1
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Integrative metabolic flux analysis reveals an indispensable dimension of phenotypes. Curr Opin Biotechnol 2022; 75:102701. [DOI: 10.1016/j.copbio.2022.102701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/26/2022] [Accepted: 02/04/2022] [Indexed: 02/06/2023]
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2
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Wasilewski T, Brito NF, Szulczyński B, Wojciechowski M, Buda N, Melo ACA, Kamysz W, Gębicki J. Olfactory Receptor-based Biosensors as Potential Future Tools in Medical Diagnosis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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3
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The development of alginate-based amperometric nanoreactors for biochemical profiling of living yeast cells. Bioelectrochemistry 2022; 145:108082. [DOI: 10.1016/j.bioelechem.2022.108082] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 12/27/2022]
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4
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Soon JW, Oohora K, Hayashi T. A disulphide bond-mediated hetero-dimer of a hemoprotein and a fluorescent protein exhibiting efficient energy transfer †. RSC Adv 2022; 12:28519-28524. [PMID: 36320522 PMCID: PMC9535469 DOI: 10.1039/d2ra05249k] [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: 08/21/2022] [Accepted: 09/22/2022] [Indexed: 11/07/2022] Open
Abstract
Artificial protein hetero-dimerization is one of the promising strategies to construct protein-based chemical tools. In this work, cytochrome b562, an electron transfer hemoprotein, and green fluorescent protein (GFP) mutants with cysteine residues added to their surfaces were conjugated via a pyridyl disulphide-based thiol–disulfide exchange reaction. The eight hetero-dimers, which have cysteine residues at different positions to form the disulphide bonds, were obtained and characterized by gel-electrophoresis, mass spectrometry and size exclusion chromatography. The fluorescence properties of the hetero-dimers were evaluated by fluorescence spectroscopy and fluorescence lifetime measurements. Efficient photoinduced energy transfer from the GFP chromophore to the heme cofactor was observed in each of the hetero-dimers. The energy transfer efficiency is strongly dependent on the cross-linking residues, reaching 96%. Furthermore, the estimated Förster distance and the structure-based maximum possible distances of the donor and acceptor suggest that one of the hetero-dimers has a rigid protein–protein structure with favourable properties for energy transfer. The disulphide bond-mediated protein hetero-dimerization is useful for screening functional protein systems towards further developments. Hetero-dimerization of a hemoprotein and green fluorescent protein via a thiol–disulphide exchange reaction is achieved. The heterodimer has suitable cross-linking points and displays efficient energy transfer.![]()
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Affiliation(s)
- Julian Wong Soon
- Department of Applied Chemistry, Graduate School of Engineering, Osaka UniversitySuita565-0871Japan
| | - Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka UniversitySuita565-0871Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka UniversitySuita565-0871Japan
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5
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Recent advances in FRET-Based biosensors for biomedical applications. Anal Biochem 2021; 630:114323. [PMID: 34339665 DOI: 10.1016/j.ab.2021.114323] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/21/2021] [Accepted: 07/29/2021] [Indexed: 01/12/2023]
Abstract
Fluorescence resonance energy transfer (FRET)-based biosensors are effective analytical tools extensively used in fields of biomedicine, pharmacology, toxicology, and food sciences. Ratiometric imaging of substantial cellular processes, molecular components, and biological interactions is widely performed by these biosensors. A variety of FRET-based biosensors have provided comprehensive insights into underlying mechanisms of pathological conditions in live cells, tissues, and organisms. Moreover, integration of FRET-based biosensors with the current bioanalytical techniques allows for accurate, rapid, and sensitive diagnosis and proposes the advanced strategies for treatment. Precise analysis of ligand-receptor interactions by FRET-based biosensors has presented a basis for determination of novel therapeutic agents. Therefore, this study was designed to review the recent developments in FRET-based biosensors and their biomedical applications. In addition, characteristics, challenges, and outlooks of these biosensors were discussed.
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Hirata Y, Oda H, Osaki T, Takeuchi S. Biohybrid sensor for odor detection. LAB ON A CHIP 2021; 21:2643-2657. [PMID: 34132291 DOI: 10.1039/d1lc00233c] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Biohybrid odorant sensors that directly integrate a biological olfactory system have been increasingly studied and are suggested to be the next generation of ultrasensitive sensors by taking advantage of the sensitivity and selectivity of living organisms. In this review, we provide a detailed description of the recent developments of biohybrid odorant sensors, especially considering the requisites for their perspective of on-site applications. We introduce the methodologies to effectively capture the biological signals from olfactory systems by readout devices, and describe the essential properties regarding the gaseous detection, stability, quality control, and portability. Moreover, we address the recent progress on multiple odorant recognition using multiple sensors as well as the current screening approaches for pairs of orphan receptors and ligands necessary for the extension of the currently available range of biohybrid sensors. Finally, we discuss our perspectives for the future for the development of practical odorant sensors.
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Affiliation(s)
- Yusuke Hirata
- Department of Mechano-Informatics, Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Haruka Oda
- Department of Mechano-Informatics, Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Toshihisa Osaki
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan and Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Shoji Takeuchi
- Department of Mechano-Informatics, Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan. and Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan and Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
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7
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Feng H, Liu L, Chen Y, Shu W, Huang Y, Zhang B, Wu T, Jin Z, Chen Y. A compact fiber-integrated optofluidic platform for highly specific microRNA Förster resonance energy transfer detection. Analyst 2021; 146:4454-4460. [PMID: 33982715 DOI: 10.1039/d1an00324k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
MicroRNAs (miRNAs) have attracted extensive interest as promising biomarkers for the profiling of diseases. However, quantitative measurement of miRNAs presents a significant challenge in biochemical studies. In this work, we developed an innovative optofluidic platform to perform a rapid, simple, quantitative and high-specificity miRNA assay using the Förster resonance energy transfer (FRET) principle. A novel three-way junction FRET probe was proposed to enable rapid and enzyme-free miRNA detection. Using this platform, we performed one-step, amplification-free miRNA detection with simple device operation and achieved miRNA identification at a low concentration. The detection system could achieve high specificity for discrimination of three-base mismatches, and the sample volume was significantly reduced, favorable for low-level miRNA detection in material-limited samples. The establishment of a compact, low-cost, highly sensitive and selective miRNA analysis platform provides a valuable tool for point-of-care diagnosis.
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Affiliation(s)
- Hongtao Feng
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Lin Liu
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Yi Chen
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Weiliang Shu
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Yuqing Huang
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Baoyue Zhang
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Tianzhun Wu
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Zongwen Jin
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Yan Chen
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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Gonçalves F, Ribeiro A, Silva C, Cavaco-Paulo A. Biotechnological applications of mammalian odorant-binding proteins. Crit Rev Biotechnol 2021; 41:441-455. [PMID: 33541154 DOI: 10.1080/07388551.2020.1853672] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The olfactory system of mammals allows the detection and discrimination of thousands of odors from the environment. In mammals, odorant-binding proteins (OBPs) are considered responsible to carry odorant molecules across the aqueous nasal mucus to the olfactory receptors (ORs). The three-dimensional structure of these proteins presents eight antiparallel β-sheets and a short α-helical segment close to the C terminus, typical of the lipocalins family. The great ability of OBPs to bind differentiated ligand molecules has driven the research to understand the mechanisms underlying the OBP function in nature and the development of advanced biotechnological applications. This review describes the role of mammalian OBPs in the olfactory perception, highlighting the influence of several key parameters (amino acids, temperature, ionic strength, and pH) in the formation of the OBP/ligand complex. The information from the literature regarding OBP structure, affinity, the strength of binding, and stability inspiring the development of several applications herein detailed.
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Affiliation(s)
- Filipa Gonçalves
- Centre of Biological Engineering, University of Minho - Campus de Gualtar, Braga, Portugal
| | - Artur Ribeiro
- Centre of Biological Engineering, University of Minho - Campus de Gualtar, Braga, Portugal
| | - Carla Silva
- Centre of Biological Engineering, University of Minho - Campus de Gualtar, Braga, Portugal
| | - Artur Cavaco-Paulo
- Centre of Biological Engineering, University of Minho - Campus de Gualtar, Braga, Portugal
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9
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Hameed MK, Parambath JBM, Kanan SM, Mohamed AA. FRET-based fluorescent probe for drug assay from amino acid@gold-carbon nanoparticles. Anal Bioanal Chem 2021; 413:1117-1125. [PMID: 33409672 DOI: 10.1007/s00216-020-03075-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/02/2020] [Accepted: 11/16/2020] [Indexed: 12/31/2022]
Abstract
Biocompatible and luminescent nanostructures synthesized by capping gold-carbon nanoparticles (HOOC-4-C6H4-AuNPs) with amino acids tyrosine, tryptophan, and cysteine were used for the quantitative estimation of ranitidine (RNH), a peptic ulcer and gastroesophageal reflux drug. We applied a fluorescence quenching mechanism to investigate the viability of the energy transfer based on gold-carbon nanosensors. Förster resonance energy transfer (FRET) calculations showed a donor-acceptor distance of 1.69 nm (Tyr@AuNPs), 2.27 nm (Trp@AuNPs), and 2.32 nm (Cys@AuNPs). The constant time-resolved fluorescence lifetime measurements supported the static quenching nature. This method was successfully utilized in the detection and quantification of RNH, with a limit of detection (LOD) of 0.174, 0.56, and 0.332 μM for Tyr@AuNP, Trp@AuNP, and Cys@AuNP bioconjugates, respectively. This approach was also successful in the quantification of RNH in spiked serum samples.
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Affiliation(s)
- Mehavesh K Hameed
- Department of Chemistry, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Javad B M Parambath
- Department of Chemistry, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Sofian M Kanan
- Department of Biology, Chemistry and Environmental Sciences, American University of Sharjah, Sharjah, 26666, United Arab Emirates
| | - Ahmed A Mohamed
- Department of Chemistry, University of Sharjah, Sharjah, 27272, United Arab Emirates.
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10
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Soleja N, Irfan, Mohsin M. Ratiometric imaging of flux dynamics of cobalt with an optical sensor. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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12
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Reimann TM. Flow Chamber Assay to Image the Response of FRET-Based Nanosensors in Pollen Tubes to Changes in Medium Composition. Methods Mol Biol 2020; 2160:257-273. [PMID: 32529443 DOI: 10.1007/978-1-0716-0672-8_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Pollen tubes growing in the transmitting tract are presented with an extracellular matrix rich in a variety of substances. The expression of a multitude of genes for transport proteins in the pollen tube indicates that pollen tubes take up at least some of the components provided by the transmitting tract, for example nutrients, ions, or signaling molecules. FRET (Förster resonance energy transfer)-based nanosensors are perfectly suited to study the uptake of these molecules into pollen tubes. They are genetically encoded and can easily be expressed in Arabidopsis pollen tubes. Furthermore, the method is noninvasive and nanosensors for a wide range of substances are available. This chapter will describe the design of plasmids required to generate stable Arabidopsis lines with a pollen tube-specific expression of nanosensor constructs. We also present a method to germinate Arabidopsis pollen tubes in a flow chamber slide that allows the perfusion of the pollen tubes with liquid medium supplemented with the substrate of the nanosensor. Simultaneous evaluation of the FRET efficiency of the nanosensor by confocal microscopy reveals whether the substance is taken up by the pollen tubes. Together with the great number of available nanosensors this method can generate a detailed picture of the substances that are taken up during pollen tubes growth.
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Affiliation(s)
- Theresa Maria Reimann
- Department of Biology, Friedrich-Alexander University Erlangen Nuremberg, Erlangen, Germany.
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13
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Real time quantification of intracellular nickel using genetically encoded FRET-based nanosensor. Int J Biol Macromol 2019; 138:648-657. [DOI: 10.1016/j.ijbiomac.2019.07.115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/13/2019] [Accepted: 07/19/2019] [Indexed: 12/19/2022]
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14
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Soleja N, Jairajpuri MA, Queen A, Mohsin M. Genetically encoded FRET-based optical sensor for Hg 2+ detection and intracellular imaging in living cells. J Ind Microbiol Biotechnol 2019; 46:1669-1683. [PMID: 31531745 DOI: 10.1007/s10295-019-02235-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 09/05/2019] [Indexed: 12/31/2022]
Abstract
Due to the potential toxicity of mercury, there is an immediate need to understand its uptake, transport and flux within living cells. Conventional techniques used to analyze Hg2+ are invasive, involve high cost and are less sensitive. In the present study, a highly efficient genetically encoded mercury FRET sensor (MerFS) was developed to measure the cellular dynamics of Hg2+ at trace level in real time. To construct MerFS, the periplasmic mercury-binding protein MerP was sandwiched between enhanced cyan fluorescent protein (ECFP) and venus. MerFS is pH stable, offers a measurable fluorescent signal and binds to Hg2+ with high sensitivity and selectivity. Mutant MerFS-51 binds with an apparent affinity (Kd) of 5.09 × 10-7 M, thus providing a detection range for Hg2+ quantification between 0.210 µM and 1.196 µM. Furthermore, MerFS-51 was targeted to Escherichia coli (E. coli), yeast and human embryonic kidney (HEK)-293T cells that allowed dynamic measurement of intracellular Hg2+ concentration with a highly responsive saturation curve, proving its potential application in cellular systems.
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Affiliation(s)
- Neha Soleja
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | | | - Aarfa Queen
- Department of Chemistry, Jamia Millia Islamia, New Delhi, 110025, India
| | - Mohd Mohsin
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India.
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15
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Soleja N, Manzoor O, Khan P, Mohsin M. Engineering genetically encoded FRET-based nanosensors for real time display of arsenic (As 3+) dynamics in living cells. Sci Rep 2019; 9:11240. [PMID: 31375744 PMCID: PMC6677752 DOI: 10.1038/s41598-019-47682-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 07/12/2019] [Indexed: 02/07/2023] Open
Abstract
Arsenic poisoning has been a major concern that causes severe toxicological damages. Therefore, intricate and inclusive understanding of arsenic flux rates is required to ascertain the cellular concentration and establish the carcinogenetic mechanism of this toxicant at real time. The lack of sufficiently sensitive sensing systems has hampered research in this area. In this study, we constructed a fluorescent resonance energy transfer (FRET)-based nanosensor, named SenALiB (Sensor for Arsenic Linked Blackfoot disease) which contains a metalloregulatory arsenic-binding protein (ArsR) as the As3+ sensing element inserted between the FRET pair enhanced cyan fluorescent protein (ECFP) and Venus. SenALiB takes advantage of the ratiometic FRET readout which measures arsenic with high specificity and selectivity. SenALiB offers rapid detection response, is stable to pH changes and provides highly accurate, real-time optical readout in cell-based assays. SenALiB-676n with a binding constant (Kd) of 0.676 × 10−6 M is the most efficient affinity mutant and can be a versatile tool for dynamic measurement of arsenic concentration in both prokaryotes and eukaryotes in vivo in a non-invasive manner.
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Affiliation(s)
- Neha Soleja
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Ovais Manzoor
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Parvez Khan
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi, 110025, India
| | - Mohd Mohsin
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India.
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