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Minoshima M, Reja SI, Hashimoto R, Iijima K, Kikuchi K. Hybrid Small-Molecule/Protein Fluorescent Probes. Chem Rev 2024; 124:6198-6270. [PMID: 38717865 DOI: 10.1021/acs.chemrev.3c00549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.
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Affiliation(s)
- Masafumi Minoshima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Shahi Imam Reja
- Immunology Frontier Research Center, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Ryu Hashimoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kohei Iijima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kazuya Kikuchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
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2
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Hellweg L, Edenhofer A, Barck L, Huppertz MC, Frei MS, Tarnawski M, Bergner A, Koch B, Johnsson K, Hiblot J. A general method for the development of multicolor biosensors with large dynamic ranges. Nat Chem Biol 2023; 19:1147-1157. [PMID: 37291200 PMCID: PMC10449634 DOI: 10.1038/s41589-023-01350-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/25/2023] [Indexed: 06/10/2023]
Abstract
Fluorescent biosensors enable the study of cell physiology with spatiotemporal resolution; yet, most biosensors suffer from relatively low dynamic ranges. Here, we introduce a family of designed Förster resonance energy transfer (FRET) pairs with near-quantitative FRET efficiencies based on the reversible interaction of fluorescent proteins with a fluorescently labeled HaloTag. These FRET pairs enabled the straightforward design of biosensors for calcium, ATP and NAD+ with unprecedented dynamic ranges. The color of each of these biosensors can be readily tuned by changing either the fluorescent protein or the synthetic fluorophore, which enables simultaneous monitoring of free NAD+ in different subcellular compartments following genotoxic stress. Minimal modifications of these biosensors furthermore allow their readout to be switched to fluorescence intensity, fluorescence lifetime or bioluminescence. These FRET pairs thus establish a new concept for the development of highly sensitive and tunable biosensors.
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Affiliation(s)
- Lars Hellweg
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Anna Edenhofer
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Lucas Barck
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Magnus-Carsten Huppertz
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Michelle S Frei
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Miroslaw Tarnawski
- Protein Expression and Characterization Facility, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Andrea Bergner
- 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
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
- Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Julien Hiblot
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.
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3
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Bednar RM, Karplus PA, Mehl RA. Site-specific dual encoding and labeling of proteins via genetic code expansion. Cell Chem Biol 2023; 30:343-361. [PMID: 36977415 PMCID: PMC10764108 DOI: 10.1016/j.chembiol.2023.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/10/2023] [Accepted: 03/03/2023] [Indexed: 03/29/2023]
Abstract
The ability to selectively modify proteins at two or more defined locations opens new avenues for manipulating, engineering, and studying living systems. As a chemical biology tool for the site-specific encoding of non-canonical amino acids into proteins in vivo, genetic code expansion (GCE) represents a powerful tool to achieve such modifications with minimal disruption to structure and function through a two-step "dual encoding and labeling" (DEAL) process. In this review, we summarize the state of the field of DEAL using GCE. In doing so, we describe the basic principles of GCE-based DEAL, catalog compatible encoding systems and reactions, explore demonstrated and potential applications, highlight emerging paradigms in DEAL methodologies, and propose novel solutions to current limitations.
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Affiliation(s)
- Riley M Bednar
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, OR 97331-7305, USA; GCE4All Research Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, OR 97331-7305, USA
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, OR 97331-7305, USA; GCE4All Research Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, OR 97331-7305, USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, OR 97331-7305, USA; GCE4All Research Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, OR 97331-7305, USA.
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4
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Li K, Li R, Kong X, Shen Q, Wan T, Wu H. A highly selective and sensitive fluorescent sensor based on a 1,8-naphthalimide with a Schiff base function for Hg 2+ in aqueous media. ZEITSCHRIFT FUR NATURFORSCHUNG SECTION B-A JOURNAL OF CHEMICAL SCIENCES 2022. [DOI: 10.1515/znb-2022-0044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
A new fluorescent sensor, N-allyl-4-[(2-(3-methoxysalicylaldimino)ethylamino]-1,8-naphthalimide (HL), for Hg2+ has been developed where the Schiff base substituent acts as a recognition group. This sensor shows a large Stokes shift of 3535–4042 cm−1 and a general fluorescence quantum yield of 0.05, 249–0.11, 866 in organic solvents of different polarity as expected. It also exhibits highly selective and a sensitive response to Hg2+ (Ф
Hg+HL/Ф
HL = 2.28) over other metal ions (Na+, K+, Ca2+, Mg2+, Al3+, Pb2+, Fe3+, Ni2+, Zn2+, Cu2+, Ag+, Co2+, Cr3+, Mn2+ and Cd2+) in solution (DMF/Tris-HCl buffer, 1:1, v/v, pH = 7.2). The Hg2+-induced fluorescence enhancement at 526 nm is proportional to the concentration of Hg2+ in the range of 0.5–4.0 µm with a detection limit of 0.18 µm. Based on the fluorescence titration and a Job’s plot analysis, the metal-to-ligand ratio of the complex is 2:1 with a binding constant of 1.56 × 1012 m
−1.
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Affiliation(s)
- Kaiyi Li
- School of Chemistry and Chemical Engineering , Lanzhou Jiaotong University , Lanzhou , Gansu , 730070 , P. R. China
| | - Ruixue Li
- School of Chemistry and Chemical Engineering , Lanzhou Jiaotong University , Lanzhou , Gansu , 730070 , P. R. China
| | - Xiaoxia Kong
- School of Chemistry and Chemical Engineering , Lanzhou Jiaotong University , Lanzhou , Gansu , 730070 , P. R. China
| | - Qinqin Shen
- School of Chemistry and Chemical Engineering , Lanzhou Jiaotong University , Lanzhou , Gansu , 730070 , P. R. China
| | - Tiantian Wan
- School of Chemistry and Chemical Engineering , Lanzhou Jiaotong University , Lanzhou , Gansu , 730070 , P. R. China
| | - Huilu Wu
- School of Chemistry and Chemical Engineering , Lanzhou Jiaotong University , Lanzhou , Gansu , 730070 , P. R. China
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5
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Wen L, Ma X, Yang J, Jiang M, Peng C, Ma Z, Yu H, Li Y. A New Ratiometric Design Strategy Based on Modulation of π-Conjugation Unit for Developing Fluorescent Probe and Imaging of Cellular Peroxynitrite. Anal Chem 2022; 94:4763-4769. [PMID: 35271267 DOI: 10.1021/acs.analchem.1c05447] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ratiometric fluorescent probes could effectively offset the changes of the autofluorescence and compartmental localization. FRET, ICT, etc. are the common strategies to design probes for biosensing, but these strategies have some deficiencies. Here, we proposed a new design strategy based on π-conjugation modulation, giving two different emission bands in the absence and presence of the target. The new fluorescence probe named Rhod-DCM-B was rationally designed and synthesized, which displayed a fluorescence emission peak at 670 nm because the electron cloud focuses on the conjugated DCM unit. With the addition of ONOO-, the fluorescence emission at 570 nm increased, accompanied by the decrease of fluorescence emission at 670 nm, showing a ratiometric signal change attributed to the opened spirane structure making the electron cloud concentrated on the xanthene core. The mechanism is well confirmed by MS and DFT calculations. Rhod-DCM-B exhibited outstanding sensitivity and excellent selectivity toward ONOO-. Moreover, Rhod-DCM-B was effectively employed to determine endogenous and exogenous ONOO- in living cells. As a marker for inflammation and drug-induced liver injury (DILI) process, ONOO- in vivo was successfully monitored by Rhod-DCM-B and presented a dramatic ratiometric response.
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Affiliation(s)
- Lei Wen
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Xinyu Ma
- Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Jing Yang
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Minmin Jiang
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, Hefei, 230032, China
| | - Chao Peng
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Zhongyun Ma
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Huan Yu
- Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Yinhui Li
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
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6
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Cheng Y, Borum RM, Clark AE, Jin Z, Moore C, Fajtová P, O'Donoghue AJ, Carlin AF, Jokerst JV. A Dual-Color Fluorescent Probe Allows Simultaneous Imaging of Main and Papain-like Proteases of SARS-CoV-2-Infected Cells for Accurate Detection and Rapid Inhibitor Screening. Angew Chem Int Ed Engl 2022; 61:e202113617. [PMID: 34889013 PMCID: PMC8854376 DOI: 10.1002/anie.202113617] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Indexed: 11/15/2022]
Abstract
The main protease (Mpro ) and papain-like protease (PLpro ) play critical roles in SARS-CoV-2 replication and are promising targets for antiviral inhibitors. The simultaneous visualization of Mpro and PLpro is extremely valuable for SARS-CoV-2 detection and rapid inhibitor screening. However, such a crucial investigation has remained challenging because of the lack of suitable probes. We have now developed a dual-color probe (3MBP5) for the simultaneous detection of Mpro and PLpro by fluorescence (or Förster) resonance energy transfer (FRET). This probe produces fluorescence from both the Cy3 and Cy5 fluorophores that are cleaved by Mpro and PLpro . 3MBP5-activatable specificity was demonstrated with recombinant proteins, inhibitors, plasmid-transfected HEK 293T cells, and SARS-CoV-2-infected TMPRSS2-Vero cells. Results from the dual-color probe first verified the simultaneous detection and intracellular distribution of SARS-CoV-2 Mpro and PLpro . This is a powerful tool for the simultaneous detection of different proteases with value for the rapid screening of inhibitors.
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Affiliation(s)
- Yong Cheng
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Raina M. Borum
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Alex E. Clark
- Department of MedicineUniversity of California, San DiegoLa JollaCA 92093USA
| | - Zhicheng Jin
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Colman Moore
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCA 92093USA
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCA 92093USA
| | - Aaron F. Carlin
- Department of MedicineUniversity of California, San DiegoLa JollaCA 92093USA
| | - Jesse V. Jokerst
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
- Materials Science and Engineering ProgramUniversity of California, San DiegoLa JollaCA 92093USA
- Department of RadiologyUniversity of California, San DiegoLa JollaCA 92093USA
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7
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Cheng Y, Borum RM, Clark AE, Jin Z, Moore C, Fajtová P, O'Donoghue AJ, Carlin AF, Jokerst JV. A Dual‐Color Fluorescent Probe Allows Simultaneous Imaging of Main and Papain‐like Proteases of SARS‐CoV‐2‐Infected Cells for Accurate Detection and Rapid Inhibitor Screening. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yong Cheng
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Raina M. Borum
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Alex E. Clark
- Department of Medicine University of California, San Diego La Jolla CA 92093 USA
| | - Zhicheng Jin
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Colman Moore
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego La Jolla CA 92093 USA
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego La Jolla CA 92093 USA
| | - Aaron F. Carlin
- Department of Medicine University of California, San Diego La Jolla CA 92093 USA
| | - Jesse V. Jokerst
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
- Materials Science and Engineering Program University of California, San Diego La Jolla CA 92093 USA
- Department of Radiology University of California, San Diego La Jolla CA 92093 USA
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8
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Lewandowski TM, An P, Ramil CP, Fang M, Lin Q. Dual fluorescent labeling of GLP-1R in live cells via enzymatic tagging and bioorthogonal chemistry. RSC Chem Biol 2022; 3:702-706. [PMID: 35755189 PMCID: PMC9175107 DOI: 10.1039/d2cb00107a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/16/2022] [Indexed: 11/21/2022] Open
Abstract
To study GPCR conformational dynamics in live cells, here we report an integrated approach combining enzymatic SNAP-tagging with bioorthogonal chemistry for dual fluorescent labeling of GLP-1R. The resulting GLP-1R conformational biosensors permit a FRET-based analysis of the receptor subdomain movement in response to ligand stimulation in live cells. To study GPCR conformational dynamics in live cells, here we report an integrated approach combining enzymatic SNAP-tagging with bioorthogonal chemistry for dual fluorescent labeling of GLP-1R.![]()
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Affiliation(s)
- Tracey M. Lewandowski
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 14260-3000, USA
| | - Peng An
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 14260-3000, USA
| | - Carlo P. Ramil
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 14260-3000, USA
| | - Ming Fang
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 14260-3000, USA
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 14260-3000, USA
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9
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Bednar RM, Jana S, Kuppa S, Franklin R, Beckman J, Antony E, Cooley RB, Mehl RA. Genetic Incorporation of Two Mutually Orthogonal Bioorthogonal Amino Acids That Enable Efficient Protein Dual-Labeling in Cells. ACS Chem Biol 2021; 16:2612-2622. [PMID: 34590824 DOI: 10.1021/acschembio.1c00649] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The ability to site-specifically modify proteins at multiple sites in vivo will enable the study of protein function in its native environment with unprecedented levels of detail. Here, we present a versatile two-step strategy to meet this goal involving site-specific encoding of two distinct noncanonical amino acids bearing bioorthogonal handles into proteins in vivo followed by mutually orthogonal labeling. This general approach, that we call dual encoding and labeling (DEAL), allowed us to efficiently encode tetrazine- and azide-bearing amino acids into a protein and demonstrate for the first time that the bioorthogonal labeling reactions with strained alkene and alkyne labels can function simultaneously and intracellularly with high yields when site-specifically encoded in a single protein. Using our DEAL system, we were able to perform topologically defined protein-protein cross-linking, intramolecular stapling, and site-specific installation of fluorophores all inside living Escherichia coli cells, as well as study the DNA-binding properties of yeast Replication Protein A in vitro. By enabling the efficient dual modification of proteins in vivo, this DEAL approach provides a tool for the characterization and engineering of proteins in vivo.
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Affiliation(s)
- Riley M. Bednar
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural & Life Sciences Building, Corvallis, Oregon 97331-7305, United States
| | - Subhashis Jana
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural & Life Sciences Building, Corvallis, Oregon 97331-7305, United States
| | - Sahiti Kuppa
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Edward A. Doisy Research Center, 1100 South Grand Blvd., St. Louis, Missouri 63104, United States
| | - Rachel Franklin
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural & Life Sciences Building, Corvallis, Oregon 97331-7305, United States
| | - Joseph Beckman
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural & Life Sciences Building, Corvallis, Oregon 97331-7305, United States
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Edward A. Doisy Research Center, 1100 South Grand Blvd., St. Louis, Missouri 63104, United States
| | - Richard B. Cooley
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural & Life Sciences Building, Corvallis, Oregon 97331-7305, United States
| | - Ryan A. Mehl
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural & Life Sciences Building, Corvallis, Oregon 97331-7305, United States
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10
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Mariam J, Hoskere Ashoka A, Gaded V, Ali F, Malvi H, Das A, Anand R. Deciphering protein microenvironment by using a cysteine specific switch-ON fluorescent probe. Org Biomol Chem 2021; 19:5161-5168. [PMID: 34037063 DOI: 10.1039/d1ob00698c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescent probes provide an unparalleled opportunity to visualize and quantify dynamic events. Here, we employ a medium-size, cysteine specific coumarin based switch-ON fluorescent probe 'L' to track protein unfolding profiles and accessibility of cysteine residues in proteins. It was established that 'L' is highly selective and exhibits no artifact due to interaction with other bystander species. 'L' is able to gauge subtle changes in protein microenvironment and proved to be effective in delineating early unfolding events that are difficult to otherwise discern by classic techniques such as circular dichroism. By solving the X-ray structure of TadA and probing the temperature dependent fluorescence-ON response with native TadA and its cysteine mutants, it was revealed that unfolding occurs in a stage-wise manner and the regions that are functionally important form compact sub-domains and unfold at later stages. Our results assert that probe 'L' serves as an efficient tool to monitor subtle changes in protein structure and can be employed as a generic dye to study processes such as protein unfolding.
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Affiliation(s)
- Jessy Mariam
- Department of Chemistry, IIT Bombay, Mumbai-400076, India.
| | - Anila Hoskere Ashoka
- Analytical Science Discipline, CSIR-Central Salt and Marine Chemicals Research Institute, G.B. Marg, Bhavnagar: 364002, Gujarat, India
| | - Vandana Gaded
- Department of Chemistry, IIT Bombay, Mumbai-400076, India.
| | - Firoj Ali
- Analytical Science Discipline, CSIR-Central Salt and Marine Chemicals Research Institute, G.B. Marg, Bhavnagar: 364002, Gujarat, India
| | - Harshada Malvi
- Department of Chemistry, IIT Bombay, Mumbai-400076, India.
| | - Amitava Das
- Analytical Science Discipline, CSIR-Central Salt and Marine Chemicals Research Institute, G.B. Marg, Bhavnagar: 364002, Gujarat, India and Department of Chemical Sciences, Indian Institute of Science and Education Research, Kolkata, Mohanpur: 742246, India.
| | - Ruchi Anand
- Department of Chemistry, IIT Bombay, Mumbai-400076, India.
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11
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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: 121] [Impact Index Per Article: 40.3] [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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12
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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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13
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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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14
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Zheng X, Li Z, Gao W, Meng X, Li X, Luk LYP, Zhao Y, Tsai YH, Wu C. Condensation of 2-((Alkylthio)(aryl)methylene)malononitrile with 1,2-Aminothiol as a Novel Bioorthogonal Reaction for Site-Specific Protein Modification and Peptide Cyclization. J Am Chem Soc 2020; 142:5097-5103. [DOI: 10.1021/jacs.9b11875] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Xiaoli Zheng
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Zhuoru Li
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Wei Gao
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Xiaoting Meng
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
| | - Xuefei Li
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
| | - Louis Y. P. Luk
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
| | - Yibing Zhao
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
| | - Chuanliu Wu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
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15
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Nödling AR, Spear LA, Williams TL, Luk LYP, Tsai YH. Using genetically incorporated unnatural amino acids to control protein functions in mammalian cells. Essays Biochem 2019; 63:237-266. [PMID: 31092687 PMCID: PMC6610526 DOI: 10.1042/ebc20180042] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 02/07/2023]
Abstract
Genetic code expansion allows unnatural (non-canonical) amino acid incorporation into proteins of interest by repurposing the cellular translation machinery. The development of this technique has enabled site-specific incorporation of many structurally and chemically diverse amino acids, facilitating a plethora of applications, including protein imaging, engineering, mechanistic and structural investigations, and functional regulation. Particularly, genetic code expansion provides great tools to study mammalian proteins, of which dysregulations often have important implications in health. In recent years, a series of methods has been developed to modulate protein function through genetically incorporated unnatural amino acids. In this review, we will first discuss the basic concept of genetic code expansion and give an up-to-date list of amino acids that can be incorporated into proteins in mammalian cells. We then focus on the use of unnatural amino acids to activate, inhibit, or reversibly modulate protein function by translational, optical or chemical control. The features of each approach will also be highlighted.
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Affiliation(s)
| | - Luke A Spear
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Thomas L Williams
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
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16
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Beyene AG, Yang SJ, Landry MP. Review Article: Tools and trends for probing brain neurochemistry. JOURNAL OF VACUUM SCIENCE & TECHNOLOGY. A, VACUUM, SURFACES, AND FILMS : AN OFFICIAL JOURNAL OF THE AMERICAN VACUUM SOCIETY 2019; 37:040802. [PMID: 31235991 PMCID: PMC6559927 DOI: 10.1116/1.5051047] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/10/2018] [Accepted: 04/29/2019] [Indexed: 05/08/2023]
Abstract
The brain is composed of complex neuronal networks that interact on spatial and temporal scales that span several orders of magnitude. Uncovering how this circuitry gives rise to multifaceted phenomena such as perception, memory, and behavior remains one of the grand challenges in science today. A wide range of investigative methods have been developed to delve deeper into the inner workings of the brain, spanning the realms of molecular biology, genetics, chemistry, optics, and engineering, thereby forming a nexus of discovery that has accelerated our understanding of the brain. Whereas neuronal electrical excitability is a hallmark property of neurons, chemical signaling between neurons-mediated by hundreds of neurotransmitters, neuromodulators, hormones, and other signaling molecules-is equally important, but far more elusive in its regulation of brain function for motor control, learning, and behavior. To date, the brain's neurochemical state has been interrogated using classical tools borrowed from analytical chemistry, such as liquid chromatography and amperometry, and more recently, newly developed fluorescent sensors. Here, the authors review advances in the development of functional fluorescent probes that are beginning to expand their understanding of the neurochemical basis of brain function alongside device-based analytical tools that have already made extensive contributions to the field. The emphasis herein is on the paradigms of probe and device development, which follow certain design principles unique to the interrogation of brain chemistry.
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Affiliation(s)
- Abraham G Beyene
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720
| | - Sarah J Yang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720
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17
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Yeh HW, Ai HW. Development and Applications of Bioluminescent and Chemiluminescent Reporters and Biosensors. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:129-150. [PMID: 30786216 PMCID: PMC6565457 DOI: 10.1146/annurev-anchem-061318-115027] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Although fluorescent reporters and biosensors have become indispensable tools in biological and biomedical fields, fluorescence measurements require external excitation light, thereby limiting their use in thick tissues and live animals. Bioluminescent reporters and biosensors may potentially overcome this hurdle because they use enzyme-catalyzed exothermic biochemical reactions to generate excited-state emitters. This review first introduces the development of bioluminescent reporters, and next, their applications in sensing biological changes in vitro and in vivo as biosensors. Lastly, we discuss chemiluminescent sensors that produce photons in the absence of luciferases. This review aims to explore fundamentals and experimental insights and to emphasize the yet-to-be-reached potential of next-generation luminescent reporters and biosensors.
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Affiliation(s)
- Hsien-Wei Yeh
- Center for Membrane and Cell Physiology, Department of Molecular Physiology and Biological Physics, and Department of Chemistry, University of Virginia, Charlottesville, Virginia 22908, USA;
| | - Hui-Wang Ai
- Center for Membrane and Cell Physiology, Department of Molecular Physiology and Biological Physics, and Department of Chemistry, University of Virginia, Charlottesville, Virginia 22908, USA;
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18
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Graphene Oxide-Based Nanostructured DNA Sensor. BIOSENSORS-BASEL 2019; 9:bios9020074. [PMID: 31151203 PMCID: PMC6627418 DOI: 10.3390/bios9020074] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/17/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022]
Abstract
Quick detection of DNA sequence is vital for many fields, especially, early-stage diagnosis. Here, we develop a graphene oxide-based fluorescence quenching sensor to quickly and accurately detect small amounts of a single strand of DNA. In this paper, fluorescent magnetic nanoparticles (FMNPs) modified with target DNA sequence (DNA-t) were bound onto the modified graphene oxide acting as the fluorescence quenching element. FMNPs are made of iron oxide (Fe3O4) core and fluorescent silica (SiO2) shell. The average particle size of FMNPs was 74 ± 6 nm and the average thickness of the silica shell, estimated from TEM results, was 30 ± 4 nm. The photoluminescence and magnetic properties of FMNPs have been investigated. Target oligonucleotide (DNA-t) was conjugated onto FMNPs through glutaraldehyde crosslinking. Meanwhile, graphene oxide (GO) nanosheets were produced by a modified Hummers method. A complementary oligonucleotide (DNA-c) was designed to interact with GO. In the presence of GO-modified with DNA-c, the fluorescence intensity of FMNPs modified with DNA-t was quenched through a FRET quenching mechanism. Our study indicates that FMNPs can not only act as a FRET donor, but also enhance the sensor accuracy by magnetically separating the sensing system from free DNA and non-hybridized GO. Results indicate that this sensing system is ideal to detect small amounts of DNA-t with limitation detection at 0.12 µM.
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19
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Wang J, Liu L, Xu W, Yang Z, Yan Y, Xie X, Wang Y, Yi T, Wang C, Hua J. Mitochondria-Targeted Ratiometric Fluorescent Probe Based on Diketopyrrolopyrrole for Detecting and Imaging of Endogenous Superoxide Anion in Vitro and in Vivo. Anal Chem 2019; 91:5786-5793. [DOI: 10.1021/acs.analchem.9b00014] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jian Wang
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Lingyan Liu
- Department of Chemistry, Fudan University, 2005 Songhu Road, Shanghai 200438, PR China
| | - Weibo Xu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, PR China
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, PR China
| | - Zhicheng Yang
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Yongchao Yan
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Xiaoxu Xie
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Yu Wang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, PR China
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, PR China
| | - Tao Yi
- Department of Chemistry, Fudan University, 2005 Songhu Road, Shanghai 200438, PR China
| | - Chengyun Wang
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Jianli Hua
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
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20
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Zou X, Zhou X, Cao C, Lu W, Yuan W, Liu Q, Feng W, Li F. Dye-sensitized upconversion nanocomposites for ratiometric semi-quantitative detection of hypochlorite in vivo. NANOSCALE 2019; 11:2959-2965. [PMID: 30693936 DOI: 10.1039/c8nr09531k] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Ratiometric fluorescent sensors, which can provide a built-in correction for environmental effects, have attracted significant attention for analytical sensing and optical imaging with the potential to provide a precise and quantitative analysis. Herein, we report a strategy based on dye-sensitized upconversion for the design of dual-excitation upconverion ratiometric probes possessing same emission peaks under a large separation in the excitation spectra (980 nm and 808 nm). Specifically, effective enhancement of upconversion luminescence could be attributed to Cy787 dyes present on the surface of nanoparticles, and it subsequently decreased upon the addition of ClO- under an 808 nm irradiation, whereas the signal under 980 nm excitation remained essentially constant, thus allowing for quantitative ratiometric monitoring of ClO-. The rationally designed dye-sensitized upconverion nanosystem exhibits excellent sensitivity for ClO- with a quantification limit of 3.6 nM in aqueous solutions. We have also demonstrated that the designed nanoprobe is a promising material for semi-quantitative detection of ClO- in an arthritis mouse model.
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Affiliation(s)
- Xianmei Zou
- Department of Chemistry & State Key Laboratory of Molecular Engineering of Polymers & Collaborative Innovation Center of Chemistry for Energy Material, Fudan University, Shanghai, 200433, P. R. China.
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21
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Deo C, Lavis LD. Synthetic and genetically encoded fluorescent neural activity indicators. Curr Opin Neurobiol 2018; 50:101-108. [DOI: 10.1016/j.conb.2018.01.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/19/2017] [Accepted: 01/10/2018] [Indexed: 10/18/2022]
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22
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Abstract
Our understanding of the complex molecular processes of living organisms at the molecular level is growing exponentially. This knowledge, together with a powerful arsenal of tools for manipulating the structures of macromolecules, is allowing chemists to to harness and reprogram the cellular machinery in ways previously unimaged. Here we review one example in which the genetic code itself has been expanded with new building blocks that allow us to probe and manipulate the structures and functions of proteins with unprecedented precision.
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Affiliation(s)
- Douglas D. Young
- Department of Chemistry, College of William & Mary,
P.O. Box 8795, Williamsburg, VA 23187 (USA)
| | - Peter G. Schultz
- Department of Chemistry, The Scripps Research Institute,
La Jolla, CA 92037 (USA),
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23
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Abstract
Chemically constructed biosensors consisting of a protein scaffold and an artificial small molecule have recently been recognized as attractive analytical tools for the specific detection and real-time monitoring of various biological substances or events in cells. Conventionally, such semisynthetic biosensors have been prepared in test tubes and then introduced into cells using invasive methods. With the impressive advances seen in bioorthogonal protein conjugation methodologies, however, it is now becoming feasible to directly construct semisynthetic biosensors in living cells, providing unprecedented tools for life-science research. We discuss here recent efforts regarding the in situ construction of protein-based semisynthetic biosensors and highlight their uses in the visualization and quantification of biomolecules and events in multimolecular and crowded cellular systems.
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Affiliation(s)
- Tsuyoshi Ueda
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- CREST(Core Research for Evolutional Science and Technology, JST), Sanbancho, Chiyodaku, Tokyo, 102-0075, Japan
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24
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Wu Z, Zhang G, Sharman E, Cui P, Jiang J. Structure-dependent luminescence of tetra-(4-pyridylphenyl)ethylene: a first-principles study. Phys Chem Chem Phys 2018; 20:41-45. [DOI: 10.1039/c7cp06643k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The relationship between the molecular structure and fluorescence properties of TPPE was investigated by TDDFT calculations.
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Affiliation(s)
- Ziye Wu
- School of Chemistry and Materials Science
- Hefei National Laboratory for Physical Sciences at the Microscale
- University of Science and Technology of China (USTC)
- Hefei
- China
| | - Guozhen Zhang
- School of Chemistry and Materials Science
- Hefei National Laboratory for Physical Sciences at the Microscale
- University of Science and Technology of China (USTC)
- Hefei
- China
| | - Edward Sharman
- Department of Neurology
- University of California
- Irvine
- USA
| | - Peng Cui
- School of Chemistry and Materials Science
- Hefei National Laboratory for Physical Sciences at the Microscale
- University of Science and Technology of China (USTC)
- Hefei
- China
| | - Jun Jiang
- School of Chemistry and Materials Science
- Hefei National Laboratory for Physical Sciences at the Microscale
- University of Science and Technology of China (USTC)
- Hefei
- China
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25
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Arts R, Ludwig SKJ, van Gerven BCB, Estirado EM, Milroy LG, Merkx M. Semisynthetic Bioluminescent Sensor Proteins for Direct Detection of Antibodies and Small Molecules in Solution. ACS Sens 2017; 2:1730-1736. [PMID: 29037030 PMCID: PMC5706068 DOI: 10.1021/acssensors.7b00695] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/17/2017] [Indexed: 01/07/2023]
Abstract
Single-step immunoassays that can be performed directly in solution are ideally suited for point-of-care diagnostics. Our group recently developed a new platform of bioluminescent sensor proteins (LUMABS; LUMinescent AntiBody Sensor) that allow antibody detection in blood plasma. Thus far, LUMABS has been limited to the detection of antibodies recognizing natural peptide epitopes. Here, we report the development of semisynthetic LUMABS sensors that recognize nonpeptide epitopes. The non-natural amino acid para-azidophenylalanine was introduced at the position of the original antibody-recognition sites as a chemical handle to enable site-specific conjugation of synthetic epitope molecules coupled to a dibenzocylcooctyne moiety via strain-promoted click chemistry. The approach was successfully demonstrated by developing semisynthetic LUMABS sensors for antibodies targeting the small molecules dinitrophenol and creatinine (DNP-LUMABS and CR-LUMABS) with affinities of 5.8 pM and 1.3 nM, respectively. An important application of these semisynthetic LUMABS is the detection of small molecules using a competitive assay format, which is demonstrated here for the detection of creatinine. Using a preassembled complex of CR-LUMABS and an anti-creatinine antibody, the detection of high micromolar concentrations of creatinine was possible both in buffer and in 1:1 diluted blood plasma. The use of semisynthetic LUMABS sensors significantly expands the range of antibody targets and enables the application of LUMABS sensors for the ratiometric bioluminescent detection of small molecules using a competitive immunoassay format.
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Affiliation(s)
- Remco Arts
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Susann K. J. Ludwig
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Benice C. B. van Gerven
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Eva Magdalena Estirado
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
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26
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Chin JW. Expanding and reprogramming the genetic code. Nature 2017; 550:53-60. [PMID: 28980641 DOI: 10.1038/nature24031] [Citation(s) in RCA: 496] [Impact Index Per Article: 70.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/22/2017] [Indexed: 12/13/2022]
Abstract
Nature uses a limited, conservative set of amino acids to synthesize proteins. The ability to genetically encode an expanded set of building blocks with new chemical and physical properties is transforming the study, manipulation and evolution of proteins, and is enabling diverse applications, including approaches to probe, image and control protein function, and to precisely engineer therapeutics. Underpinning this transformation are strategies to engineer and rewire translation. Emerging strategies aim to reprogram the genetic code so that noncanonical biopolymers can be synthesized and evolved, and to test the limits of our ability to engineer the translational machinery and systematically recode genomes.
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Affiliation(s)
- Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.,Department of Chemistry, Cambridge University, Cambridge CB2 1EW, UK
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27
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Hiblot J, Yu Q, Sabbadini MD, Reymond L, Xue L, Schena A, Sallin O, Hill N, Griss R, Johnsson K. Luciferases with Tunable Emission Wavelengths. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708277] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Julien Hiblot
- Ecole Polytechnique Fédérale de Lausanne, EPFL; Institute of Chemical Sciences and Engineering, ISIC, NCCR in Chemical Biology; 1015 Lausanne Switzerland
- Max-Planck-Institute for Medical Research; Department of Chemical Biology; 69120 Heidelberg Germany
| | - Qiuliyang Yu
- Ecole Polytechnique Fédérale de Lausanne, EPFL; Institute of Chemical Sciences and Engineering, ISIC, NCCR in Chemical Biology; 1015 Lausanne Switzerland
- Max-Planck-Institute for Medical Research; Department of Chemical Biology; 69120 Heidelberg Germany
| | - Marina D.B. Sabbadini
- Ecole Polytechnique Fédérale de Lausanne, EPFL; Institute of Chemical Sciences and Engineering, ISIC, NCCR in Chemical Biology; 1015 Lausanne Switzerland
| | - Luc Reymond
- Ecole Polytechnique Fédérale de Lausanne, EPFL; Institute of Chemical Sciences and Engineering, ISIC, NCCR in Chemical Biology; 1015 Lausanne Switzerland
| | - Lin Xue
- Ecole Polytechnique Fédérale de Lausanne, EPFL; Institute of Chemical Sciences and Engineering, ISIC, NCCR in Chemical Biology; 1015 Lausanne Switzerland
- Max-Planck-Institute for Medical Research; Department of Chemical Biology; 69120 Heidelberg Germany
| | - Alberto Schena
- Ecole Polytechnique Fédérale de Lausanne, EPFL; Institute of Chemical Sciences and Engineering, ISIC, NCCR in Chemical Biology; 1015 Lausanne Switzerland
| | - Olivier Sallin
- Ecole Polytechnique Fédérale de Lausanne, EPFL; Institute of Chemical Sciences and Engineering, ISIC, NCCR in Chemical Biology; 1015 Lausanne Switzerland
| | - Nicholas Hill
- Ecole Polytechnique Fédérale de Lausanne, EPFL; Institute of Chemical Sciences and Engineering, ISIC, NCCR in Chemical Biology; 1015 Lausanne Switzerland
| | - Rudolf Griss
- Ecole Polytechnique Fédérale de Lausanne, EPFL; Institute of Chemical Sciences and Engineering, ISIC, NCCR in Chemical Biology; 1015 Lausanne Switzerland
| | - Kai Johnsson
- Ecole Polytechnique Fédérale de Lausanne, EPFL; Institute of Chemical Sciences and Engineering, ISIC, NCCR in Chemical Biology; 1015 Lausanne Switzerland
- Max-Planck-Institute for Medical Research; Department of Chemical Biology; 69120 Heidelberg Germany
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28
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Hiblot J, Yu Q, Sabbadini MD, Reymond L, Xue L, Schena A, Sallin O, Hill N, Griss R, Johnsson K. Luciferases with Tunable Emission Wavelengths. Angew Chem Int Ed Engl 2017; 56:14556-14560. [DOI: 10.1002/anie.201708277] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Julien Hiblot
- Ecole Polytechnique Fédérale de Lausanne, EPFL; Institute of Chemical Sciences and Engineering, ISIC, NCCR in Chemical Biology; 1015 Lausanne Switzerland
- Max-Planck-Institute for Medical Research; Department of Chemical Biology; 69120 Heidelberg Germany
| | - Qiuliyang Yu
- Ecole Polytechnique Fédérale de Lausanne, EPFL; Institute of Chemical Sciences and Engineering, ISIC, NCCR in Chemical Biology; 1015 Lausanne Switzerland
- Max-Planck-Institute for Medical Research; Department of Chemical Biology; 69120 Heidelberg Germany
| | - Marina D.B. Sabbadini
- Ecole Polytechnique Fédérale de Lausanne, EPFL; Institute of Chemical Sciences and Engineering, ISIC, NCCR in Chemical Biology; 1015 Lausanne Switzerland
| | - Luc Reymond
- Ecole Polytechnique Fédérale de Lausanne, EPFL; Institute of Chemical Sciences and Engineering, ISIC, NCCR in Chemical Biology; 1015 Lausanne Switzerland
| | - Lin Xue
- Ecole Polytechnique Fédérale de Lausanne, EPFL; Institute of Chemical Sciences and Engineering, ISIC, NCCR in Chemical Biology; 1015 Lausanne Switzerland
- Max-Planck-Institute for Medical Research; Department of Chemical Biology; 69120 Heidelberg Germany
| | - Alberto Schena
- Ecole Polytechnique Fédérale de Lausanne, EPFL; Institute of Chemical Sciences and Engineering, ISIC, NCCR in Chemical Biology; 1015 Lausanne Switzerland
| | - Olivier Sallin
- Ecole Polytechnique Fédérale de Lausanne, EPFL; Institute of Chemical Sciences and Engineering, ISIC, NCCR in Chemical Biology; 1015 Lausanne Switzerland
| | - Nicholas Hill
- Ecole Polytechnique Fédérale de Lausanne, EPFL; Institute of Chemical Sciences and Engineering, ISIC, NCCR in Chemical Biology; 1015 Lausanne Switzerland
| | - Rudolf Griss
- Ecole Polytechnique Fédérale de Lausanne, EPFL; Institute of Chemical Sciences and Engineering, ISIC, NCCR in Chemical Biology; 1015 Lausanne Switzerland
| | - Kai Johnsson
- Ecole Polytechnique Fédérale de Lausanne, EPFL; Institute of Chemical Sciences and Engineering, ISIC, NCCR in Chemical Biology; 1015 Lausanne Switzerland
- Max-Planck-Institute for Medical Research; Department of Chemical Biology; 69120 Heidelberg Germany
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29
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Reactivity of 7-Azanorbornenes in Bioorthogonal Inverse Electron-Demand Diels-Alder Reactions. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700411] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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30
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Kuriki Y, Komatsu T, Ycas PD, Coulup SK, Carlson EJ, Pomerantz WCK. Meeting Proceedings ICBS2016-Translating the Power of Chemical Biology to Clinical Advances. ACS Chem Biol 2017; 12:869-877. [PMID: 28303709 DOI: 10.1021/acschembio.7b00205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Yugo Kuriki
- Graduate School
of Pharmaceutical Sciences, University of Tokyo, 7-3-1, Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toru Komatsu
- Graduate School
of Pharmaceutical Sciences, University of Tokyo, 7-3-1, Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
- Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Peter D. Ycas
- Department of Chemistry, University of Minnesota, 312 Smith
Hall, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
| | - Sara K. Coulup
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware Street, SE, Minneapolis, Minnesota 55414, United States
| | - Erick J. Carlson
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware Street, SE, Minneapolis, Minnesota 55414, United States
| | - William C. K. Pomerantz
- Department of Chemistry, University of Minnesota, 312 Smith
Hall, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware Street, SE, Minneapolis, Minnesota 55414, United States
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31
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Abstract
FRET-sensors have become important tools for intracellular imaging, but their dependence on external illumination presents some limitations, such as photobleaching and phototoxicity, which limit measurements over extended periods of time. Fluorescence measurements also suffer from autofluorescence and light scattering, which hampers in vivo imaging and measurements in strongly absorbing and scattering media such as blood. In principle, these issues can be resolved by using sensors based on bioluminescence resonance energy transfer (BRET). The recent development of brighter and more stable luciferases and the concomitant improvement in luciferase substrates have substantially decreased the sensitivity gap between fluorescence and bioluminescence. As a result, the application of BRET-sensors is no longer restricted to measurements on cell populations, but they can also be used for imaging of single living cells, and BRET has started to emerge as an attractive sensor format for point-of-care diagnostics. The aim of this chapter is to first provide a brief overview of the basic design principles for BRET-sensors. Next, important design considerations will be discussed in more detail by describing the development of three different classes of BRET-sensors, both from our own work and that of others. These examples are all based on the NanoLuc luciferase, a bright and very stable blue light-emitting luciferase developed by Promega that has quickly risen to prominence in the bioluminescence field.
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Affiliation(s)
- Remco Arts
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Stijn J A Aper
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
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32
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Wang Z, Luo M, Mao C, Wei Q, Zhao T, Li Y, Huang G, Gao J. A Redox-Activatable Fluorescent Sensor for the High-Throughput Quantification of Cytosolic Delivery of Macromolecules. Angew Chem Int Ed Engl 2016; 56:1319-1323. [PMID: 27981718 DOI: 10.1002/anie.201610302] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Indexed: 12/19/2022]
Abstract
Efficient delivery of biomacromolecules (e.g., proteins, nucleic acids) into cell cytosol remains a critical challenge for the development of macromolecular therapeutics or diagnostics. To date, most common approaches to assess cytosolic delivery rely on fluorescent labeling of macromolecules with an "always on" reporter and subcellular imaging of endolysosomal escape by confocal microscopy. This strategy is limited by poor signal-to-noise ratio and only offers low throughput, qualitative information. Herein we describe a quantitative redox-activatable sensor (qRAS) for the real-time monitoring of cytosolic delivery of macromolecules. qRAS-labeled macromolecules are silent (off) inside the intact endocytic organelles, but can be turned on by redox activation after endolysosomal disruption and delivery into the cytosol, thereby greatly improving the detection accuracy. In addition to confocal microscopy, this quantitative sensing technology allowed for a high-throughput screening of a panel of polymer carriers toward efficient cytosolic delivery of model proteins on a plate reader. The simple and versatile qRAS design offers a useful tool for the investigation of new strategies for endolysosomal escape of biomacromolecules to facilitate the development of macromolecular therapeutics for a variety of disease indications.
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Affiliation(s)
- Zhaohui Wang
- Department of Pharmacology, Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Min Luo
- Department of Pharmacology, Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Chengqiong Mao
- Department of Pharmacology, Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Qi Wei
- Department of Pharmacology, Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Tian Zhao
- Department of Pharmacology, Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Yang Li
- Department of Pharmacology, Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Gang Huang
- Department of Pharmacology, Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Jinming Gao
- Department of Pharmacology, Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
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33
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Wang Z, Luo M, Mao C, Wei Q, Zhao T, Li Y, Huang G, Gao J. A Redox‐Activatable Fluorescent Sensor for the High‐Throughput Quantification of Cytosolic Delivery of Macromolecules. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610302] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Zhaohui Wang
- Department of Pharmacology Harold C. Simmons Comprehensive Cancer Center UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas TX 75390 USA
| | - Min Luo
- Department of Pharmacology Harold C. Simmons Comprehensive Cancer Center UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas TX 75390 USA
| | - Chengqiong Mao
- Department of Pharmacology Harold C. Simmons Comprehensive Cancer Center UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas TX 75390 USA
| | - Qi Wei
- Department of Pharmacology Harold C. Simmons Comprehensive Cancer Center UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas TX 75390 USA
| | - Tian Zhao
- Department of Pharmacology Harold C. Simmons Comprehensive Cancer Center UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas TX 75390 USA
| | - Yang Li
- Department of Pharmacology Harold C. Simmons Comprehensive Cancer Center UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas TX 75390 USA
| | - Gang Huang
- Department of Pharmacology Harold C. Simmons Comprehensive Cancer Center UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas TX 75390 USA
| | - Jinming Gao
- Department of Pharmacology Harold C. Simmons Comprehensive Cancer Center UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas TX 75390 USA
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34
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Wang L, Ma R, Jiang L, Jia L, Jia W, Wang H. A novel "signal-on/off" sensing platform for selective detection of thrombin based on target-induced ratiometric electrochemical biosensing and bio-bar-coded nanoprobe amplification strategy. Biosens Bioelectron 2016; 92:390-395. [PMID: 27836592 DOI: 10.1016/j.bios.2016.10.089] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/27/2016] [Accepted: 10/28/2016] [Indexed: 10/20/2022]
Abstract
A novel dual-signal ratiometric electrochemical aptasensor for highly sensitive and selective detection of thrombin has been designed on the basis of signal-on and signal-off strategy. Ferrocene labeled hairpin probe (Fc-HP), thrombin aptamer and methyl blue labeled bio-bar-coded AuNPs (MB-P3-AuNPs) were rationally introduced for the construction of the assay platform, which combined the advantages of the recognition of aptamer, the amplification of bio-bar-coded nanoprobe, and the ratiometric signaling readout. In the presence of thrombin, the interaction between thrombin and the aptamer leads to the departure of MB-P3-AuNPs from the sensing interface, and the conformation of the single stranded Fc-HP to a hairpin structure to take the Fc confined near the electrode surface. Such conformational changes resulted in the oxidation current of Fc increased and that of MB decreased. Therefore, the recognition event of the target can be dual-signal ratiometric electrochemical readout in both the "signal-off" of MB and the "signal-on" of Fc. The proposed strategy showed a wide linear detection range from 0.003 to 30nM with a detection limit of 1.1 pM. Moreover, it exhibits good performance of excellent selectivity, good stability, and acceptable fabrication reproducibility. By changing the recognition probe, this protocol could be easily expanded into the detection of other targets, showing promising potential applications in disease diagnostics and bioanalysis.
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Affiliation(s)
- Lanlan Wang
- Department of Chemistry, Liaocheng University, Liaocheng 252059, Shandong, PR China
| | - Rongna Ma
- Department of Chemistry, Liaocheng University, Liaocheng 252059, Shandong, PR China.
| | - Liushan Jiang
- Department of Chemistry, Liaocheng University, Liaocheng 252059, Shandong, PR China
| | - Liping Jia
- Department of Chemistry, Liaocheng University, Liaocheng 252059, Shandong, PR China
| | - Wenli Jia
- Department of Chemistry, Liaocheng University, Liaocheng 252059, Shandong, PR China
| | - Huaisheng Wang
- Department of Chemistry, Liaocheng University, Liaocheng 252059, Shandong, PR China.
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35
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Ohta Y, Kamagata T, Mukai A, Takada S, Nagai T, Horikawa K. Nontrivial Effect of the Color-Exchange of a Donor/Acceptor Pair in the Engineering of Förster Resonance Energy Transfer (FRET)-Based Indicators. ACS Chem Biol 2016; 11:1816-22. [PMID: 27232891 DOI: 10.1021/acschembio.6b00221] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genetically encoded indicators driven by the Förster resonance energy transfer (FRET) mechanism are reliable tools for live imaging. While the properties of FRET-based indicators have been improved over the years, they often suffer from a poor dynamic range due to the lack of comprehensive understanding about how to apply an appropriate strategy to optimize the FRET parameters. One of the most successful optimizations is the incorporation of circularly permuted fluorescent proteins (cpFPs). To better understand the effects of this strategy, we systematically investigated the properties of the indicators by utilizing a set of FRET backbones consisting of native or one of the most effective cp variants (cp173FPs) with considerations of their order. As a result, the ordering of donor and acceptor FPs, which has been ignored in previous studies, was found to significantly affect the dynamic range of indicators. By utilizing these backbones, we succeeded in improving a cGMP indicator with 3.6-fold increased dynamic range and in generating an ultrasensitive cAMP indicator capable of environmental imaging, demonstrating the practical importance of the ordering of donors and acceptors in the engineering of FRET-based indicators.
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Affiliation(s)
- Yusaku Ohta
- Division
of Bioimaging, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15 Kuramoto-cho, Tokushima
City, Tokushima 770-8503, Japan
| | - Takanori Kamagata
- Division
of Bioimaging, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15 Kuramoto-cho, Tokushima
City, Tokushima 770-8503, Japan
- Okazaki
Institute for Integrative Bioscience and National Institute for Basic
Biology, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
| | - Asuka Mukai
- Division
of Bioimaging, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15 Kuramoto-cho, Tokushima
City, Tokushima 770-8503, Japan
| | - Shinji Takada
- Okazaki
Institute for Integrative Bioscience and National Institute for Basic
Biology, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
| | - Takeharu Nagai
- The
Institute of Scientific and Industrial Research, Osaka University, Mihogaoka
8-1, Ibaraki, Osaka 567-0047, Japan
| | - Kazuki Horikawa
- Division
of Bioimaging, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15 Kuramoto-cho, Tokushima
City, Tokushima 770-8503, Japan
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