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Zhang Z, Nakata E, Shibano Y, Morii T. FRET-based cathepsin probes for simultaneous detection of cathepsin B and D activities. Chembiochem 2022; 23:e202200319. [PMID: 35929606 DOI: 10.1002/cbic.202200319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/05/2022] [Indexed: 11/09/2022]
Abstract
Fluorescent cathepsin probes were prepared by modification of peptidic substrates for cathepsin B (CTSB) and cathepsin D (CTSD) with FRET pairs. Fluorophores with distinguishable emission characteristics were applied to CTSB and CTSD probes with their appropriate quenchers to simultaneously monitor the activity of CTSB and/or CTSD. Conjugation of both the CTSB and CTSD probes with short single-stranded DNA drastically increased their reactivity to cathepsins over the parent probes possibly by improving their solubility. The activity of CTSB and CTSD were simultaneously detected by using these orthogonal FRET-based cathepsin probes.
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Affiliation(s)
- Zhengxiao Zhang
- Kyoto University: Kyoto Daigaku, Institute of Advanced Energy, Gokasyo, 611-0011, Uji, JAPAN
| | - Eiji Nakata
- Kyoto University: Kyoto Daigaku, Institute of Advanced Energy, Gokasyo, 611-0011, Uji, JAPAN
| | - Yuya Shibano
- Kyoto University - Uji Campus: Kyoto Daigaku - Uji Campus, Institute of Advanced energy, Gokasyo, 6110011, Uji, JAPAN
| | - Takashi Morii
- Kyoto University: Kyoto Daigaku, Institute of Advanced Energy, Gokasyo, 611-0011, Uji, JAPAN
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2
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Marongiu L, Mingozzi F, Cigni C, Marzi R, Di Gioia M, Garrè M, Parazzoli D, Sironi L, Collini M, Sakaguchi R, Morii T, Crosti M, Moro M, Schurmans S, Catelani T, Rotem R, Colombo M, Shears S, Prosperi D, Zanoni I, Granucci F. Inositol 1,4,5-trisphosphate 3-kinase B promotes Ca 2+ mobilization and the inflammatory activity of dendritic cells. Sci Signal 2021; 14:14/676/eaaz2120. [PMID: 33785611 DOI: 10.1126/scisignal.aaz2120] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Innate immune responses to Gram-negative bacteria depend on the recognition of lipopolysaccharide (LPS) by a receptor complex that includes CD14 and TLR4. In dendritic cells (DCs), CD14 enhances the activation not only of TLR4 but also that of the NFAT family of transcription factors, which suppresses cell survival and promotes the production of inflammatory mediators. NFAT activation requires Ca2+ mobilization. In DCs, Ca2+ mobilization in response to LPS depends on phospholipase C γ2 (PLCγ2), which produces inositol 1,4,5-trisphosphate (IP3). Here, we showed that the IP3 receptor 3 (IP3R3) and ITPKB, a kinase that converts IP3 to inositol 1,3,4,5-tetrakisphosphate (IP4), were both necessary for Ca2+ mobilization and NFAT activation in mouse and human DCs. A pool of IP3R3 was located on the plasma membrane of DCs, where it colocalized with CD14 and ITPKB. Upon LPS binding to CD14, ITPKB was required for Ca2+ mobilization through plasma membrane-localized IP3R3 and for NFAT nuclear translocation. Pharmacological inhibition of ITPKB in mice reduced both LPS-induced tissue swelling and the severity of inflammatory arthritis to a similar extent as that induced by the inhibition of NFAT using nanoparticles that delivered an NFAT-inhibiting peptide specifically to phagocytic cells. Our results suggest that ITPKB may represent a promising target for anti-inflammatory therapies that aim to inhibit specific DC functions.
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Affiliation(s)
- Laura Marongiu
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Francesca Mingozzi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Clara Cigni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Roberta Marzi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Marco Di Gioia
- Harvard Medical School and Division of Immunology, Division of Gastroenterology, Boston Children's Hospital, Boston, MA 02115, USA
| | | | | | - Laura Sironi
- Department of Physics, University of Milano-Bicocca, Piazza della Scienza 3, 20126 Milan, Italy
| | - Maddalena Collini
- Department of Physics, University of Milano-Bicocca, Piazza della Scienza 3, 20126 Milan, Italy
| | - Reiko Sakaguchi
- Institute for Integrated Cell-Material Sciences, Kyoto University Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Mariacristina Crosti
- INGM, Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milan, Italy
| | - Monica Moro
- INGM, Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milan, Italy
| | - Stéphane Schurmans
- Laboratory of Functional Genetics, GIGA-B34, University of Liège, 4000 Liège, Belgium
| | - Tiziano Catelani
- Piattaforma Interdipartimentale di Microscopia, University of Milano-Bicocca, Piazza della Scienza 3, 20126 Milan, Italy
| | - Rany Rotem
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Miriam Colombo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Stephen Shears
- Signal Transduction Laboratory, NIEHS/NIH, 111 TW Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Davide Prosperi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Ivan Zanoni
- Harvard Medical School and Division of Immunology, Division of Gastroenterology, Boston Children's Hospital, Boston, MA 02115, USA.,Division of Immunology, Harvard Medical School, Boston Children's Hospital, Boston, MA 02115, USA
| | - Francesca Granucci
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy. .,INGM, Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milan, Italy
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3
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Nakano S, Konishi H, Morii T. Receptor-based fluorescent sensors constructed from ribonucleopeptide. Methods Enzymol 2020; 641:183-223. [PMID: 32713523 DOI: 10.1016/bs.mie.2020.04.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Receptor-based fluorescent sensors are the representative tool for quantitative detection of target ligands. The high substrate-selectivity originated from biomacromolecule receptor is one of the advantages of this tool, but a laborious trial and error is usually required to construct sensors showing satisfactory fluorescence intensity changes without diminishing the function of parent receptor. Ribonucleopeptide (RNP) provides a scaffold of fluorescent sensors to improve such issues. RNP receptors for the ligand of interest are constructed by applying in vitro selection for RNA-derived RNP library. Simple modification of the N-terminal of peptide in RNP by an appropriate fluorophore converts the RNP receptor into the fluorescent sensor with retaining the affinity and selectivity for the substrate. In this chapter, we introduce the protocols for construction of fluorescent RNP sensors through selection from a library of fluorophore-modified RNP complex or by a structure-based modular design. Furthermore, we describe the application of covalently linked RNP sensors for simultaneous detection of multiple ligands.
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Affiliation(s)
- Shun Nakano
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Hiroaki Konishi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan.
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4
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Abstract
The multitudinous inositol phosphate family elicits a wide range of molecular effects that regulate countless biological responses. In this review, I provide a methodological viewpoint of the manner in which key advances in the field of inositol phosphate research were made. I also note some of the considerable challenges that still lie ahead.
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Affiliation(s)
- Stephen B Shears
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
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5
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Kiyonaka S, Sakamoto S, Wakayama S, Morikawa Y, Tsujikawa M, Hamachi I. Ligand-Directed Chemistry of AMPA Receptors Confers Live-Cell Fluorescent Biosensors. ACS Chem Biol 2018; 13:1880-1889. [PMID: 29437380 DOI: 10.1021/acschembio.7b01042] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AMPA-type glutamate receptors (AMPARs) mediate fast excitatory synaptic transmission in the central nervous system. Dysregulation of AMPAR function is associated with many kinds of neurological, neurodegenerative, and psychiatric disorders. As a result, molecules capable of controlling AMPAR functions are potential therapeutic agents. Fluorescent semisynthetic biosensors have attracted considerable interest for the discovery of ligands selectively acting on target proteins. Given the large protein complex formation of AMPARs in live cells, biosensors using full-length AMPARs retaining original functionality are ideal for drug screening. Here, we demonstrate that fluorophore-labeled AMPARs prepared by ligand-directed acyl imidazole chemistry can act as turn-on fluorescent biosensors for AMPAR ligands in living cells. These biosensors selectively detect orthosteric ligands of AMPARs among the glutamate receptor family. Notably, the dissociation constants of agonists and antagonists for AMPARs were determined in live cells, which revealed that the ligand-binding properties of AMPARs to agonists are largely different in living cells, compared with noncellular conditions. We also show that these sensors can be applied to detecting allosteric modulators or subunit-selective ligands of AMPARs. Thus, our protein-based biosensors can be useful for discovering pharmaceutical agents to treat AMPAR-related neurological disorders.
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Affiliation(s)
- Shigeki Kiyonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Sho Wakayama
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yuma Morikawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Muneo Tsujikawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
- CREST(Core Research for Evolutional Science and Technology, JST), Chiyodaku, Tokyo, 102-0075, Japan
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6
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Discovery of allosteric modulators for GABAA receptors by ligand-directed chemistry. Nat Chem Biol 2016; 12:822-30. [DOI: 10.1038/nchembio.2150] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/17/2016] [Indexed: 12/26/2022]
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7
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Takaoka Y, Ojida A, Hamachi I. Organische Proteinchemie und ihre Anwendung für Markierungen und Engineering in Lebendzellsystemen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201207089] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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8
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Nakano S, Fukuda M, Tamura T, Sakaguchi R, Nakata E, Morii T. Simultaneous detection of ATP and GTP by covalently linked fluorescent ribonucleopeptide sensors. J Am Chem Soc 2013; 135:3465-73. [PMID: 23373863 DOI: 10.1021/ja3097652] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A noncovalent RNA complex embedding an aptamer function and a fluorophore-labeled peptide affords a fluorescent ribonucleopeptide (RNP) framework for constructing fluorescent sensors. By taking an advantage of the noncovalent properties of the RNP complex, the ligand-binding and fluorescence characteristics of the fluorescent RNP can be independently tuned by taking advantage of the nature of the RNA and peptide subunits, respectively. Fluorescent sensors tailored for given measurement conditions, such as a detection wavelength and a detection concentration range for a ligand of interest can be easily identified by screening of fluorescent RNP libraries. The noncovalent configuration of a RNP becomes a disadvantage when the sensor is to be utilized at very low concentrations or when multiple sensors are applied to the same solution. Here, we report a strategy to convert a fluorescent RNP sensor in the noncovalent configuration into a covalently linked stable fluorescent RNP sensor. This covalently linked fluorescent RNP sensor enabled ligand detection at a low sensor concentration, even in cell extracts. Furthermore, application of both ATP and GTP sensors enabled simultaneous detection of ATP and GTP by monitoring each wavelength corresponding to the respective sensor. Importantly, when a fluorescein-modified ATP sensor and a pyrene-modified GTP sensor were co-incubated in the same solution, the ATP sensor responded at 535 nm only to changes in the concentration of ATP, whereas the GTP sensor detected GTP at 390 nm without any effect on the ATP sensor. Finally, simultaneous monitoring by these sensors enabled real-time measurement of adenosine deaminase enzyme reactions.
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Affiliation(s)
- Shun Nakano
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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9
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Takaoka Y, Ojida A, Hamachi I. Protein organic chemistry and applications for labeling and engineering in live-cell systems. Angew Chem Int Ed Engl 2013; 52:4088-106. [PMID: 23426903 DOI: 10.1002/anie.201207089] [Citation(s) in RCA: 261] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Indexed: 12/11/2022]
Abstract
The modification of proteins with synthetic probes is a powerful means of elucidating and engineering the functions of proteins both in vitro and in live cells or in vivo. Herein we review recent progress in chemistry-based protein modification methods and their application in protein engineering, with particular emphasis on the following four strategies: 1) the bioconjugation reactions of amino acids on the surfaces of natural proteins, mainly applied in test-tube settings; 2) the bioorthogonal reactions of proteins with non-natural functional groups; 3) the coupling of recognition and reactive sites using an enzyme or short peptide tag-probe pair for labeling natural amino acids; and 4) ligand-directed labeling chemistries for the selective labeling of endogenous proteins in living systems. Overall, these techniques represent a useful set of tools for application in chemical biology, with the methods 2-4 in particular being applicable to crude (living) habitats. Although still in its infancy, the use of organic chemistry for the manipulation of endogenous proteins, with subsequent applications in living systems, represents a worthy challenge for many chemists.
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Affiliation(s)
- Yousuke Takaoka
- Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan
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10
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Shears SB, Ganapathi SB, Gokhale NA, Schenk TMH, Wang H, Weaver JD, Zaremba A, Zhou Y. Defining signal transduction by inositol phosphates. Subcell Biochem 2012; 59:389-412. [PMID: 22374098 PMCID: PMC3925325 DOI: 10.1007/978-94-007-3015-1_13] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Ins(1,4,5)P(3) is a classical intracellular messenger: stimulus-dependent changes in its levels elicits biological effects through its release of intracellular Ca(2+) stores. The Ins(1,4,5)P(3) response is "switched off" by its metabolism to a range of additional inositol phosphates. These metabolites have themselves come to be collectively described as a signaling "family". The validity of that latter definition is critically examined in this review. That is, we assess the strength of the hypothesis that Ins(1,4,5)P(3) metabolites are themselves "classical" signals. Put another way, what is the evidence that the biological function of a particular inositol phosphate depends upon stimulus dependent changes in its levels? In this assessment, examples of an inositol phosphate acting as a cofactor (i.e. its function is not stimulus-dependent) do not satisfy our signaling criteria. We conclude that Ins(3,4,5,6)P(4) is, to date, the only Ins(1,4,5)P(3) metabolite that has been validated to act as a second messenger.
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Key Words
- adenosine deaminase
- akt
- β-cells
- calcium
- camp
- camkii
- chloride channel
- clc3
- compartmentalization
- dna repair
- endosomes
- erk
- frizzled receptor
- gap1ip4bp
- mrna export
- ins(1,4,5)p3
- ins(1,4,5)p4 receptor
- ins(1,3,4)p3
- ins(1,3,4,5)p4
- ins(1,3,4,5)p4 receptor
- ins(1,4,5,6)p4
- ins(3,4,5,6)p4
- ins(1,3,4,5,6)p5
- insp6
- insulin
- ipmk
- ipk2
- ip5k
- itp
- itpk1
- itpkb
- lymphocytes
- ku
- neutrophils
- protein phosphatase
- ptdins(4,5)p2
- ptdins(3,4,5)p3
- ph domain
- pten
- rasa3
- transcription
- wnt ligand
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Affiliation(s)
- Stephen B Shears
- Inositol Signaling Section, Laboratory of Signal Transduction, NIEHS, NIH, DHHS, Research Triangle Park, 27709, NC, USA, USA,
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11
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Ho CL, Koh SL, Chuah MLC, Luo Z, Tan WJ, Low DKS, Liang ZX. Rational design of fluorescent biosensor for cyclic di-GMP. Chembiochem 2011; 12:2753-8. [PMID: 22021215 DOI: 10.1002/cbic.201100557] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Indexed: 01/19/2023]
Abstract
Messenger bagged: The design of a fluorophore-labeled protein biosensor for the bacterial messenger cyclic di-GMP is described. The biosensor responds to c-di-GMP with sub-micromolar sensitivity in a real-time fashion. The biosensor can be used for enzyme assays for diguanylate cyclases and c-di-GMP phosphodiesterases as well as the high-throughput screening of inhibitors.
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Affiliation(s)
- Chun Loong Ho
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore
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12
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Zheng ML, Fujita K, Chen WQ, Smith NI, Duan XM, Kawata S. Comparison of Staining Selectivity for Subcellular Structures by Carbazole-Based Cyanine Probes in Nonlinear Optical Microscopy. Chembiochem 2010; 12:52-5. [DOI: 10.1002/cbic.201000593] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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13
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Orner B. The first Asian Chemical Biology conference meets at Seoul National University. ACS Chem Biol 2010; 5:725-7. [PMID: 20722456 DOI: 10.1021/cb100206k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Brendan Orner
- Nanyang Technological University, Singapore, Singapore.
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14
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Design strategies of fluorescent biosensors based on biological macromolecular receptors. SENSORS 2010; 10:1355-76. [PMID: 22205872 PMCID: PMC3244018 DOI: 10.3390/s100201355] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 01/29/2010] [Accepted: 02/04/2010] [Indexed: 11/17/2022]
Abstract
Fluorescent biosensors to detect the bona fide events of biologically important molecules in living cells are increasingly demanded in the field of molecular cell biology. Recent advances in the development of fluorescent biosensors have made an outstanding contribution to elucidating not only the roles of individual biomolecules, but also the dynamic intracellular relationships between these molecules. However, rational design strategies of fluorescent biosensors are not as mature as they look. An insatiable request for the establishment of a more universal and versatile strategy continues to provide an attractive alternative, so-called modular strategy, which permits facile preparation of biosensors with tailored characteristics by a simple combination of a receptor and a signal transducer. This review describes an overview of the progress in design strategies of fluorescent biosensors, such as auto-fluorescent protein-based biosensors, protein-based biosensors covalently modified with synthetic fluorophores, and signaling aptamers, and highlights the insight into how a given receptor is converted to a fluorescent biosensor. Furthermore, we will demonstrate a significance of the modular strategy for the sensor design.
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