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Smith DD, Girodat D, Abbott DW, Wieden HJ. Construction of a highly selective and sensitive carbohydrate-detecting biosensor utilizing Computational Identification of Non-disruptive Conjugation sites (CINC) for flexible and streamlined biosensor design. Biosens Bioelectron 2022; 200:113899. [PMID: 34974264 DOI: 10.1016/j.bios.2021.113899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/18/2021] [Accepted: 12/16/2021] [Indexed: 01/30/2023]
Abstract
Fluorescently-labeled solute-binding proteins that alter their fluorescence output in response to ligand binding have been utilized as biosensors for a variety of applications. Coupling protein ligand binding to altered fluorescence output often requires trial and error-based testing of both multiple labeling positions and fluorophores to produce a functional biosensor with the desired properties. This approach is laborious and can lead to reduced ligand binding affinity or altered ligand specificity. Here we report the Computational Identification of Non-disruptive Conjugation sites (CINC) for streamlined identification of fluorophore conjugation sites. By exploiting the structural dynamics properties of proteins, CINC identifies positions where conjugation of a fluorophore results in a fluorescence change upon ligand binding without disrupting protein function. We show that a CINC-developed maltooligosaccharide (MOS)-detecting biosensor is capable of rapid (kon = 20 μM-1s-1), sensitive (sub-μM KD) and selective MOS detection. The MOS-detecting biosensor is modular with respect to the spectroscopic properties and demonstrates portability to detecting MOS released via α-amylase-catalyzed depolymerization of starch using both a stopped-flow and a microplate reader assay. Our MOS-detecting biosensor represents a first-in-class probe whose design was guided by changes in localized dynamics of individual amino acid positions, supporting expansion of the CINC pipeline as an indispensable tool for a wide range of protein engineering applications.
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Affiliation(s)
- Dustin D Smith
- Alberta RNA Research and Training Institute (ARRTI), University of Lethbridge, Lethbridge, AB, Canada; Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
| | - Dylan Girodat
- Alberta RNA Research and Training Institute (ARRTI), University of Lethbridge, Lethbridge, AB, Canada; Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
| | - D Wade Abbott
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada; Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Hans-Joachim Wieden
- Alberta RNA Research and Training Institute (ARRTI), University of Lethbridge, Lethbridge, AB, Canada; Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada; Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada.
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2
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Allert MJ, Hellinga HW. Discovery of Thermostable, Fluorescently Responsive Glucose Biosensors by Structure-Assisted Function Extrapolation. Biochemistry 2022; 61:276-293. [PMID: 35084821 DOI: 10.1021/acs.biochem.1c00738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate assignment of protein function from sequence remains a fascinating and difficult challenge. The periplasmic-binding protein (PBP) superfamily present an interesting case of function prediction because they are both ubiquitous in prokaryotes and tend to diversify through gene duplication "explosions" that can lead to large numbers of paralogs in a genome. An engineered version of the moderately thermostable glucose-binding PBP from Escherichia coli has been used successfully as a reagentless fluorescent biosensor both in vitro and in vivo. To develop more robust sensors that meet the challenges of real-world applications, we report the discovery of thermostable homologues that retain a glucose-mediated conformationally coupled fluorescence response. Accurately identifying a glucose-binding PBP homologue among closely related paralogs is challenging. We demonstrate that a structure-based method that filters sequences by residues that bind glucose in an archetype structure is highly effective. Using fully sequenced bacterial genomes, we found that this filter reduced high paralog numbers to single hits in a genome, consistent with the accurate separation of glucose binding from other functions. We expressed engineered proteins for eight homologues, chosen to represent different degrees of sequence identity, and tested their glucose-mediated fluorescence responses. We accurately predicted the presence of glucose binding down to 31% sequence identity. We have also successfully identified suitable candidates for next-generation robust, fluorescent glucose sensors.
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Affiliation(s)
- Malin J Allert
- Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, North Carolina 27710, United States
| | - Homme W Hellinga
- Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, North Carolina 27710, United States
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3
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Development of a Real-Time Pectic Oligosaccharide-Detecting Biosensor Using the Rapid and Flexible Computational Identification of Non-Disruptive Conjugation Sites (CINC) Biosensor Design Platform. SENSORS 2022; 22:s22030948. [PMID: 35161692 PMCID: PMC8839585 DOI: 10.3390/s22030948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 01/25/2023]
Abstract
Fluorescently labeled, solute-binding proteins that change their fluorescent output in response to ligand binding are frequently used as biosensors for a wide range of applications. We have previously developed a "Computational Identification of Non-disruptive Conjugation sites" (CINC) approach, an in silico pipeline utilizing molecular dynamics simulations for the rapid design and construction of novel protein-fluorophore conjugate-type biosensors. Here, we report an improved in silico scoring algorithm for use in CINC and its use in the construction of an oligogalacturonide-detecting biosensor set. Using both 4,5-unsaturated and saturated oligogalacturonides, we demonstrate that signal transmission from the ligand-binding pocket of the starting protein scaffold to the CINC-selected reporter positions is effective for multiple different ligands. The utility of an oligogalacturonide-detecting biosensor is shown in Carbohydrate Active Enzyme (CAZyme) activity assays, where the biosensor is used to follow product release upon polygalacturonic acid (PGA) depolymerization in real time. The oligogalacturonide-detecting biosensor set represents a novel enabling tool integral to our rapidly expanding platform for biosensor-based carbohydrate detection, and moving forward, the CINC pipeline will continue to enable the rational design of biomolecular tools to detect additional chemically distinct oligosaccharides and other solutes.
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4
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Periplasmic-binding protein-based biosensors and bioanalytical assay platforms: Advances, considerations, and strategies for optimal utility. TALANTA OPEN 2021. [DOI: 10.1016/j.talo.2021.100038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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5
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Bearham J, Krutrök N, Lindberg B, Woodall M, Astrand A, Taylor JD, Biggart M, Vasiljevs S, Tarran R, Baines DL. A modified fluorescent sensor for reporting glucose concentration in the airway lumen. PLoS One 2021; 16:e0254248. [PMID: 34242292 PMCID: PMC8270177 DOI: 10.1371/journal.pone.0254248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 06/23/2021] [Indexed: 11/19/2022] Open
Abstract
We have modified the periplasmic Escherichia coli glucose/galactose binding protein (GBP) and labelled with environmentally sensitive fluorophores to further explore its potential as a sensor for the evaluation of glucose concentration in airway surface liquid (ASL). We identified E149C/A213R GBP labelled with N,N'-Dimethyl-N-(iodoacetyl)-N'-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)ethylenediamine (IANBD, emission wavelength maximum 536nm) with a Kd for D-glucose of 1.02mM and a fluorescence dynamic range of 5.8. This sensor was specific for D-glucose and exhibited fluorescence stability in experiments for several hours. The use of E149C/A213R GBP-IANBD in the ASL of airway cells grown at air-liquid-interface (ALI) detected an increase in glucose concentration 10 minutes after raising basolateral glucose from 5 to 15mM. This sensor also reported a greater change in ASL glucose concentration in response to increased basolateral glucose in H441 airway cells compared to human bronchial epithelial cells (HBEC) and there was less variability with HBEC data than that of H441 indicating that HBEC more effectively regulate glucose movement into the ASL. The sensor detected glucose in bronchoalveolar lavage fluid (BALf) from diabetic db/db mice but not normoglycaemic wildtype mice, indicating limited sensitivity of the sensor at glucose concentrations <50μM. Using nasal inhalation of the sensor and spectral unmixing to generate images, E149C/A213R GBP-IANBD fluorescence was detected in luminal regions of cryosections of the murine distal lung that was greater in db/db than wildtype mice. In conclusion, this sensor provides a useful tool for further development to measure luminal glucose concentration in models of lung/airway to explore how this may change in disease.
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Affiliation(s)
- Jade Bearham
- Institute for Infection and Immunity, St George’s University of London, London, United Kingdom
| | - Nina Krutrök
- Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Botilda Lindberg
- Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Maximillian Woodall
- Institute for Infection and Immunity, St George’s University of London, London, United Kingdom
| | - Annika Astrand
- Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - John D. Taylor
- Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Matthew Biggart
- Institute for Infection and Immunity, St George’s University of London, London, United Kingdom
| | - Stanislavs Vasiljevs
- Institute for Infection and Immunity, St George’s University of London, London, United Kingdom
| | - Robert Tarran
- Department of Cell Biology & Physiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Deborah L. Baines
- Institute for Infection and Immunity, St George’s University of London, London, United Kingdom
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6
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Tankasala D, Linnes JC. Noninvasive glucose detection in exhaled breath condensate. Transl Res 2019; 213:1-22. [PMID: 31194942 PMCID: PMC6783357 DOI: 10.1016/j.trsl.2019.05.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 05/02/2019] [Accepted: 05/26/2019] [Indexed: 01/04/2023]
Abstract
Two-thirds of patients with diabetes avoid regularly monitoring their blood glucose levels because of the painful and invasive nature of current blood glucose detection. As an alternative to blood sample collection, exhaled breath condensate (EBC) has emerged as a promising noninvasive sample from which to monitor glucose levels. However, this dilute sample matrix requires sensors capable of detecting glucose with high resolution at nanomolar and micromolar concentrations. Recent developments in EBC collection methods and highly sensitive glucose biosensors provide a path toward enabling robust and sensitive glucose detection in EBC. This review addresses current and emerging EBC collection and glucose sensing modalities capable of quantifying glucose in EBC samples. We highlight the opportunities and challenges for development and integration of EBC glucose detection systems that will enable clinically robust and accurate EBC glucose measurements for improved glycemic control.
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Affiliation(s)
- Divya Tankasala
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana
| | - Jacqueline C Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana.
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7
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Li D, Su J, Yang J, Yu S, Zhang J, Xu K, Yu H. Optical surface plasmon resonance sensor modified by mutant glucose/galactose-binding protein for affinity detection of glucose molecules. BIOMEDICAL OPTICS EXPRESS 2017; 8:5206-5217. [PMID: 29188114 PMCID: PMC5695964 DOI: 10.1364/boe.8.005206] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 10/18/2017] [Accepted: 10/18/2017] [Indexed: 06/07/2023]
Abstract
Transdermal extraction of interstitial fluid (ISF) offers an attractive method for minimally invasive blood glucose monitoring. However, only a minute volume of ISF could be transdermally extracted, which is required to be diluted to form a manipulable volume of fluid for easy collection, transportation, and glucose detection. Therefore, a high-resolution glucose detection method is required for detecting glucose concentration in diluted ISF. In this paper, an optical surface plasmon resonance (SPR) sensor modified by the glucose/galactose-binding (GGB) protein which has good affinity to glucose molecules was presented for specific and sensitive glucose detection. The GGB protein was mutated at different sites for thiol coupling with the SPR surface and adjusting the affinity between glucose molecules and GGB protein. And the immobilization process of the GGB protein onto the surface of SPR sensor was optimized. Then, the stability of the SPR sensor modified with GGB protein was tested immediately and two weeks after immobilization. The coefficient of variation for glucose concentration measurement was less than 4.5%. By further mutation of the GGB protein at the A213S and L238S sites, the measurement range of the SPR sensor was adjusted to 0.1-100 mg/dL, which matches the glucose concentration range of 5-10 times diluted ISF (3-100 mg/dL). These results suggest that the SPR biosensor immobilized with GGB protein has the potential for continuous glucose monitoring by integrating into the microfluidic ISF extraction chip.
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Affiliation(s)
- Dachao Li
- School of Precision Instrument and Opto-Electronics Engineering at Tianjin University, Tianjin 300072, China
| | - Jie Su
- School of Precision Instrument and Opto-Electronics Engineering at Tianjin University, Tianjin 300072, China
| | - Jia Yang
- Tianjin Institute of Metrological Supervision and Testing, Tianjin 300192, China
| | - Songlin Yu
- Tianjin Institute of Metrological Supervision and Testing, Tianjin 300192, China
| | - Jingxin Zhang
- School of Precision Instrument and Opto-Electronics Engineering at Tianjin University, Tianjin 300072, China
| | - Kexin Xu
- School of Precision Instrument and Opto-Electronics Engineering at Tianjin University, Tianjin 300072, China
| | - Haixia Yu
- School of Precision Instrument and Opto-Electronics Engineering at Tianjin University, Tianjin 300072, China
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8
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Ibáñez-Fonseca A, Alonso M, Arias FJ, Rodríguez-Cabello JC. Förster Resonance Energy Transfer-Paired Hydrogel Forming Silk-Elastin-Like Recombinamers by Recombinant Conjugation of Fluorescent Proteins. Bioconjug Chem 2017; 28:828-835. [DOI: 10.1021/acs.bioconjchem.6b00738] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Arturo Ibáñez-Fonseca
- BIOFORGE Lab, University of Valladolid − CIBER-BBN, Paseo de Belén 19, 47011 Valladolid, Spain
| | - Matilde Alonso
- BIOFORGE Lab, University of Valladolid − CIBER-BBN, Paseo de Belén 19, 47011 Valladolid, Spain
| | - Francisco Javier Arias
- BIOFORGE Lab, University of Valladolid − CIBER-BBN, Paseo de Belén 19, 47011 Valladolid, Spain
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9
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Mitchell JA, Whitfield JH, Zhang WH, Henneberger C, Janovjak H, O’Mara ML, Jackson CJ. Rangefinder: A Semisynthetic FRET Sensor Design Algorithm. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00576] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joshua A. Mitchell
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| | - Jason H. Whitfield
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| | - William H. Zhang
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| | - Christian Henneberger
- Institute
of Neurology, University College London, London, WC1E 6BT, United Kingdom
- German Center for Neurodegenerative Diseases (DZNE), 53175 Bonn, Germany
- Institute
of Cellular Neurosciences, University of Bonn, 53113 Bonn, Germany
| | - Harald Janovjak
- Institute of Science and Technology, 3400 Klosterneuburg, Austria
| | - Megan L. O’Mara
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| | - Colin J. Jackson
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
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10
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Kasák P, Mosnáček J, Danko M, Krupa I, Hloušková G, Chorvát D, Koukaki M, Karamanou S, Economou A, Lacík I. A polysulfobetaine hydrogel for immobilization of a glucose-binding protein. RSC Adv 2016. [DOI: 10.1039/c6ra14423c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A hydrogel based on sulfobetaine methacrylate monomer and crosslinker was investigated as a potential material for fluorescent glucose biosensor applications.
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Affiliation(s)
- Peter Kasák
- Center for Advanced Materials
- Qatar University
- 2713 Doha
- Qatar
| | - Jaroslav Mosnáček
- Polymer Institute of the Slovak Academy of Sciences
- 845 41 Bratislava
- Slovakia
| | - Martin Danko
- Polymer Institute of the Slovak Academy of Sciences
- 845 41 Bratislava
- Slovakia
| | - Igor Krupa
- Center for Advanced Materials
- Qatar University
- 2713 Doha
- Qatar
| | - Gabriela Hloušková
- Polymer Institute of the Slovak Academy of Sciences
- 845 41 Bratislava
- Slovakia
| | | | | | - Spyridoula Karamanou
- KU Leuven
- Department of Microbiology and Immunology
- Rega Institute for Medical Research
- Laboratory of Molecular Bacteriology
- B-3000 Leuven
| | | | - Igor Lacík
- Polymer Institute of the Slovak Academy of Sciences
- 845 41 Bratislava
- Slovakia
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11
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Kameya M, Sakaguchi-Mikami A, Ferri S, Tsugawa W, Sode K. Advancing the development of glycated protein biosensing technology: next-generation sensing molecules. J Diabetes Sci Technol 2015; 9:183-91. [PMID: 25627465 PMCID: PMC4604589 DOI: 10.1177/1932296814565784] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Research advances in biochemical molecules have led to the development of convenient and reproducible biosensing molecules for glycated proteins, such as those based on the enzymes fructosyl amino acid oxidase (FAOX) or fructosyl peptide oxidase (FPOX). Recently, more attractive biosensing molecules with potential applications in next-generation biosensing of glycated proteins have been aggressively reported. We review 2 such molecules, fructosamine 6-kinase (FN6K) and fructosyl amino acid-binding protein, as well as their recent applications in the development of glycated protein biosensing systems. Research on FN6K and fructosyl amino acid-binding protein has been opening up new possibilities for the development of highly sensitive and proteolytic-digestion-free biosensing systems for glycated proteins.
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Affiliation(s)
- Miho Kameya
- Department of Biotechnology & Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Akane Sakaguchi-Mikami
- Department of Medical Technology, School of Health Sciences, Graduate School of Bionics, Computer and Media Sciences, Tokyo University of Technology, Tokyo, Japan
| | - Stefano Ferri
- Department of Biotechnology & Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Wakako Tsugawa
- Department of Biotechnology & Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Koji Sode
- Department of Biotechnology & Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan Ultizyme International Ltd, Tokyo, Japan
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12
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Near-infrared fluorescence glucose sensing based on glucose/galactose-binding protein coupled to 651-Blue Oxazine. Biochem Biophys Res Commun 2013; 438:488-92. [PMID: 23928160 DOI: 10.1016/j.bbrc.2013.07.111] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 07/28/2013] [Indexed: 01/14/2023]
Abstract
Near-infrared (NIR) fluorescent dyes that are environmentally sensitive or solvatochromic are useful tools for protein labelling in in vivo biosensor applications such as glucose monitoring in diabetes since their spectral properties are mostly independent of tissue autofluorescence and light scattering, and they offer potential for non-invasive analyte sensing. We showed that the fluorophore 651-Blue Oxazine is polarity-sensitive, with a marked reduction in NIR fluorescence on increasing solvent polarity. Mutants of glucose/galactose-binding protein (GBP) used as the glucose receptor were site-specifically and covalently labelled with Blue Oxazine using click chemistry. Mutants H152C/A213R and H152C/A213R/L238S showed fluorescence increases of 15% and 21% on addition of saturating glucose concentrations and binding constants of 6 and 25mM respectively. Fluorescence responses to glucose were preserved when GBP-Blue Oxazine was immobilised to agarose beads, and the beads were excited by NIR light through a mouse skin preparation studied in vitro. We conclude GBP-Blue Oxazine shows proof-of-concept as a non-invasive continuous glucose sensing system.
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