
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Munich, Germany
| | - Edzard Schwedhelm
- Institute of Clinical Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Hamburg / Kiel / Lübeck, Hamburg, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Munich, Germany
| | - Martin Dichgans
- Institute for Stroke and Dementia Research, University Hospital, LMU Munich, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
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71
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Love AC, Prescher JA. Seeing (and Using) the Light: Recent Developments in Bioluminescence Technology. Cell Chem Biol 2020; 27:904-920. [PMID: 32795417 PMCID: PMC7472846 DOI: 10.1016/j.chembiol.2020.07.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/10/2020] [Accepted: 07/24/2020] [Indexed: 02/08/2023]
Abstract
Bioluminescence has long been used to image biological processes in vivo. This technology features luciferase enzymes and luciferin small molecules that produce visible light. Bioluminescent photons can be detected in tissues and live organisms, enabling sensitive and noninvasive readouts on physiological function. Traditional applications have focused on tracking cells and gene expression patterns, but new probes are pushing the frontiers of what can be visualized. The past few years have also seen the merger of bioluminescence with optogenetic platforms. Luciferase-luciferin reactions can drive light-activatable proteins, ultimately triggering signal transduction and other downstream events. This review highlights these and other recent advances in bioluminescence technology, with an emphasis on tool development. We showcase how new luciferins and engineered luciferases are expanding the scope of optical imaging. We also highlight how bioluminescent systems are being leveraged not just for sensing-but also controlling-biological processes.
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Affiliation(s)
- Anna C Love
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Jennifer A Prescher
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA.
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72
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Quijano-Rubio A, Yeh HW, Park J, Lee H, Langan RA, Boyken SE, Lajoie MJ, Cao L, Chow CM, Miranda MC, Wi J, Hong HJ, Stewart L, Oh BH, Baker D. De novo design of modular and tunable allosteric biosensors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32743576 DOI: 10.1101/2020.07.18.206946] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Naturally occurring allosteric protein switches have been repurposed for developing novel biosensors and reporters for cellular and clinical applications 1 , but the number of such switches is limited, and engineering them is often challenging as each is different. Here, we show that a very general class of allosteric protein-based biosensors can be created by inverting the flow of information through de novo designed protein switches in which binding of a peptide key triggers biological outputs of interest 2 . Using broadly applicable design principles, we allosterically couple binding of protein analytes of interest to the reconstitution of luciferase activity and a bioluminescent readout through the association of designed lock and key proteins. Because the sensor is based purely on thermodynamic coupling of analyte binding to switch activation, only one target binding domain is required, which simplifies sensor design and allows direct readout in solution. We demonstrate the modularity of this platform by creating biosensors that, with little optimization, sensitively detect the anti-apoptosis protein Bcl-2, the hIgG1 Fc domain, the Her2 receptor, and Botulinum neurotoxin B, as well as biosensors for cardiac Troponin I and an anti-Hepatitis B virus (HBV) antibody that achieve the sub-nanomolar sensitivity necessary to detect clinically relevant concentrations of these molecules. Given the current need for diagnostic tools for tracking COVID-19 3 , we use the approach to design sensors of antibodies against SARS-CoV-2 protein epitopes and of the receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein. The latter, which incorporates a de novo designed RBD binder, has a limit of detection of 15pM with an up to seventeen fold increase in luminescence upon addition of RBD. The modularity and sensitivity of the platform should enable the rapid construction of sensors for a wide range of analytes and highlights the power of de novo protein design to create multi-state protein systems with new and useful functions.
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73
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Broch F, Gautier A. Illuminating Cellular Biochemistry: Fluorogenic Chemogenetic Biosensors for Biological Imaging. Chempluschem 2020; 85:1487-1497. [PMID: 32644262 DOI: 10.1002/cplu.202000413] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/18/2020] [Indexed: 12/19/2022]
Abstract
Cellular activity is defined by the precise spatiotemporal regulation of various components, such as ions, small molecules, or proteins. Studying cell physiology consequently requires the optical recording of these processes, notably by using fluorescent biosensors. The recent development of various fluorogenic systems greatly expanded the palette of reporters to be included in these sensors design. Fluorogenic reporters consist of a protein or RNA tag that can complex either an endogenous or a synthetic fluorogenic dye (so-called fluorogen). The intrinsic nature of these tags, along with the high tunability of their cognate chromophore provide interesting features such as far-red to near-infrared emission, oxygen independence, or unprecedented color versatility. These engineered photoreceptors, self-labelling proteins, or noncovalent aptamers and protein tags were rapidly identified as promising reporters to observe biological events. This Minireview focuses on the new perspectives they offer to design unique and innovative biosensors, thus pushing the boundaries of cellular imaging.
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Affiliation(s)
- Fanny Broch
- Sorbonne Université, École normale supérieure, PSL University, CNRS Laboratoire des biomolécules, LBM, 75005, Paris, France
| | - Arnaud Gautier
- Sorbonne Université, École normale supérieure, PSL University, CNRS Laboratoire des biomolécules, LBM, 75005, Paris, France.,Institut Universitaire de France, France
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74
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Tomimuro K, Tenda K, Ni Y, Hiruta Y, Merkx M, Citterio D. Thread-Based Bioluminescent Sensor for Detecting Multiple Antibodies in a Single Drop of Whole Blood. ACS Sens 2020; 5:1786-1794. [PMID: 32441095 DOI: 10.1021/acssensors.0c00564] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Antibodies are important biomarkers in clinical diagnostics in addition to being increasingly used for therapeutic purposes. Although numerous methods for their detection and quantification exist, they predominantly require benchtop instruments operated by specialists. To enable the detection of antibodies at point-of-care (POC), the development of simple and rapid assay methods independent of laboratory equipment is of high relevance. In this study, we demonstrate microfluidic thread-based analytical devices (μTADs) as a new platform for antibody detection by means of bioluminescence resonance energy-transfer (BRET) switching sensor proteins. The devices consist of vertically assembled layers including a blood separation membrane and a plastic film with a sewn-in cotton thread, onto which the BRET sensor proteins together with the substrate furimazine have been predeposited. In contrast to intensity-based signaling, the BRET mechanism enables time-independent, ratiometric readout of bioluminescence signals with a digital camera in a darkroom or a smartphone camera with a 3D-printed lens adapter. The device design allows spatially separated deposition of multiple bioluminescent proteins on a single sewn thread, enabling quantification of multiple antibodies in 5 μL of whole blood within 5 min. The bioluminescence response is independent of the applied sample volume within the range of 5-15 μL. Therefore, μTADs in combination with BRET-based sensor proteins represent user-friendly analytical tools for POC quantification of antibodies without any laboratory equipment in a finger prick (5 μL) of whole blood.
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Affiliation(s)
- Kosuke Tomimuro
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi,
Kohoku-ku, 223-8522 Yokohama, Japan
| | - Keisuke Tenda
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi,
Kohoku-ku, 223-8522 Yokohama, Japan
| | - Yan Ni
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Yuki Hiruta
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi,
Kohoku-ku, 223-8522 Yokohama, Japan
| | - Maarten Merkx
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi,
Kohoku-ku, 223-8522 Yokohama, Japan
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Daniel Citterio
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi,
Kohoku-ku, 223-8522 Yokohama, Japan
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75
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Gautier A, Tebo AG. Sensing cellular biochemistry with fluorescent chemical-genetic hybrids. Curr Opin Chem Biol 2020; 57:58-64. [PMID: 32580134 DOI: 10.1016/j.cbpa.2020.04.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/19/2020] [Accepted: 04/08/2020] [Indexed: 11/26/2022]
Abstract
Fluorescent biosensors are powerful tools for the detection of biochemical events inside cells with high spatiotemporal resolution. Biosensors based on fluorescent proteins often suffer from issues with photostability and brightness. On the other hand, hybrid, chemical-genetic systems present unique opportunities to combine the strengths of synthetic, organic chemistry with biological macromolecules to generate exquisitely tailored semisynthetic sensors.
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Affiliation(s)
- Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France; Institut Universitaire de France, France.
| | - Alison G Tebo
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France.
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76
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Moeyaert B, Dedecker P. Genetically encoded biosensors based on innovative scaffolds. Int J Biochem Cell Biol 2020; 125:105761. [PMID: 32504671 DOI: 10.1016/j.biocel.2020.105761] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022]
Abstract
Genetically encoded biosensors are indispensable tools for visualizing the spatiotemporal dynamics of analytes or processes in living cells in vitro and in vivo. Their widespread adaptation has gone hand in hand with the development of sensors for new analytes or processes and improved functionality and robustness. In this review, we highlight some of the recent advances in genetically encoded biosensor development, with a special focus on novel and innovative scaffolds that will lead to new possibilities in the future.
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Affiliation(s)
- Benjamien Moeyaert
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Heverlee, Belgium
| | - Peter Dedecker
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Heverlee, Belgium.
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77
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Liu J, Cai C, Wang Y, Liu Y, Huang L, Tian T, Yao Y, Wei J, Chen R, Zhang K, Liu B, Qian K. A Biomimetic Plasmonic Nanoreactor for Reliable Metabolite Detection. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1903730. [PMID: 32440487 PMCID: PMC7237842 DOI: 10.1002/advs.201903730] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/30/2020] [Accepted: 02/17/2020] [Indexed: 05/20/2023]
Abstract
Reliable monitoring of metabolites in biofluids is critical for diagnosis, treatment, and long-term management of various diseases. Although widely used, existing enzymatic metabolite assays face challenges in clinical practice primarily due to the susceptibility of enzyme activity to external conditions and the low sensitivity of sensing strategies. Inspired by the micro/nanoscale confined catalytic environment in living cells, the coencapsulation of oxidoreductase and metal nanoparticles within the nanopores of macroporous silica foams to fabricate all-in-one bio-nanoreactors is reported herein for use in surface-enhanced Raman scattering (SERS)-based metabolic assays. The enhancement of catalytical activity and stability of enzyme against high temperatures, long-time storage or proteolytic agents are demonstrated. The nanoreactors recognize and catalyze oxidation of the metabolite, and provide ratiometric SERS response in the presence of the enzymatic by-product H2O2, enabling sensitive metabolite quantification in a "sample in and answer out" manner. The nanoreactor makes any oxidoreductase-responsible metabolite a candidate for quantitative SERS sensing, as shown for glucose and lactate. Glucose levels of patients with bacterial infection are accurately analyzed with only 20 µL of cerebrospinal fluids, indicating the potential application of the nanoreactor in vitro clinical testing.
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Affiliation(s)
- Jiangang Liu
- Department of NeurosurgeryShanghai Children's HospitalMed‐X Research Institute and School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200062China
| | - Chenlei Cai
- Department of Medical OncologyShanghai Pulmonary HospitalTongji University School of MedicineShanghai200433China
| | - Yuning Wang
- Department of ChemistryInstitutes of Biomedical Sciences and State Key Lab of Molecular Engineering of PolymersFudan UniversityShanghai200438China
| | - Yu Liu
- Department of NeurosurgeryShanghai Children's HospitalMed‐X Research Institute and School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200062China
| | - Lin Huang
- Department of NeurosurgeryShanghai Children's HospitalMed‐X Research Institute and School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200062China
| | - Tongtong Tian
- Department of ChemistryInstitutes of Biomedical Sciences and State Key Lab of Molecular Engineering of PolymersFudan UniversityShanghai200438China
| | - Yuanyuan Yao
- Department of ChemistryInstitutes of Biomedical Sciences and State Key Lab of Molecular Engineering of PolymersFudan UniversityShanghai200438China
| | - Jia Wei
- Department of NeurosurgeryShanghai Children's HospitalMed‐X Research Institute and School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200062China
| | - Ruoping Chen
- Department of NeurosurgeryShanghai Children's HospitalMed‐X Research Institute and School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200062China
| | - Kun Zhang
- Department of NeurosurgeryShanghai Children's HospitalMed‐X Research Institute and School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200062China
| | - Baohong Liu
- Department of ChemistryInstitutes of Biomedical Sciences and State Key Lab of Molecular Engineering of PolymersFudan UniversityShanghai200438China
| | - Kun Qian
- Department of NeurosurgeryShanghai Children's HospitalMed‐X Research Institute and School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200062China
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78
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Yan J, van Smeden L, Merkx M, Zijlstra P, Prins MWJ. Continuous Small-Molecule Monitoring with a Digital Single-Particle Switch. ACS Sens 2020; 5:1168-1176. [PMID: 32189498 PMCID: PMC8177406 DOI: 10.1021/acssensors.0c00220] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
The
ability to continuously measure concentrations of small molecules
is important for biomedical, environmental, and industrial monitoring.
However, because of their low molecular mass, it is difficult to quantify
concentrations of such molecules, particularly at low concentrations.
Here, we describe a small-molecule sensor that is generalizable, sensitive,
specific, reversible, and suited for continuous monitoring over long
durations. The sensor consists of particles attached to a sensing
surface via a double-stranded DNA tether. The particles transiently
bind to the sensing surface via single-molecular affinity interactions,
and the transient binding is optically detected as digital binding
events via the Brownian motion of the particles. The rate of binding
events decreases with increasing analyte concentration because analyte
molecules inhibit binding of the tethered particle to the surface.
The sensor enables continuous measurements of analyte concentrations
because of the reversibility of the intermolecular bonds and digital
read-out of particle motion. We show results for the monitoring of
short single-stranded DNA sequences and creatinine, a small-molecule
biomarker (113 Da) for kidney function, demonstrating a temporal resolution
of a few minutes. The precision of the sensor is determined by the
statistics of the digital switching events, which means that the precision
is tunable by the number of particles and the measurement time.
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Affiliation(s)
- Junhong Yan
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
| | - Laura van Smeden
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
| | - Maarten Merkx
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
| | - Peter Zijlstra
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
| | - Menno W. J. Prins
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
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79
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Tian G, Zhang Z, Li H, Li D, Wang X, Qin C. Design, Synthesis and Application in Analytical Chemistry of Photo-Sensitive Probes Based on Coumarin. Crit Rev Anal Chem 2020; 51:565-581. [DOI: 10.1080/10408347.2020.1753163] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Guang Tian
- Department of Applied Chemistry, Shanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernomal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi’an, P. R. China
| | - Zixin Zhang
- Department of Applied Chemistry, Shanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernomal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi’an, P. R. China
| | - Haidi Li
- Department of Applied Chemistry, Shanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernomal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi’an, P. R. China
| | - Dongsheng Li
- Department of Applied Chemistry, Shanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernomal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi’an, P. R. China
| | - Xinrui Wang
- Department of Applied Chemistry, Shanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernomal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi’an, P. R. China
| | - Chuanguang Qin
- Department of Applied Chemistry, Shanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernomal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi’an, P. R. China
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80
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Chang D, Kim KT, Lindberg E, Winssinger N. Smartphone DNA or RNA Sensing Using Semisynthetic Luciferase-Based Logic Device. ACS Sens 2020; 5:807-813. [PMID: 32124606 DOI: 10.1021/acssensors.9b02454] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Detection of specific oligonucleotide sequences is central to numerous applications, and technologies amenable to point-of-care diagnostics or end users are needed. Here, we report a technology making use of a bioluminescent readout and smartphone quantification. The sensor is a semisynthetic luciferase (H-Luc-PNA conjugate) that is turned on by a strand-displacement reaction. We demonstrated sensing of three different microRNAs (miRs), as representative cancer biomarkers, and demonstrate the possibility to integrate an AND gate to sense two sequences simultaneously.
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Affiliation(s)
- Dalu Chang
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Ki Tae Kim
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Eric Lindberg
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
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81
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Smartphone-assisted robust enzymes@MOFs-based paper biosensor for point-of-care detection. Biosens Bioelectron 2020; 156:112095. [PMID: 32174563 DOI: 10.1016/j.bios.2020.112095] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/01/2020] [Accepted: 02/12/2020] [Indexed: 11/24/2022]
Abstract
Portable devices featured with fast analysis and affordable methodologies for clinical diagnostics have stimulated the rapid development of point-of-care (POC) technologies, potentially lowering the mortality rate. Herein, we demonstrated a portable, robust, and user-friendly intelligent metal-organic frameworks (MOFs) paper device, called smartphone-assisted biomimetic MOFs nanoreactor colorimetric paper (SBMCP), for on-demand POC detection of endogenous biomolecules. The concept of this paper platform was analogous to the intracellular cascades signal transduction, wherein the single/multiple enzymes components trapped within a ZIF-8 exoskeleton allowed the sensitive and selective recognition of target analyte via the accessible micropores network of ZIF-8, and then transferred the recognition event to a visual color signal based on the cascade reaction. Meanwhile, the ZIF-8 exoskeleton also endowed the enzymes with significantly elevated stability. As a result, this robust and portable SBMCP sensor enabled the on-site analysis of different important disease-related biomolecules through modulating the enzyme cascades, combining with a custom-designed smartphone application for signal readout. In the SBMCP assay, no sophisticated instruments or professional skill of the user was required, only 5 μL sample volume was needed, and the whole analysis process could be achieved within a portable MOFs paper and pervasive smartphone, endowing this new assay with the merits of low-cost, time-saving and easy-to-use. We demonstrated this SBMCP sensor was capable of real-time colorimetric detection of glucose and uric acid in diabetes and gout events. It is believed that this portable biosensor platform proposed herein potentially represents promising alternatives for POC diagnosis, especially applicable in developing world and resource-limited settings.
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82
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Farrants H, Tarnawski M, Müller TG, Otsuka S, Hiblot J, Koch B, Kueblbeck M, Kräusslich HG, Ellenberg J, Johnsson K. Chemogenetic Control of Nanobodies. Nat Methods 2020; 17:279-282. [PMID: 32066961 DOI: 10.1038/s41592-020-0746-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 12/01/2019] [Accepted: 01/15/2020] [Indexed: 12/30/2022]
Abstract
We introduce an engineered nanobody whose affinity to green fluorescent protein (GFP) can be switched on and off with small molecules. By controlling the cellular localization of GFP fusion proteins, the engineered nanobody allows interrogation of their roles in basic biological processes, an approach that should be applicable to numerous previously described GFP fusions. We also outline how the binding affinities of other nanobodies can be controlled by small molecules.
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Affiliation(s)
- Helen Farrants
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.,Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Miroslaw Tarnawski
- Protein Expression and Characterization Facility, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Thorsten G Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Shotaro Otsuka
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Max Perutz Labs, a joint venture of the University of Vienna and the Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Julien Hiblot
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Birgit Koch
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Moritz Kueblbeck
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany. .,Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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83
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Wentland L, Polaski R, Fu E. Characterization methods in porous materials for the rational design of multi-step processing in the context of a paper microfluidic phenylalanine test. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:768-780. [PMID: 34887944 PMCID: PMC8654261 DOI: 10.1039/c9ay02500f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A promising application of paper microfluidics is the translation of gold-standard multi-step laboratory tests to a disposable paper-based format for decentralized diagnostic or therapeutic testing. This often entails conversion of bench-top processing of macro-volume samples to the processing of micro-volume samples within a porous matrix, and requires detailed characterization of fluid and reagent interactions within the porous material(s) of the device. The current study focuses on rational device design through the characterization of fluid and reagent interactions in polysulfone and glass fiber substrates for multi-step sample processing. Specifically, we demonstrate how the characterization of fluidic compatibility between substrates, chemical compatibility between reagents and substrates, sample pH, and sample transport can be used to inform device design in the context of a two-reaction detection scheme for phenylalanine in porous materials. Finally, we demonstrate detection of phenylalanine from human whole blood, and discuss the multiple strengths of the current design over a previous version.
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Affiliation(s)
- Lael Wentland
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, OR 97331
| | - Rachel Polaski
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, OR 97331
| | - Elain Fu
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, OR 97331
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84
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Shi L, Yan C, Guo Z, Chi W, Wei J, Liu W, Liu X, Tian H, Zhu WH. De novo strategy with engineering anti-Kasha/Kasha fluorophores enables reliable ratiometric quantification of biomolecules. Nat Commun 2020; 11:793. [PMID: 32034152 PMCID: PMC7005775 DOI: 10.1038/s41467-020-14615-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 01/09/2020] [Indexed: 01/05/2023] Open
Abstract
Fluorescence-based technologies have revolutionized in vivo monitoring of biomolecules. However, significant technical hurdles in both probe chemistry and complex cellular environments have limited the accuracy of quantifying these biomolecules. Herein, we report a generalizable engineering strategy for dual-emission anti-Kasha-active fluorophores, which combine an integrated fluorescein with chromene (IFC) building block with donor-π-acceptor structural modification. These fluorophores exhibit an invariant near-infrared Kasha emission from the S1 state, while their anti-Kasha emission from the S2 state at around 520 nm can be finely regulated via a spirolactone open/closed switch. We introduce bio-recognition moieties to IFC structures, and demonstrate ratiometric quantification of cysteine and glutathione in living cells and animals, using the ratio (S2/S1) with the S1 emission as a reliable internal reference signal. This de novo strategy of tuning anti-Kasha-active properties expands the in vivo ratiometric quantification toolbox for highly accurate analysis in both basic life science research and clinical applications.
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Grants
- This work was supported by NSFC/China (21788102, 21636002, 21622602 and 21908060), National Key Research and Development Program (2017YFC0906902 and 2016YFA0200300), Shanghai Municipal Science and Technology Major Project (Grant 2018SHZDZX03), the Innovation Program of Shanghai Municipal Education Commission, Scientific Committee of Shanghai (15XD1501400), Programme of Introducing Talents of Discipline to Universities (B16017), the Shuguang Program (18SG27), the China Postdoctoral Science Foundation (2019M651417), and Singapore University of Technology and Design (SUTD) and the SUTD-MIT International Design Centre (IDC) [T1SRCI17126, IDG31800104]. The authors would like to acknowledge the use of the computing service of SUTD-MIT IDC and National Supercomputing Centre, Singapore.
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Affiliation(s)
- Limin Shi
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Chenxu Yan
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Zhiqian Guo
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Weijie Chi
- Science and Math Cluster, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
| | - Jingle Wei
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Weimin Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Xiaogang Liu
- Science and Math Cluster, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore.
| | - He Tian
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Wei-Hong Zhu
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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85
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Luo Z, Lv T, Zhu K, Li Y, Wang L, Gooding JJ, Liu G, Liu B. Paper‐Based Ratiometric Fluorescence Analytical Devices towards Point‐of‐Care Testing of Human Serum Albumin. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915046] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Zijie Luo
- Shenzhen Key Laboratory of Polymer Science and Technology College of Materials Science and Engineering Shenzhen University Shenzhen 518060 China
- Graduate School of Biomedical Engineering Faculty of Engineering Australian Centre for NanoMedicine University of New South Wales (UNSW) Sydney 2052 Australia
| | - Taoyuze Lv
- Shenzhen Key Laboratory of Polymer Science and Technology College of Materials Science and Engineering Shenzhen University Shenzhen 518060 China
| | - Kangning Zhu
- Shenzhen Key Laboratory of Polymer Science and Technology College of Materials Science and Engineering Shenzhen University Shenzhen 518060 China
| | - Yi Li
- Graduate School of Biomedical Engineering Faculty of Engineering Australian Centre for NanoMedicine University of New South Wales (UNSW) Sydney 2052 Australia
| | - Lei Wang
- Shenzhen Key Laboratory of Polymer Science and Technology College of Materials Science and Engineering Shenzhen University Shenzhen 518060 China
| | - J. Justin Gooding
- School of Chemistry Australian Centre for NanoMedicine and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology University of New South Wales Sydney 2052 Australia
| | - Guozhen Liu
- Graduate School of Biomedical Engineering Faculty of Engineering Australian Centre for NanoMedicine University of New South Wales (UNSW) Sydney 2052 Australia
| | - Bin Liu
- Shenzhen Key Laboratory of Polymer Science and Technology College of Materials Science and Engineering Shenzhen University Shenzhen 518060 China
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86
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Luo Z, Lv T, Zhu K, Li Y, Wang L, Gooding JJ, Liu G, Liu B. Paper‐Based Ratiometric Fluorescence Analytical Devices towards Point‐of‐Care Testing of Human Serum Albumin. Angew Chem Int Ed Engl 2020; 59:3131-3136. [DOI: 10.1002/anie.201915046] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Zijie Luo
- Shenzhen Key Laboratory of Polymer Science and Technology College of Materials Science and Engineering Shenzhen University Shenzhen 518060 China
- Graduate School of Biomedical Engineering Faculty of Engineering Australian Centre for NanoMedicine University of New South Wales (UNSW) Sydney 2052 Australia
| | - Taoyuze Lv
- Shenzhen Key Laboratory of Polymer Science and Technology College of Materials Science and Engineering Shenzhen University Shenzhen 518060 China
| | - Kangning Zhu
- Shenzhen Key Laboratory of Polymer Science and Technology College of Materials Science and Engineering Shenzhen University Shenzhen 518060 China
| | - Yi Li
- Graduate School of Biomedical Engineering Faculty of Engineering Australian Centre for NanoMedicine University of New South Wales (UNSW) Sydney 2052 Australia
| | - Lei Wang
- Shenzhen Key Laboratory of Polymer Science and Technology College of Materials Science and Engineering Shenzhen University Shenzhen 518060 China
| | - J. Justin Gooding
- School of Chemistry Australian Centre for NanoMedicine and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology University of New South Wales Sydney 2052 Australia
| | - Guozhen Liu
- Graduate School of Biomedical Engineering Faculty of Engineering Australian Centre for NanoMedicine University of New South Wales (UNSW) Sydney 2052 Australia
| | - Bin Liu
- Shenzhen Key Laboratory of Polymer Science and Technology College of Materials Science and Engineering Shenzhen University Shenzhen 518060 China
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87
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Song J, Zheng Y, Huang M, Wu L, Wang W, Zhu Z, Song Y, Yang C. A Sequential Multidimensional Analysis Algorithm for Aptamer Identification based on Structure Analysis and Machine Learning. Anal Chem 2020; 92:3307-3314. [PMID: 31876151 DOI: 10.1021/acs.analchem.9b05203] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Molecular recognition ligands are of great significance in many fields, but our ability to develop new recognition molecules remains to be expanded. Here, we developed a Sequential Multidimensional Analysis algoRiThm for aptamer discovery (SMART-Aptamer) from high-throughput sequencing (HTS) data of SELEX libraries based on multilevel structure analysis and unsupervised machine learning to discover nucleic acid recognition ligands with high accuracy and efficiency. We validated SMART-Aptamer with three sets of HTS data from screening pools against hESCs, EpCAM, and CSV. High affinity aptamers for all three targets were successfully obtained, and the results revealed that SMART-Aptamer is able to pick out high affinity aptamers with low false positive and negative rates. With the advantages of accuracy, efficiency, and robustness, SMART-Aptamer represents a paradigm-shift strategy for the discovery of binding ligands for a variety of biomedical applications.
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Affiliation(s)
- Jia Song
- Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Yuan Zheng
- Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Mengjiao Huang
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , 361005 , People's Republic of China
| | - Lingling Wu
- Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Wei Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Zhi Zhu
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , 361005 , People's Republic of China
| | - Yanling Song
- Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China.,State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , 361005 , People's Republic of China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China.,State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , 361005 , People's Republic of China
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88
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Idili A, Parolo C, Ortega G, Plaxco KW. Calibration-Free Measurement of Phenylalanine Levels in the Blood Using an Electrochemical Aptamer-Based Sensor Suitable for Point-of-Care Applications. ACS Sens 2019; 4:3227-3233. [PMID: 31789505 PMCID: PMC8097980 DOI: 10.1021/acssensors.9b01703] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
By analogy to the revolution the "home glucose monitor" created in the treatment of diabetes, the availability of a modular, "platform" technology able to measure nearly any metabolite, biomarker, or drug "at-home" in unprocessed, finger-prick volumes of whole blood could revolutionize the monitoring and treatment of disease. Thus motivated, we have adapted here the electrochemical aptamer-based sensing platform to the problem of rapidly and conveniently measuring the level of phenylalanine in the blood, an ability that would aid the monitoring and management of phenylketonuria (PKU). To achieve this, we exploited a previously reported DNA aptamer that recognizes phenylalanine in complex with a rhodium-based "receptor" that improves affinity. We re-engineered this to undergo a large-scale, binding-induced conformational change before modifying it with a methylene blue redox reporter and attaching it to a gold electrode that supports the appropriate electrochemical interrogation. The resultant sensor achieves a useful dynamic range of 90 nM to 7 μM. When challenged with finger-prick-scale sample volumes of the whole blood (diluted 1000-fold to match the sensor's dynamic range), the device achieves the accurate (±20%), calibration-free measurement of blood phenylalanine levels in minutes.
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Affiliation(s)
- Andrea Idili
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
- Center for Bioengineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Claudio Parolo
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
- Center for Bioengineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Gabriel Ortega
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
- Center for Bioengineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Kevin W. Plaxco
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
- Center for Bioengineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
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89
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Yu Q, Pourmandi N, Xue L, Gondrand C, Fabritz S, Bardy D, Patiny L, Katsyuba E, Auwerx J, Johnsson K. A biosensor for measuring NAD + levels at the point of care. Nat Metab 2019; 1:1219-1225. [PMID: 32694678 DOI: 10.1038/s42255-019-0151-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 11/12/2019] [Indexed: 01/08/2023]
Abstract
The cellular level of nicotinamide adenine dinucleotide (NAD+), through its different functions, affects cellular metabolism and signalling1-3. A decrease in the NAD+ content has been associated with various pathologies and physiological aging4,5, while strategies to boost cellular NAD+ levels have been shown to be effective against age-related diseases in many animal models6. The link between decreased NAD+ levels and numerous pathologies and physiological aging has triggered the need for a simple quantification method for NAD+, ideally applicable at the point of care. Here, we introduce a bioluminescent biosensor for the rapid quantification of NAD+ levels in biological samples, which can be used either in laboratories or at the point of care. The biosensor is a semisynthetic, light-emitting sensor protein that changes the colour of emitted light from blue to red on binding of NAD+. This NAD+-dependent colour change enables the use of the biosensor in paper-based assays in which NAD+ is quantified by measuring the colour of the emitted light by using either a simple digital camera or a plate reader. We used the approach to quantify NAD+ levels in cell culture, tissue and blood samples, yielding results that agreed with those from standard testing methods. The same biosensor furthermore allows the quantification of NAD+-dependent enzymatic activities in blood samples, thus expanding its utility as a tool for point-of-care diagnostics.
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Affiliation(s)
- Qiuliyang Yu
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Narges Pourmandi
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Lin Xue
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Corentin Gondrand
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Sebastian Fabritz
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Daniel Bardy
- Clinical Chemistry Laboratory, Service of Biomedicine, University Hospital of Lausanne, Lausanne, Switzerland
| | - Luc Patiny
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Elena Katsyuba
- Laboratory of Integrative Systems Physiology, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Nagi Biosciences, Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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90
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Adamson H, Ajayi MO, Campbell E, Brachi E, Tiede C, Tang AA, Adams TL, Ford R, Davidson A, Johnson M, McPherson MJ, Tomlinson DC, Jeuken LJC. Affimer-Enzyme-Inhibitor Switch Sensor for Rapid Wash-free Assays of Multimeric Proteins. ACS Sens 2019; 4:3014-3022. [PMID: 31578863 DOI: 10.1021/acssensors.9b01574] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Robust technology is required to underpin rapid point-of-care and in-field diagnostics to improve timely decision making across broad sectors. An attractive strategy combines target recognition and signal generating elements into an "active" enzyme-switch that directly transduces target-binding into a signal. However, approaches that are broadly applicable to diverse targets remain elusive. Here, an enzyme-inhibitor switch sensor was developed by insertion of non-immunoglobulin Affimer binding proteins, between TEM1-β-lactamase and its inhibitor protein, such that target binding disrupts the enzyme-inhibitor complex. Design principles for a successful switch architecture are illustrated by the rapid (min), simple (wash-free), and sensitive (pM) quantification of multimeric target analytes in biological samples (serum, plasma, leaf extracts), across three application areas. A therapeutic antibody (Herceptin), protein biomarker (human C-reactive protein), and plant virus (cow pea mosaic virus) were targeted, demonstrating assays for therapeutic drug monitoring, health diagnostics, and plant pathogen detection, respectively. Batch-to-batch reproducibility, shelf-life stability, and consistency with validated enzyme-linked immunosorbent assay analysis confirm that the principle of an Affimer-enzyme-inhibitor switch provides a platform for point-of-care and in-field diagnostics.
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Affiliation(s)
| | | | | | | | | | | | | | - Robert Ford
- Avacta Life Sciences Limited, Unit 20, Ash Way, Thorp Arch Estate, Wetherby LS23 7FA, U.K
| | - Alex Davidson
- Avacta Life Sciences Limited, Unit 20, Ash Way, Thorp Arch Estate, Wetherby LS23 7FA, U.K
| | - Matt Johnson
- Avacta Life Sciences Limited, Unit 20, Ash Way, Thorp Arch Estate, Wetherby LS23 7FA, U.K
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91
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Xiao W, Deng Z, Huang J, Huang Z, Zhuang M, Yuan Y, Nie J, Zhang Y. Highly Sensitive Colorimetric Detection of a Variety of Analytes via the Tyndall Effect. Anal Chem 2019; 91:15114-15122. [DOI: 10.1021/acs.analchem.9b03824] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Wencheng Xiao
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Zihao Deng
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Jinkun Huang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Ziheng Huang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Miaomiao Zhuang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Yali Yuan
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Jinfang Nie
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Yun Zhang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
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92
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Monitoring Nicotinamide Adenine Dinucleotide and its phosphorylated redox metabolism using genetically encoded fluorescent biosensors. SENSING AND BIO-SENSING RESEARCH 2019. [DOI: 10.1016/j.sbsr.2019.100307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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93
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Song F, Deng R, Liu H, Wang A, Ma C, Wei Y, Cui X, Wan Y, Li J. Trypsin-Amplified Aerolysin Nanopore Amplified Sandwich Assay for Attomolar Nucleic Acid and Single Bacteria Detection. Anal Chem 2019; 91:14043-14048. [PMID: 31577421 DOI: 10.1021/acs.analchem.9b03717] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nanopore technology is promising for the next-generation of nucleic acid-based diagnosis. However, sequence reservation could still be hardly achieved in low-concentration. Herein, we propose a trypsin-activated catalysis reaction for amplified detection, which substantially improves the sensitivity of nanopore technique. The proposed trypsin-amplified nanopore amplified sandwich assay (tNASA) could contribute to a sensitivity approximately 100 000 times higher based on nucleic acid probe design. Remarkably, tNASA is capable of attomolar nucleic acid and single cell detection by using a miniaturized current amplifier without alignment algorithm. Also it allows 10 pathogenic species in serum to be accurately and robustly profiled, thus be utilized for the diagnosis of infectious diseases. tNASA may evolve the construction of nanopore techniques for nucleic acid detection and would facilitate its translation for pocket diagnosis and precision medicine.
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Affiliation(s)
- Fengge Song
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Marine College, State Key Laboratory of Marine Resource Utilization in South China Sea , Hainan University , Haikou 570228 , China
| | - Ruijie Deng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China.,College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Centre , Sichuan University , Chengdu 610065 , China
| | - Hong Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Marine College, State Key Laboratory of Marine Resource Utilization in South China Sea , Hainan University , Haikou 570228 , China
| | - Aimin Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Marine College, State Key Laboratory of Marine Resource Utilization in South China Sea , Hainan University , Haikou 570228 , China
| | - Chunxin Ma
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Marine College, State Key Laboratory of Marine Resource Utilization in South China Sea , Hainan University , Haikou 570228 , China
| | - Yangdao Wei
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Marine College, State Key Laboratory of Marine Resource Utilization in South China Sea , Hainan University , Haikou 570228 , China
| | - Xiaojian Cui
- National Marine Data & Information Service , Tianjin 300170 , China
| | - Yi Wan
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Marine College, State Key Laboratory of Marine Resource Utilization in South China Sea , Hainan University , Haikou 570228 , China.,Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China
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94
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Chang D, Lindberg E, Feng S, Angerani S, Riezman H, Winssinger N. Luciferase‐Induced Photouncaging: Bioluminolysis. Angew Chem Int Ed Engl 2019; 58:16033-16037. [DOI: 10.1002/anie.201907734] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/06/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Dalu Chang
- School of Chemistry and Biochemistry, NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
| | - Eric Lindberg
- School of Chemistry and Biochemistry, NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
- Present address: National Heart, Lung, and Blood Institute National Institutes of Health Bethesda MD 20892 USA
| | - Suihan Feng
- School of Chemistry and Biochemistry, NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
| | - Simona Angerani
- School of Chemistry and Biochemistry, NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
| | - Howard Riezman
- School of Chemistry and Biochemistry, NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
| | - Nicolas Winssinger
- School of Chemistry and Biochemistry, NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
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95
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Chang D, Lindberg E, Feng S, Angerani S, Riezman H, Winssinger N. Luciferase‐Induced Photouncaging: Bioluminolysis. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Dalu Chang
- School of Chemistry and Biochemistry, NCCR Chemical BiologyFaculty of ScienceUniversity of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
| | - Eric Lindberg
- School of Chemistry and Biochemistry, NCCR Chemical BiologyFaculty of ScienceUniversity of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
- Present address: National Heart, Lung, and Blood InstituteNational Institutes of Health Bethesda MD 20892 USA
| | - Suihan Feng
- School of Chemistry and Biochemistry, NCCR Chemical BiologyFaculty of ScienceUniversity of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
| | - Simona Angerani
- School of Chemistry and Biochemistry, NCCR Chemical BiologyFaculty of ScienceUniversity of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
| | - Howard Riezman
- School of Chemistry and Biochemistry, NCCR Chemical BiologyFaculty of ScienceUniversity of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
| | - Nicolas Winssinger
- School of Chemistry and Biochemistry, NCCR Chemical BiologyFaculty of ScienceUniversity of Geneva 30 quai Ernest-Ansermet Geneva Switzerland
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96
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97
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Huang M, Song J, Huang P, Chen X, Wang W, Zhu Z, Song Y, Yang C. Molecular Crowding Evolution for Enabling Discovery of Enthalpy-Driven Aptamers for Robust Biomedical Applications. Anal Chem 2019; 91:10879-10886. [PMID: 31347355 DOI: 10.1021/acs.analchem.9b02697] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An enthalpy-driven ligand is an ideal probe for practical applications because of the formation of abundant specific bonds between the ligand and target, compared to an entropy-driven ligand with a similar Gibbs free energy change. However, there has been a lack of direct discovery strategy for identifying enthalpy-driven ligands. In this work, a molecular crowding SELEX (systematic evolution of ligands by exponential enrichment) strategy for discovering enthalpy-driven aptamers was developed to improve the affinity and selectivity of aptamers in complex samples. Three aptamer sequences were successfully evolved against a tumor biomarker protein, and all proved to be enthalpy-driven by thermodynamics analysis, establishing the feasibility of molecular crowding SELEX for effective discovery of enthalpy-driven aptamers. Further comparison of aptamers evolved from conventional SELEX in buffer and molecular crowding SELEX (SYL-H2C) revealed much higher affinity of SYL-H2C. With its improved thermodynamic properties, the enthalpy-driven SYL-H2C aptamer was able to detect circulating tumor cells in real cancer patient blood samples with excellent detection accuracy (10/10). The proposed molecular crowding screening strategy offers a promising direction for discovering robust binding probes for a great variety of biomedical applications.
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Affiliation(s)
- Mengjiao Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China
| | - Jia Song
- Institute of Molecular Medicine, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , 200127 , China
| | - Peifeng Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China
| | - Xiaofeng Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China
| | - Wei Wang
- Institute of Molecular Medicine, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , 200127 , China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China.,Institute of Molecular Medicine, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , 200127 , China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China.,Institute of Molecular Medicine, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , 200127 , China
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98
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Han X, Cao M, Wu M, Wang YJ, Yu C, Zhang C, Yu H, Wei JF, Li L, Huang W. A paper-based chemiluminescence immunoassay device for rapid and high-throughput detection of allergen-specific IgE. Analyst 2019; 144:2584-2593. [PMID: 30830127 DOI: 10.1039/c8an02020e] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The fast and precise detection of potential allergen-specific immunoglobulin E (sIgE) is imperative for the diagnosis and appropriate treatment of allergic diseases. In this study, we have successfully fabricated a novel paper-based immunoassay device for the detection of sIgE in allergic diseases. We used Can f 1, one of the main dog allergens, as a model allergen to detect sIgE in human sera. To achieve excellent performance, the experimental parameters were optimized. Further, we extended this device for potential applications in the clinical diagnosis of allergic diseases: worthwhile clinical performance in the detection of allergens was achieved as compared to that achieved by commercial enzyme-linked immunosorbent assay (ELISA) kit. Therefore, it was proven that this strategy has the advantages of high-throughput, rapid, sensitive, and highly accurate detection of trace amounts of sIgEs. Furthermore, by simply changing the antigen and antibody, this device could be used for the high-throughput detection of other allergens, so as to achieve multiallergen detection and appropriate desensitization therapy, thereby making it promising in the determination of allergic diseases in clinics.
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Affiliation(s)
- Xisi Han
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211800, P. R. China.
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99
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Xu X, Ji D, Zhang Y, Gao X, Xu P, Li X, Liu CC, Wen W. Detection of Phenylketonuria Markers Using a ZIF-67 Encapsulated PtPd Alloy Nanoparticle (PtPd@ZIF-67)-Based Disposable Electrochemical Microsensor. ACS APPLIED MATERIALS & INTERFACES 2019; 11:20734-20742. [PMID: 31094505 DOI: 10.1021/acsami.9b05431] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phenylketonuria (PKU) is a common disease in congenital disorder of amino acid metabolism, which can lead to intellectual disability, seizures, behavioral problems, and mental disorders. We report herein a facile method to screen for PKU by the measurements of its metabolites (markers). In this work, a disposable electrochemical microsensor modified with a ZIF (zeolitic imidazolate framework)-based nanocomposite is constructed, in which ZIF-67 crystals are encapsulated with PtPd alloy nanoparticles (NPs) forming the nanocomposite (PtPd@ZIF-67). According to electrochemical measurements, the PtPd@ZIF-67-modified microsensor shows good responses and selectivity to phenylpyruvic acid and phenylacetic acid, while almost no response toward other amino acid analogues is observed. Here, a new sensing mechanism based on the acylation reaction between the imidazole linker in ZIF-67 and carboxyl in PKU markers has been proposed and verified through the Fourier-transform infrared spectroscopy study. Moreover, the encapsulated PtPd NPs elevate the electron transfer capability of the PtPd@ZIF-67-modified microsensor and further improve the electrochemical sensing performance. Finally, we demonstrate that the developed PtPd@ZIF-67-modified microsensor has the possibility to sensing of PKU markers with high response and good specificity and may be extended to exploit the point-of-care rapid PKU screening.
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Affiliation(s)
- Xinyue Xu
- Materials Genome Institute , Shanghai University , Shanghai 200444 , China
| | - Dongqing Ji
- Materials Genome Institute , Shanghai University , Shanghai 200444 , China
| | - Yuan Zhang
- Materials Genome Institute , Shanghai University , Shanghai 200444 , China
| | - Xinghua Gao
- Materials Genome Institute , Shanghai University , Shanghai 200444 , China
| | - Pengcheng Xu
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology , Chinese Academy of Sciences , Shanghai 200050 , China
| | - Xinxin Li
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology , Chinese Academy of Sciences , Shanghai 200050 , China
| | - Chung-Chiun Liu
- Department of Chemical Engineering , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Weijia Wen
- Materials Genome Institute , Shanghai University , Shanghai 200444 , China
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100
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Guerra M, Frey D, Hagner M, Dittrich S, Paulsen M, Mall MA, Schultz C. Cathepsin G Activity as a New Marker for Detecting Airway Inflammation by Microscopy and Flow Cytometry. ACS CENTRAL SCIENCE 2019; 5:539-548. [PMID: 30937381 PMCID: PMC6439450 DOI: 10.1021/acscentsci.8b00933] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Indexed: 06/01/2023]
Abstract
Muco-obstructive lung diseases feature extensive bronchiectasis due to the uncontrolled release of neutrophil serine proteases into the airways. To assess if cathepsin G (CG) is a novel key player in chronic lung inflammation, we developed membrane-bound (mSAM) and soluble (sSAM) FRET reporters. The probes quantitatively revealed elevated CG activity in samples from 46 patients. For future basic science and personalized clinical applications, we developed a rapid, highly informative, and easily translatable small-molecule FRET flow cytometry assay for monitoring protease activity including cathepsin G. We demonstrated that mSAM distinguished healthy from patient cells by FRET-based flow cytometry with excellent correlation to confocal microscopy data.
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Affiliation(s)
- Matteo Guerra
- Molecular
Medicine Partnership Unit (MMPU), European
Molecular Biology Laboratory (EMBL) and University of Heidelberg, 69117 Heidelberg, Germany
- Faculty
of Biosciences, Collaboration for Joint
Ph.D. Degree between EMBL and Heidelberg University, 69117 Heidelberg, Germany
- Translational
Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Dario Frey
- Department
of Translational Pulmonology, University
of Heidelberg, 69120 Heidelberg, Germany
- Translational
Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Matthias Hagner
- Department
of Translational Pulmonology, University
of Heidelberg, 69120 Heidelberg, Germany
- Translational
Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Susanne Dittrich
- Department
of Translational Pulmonology, University
of Heidelberg, 69120 Heidelberg, Germany
- Translational
Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Michelle Paulsen
- Department
of Translational Pulmonology, University
of Heidelberg, 69120 Heidelberg, Germany
- Translational
Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Marcus A. Mall
- Department
of Translational Pulmonology, University
of Heidelberg, 69120 Heidelberg, Germany
- Translational
Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
- Department
of Pediatric Pulmonology, Immunology and Intensive Care Medicine, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
- Berlin Institute
of Health (BIH), 10178 Berlin, Germany
| | - Carsten Schultz
- Molecular
Medicine Partnership Unit (MMPU), European
Molecular Biology Laboratory (EMBL) and University of Heidelberg, 69117 Heidelberg, Germany
- Translational
Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
- Department
of Physiology and Pharmacology, Oregon Health
& Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239-3098, United States
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