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Liu L, Ma N, Wang L, Zhang Y, Wan YZ, Wang T, Qian W. Development of a Methodology Based on Optical Interferometry for Measuring Fibrinolytic Activity. Anal Chem 2024; 96:13482-13493. [PMID: 39094103 DOI: 10.1021/acs.analchem.4c01646] [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: 08/04/2024]
Abstract
Fibrinolytic activity assay is particularly important for the detection, diagnosis, and treatment of cardiovascular disease and the development of fibrinolytic drugs. A novel efficacious strategy for real-time and label-free dynamic detection of fibrinolytic activity based on ordered porous layer interferometry (OPLI) was developed. Fibrin or a mixture of fibrin and plasminogen (Plg) was loaded into the highly ordered silica colloidal crystal (SCC) film scaffold to construct a fibrinolytic response interference layer to measure fibrinolytic activity with different mechanisms of action. Fibrinolytic enzyme-triggered fibrinolysis led to the migration of interference fringes in the interferogram, which could be represented by optical thickness changes (ΔOT) tracked in real time by the OPLI system. The morphology and optical property of the fibrinolytic response interference layer were characterized, and the Plg content in the fibrinolytic response interference layer and experimental parameters of the system were optimized. The method showed adequate sensitivity for the fibrinolytic activity of lumbrokinase and streptokinase, with wide linear ranges of 12-6000 and 10-2000 U/mL, respectively. Compared with the traditional fibrin plate method, it has a lower detection limit and higher linearity. The whole kinetic process of fibrinolysis by these two fibrinolytic drug models was recorded in real time, and the Michaelis constant and apparent kinetic parameters were calculated. Importantly, some other blood proteins were less interfering with this system, and it showed reliability in fibrin activity detection in real whole blood samples. This study established a better and more targeted research method of in vitro fibrinolysis and provided dynamic monitoring data for the analysis of fibrinolytic activity of whole blood.
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Affiliation(s)
- Liming Liu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Ning Ma
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Lu Wang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yu Zhang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yi-Zhen Wan
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Tianze Wang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Weiping Qian
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- OPLI (Suzhou) Biotechnology Company Limited, New District, Suzhou 215163, China
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Yin S, Siahaan EA, Niu L, Shibata M, Liu Y, Hagiwara T. Real time monitoring and evaluation of the inhibition effect of fucoxanthin against α-amylase activity by using QCM-A. Front Nutr 2023; 9:1110615. [PMID: 36712503 PMCID: PMC9877462 DOI: 10.3389/fnut.2022.1110615] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 12/30/2022] [Indexed: 01/13/2023] Open
Abstract
The main symptoms of diabetes are hyperglycemia and insulin resistance. The inhibition of the starch digestion enzymes could effectively regulate starch digestion and glucose absorption, thereby slowing or treating the symptoms of postprandial hyperglycemia. Herein, we used fucoxanthin isolated from Undaria pinnatifida stems, as α-amylase inhibitor, and monitored the interactions of both biomolecules by using quartz crystal microbalance-admittance (QCM-A) instrument. All the processes of α-amylase hydrolysis of starch were also dynamically tracked by using amylose-immobilized QCM technology. In our work, we found that the kinetic parameter (k off, k on, and k cat) values obtained by the QCM-A analysis were relatively consistent compared to the kinetic parameter values obtained by the conventional Michaelis-Menten analysis. For the inhibitory reactions, the results showed that fucoxanthin significantly reduced the activity of α-amylase in a dose-dependent manner. The QCM-A technology shown to be an excellent approach in obtaining comprehensive and accurate kinetic parameters, thereby providing real and accurate data for kinetic studies. It is helpful to clarify the mechanism of action of fucoxanthin on α-amylase, which further proved the potential of fucoxanthin to improve and treat postprandial hyperglycemia.
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Affiliation(s)
- Shipeng Yin
- State Key Laboratory of Food Science and Technology, National Engineering Laboratory for Cereal Fermentation Technology, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Evi Amelia Siahaan
- Research Centre for Marine and Land Bioindustry, National Research and Innovation Agency, Bogor, Indonesia
| | - Liqiong Niu
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Mario Shibata
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Technology, National Engineering Laboratory for Cereal Fermentation Technology, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Tomoaki Hagiwara
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
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Gagliardi M, Agostini M, Lunardelli F, Miranda A, Luminare AG, Cervelli F, Gambineri F, Cecchini M. A Surface Acoustic Wave (SAW)-Based Lab-on-Chip for the Detection of Active α-Glycosidase. BIOSENSORS 2022; 12:1010. [PMID: 36421128 PMCID: PMC9688093 DOI: 10.3390/bios12111010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/03/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Enzyme detection in liquid samples is a complex laboratory procedure, based on assays that are generally time- and cost-consuming, and require specialized personnel. Surface acoustic wave sensors can be used for this application, overcoming the cited limitations. To give our contribution, in this work we present the bottom-up development of a surface acoustic wave biosensor to detect active α-glycosidase in aqueous solutions. Our device, optimized to work at an ultra-high frequency (around 740 MHz), is functionalized with a newly synthesized probe 7-mercapto-1-eptyl-D-maltoside, bringing one maltoside terminal moiety. The probe is designed ad hoc for this application and tested in-cuvette to analyze the enzymatic conversion kinetics at different times, temperatures and enzyme concentrations. Preliminary data are used to optimize the detection protocol with the SAW device. In around 60 min, the SAW device is able to detect the enzymatic conversion of the maltoside unit into glucose in the presence of the active enzyme. We obtained successful α-glycosidase detection in the concentration range 0.15-150 U/mL, with an increasing signal in the range up to 15 U/mL. We also checked the sensor performance in the presence of an enzyme inhibitor as a control test, with a signal decrease of 80% in the presence of the inhibitor. The results demonstrate the synergic effect of our SAW Lab-on-a-Chip and probe design as a valid alternative to conventional laboratory tests.
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Affiliation(s)
- Mariacristina Gagliardi
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro, 56127 Pisa, Italy
| | - Matteo Agostini
- INTA S.R.L., Intelligent Acoustics Systems, Via Nino Pisano 14, 56122 Pisa, Italy
| | - Francesco Lunardelli
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro, 56127 Pisa, Italy
- INTA S.R.L., Intelligent Acoustics Systems, Via Nino Pisano 14, 56122 Pisa, Italy
| | - Alessio Miranda
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro, 56127 Pisa, Italy
| | | | | | | | - Marco Cecchini
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro, 56127 Pisa, Italy
- INTA S.R.L., Intelligent Acoustics Systems, Via Nino Pisano 14, 56122 Pisa, Italy
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4
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Raguin A, Ebenhöh O. Design starch: stochastic modeling of starch granule biogenesis. Biochem Soc Trans 2017; 45:885-893. [PMID: 28673938 PMCID: PMC5652221 DOI: 10.1042/bst20160407] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/15/2017] [Accepted: 05/19/2017] [Indexed: 12/03/2022]
Abstract
Starch is the most widespread and abundant storage carbohydrate in plants and the main source of carbohydrate in the human diet. Owing to its remarkable properties and commercial applications, starch is still of growing interest. Its unique granular structure made of intercalated layers of amylopectin and amylose has been unraveled thanks to recent progress in microscopic imaging, but the origin of such periodicity is still under debate. Both amylose and amylopectin are made of linear chains of α-1,4-bound glucose residues, with branch points formed by α-1,6 linkages. The net difference in the distribution of chain lengths and the branching pattern of amylose (mainly linear), compared with amylopectin (racemose structure), leads to different physico-chemical properties. Amylose is an amorphous and soluble polysaccharide, whereas amylopectin is insoluble and exhibits a highly organized structure of densely packed double helices formed between neighboring linear chains. Contrarily to starch degradation that has been investigated since the early 20th century, starch production is still poorly understood. Most enzymes involved in starch growth (elongation, branching, debranching, and partial hydrolysis) are now identified. However, their specific action, their interplay (cooperative or competitive), and their kinetic properties are still largely unknown. After reviewing recent results on starch structure and starch growth and degradation enzymatic activity, we discuss recent results and current challenges for growing polysaccharides on granular surface. Finally, we highlight the importance of novel stochastic models to support the analysis of recent and complex experimental results, and to address how macroscopic properties emerge from enzymatic activity and structural rearrangements.
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Affiliation(s)
- Adélaïde Raguin
- Institute of Quantitative and Theoretical Biology, Heinrich-Heine University, Düsseldorf 40225, Germany
| | - Oliver Ebenhöh
- Institute of Quantitative and Theoretical Biology, Heinrich-Heine University, Düsseldorf 40225, Germany
- Cluster of Excellence on Plant Sciences, Institute of Quantitative and Theoretical Biology, Heinrich-Heine University, Düsseldorf 40225, Germany
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5
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O'Neill EC, Field RA. Underpinning Starch Biology with in vitro Studies on Carbohydrate-Active Enzymes and Biosynthetic Glycomaterials. Front Bioeng Biotechnol 2015; 3:136. [PMID: 26442250 PMCID: PMC4561517 DOI: 10.3389/fbioe.2015.00136] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 08/24/2015] [Indexed: 12/21/2022] Open
Abstract
Starch makes up more than half of the calories in the human diet and is also a valuable bulk commodity that is used across the food, brewing and distilling, medicines and renewable materials sectors. Despite its importance, our understanding of how plants make starch, and what controls the deposition of this insoluble, polymeric, liquid crystalline material, remains rather limited. Advances are hampered by the challenges inherent in analyzing enzymes that operate across the solid-liquid interface. Glyconanotechnology, in the form of glucan-coated sensor chips and metal nanoparticles, present novel opportunities to address this problem. Herein, we review recent developments aimed at the bottom-up generation and self-assembly of starch-like materials, in order to better understand which enzymes are required for starch granule biogenesis and metabolism.
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Affiliation(s)
- Ellis C O'Neill
- Department of Plant Sciences, University of Oxford , Oxford , UK
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park , Norwich , UK
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6
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Raja DS, Liu WL, Huang HY, Lin CH. Immobilization of Protein on Nanoporous Metal-Organic Framework Materials. COMMENT INORG CHEM 2015. [DOI: 10.1080/02603594.2015.1059827] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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7
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Fang Y, Wu J, Xu ZK. Dextransucrase-catalyzed elongation of polysaccharide brushes with immobilized mono-/di-saccharides as acceptors. Chem Commun (Camb) 2015; 51:129-32. [PMID: 25383964 DOI: 10.1039/c4cc06137c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A quartz crystal microbalance (QCM) was used to monitor dextransucrase (DSase)-catalyzed polysaccharide elongation on the glucose-/maltose-ended self-assembly monolayer (SAM) surfaces. Kinetic parameters of the enzymatic elongation indicate that maltose is a promising substrate acceptor for DSase.
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Affiliation(s)
- Yan Fang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China.
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8
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Huang Y, Zhang Q, Liu G, Zhao R. A continuous-flow mass biosensor for the real-time dynamic analysis of protease inhibition. Chem Commun (Camb) 2015; 51:6601-4. [DOI: 10.1039/c5cc00885a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A flow injection analysis–quartz crystal microbalance (FIA–QCM) biosensor system was introduced for probing the dynamic interactions during protease inhibition.
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Affiliation(s)
- Yanyan Huang
- Beijing National Laboratory for Molecular Sciences
- CAS Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Qundan Zhang
- Beijing National Laboratory for Molecular Sciences
- CAS Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Guoquan Liu
- Beijing National Laboratory for Molecular Sciences
- CAS Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Rui Zhao
- Beijing National Laboratory for Molecular Sciences
- CAS Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
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9
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Gray CJ, Weissenborn MJ, Eyers CE, Flitsch SL. Enzymatic reactions on immobilised substrates. Chem Soc Rev 2014; 42:6378-405. [PMID: 23579870 DOI: 10.1039/c3cs60018a] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This review gives an overview of enzymatic reactions that have been conducted on substrates attached to solid surfaces. Such biochemical reactions have become more important with the drive to miniaturisation and automation in chemistry, biology and medicine. Technical aspects such as choice of solid surface and analytical methods are discussed and examples of enzyme reactions that have been successful on these surfaces are provided.
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Affiliation(s)
- Christopher J Gray
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Road, Manchester, M1 7DN, UK
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10
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O'Neill EC, Rashid AM, Stevenson CEM, Hetru AC, Gunning AP, Rejzek M, Nepogodiev SA, Bornemann S, Lawson DM, Field RA. Sugar-coated sensor chip and nanoparticle surfaces for the in vitro enzymatic synthesis of starch-like materials. Chem Sci 2014. [DOI: 10.1039/c3sc51829a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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11
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Bouchet-Spinelli A, Reuillard B, Coche-Guérente L, Armand S, Labbé P, Fort S. Oligosaccharide biosensor for direct monitoring of enzymatic activities using QCM-D. Biosens Bioelectron 2013; 49:290-6. [PMID: 23774166 DOI: 10.1016/j.bios.2013.05.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 05/13/2013] [Accepted: 05/20/2013] [Indexed: 11/30/2022]
Abstract
Enzymatic modification of saccharidic biomass is a subject of intensive research with potential applications in plant or human health, design of biomaterials and biofuel production. Bioengineering and metagenomics provide access to libraries of glycoside hydrolases but the biochemical characterization of these enzymes remains challenging, requiring fastidious colorimetric tests in discontinuous assays. Here, we describe a highly sensitive carbohydrate biosensor for the detection and characterization of glycoside hydrolases. Immobilization of oligosaccharides was achieved using copper-catalyzed azide-alkyne cycloaddition of maltoheptaose-modified probes onto self-assembled monolayers bearing azide reactive groups. This biosensor allowed detection of glycoside hydrolase activities at the picomolar level using quartz-crystal microbalance with dissipation monitoring (QCM-D). To our knowledge, this protocol provides the best performance to date for the detection of glycoside hydrolase activities. For each enzyme tested, we could determine the kinetic constant from the QCM-D data, and derive conclusions that correlated well with those of standard colorimetric tests. This opens the way to a new generation of rapid and direct tests characterizing functionally carbohydrate-active enzymes.
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Affiliation(s)
- Aurélie Bouchet-Spinelli
- Centre de Recherches sur les Macromolécules Végétales (CERMAV-CNRS), affiliated with Université de Grenoble, 38041 Grenoble cedex 9, France.
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12
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Anne A, Demaille C. Kinetics of enzyme action on surface-attached substrates: a practical guide to progress curve analysis in any kinetic situation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:14665-14671. [PMID: 22978617 DOI: 10.1021/la3030827] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In the present work, exact kinetic equations describing the action of an enzyme in solution on a substrate attached to a surface have been derived in the framework of the Michaelis-Menten mechanism but without resorting to the often-used steady-state approximation. The here-derived kinetic equations are cast in a workable format, allowing us to introduce a simple and universal procedure for the quantitative analysis of enzyme surface kinetics that is valid for any kinetic situation. The results presented here should allow experimentalists studying the kinetics of enzyme action on immobilized substrates to analyze their data in a perfectly rigorous way.
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Affiliation(s)
- Agnès Anne
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
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13
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Anne A, Chovin A, Demaille C. Optimizing electrode-attached redox-peptide systems for kinetic characterization of protease action on immobilized substrates. Observation of dissimilar behavior of trypsin and thrombin enzymes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:8804-8813. [PMID: 22591015 DOI: 10.1021/la301316r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In this work, we experimentally address the issue of optimizing gold electrode attached ferrocene (Fc)-peptide systems for kinetic measurements of protease action. Considering human α-thrombin and bovine trypsin as proteases of interest, we show that the recurring problem of incomplete cleavage of the peptide layer by these enzymes can be solved by using ultraflat template-stripped gold, instead of polished polycrystalline gold, as the Fc-peptide bearing electrode material. We describe how these fragile surfaces can be mounted in a rotating disk configuration so that enzyme mass transfer no longer limits the overall measured cleavage kinetics. Finally, we demonstrate that, once the system has been optimized, in situ real-time cyclic voltammetry monitoring of the protease action can yield high-quality kinetic data, showing no sign of interfering effects. The cleavage progress curves then closely match the Langmuirian variation expected for a kinetically controlled surface process. Global fit of the progress curves yield accurate values of the peptide cleavage rate for both trypsin and thrombin. It is shown that, whereas trypsin action on the surface-attached peptide closely follows Michaelis-Menten kinetics, thrombin displays a specific and unexpected behavior characterized by a nearly enzyme-concentration-independent cleavage rate in the subnanomolar enzyme concentration range. The reason for this behavior has still to be clarified, but its occurrence may limit the sensitivity of thrombin sensors based on Fc-peptide layers.
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Affiliation(s)
- Agnès Anne
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Univ Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France.
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14
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Mori T, Kodera T, Yoshimine H, Kakuta Y, Sugiura N, Kimata K, Okahata Y. Kinetics of Iterative Carbohydrate Transfer to Polysaccharide Catalyzed by Chondroitin Polymerase on a Highly Sensitive Flow-Type 27 MHz Quartz-Crystal Microbalance. Chemistry 2012; 18:7388-93. [DOI: 10.1002/chem.201200342] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Indexed: 11/07/2022]
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15
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Fang Y, Xu W, Wu J, Xu ZK. Enzymatic transglycosylation of PEG brushes by β-galactosidase. Chem Commun (Camb) 2012; 48:11208-10. [DOI: 10.1039/c2cc35369e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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16
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Cheng CI, Chang YP, Chu YH. Biomolecular interactions and tools for their recognition: focus on the quartz crystal microbalance and its diverse surface chemistries and applications. Chem Soc Rev 2012; 41:1947-71. [DOI: 10.1039/c1cs15168a] [Citation(s) in RCA: 170] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Mori T, Asakura M, Okahata Y. Single-Molecule Force Spectroscopy for Studying Kinetics of Enzymatic Dextran Elongations. J Am Chem Soc 2011; 133:5701-3. [DOI: 10.1021/ja200094f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Nihira T, Mori T, Asakura M, Okahata Y. Kinetic studies of dextransucrase enzyme reactions on a substrate- or enzyme-immobilized 27 MHz quartz crystal microbalance. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:2107-2111. [PMID: 21280619 DOI: 10.1021/la104550m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Catalytic elongation by dextransucrase (DSase) was monitored directly on a dextran-acceptor- or DSase-immobilized 27 MHz quartz crystal microbalance (QCM). Kinetic parameters for the binding of the enzyme to the dextran acceptor (k(on), k(off), and K(d)) and enzymatic elongation in the presence of a sucrose monomer (K(m) for sucrose and k(cat)) were determined. The kinetic parameters obtained by both methods were consistent.
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Affiliation(s)
- Takanori Nihira
- Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501 Japan
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19
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Su Z, Chen L, Liu Y, He X, Zhou Y, Xie Q, Yao S. 35MHz quartz crystal microbalance and surface plasmon resonance studies on the binding of angiotensin converting enzyme with lisinopril. Biosens Bioelectron 2011; 26:3240-5. [DOI: 10.1016/j.bios.2010.12.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 12/12/2010] [Accepted: 12/21/2010] [Indexed: 11/25/2022]
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20
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Mori T, Ohtsuka T, Okahata Y. Kinetic analyses of bindings of Shiga-like toxin to clustered and dispersed Gb3 glyco-arrays on a quartz-crystal microbalance. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:14118-14125. [PMID: 20666463 DOI: 10.1021/la102260k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
One-, two-, four-, and eight-branched globotriaosyl saccharides (Gb(3): Gal-alpha1,4-Gal-beta1,4-Glc), whose reducing ends were biotinylated, were prepared (1Gb(3)-bio, 2Gb(3)-bio, 4Gb(3)-bio, and 8Gb(3)-bio, respectively). They are dispersively immobilized as a glyco-array in the matrix of biotinylated maltotriose (Glc(3)-bio) on a streptavidin-covered 27 MHz quartz-crystal microbalance (QCM). The binding kinetics of the verotoxin B subunit (VTB) to various branched Gb(3)-bio ligands in the Glc(3)-bio matrix could be obtained from frequency decreases (mass increases) of the QCM. VTB can recognize the Gb(3) unit but not the Glc(3) unit, where VTB is a pentamer having five binding sites for one Gb(3) unit per each B subunit (having a total of 15 binding sites for Gb(3)). By changing the Gb(3) multivalency, the Gb(3) packing density, and the Gb(3) cluster size in the Glc(3) matrix, association constants (K(a)), maximum amounts bound (Delta m(max)), and binding and dissociation rate constants (k(on) and k(off)) were obtained. When 15 sites of VTB were recognized by 16 Gb(3) units, K(a) was 100 times larger than that when 15 sites of VTB were recognized by only 2 Gb(3) units, with a 6-fold-larger k(on) and a 25-fold-smaller k(off). When the Gb(3) multivalency was changed by covering with two 1Gb(3)-bio, 2Gb(3)-bio, 4Gb(3)-bio, or 8Gb(3)-bio ligands on two pockets of one streptavidin, the K(a) values increased with increasing branch number from one to eight. When the Gb(3) cluster size was changed from eight 1Gb(3)-bio units to one 8Gb(3)-bio unit in the matrix, the K(a) values increased but the Delta m(max) values decreased with increasing cluster size from eight 1Gb(3)-bio units to one 8Gb(3)-bio unit. This is the first example of systematically obtaining all kinetic parameters of sugar-binding proteins to sugars on a glyco-array by changing the sugar multivalency, the sugar packing density, and the sugar cluster size in the matrix.
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Affiliation(s)
- Toshiaki Mori
- Japan Science and Technology Agency-Precursory Research for Embryonic Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501 Japan.
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Clé C, Martin C, Field RA, Kuzmič P, Bornemann S. Detection of enzyme-catalyzed polysaccharide synthesis on surfaces. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.3109/10242420903388744] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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22
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Mori T, Toyoda M, Ohtsuka T, Okahata Y. Kinetic analyses for bindings of concanavalin A to dispersed and condensed mannose surfaces on a quartz crystal microbalance. Anal Biochem 2009; 395:211-6. [DOI: 10.1016/j.ab.2009.08.029] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2009] [Revised: 08/13/2009] [Accepted: 08/19/2009] [Indexed: 11/25/2022]
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23
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Bi X, Yang KL. On-line monitoring imidacloprid and thiacloprid in celery juice using quartz crystal microbalance. Anal Chem 2009; 81:527-32. [PMID: 19086904 DOI: 10.1021/ac801786a] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this article, we report a quartz crystal microbalance (QCM)-based detection method which allows the identification and quantification of two neonicotinoid pesticides, imidacloprid and thiacloprid, in aqueous solutions and celery juice. To achieve high selectivity, molecular imprinted monolayers (MIMs), which can either recognize 1 muM of imidacloprid or 1 muM of thiacloprid, are prepared from alkanethiols self-assembled on QCM sensor chips with preadsorbed templates (either imidacloprid or thiacloprid). Our experimental results show that the detection limit can be improved by using alkanethiols having longer hydrocarbon chains. For example, MIMs prepared from hexadecanethiol have dissociation constants 2-5 times smaller than those prepared from octanethiol. To detect two neonicotinoids in vegetable samples simultaneously, we also develop a new type of MIM with two different templates. A single QCM decorated with this MIM can respond to 10 muM of imidacloprid and 10 muM thiacloprid in celery juice in a real-time manner.
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Affiliation(s)
- Xinyan Bi
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore
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Furusawa H, Ozeki T, Morita M, Okahata Y. Added Mass Effect on Immobilizations of Proteins on a 27 MHz Quartz Crystal Microbalance in Aqueous Solution. Anal Chem 2009; 81:2268-73. [DOI: 10.1021/ac802412t] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hiroyuki Furusawa
- Department of Biomolecular Engineering, Tokyo Institute of Technology and SENTAN, JST, 4259 Nagatsuda, Midori-ku, Yokohama 226-8501, Japan, and Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Tomomitsu Ozeki
- Department of Biomolecular Engineering, Tokyo Institute of Technology and SENTAN, JST, 4259 Nagatsuda, Midori-ku, Yokohama 226-8501, Japan, and Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Mizuki Morita
- Department of Biomolecular Engineering, Tokyo Institute of Technology and SENTAN, JST, 4259 Nagatsuda, Midori-ku, Yokohama 226-8501, Japan, and Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yoshio Okahata
- Department of Biomolecular Engineering, Tokyo Institute of Technology and SENTAN, JST, 4259 Nagatsuda, Midori-ku, Yokohama 226-8501, Japan, and Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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25
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Furusawa H, Komatsu M, Okahata Y. In Situ Monitoring of Conformational Changes of and Peptide Bindings to Calmodulin on a 27 MHz Quartz-Crystal Microbalance. Anal Chem 2009; 81:1841-7. [DOI: 10.1021/ac8022229] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hiroyuki Furusawa
- Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Mayu Komatsu
- Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Yoshio Okahata
- Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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26
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Enzyme catalysis on solid surfaces. Trends Biotechnol 2008; 26:328-37. [DOI: 10.1016/j.tibtech.2008.03.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Revised: 03/10/2008] [Accepted: 03/11/2008] [Indexed: 11/20/2022]
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27
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Takahashi S, Matsuno H, Furusawa H, Okahata Y. Direct monitoring of allosteric recognition of type IIE restriction endonuclease EcoRII. J Biol Chem 2008; 283:15023-30. [PMID: 18367450 PMCID: PMC3258892 DOI: 10.1074/jbc.m800334200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Revised: 03/13/2008] [Indexed: 11/06/2022] Open
Abstract
EcoRII is a homodimer with two domains consisting of a DNA-binding N terminus and a catalytic C terminus and recognizes two specific sequences on DNA. It shows a relatively complicated cleavage reaction in bulk solution. After binding to either recognition site, EcoRII cleaves the other recognition site of the same DNA (cis-binding) strand and/or the recognition site of the other DNA (trans-binding) strand. Although it is difficult to separate these two reactions in bulk solution, we could simply obtain the binding and cleavage kinetics of only the cis-binding by following the frequency (mass) changes of a DNA-immobilized quartz-crystal microbalance (QCM) responding to the addition of EcoRII in aqueous solution. We obtained the maximum binding amounts (Deltam(max)), the dissociation constants (K(d)), the binding and dissociation rate constants (k(on) and k(off)), and the catalytic cleavage reaction rate constants (k(cat)) for wild-type EcoRII, the N-terminal-truncated form (EcoRII N-domain), and the mutant derivatives in its C-terminal domain (K263A and R330A). It was determined from the kinetic analyses that the N-domain, which covers the catalytic C-domain in the absence of DNA, preferentially binds to the one DNA recognition site while transforming EcoRII into an active form allosterically, and then the secondary C-domain binds to and cleaves the other recognition site of the DNA strand.
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Affiliation(s)
| | | | | | - Yoshio Okahata
- Frontier Research Center, Department of Biomolecular Engineering, Tokyo Institute of Technology, B-53 4259 Nagatsuda, Midori-ku, Yokohama, Japan
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28
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Takahashi S, Akita R, Matsuno H, Furusawa H, Shimizu Y, Ueda T, Okahata Y. 70 S Ribosomes Bind to Shine–Dalgarno Sequences without Required Dissociations. Chembiochem 2008; 9:870-3. [DOI: 10.1002/cbic.200700679] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Furusawa H, Takano H, Okahata Y. Transient kinetic studies of protein hydrolyses by endo- and exo-proteases on a 27 MHz quartz-crystal microbalance. Org Biomol Chem 2008; 6:727-31. [DOI: 10.1039/b717171d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Tang D, Yuan R, Chai Y. Quartz crystal microbalance immunoassay for carcinoma antigen 125 based on gold nanowire-functionalized biomimetic interface. Analyst 2008; 133:933-8. [DOI: 10.1039/b719389k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Takakusagi Y, Takakusagi K, Kuramochi K, Kobayashi S, Sugawara F, Sakaguchi K. Identification of C10 biotinylated camptothecin (CPT-10-B) binding peptides using T7 phage display screen on a QCM device. Bioorg Med Chem 2007; 15:7590-8. [PMID: 17897832 DOI: 10.1016/j.bmc.2007.09.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Revised: 09/05/2007] [Accepted: 09/06/2007] [Indexed: 11/20/2022]
Abstract
A peptide sequence that can bind to camptothecin (CPT), a natural cytotoxic compound, was screened for using a T7 phage display system combined with a cuvette type quartz crystal microbalance (QCM) device. In this screen, after only 10min of monitoring of the interaction between injected T7 phage pool with immobilized C10 biotinylated CPT (CPT-10-B) on a gold electrode surface, six different kinds of phage (A-F) were identified as judged by the size of PCR product on agarose gel electrophoresis. Injection of each single phage (A-E) pool individually caused a frequency decrease, suggesting interaction with the immobilized CPT-10-B. In addition, the peptide sequence displayed on phages A-C is consistent with chemical and biological studies of the interaction of CPTs with topoisomerase I (TopI), human E prostanoid receptor third cytoplasmic polypeptide, and a series of esterases. The efficacy of T7 phage display screening for small molecules on QCM devices, target discovery from primary peptide sequence, and application of this strategy to various drug-like small molecules are discussed.
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Affiliation(s)
- Yoichi Takakusagi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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32
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Takahashi S, Matsuno H, Furusawa H, Okahata Y. Monitoring of EcoRV Digestions on a DNA-immobilized Quartz Crystal Microbalance. CHEM LETT 2007. [DOI: 10.1246/cl.2007.230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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33
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Murakawa A, Mori T, Okahata Y. Direct Monitoring of Both Phosphorolysis and Elongation of Amylopectin Catalyzed by Phosphorylase on a 27-MHz Quartz-crystal Microbalance. CHEM LETT 2007. [DOI: 10.1246/cl.2007.312] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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34
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Cooper MA, Singleton VT. A survey of the 2001 to 2005 quartz crystal microbalance biosensor literature: applications of acoustic physics to the analysis of biomolecular interactions. J Mol Recognit 2007; 20:154-84. [PMID: 17582799 DOI: 10.1002/jmr.826] [Citation(s) in RCA: 294] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The widespread exploitation of biosensors in the analysis of molecular recognition has its origins in the mid-1990s following the release of commercial systems based on surface plasmon resonance (SPR). More recently, platforms based on piezoelectric acoustic sensors (principally 'bulk acoustic wave' (BAW), 'thickness shear mode' (TSM) sensors or 'quartz crystal microbalances' (QCM)), have been released that are driving the publication of a large number of papers analysing binding specificities, affinities, kinetics and conformational changes associated with a molecular recognition event. This article highlights salient theoretical and practical aspects of the technologies that underpin acoustic analysis, then reviews exemplary papers in key application areas involving small molecular weight ligands, carbohydrates, proteins, nucleic acids, viruses, bacteria, cells and lipidic and polymeric interfaces. Key differentiators between optical and acoustic sensing modalities are also reviewed.
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Affiliation(s)
- Matthew A Cooper
- Akubio Ltd., 181 Cambridge Science Park, Cambridge, United Kingdom, UK.
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35
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Manaka Y, Kudo Y, Yoshimine H, Kawasaki T, Kajikawa K, Okahata Y. Simultaneous anomalous reflection and quartz-crystal microbalance measurements of protein bindings on a gold surface. Chem Commun (Camb) 2007:3574-6. [DOI: 10.1039/b708901e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Hoshiba T, Cho CS, Murakawa A, Okahata Y, Akaike T. The effect of natural extracellular matrix deposited on synthetic polymers on cultured primary hepatocytes. Biomaterials 2006; 27:4519-28. [PMID: 16697038 DOI: 10.1016/j.biomaterials.2006.04.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Accepted: 04/12/2006] [Indexed: 11/27/2022]
Abstract
It is well known that natural extracellular matrix (ECM) molecules are deposited on the surface of biomaterials during culture of cells and affect cellular behaviors. However, it has not been fully understood what kinds of ECM molecules are deposited on the surface of biomaterials although the cellular behaviors were affected by deposited ECM. In this study, to investigate the effect of deposited natural ECM on behaviors of hepatocytes cultured on biomaterials such as poly (N-p-vinylbenzyl-4-O-beta-D-galactopyranosyl-D-gluconamide) (PVLA) as a hepatocyte-specific matrix and poly (L-lysine) (PLL) as a non-specific one during the culture of hepatocytes in vitro, we investigated expression pattern of ECM genes and adsorption of ECM molecules onto PVLA- and PLL-coated surfaces. It was found that the expression levels of type I collagen and fibronectin genes in the hepatocytes cultured on PVLA-coated surface were different from them in the hepatocytes cultured on PLL-coated one. Also, the results showed that laminin was dominantly deposited on PVLA-coated surface whereas fibronectin was dominantly deposited on PLL-coated one. Hepatocytes maintained liver-specific functions on PVLA- and laminin-coated surfaces. It is thought that deposited laminin during the culture of hepatocytes affects the liver-specific functions of hepatocytes cultured on PVLA-coated surface.
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Affiliation(s)
- Takashi Hoshiba
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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37
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Halling PJ, Ulijn RV, Flitsch SL. Understanding enzyme action on immobilised substrates. Curr Opin Biotechnol 2005; 16:385-92. [PMID: 16005203 DOI: 10.1016/j.copbio.2005.06.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2005] [Revised: 06/10/2005] [Accepted: 06/24/2005] [Indexed: 11/22/2022]
Abstract
With increasing interest in automated synthesis and screening protocols, solid supported chemistry and biochemistry are attractive technologies. Studies with surface-immobilised substrates have been carried out to analyse enzyme accessibility, kinetics and thermodynamics. Several interesting new methods have been developed to monitor enzyme action on substrates attached to a solid phase such as polymer beads glass or gold surfaces. These include fluorescence measurements, MALDI-TOF mass spectrometry, and the use of quartz crystal microbalances to measure weight changes of immobilised molecules directly on the surface. Approaches that allow spatial resolution in single beads have also been reported. The ability of enzymes to reach the inside of beads is becoming better characterised and new supports have been developed that allow improved accessibility. The equilibrium position of reactions on the solid surface can be substantially shifted compared with reactions in solution, and this can be usefully exploited using hydrolases in reverse. Research is also starting to tackle the way in which kinetics are modified when the substrates are surface immobilised.
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Affiliation(s)
- Peter J Halling
- Department of Pure & Applied Chemistry, University of Strathclyde, Glasgow G1 1XW, UK.
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