1
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Cano-Garrido O, Serna N, Unzueta U, Parladé E, Mangues R, Villaverde A, Vázquez E. Protein scaffolds in human clinics. Biotechnol Adv 2022; 61:108032. [PMID: 36089254 DOI: 10.1016/j.biotechadv.2022.108032] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 07/30/2022] [Accepted: 09/03/2022] [Indexed: 11/02/2022]
Abstract
Fundamental clinical areas such as drug delivery and regenerative medicine require biocompatible materials as mechanically stable scaffolds or as nanoscale drug carriers. Among the wide set of emerging biomaterials, polypeptides offer enticing properties over alternative polymers, including full biocompatibility, biodegradability, precise interactivity, structural stability and conformational and functional versatility, all of them tunable by conventional protein engineering. However, proteins from non-human sources elicit immunotoxicities that might bottleneck further development and narrow their clinical applicability. In this context, selecting human proteins or developing humanized protein versions as building blocks is a strict demand to design non-immunogenic protein materials. We review here the expanding catalogue of human or humanized proteins tailored to execute different levels of scaffolding functions and how they can be engineered as self-assembling materials in form of oligomers, polymers or complex networks. In particular, we emphasize those that are under clinical development, revising their fields of applicability and how they have been adapted to offer, apart from mere mechanical support, highly refined functions and precise molecular interactions.
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Affiliation(s)
- Olivia Cano-Garrido
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain
| | - Naroa Serna
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 08193 Cerdanyola del Vallès (Barcelona), Spain
| | - Ugutz Unzueta
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 08193 Cerdanyola del Vallès (Barcelona), Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain; Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025 Barcelona, Spain; Josep Carreras Leukaemia Research Institute, 08916 Badalona (Barcelona), Spain
| | - Eloi Parladé
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 08193 Cerdanyola del Vallès (Barcelona), Spain
| | - Ramón Mangues
- Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025 Barcelona, Spain; Josep Carreras Leukaemia Research Institute, 08916 Badalona (Barcelona), Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 08193 Cerdanyola del Vallès (Barcelona), Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain.
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 08193 Cerdanyola del Vallès (Barcelona), Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain.
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2
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Dong J, Salem DP, Sun JH, Strano MS. Analysis of Multiplexed Nanosensor Arrays Based on Near-Infrared Fluorescent Single-Walled Carbon Nanotubes. ACS NANO 2018; 12:3769-3779. [PMID: 29614219 DOI: 10.1021/acsnano.8b00980] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The high-throughput, label-free detection of biomolecules remains an important challenge in analytical chemistry with the potential of nanosensors to significantly increase the ability to multiplex such assays. In this work, we develop an optical sensor array, printable from a single-walled carbon nanotube/chitosan ink and functionalized to enable a divalent ion-based proximity quenching mechanism for transducing binding between a capture protein or an antibody with the target analyte. Arrays of 5 × 6, 200 μm near-infrared (nIR) spots at a density of ≈300 spots/cm2 are conjugated with immunoglobulin-binding proteins (proteins A, G, and L) for the detection of human IgG, mouse IgM, rat IgG2a, and human IgD. Binding kinetics are measured in a parallel, multiplexed fashion from each sensor spot using a custom laser scanning imaging configuration with an nIR photomultiplier tube detector. These arrays are used to examine cross-reactivity, competitive and nonspecific binding of analyte mixtures. We find that protein G and protein L functionalized sensors report selective responses to mouse IgM on the latter, as anticipated. Optically addressable platforms such as the one examined in this work have potential to significantly advance the real-time, multiplexed biomolecular detection of complex mixtures.
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Affiliation(s)
- Juyao Dong
- Department of Chemical Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Daniel P Salem
- Department of Chemical Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Jessica H Sun
- Department of Chemical Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Michael S Strano
- Department of Chemical Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
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3
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Berto M, Diacci C, D'Agata R, Pinti M, Bianchini E, Lauro MD, Casalini S, Cossarizza A, Berggren M, Simon D, Spoto G, Biscarini F, Bortolotti CA. EGOFET Peptide Aptasensor for Label-Free Detection of Inflammatory Cytokines in Complex Fluids. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/adbi.201700072] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Marcello Berto
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Chiara Diacci
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Roberta D'Agata
- Dipartimento di Scienze Chimiche; Università di Catania; V.le A. Doria 6 95131 Catania
| | - Marcello Pinti
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Elena Bianchini
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Michele Di Lauro
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Stefano Casalini
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Andrea Cossarizza
- Dipartimento di Scienze Mediche e Chirurgiche Materno-Infantili e dell'Adulto; Università di Modena e Reggio Emilia; Via Campi 287 41125 Modena Italy
| | - Magnus Berggren
- Laboratory of Organic Electronics; Department of Science and Technology; ITN; Linköping University; S-601 74 Norrköping Sweden
| | - Daniel Simon
- Laboratory of Organic Electronics; Department of Science and Technology; ITN; Linköping University; S-601 74 Norrköping Sweden
| | - Giuseppe Spoto
- Dipartimento di Scienze Chimiche; Università di Catania; V.le A. Doria 6 95131 Catania
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici; c/o Dipartimento di Scienze Chimiche; Università di Catania; Viale Andrea Doria 6 95131 Catania Italy
| | - Fabio Biscarini
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Carlo A. Bortolotti
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
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4
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Abstract
Biosensors that depend on a physical or chemical measurement can be adversely affected by non-specific interactions. For example, a biosensor designed to measure specifically the levels of a rare analyte can give false positive results if there is even a small amount of interaction with a highly abundant but irrelevant molecule. To overcome this limitation, the biosensor community has frequently turned to antibody molecules as recognition elements because they are renowned for their exquisite specificity. Unfortunately antibodies can often fail when immobilised on inorganic surfaces, and alternative biological recognition elements are needed. This article reviews the available non-antibody-binding proteins that have been successfully used in electrical and micro-mechanical biosensor platforms.
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5
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Johnson S, Krauss TF. Label-free affinity biosensor arrays: novel technology for molecular diagnostics. Expert Rev Med Devices 2017; 14:177-179. [DOI: 10.1080/17434440.2017.1283982] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Steven Johnson
- University of York – Electronics, York, UK
- University of York – Physics, York, North Yorkshire, UK
| | - Thomas F Krauss
- University of York – Electronics, York, UK
- University of York – Physics, York, North Yorkshire, UK
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6
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Abstract
Speed and throughput are vital ingredients for discovery driven, "-omics" research. The small molecule microarray (SMM) succeeds at delivering phenomenal screening throughput and versatility. The concept at the heart of the technology is elegant, yet simple: by presenting large collections of molecules in high density on a flat surface, one is able to interrogate all possible interactions with desired targets, in just a single step. SMMs have become established as the choice platform for screening, lead discovery, and molecular characterization. This introduction describes the principles governing microarray construction and use, focusing on practical challenges faced when conducting SMM experiments. It will explain the key design considerations and lay the foundation for the chapters that follow. (An earlier version of this chapter appeared in Small Molecule Microarrays: Methods and Protocols, published in 2010.).
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Affiliation(s)
- Mahesh Uttamchandani
- Defence Medical and Environmental Research Institute, DMERI, DSO National Laboratories, #09-01, 27 Medical Drive, Singapore, Singapore, 117510. .,Department of Chemistry, Faculty of Science, National University of Singapore, 3 Science Drive 3, Singapore, Singapore, 117543.
| | - Shao Q Yao
- Department of Chemistry, Faculty of Science, National University of Singapore, 3 Science Drive 3, Singapore, Singapore, 117543.
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7
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Szymonik M, Davies AG, Wälti C. DNA self-assembly-driven positioning of molecular components on nanopatterned surfaces. NANOTECHNOLOGY 2016; 27:395301. [PMID: 27559837 DOI: 10.1088/0957-4484/27/39/395301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We present a method for the specific, spatially targeted attachment of DNA molecules to lithographically patterned gold surfaces-demonstrated by bridging DNA strands across nanogap electrode structures. An alkanethiol self-assembled monolayer was employed as a molecular resist, which could be selectively removed via electrochemical desorption, allowing the binding of thiolated DNA anchoring oligonucleotides to each electrode. After introducing a bridging DNA molecule with single-stranded ends complementary to the electrode-tethered anchoring oligonucleotides, the positioning of the DNA molecule across the electrode gap, driven by self-assembly, occurred autonomously. This demonstrates control of molecule positioning with resolution limited only by the underlying patterned structure, does not require any alignment, is carried out entirely under biologically compatible conditions, and is scalable.
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Affiliation(s)
- M Szymonik
- School of Electronic and Electrical Engineering, University of Leeds, Leeds LS2 9JT, UK
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8
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Sharma R, Deacon SE, Nowak D, George SE, Szymonik MP, Tang AAS, Tomlinson DC, Davies AG, McPherson MJ, Wälti C. Label-free electrochemical impedance biosensor to detect human interleukin-8 in serum with sub-pg/ml sensitivity. Biosens Bioelectron 2016; 80:607-613. [PMID: 26897263 PMCID: PMC4785862 DOI: 10.1016/j.bios.2016.02.028] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 02/08/2016] [Accepted: 02/10/2016] [Indexed: 01/01/2023]
Abstract
Biosensors with high sensitivity and short time-to-result that are capable of detecting biomarkers in body fluids such as serum are an important prerequisite for early diagnostics in modern healthcare provision. Here, we report the development of an electrochemical impedance-based sensor for the detection in serum of human interleukin-8 (IL-8), a pro-angiogenic chemokine implicated in a wide range of inflammatory diseases. The sensor employs a small and robust synthetic non-antibody capture protein based on a cystatin scaffold that displays high affinity for human IL-8 with a KD of 35±10 nM and excellent ligand specificity. The change in the phase of the electrochemical impedance from the serum baseline, ∆θ(ƒ), measured at 0.1 Hz, was used as the measure for quantifying IL-8 concentration in the fluid. Optimal sensor signal was observed after 15 min incubation, and the sensor exhibited a linear response versus logarithm of IL-8 concentration from 900 fg/ml to 900 ng/ml. A detection limit of around 90 fg/ml, which is significantly lower than the basal clinical levels of 5–10 pg/ml, was observed. Our results are significant for the development of point-of-care and early diagnostics where high sensitivity and short time-to-results are essential. A label-free electrochemical impedance-based sensor for the detection of human interleukin-8 (IL-8) in full serum was developed. Detection limit of 90 fg/ml and time-to-result of 15 min was found. A large dynamic range of the sensor was observed, with sensor response linear vs logarithm of IL-8 concentration from 900 fg/ml to 900 ng/ml. The sensor employs a small and robust synthetic non-antibody capture protein, with high stability and excellent ligand specificity. Findings are particularly relevant for the development of point-of-care and early diagnosis sensors where high sensitivity and short time-to-results are essential.
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Affiliation(s)
- R Sharma
- School of Electronic and Electrical Engineering, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - S E Deacon
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - D Nowak
- School of Electronic and Electrical Engineering, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - S E George
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - M P Szymonik
- School of Electronic and Electrical Engineering, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - A A S Tang
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK; BioScreening Technology Group, Astbury Building, University of Leeds, Leeds LS2 9JT, UK
| | - D C Tomlinson
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK; BioScreening Technology Group, Astbury Building, University of Leeds, Leeds LS2 9JT, UK
| | - A G Davies
- School of Electronic and Electrical Engineering, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - M J McPherson
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK; BioScreening Technology Group, Astbury Building, University of Leeds, Leeds LS2 9JT, UK.
| | - C Wälti
- School of Electronic and Electrical Engineering, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.
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9
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Weckman NE, McRae C, Ko Ferrigno P, Seshia AA. Comparison of the specificity and affinity of surface immobilised Affimer binders using the quartz crystal microbalance. Analyst 2016; 141:6278-6286. [DOI: 10.1039/c6an01602b] [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
This study investigates the performance of surface bound Affimer proteins, comparing the affinity and specificity of different binders for closely related immunoglobulin molecules using the quartz crystal microbalance with dissipation monitoring (QCM-D).
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Affiliation(s)
| | | | | | - Ashwin A. Seshia
- Nanoscience Centre
- University of Cambridge
- Cambridge CB3 0FF
- UK
- Department of Engineering
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10
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Paleček E, Tkáč J, Bartošík M, Bertók T, Ostatná V, Paleček J. Electrochemistry of nonconjugated proteins and glycoproteins. Toward sensors for biomedicine and glycomics. Chem Rev 2015; 115:2045-108. [PMID: 25659975 PMCID: PMC4360380 DOI: 10.1021/cr500279h] [Citation(s) in RCA: 214] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Indexed: 02/07/2023]
Affiliation(s)
- Emil Paleček
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Tkáč
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Martin Bartošík
- Regional
Centre for Applied Molecular Oncology, Masaryk
Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Tomáš Bertók
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Veronika Ostatná
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Paleček
- Central
European Institute of Technology, Masaryk
University, Kamenice
5, 625 00 Brno, Czech Republic
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11
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Raina M, Sharma R, Deacon SE, Tiede C, Tomlinson D, Davies AG, McPherson MJ, Wälti C. Antibody mimetic receptor proteins for label-free biosensors. Analyst 2015; 140:803-10. [DOI: 10.1039/c4an01418a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small synthetic antibody mimetic receptor proteins which offer high stability, specificity and affinity are presented as capture molecules in solid-state electro-chemical biosensors.
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Affiliation(s)
- M. Raina
- Bioelectronics
- School of Electronic and Electrical Engineering
- University of Leeds
- Leeds
- UK
| | - R. Sharma
- Bioelectronics
- School of Electronic and Electrical Engineering
- University of Leeds
- Leeds
- UK
| | - S. E. Deacon
- School of Molecular and Cellular Biology
- University of Leeds
- Leeds
- UK
| | - C. Tiede
- School of Molecular and Cellular Biology
- University of Leeds
- Leeds
- UK
| | - D. Tomlinson
- School of Molecular and Cellular Biology
- University of Leeds
- Leeds
- UK
- Astbury Centre for Structural Molecular Biology
| | - A. G. Davies
- Bioelectronics
- School of Electronic and Electrical Engineering
- University of Leeds
- Leeds
- UK
| | - M. J. McPherson
- School of Molecular and Cellular Biology
- University of Leeds
- Leeds
- UK
- Astbury Centre for Structural Molecular Biology
| | - C. Wälti
- Bioelectronics
- School of Electronic and Electrical Engineering
- University of Leeds
- Leeds
- UK
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12
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Kluková L, Bertók T, Kasák P, Tkac J. Nanoscale controlled architecture for development of ultrasensitive lectin biosensors applicable in glycomics. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2014; 6:4922-4931. [PMID: 27231486 PMCID: PMC4878709 DOI: 10.1039/c4ay00495g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
In this Minireview the most advanced patterning protocols and transducing schemes for development of ultrasensitive label-free and label-based lectin biosensors for glycoprofiling of disease markers and some cancerous cells are described. Performance of such lectin biosensors with interfacial properties tuned at a nanoscale are critically compared to the most sensitive immunoassay format of analysis and challenges ahead in the field are discussed. Moreover, key elements for future advances of such devices on the way to enhance robustness and practical applicability of lectin biosensors are revealed.
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Affiliation(s)
- L Kluková
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - T Bertók
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - P Kasák
- Center for Advanced Materials, Qatar University, P.O. Box 2713, Doha, Qatar; Department for Biomaterial Research, Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 845 38, Slovakia
| | - J Tkac
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
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13
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Gopinath SC, Tang TH, Citartan M, Chen Y, Lakshmipriya T. Current aspects in immunosensors. Biosens Bioelectron 2014; 57:292-302. [DOI: 10.1016/j.bios.2014.02.029] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 02/11/2014] [Accepted: 02/11/2014] [Indexed: 02/08/2023]
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14
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Conidi A, van den Berghe V, Huylebroeck D. Aptamers and their potential to selectively target aspects of EGF, Wnt/β-catenin and TGFβ-smad family signaling. Int J Mol Sci 2013; 14:6690-719. [PMID: 23531534 PMCID: PMC3645661 DOI: 10.3390/ijms14046690] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 03/05/2013] [Accepted: 03/12/2013] [Indexed: 02/07/2023] Open
Abstract
The smooth identification and low-cost production of highly specific agents that interfere with signaling cascades by targeting an active domain in surface receptors, cytoplasmic and nuclear effector proteins, remain important challenges in biomedical research. We propose that peptide aptamers can provide a very useful and new alternative for interfering with protein–protein interactions in intracellular signal transduction cascades, including those emanating from activated receptors for growth factors. By their targeting of short, linear motif type of interactions, peptide aptamers have joined nucleic acid aptamers for use in signaling studies because of their ease of production, their stability, their high specificity and affinity for individual target proteins, and their use in high-throughput screening protocols. Furthermore, they are entering clinical trials for treatment of several complex, pathological conditions. Here, we present a brief survey of the use of aptamers in signaling pathways, in particular of polypeptide growth factors, starting with the published as well as potential applications of aptamers targeting Epidermal Growth Factor Receptor signaling. We then discuss the opportunities for using aptamers in other complex pathways, including Wnt/β-catenin, and focus on Transforming Growth Factor-β/Smad family signaling.
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Affiliation(s)
- Andrea Conidi
- Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, KU Leuven, Campus Gasthuisberg, Building Ond & Nav4 p.o.box 812, room 05.313, Stem Cell Institute, Herestraat 49, B-3000 Leuven, Belgium.
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15
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White SJ, Johnson S, Szymonik M, Wardingley RA, Pye D, Davies AG, Wälti C, Stockley PG. Directed surface attachment of nanomaterials via coiled-coil-driven self-assembly. NANOTECHNOLOGY 2012; 23:495304. [PMID: 23154792 PMCID: PMC4785676 DOI: 10.1088/0957-4484/23/49/495304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Numerous nanoscale devices and materials have been fabricated in recent years using a variety of biological scaffolds. However, the interfacing of these devices and materials into existing circuits and ordered arrays has proved problematic. Here, we describe a simple solution to this problem using self-assembly of the peptide coiled-coil heterodimer ACID:BASE to immobilize M13 bacteriophage particles to specific locations on a patterned gold surface. Surface plasmon resonance demonstrated that free ACID peptides will assemble onto a surface derivatized with BASE. We then displayed the ACID peptide on the pIX coat protein of M13 and showed that these phage particles permit formation of the coiled-coil resulting in specific surface attachment. The ACID:immobilized BASE affinities appear to be similar for free peptide and phage-displayed ACID. Finally, we fabricated two gold electrodes, separated by a 200 nm gap, coated one of them with BASE and showed that this allows localization of the M13:ACID onto the functionalized electrode.
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Affiliation(s)
- Simon J White
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Steven Johnson
- School of Electronic and Electrical Engineering, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- Department of Electronics, University of York, Heslington, York, Y010 5DD, UK
| | - Michal Szymonik
- School of Electronic and Electrical Engineering, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Richard A Wardingley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Douglas Pye
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - A Giles Davies
- School of Electronic and Electrical Engineering, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Christoph Wälti
- School of Electronic and Electrical Engineering, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
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16
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White SJ, Morton DWA, Cheah BC, Bronowska A, Davies AG, Stockley PG, Wälti C, Johnson S. On-surface assembly of coiled-coil heterodimers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:13877-82. [PMID: 22934624 PMCID: PMC4820041 DOI: 10.1021/la3025149] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The coiled coil is a widespread protein motif responsible for directing the assembly of a wide range of protein complexes. To date, research has focused largely on the solution phase assembly of coiled-coil complexes. Here, we describe an investigation into coiled-coil heterodimer assembly where one of the peptides is immobilized directly onto a gold electrode. Immobilization is achieved by the introduction of a unique cysteine residue at the C terminus, allowing for covalent and orientated attachment to a thiol-reactive surface, here the gold electrode. We show an electrochemical impedance of the resulting self-assembled polypeptide monolayer around |Z| = 4 × 10(4) Ω cm(2) at 100 mHz with a minimum phase angle of -84°, consistent with the formation of a densely packed, insulating layer. The thickness of the peptide monolayer, as measured using ellipsometry, is around 3 nm, close to that expected for a self-assembled monolayer assembled from helical peptides. Crucially, we find that the efficiency of dimerization between a peptide in solution and its coiled-coil partner peptide immobilized on a surface is strongly dependent upon the density of the immobilized peptide layer, with dimer assembly being strongly suppressed by high-density peptide monolayers. We thus develop an approach for controlling the density of the immobilized peptide by diluting the monolayer with a thiolated, random-coil peptide to modulate dimerization efficiency and demonstrate electrochemical detection of highly specific, coiled-coil heterodimer on-surface assembly.
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Affiliation(s)
- Simon J White
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
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17
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Johnson A, Song Q, Ko Ferrigno P, Bueno PR, Davis JJ. Sensitive Affimer and Antibody Based Impedimetric Label-Free Assays for C-Reactive Protein. Anal Chem 2012; 84:6553-60. [DOI: 10.1021/ac300835b] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Anthony Johnson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1
3TA, United Kingdom
| | - Qifeng Song
- Wellcome
Trust/EPSRC/Leeds Medical
Engineering Centre, Leeds Institute of Molecular Medicine, Wellcome
Trust Brenner Building, St James’s University Hospital, Leeds LS9 7TF, United Kingdom
| | - Paul Ko Ferrigno
- Wellcome
Trust/EPSRC/Leeds Medical
Engineering Centre, Leeds Institute of Molecular Medicine, Wellcome
Trust Brenner Building, St James’s University Hospital, Leeds LS9 7TF, United Kingdom
| | - Paulo R. Bueno
- Instituto de Química (Institute
of Chemistry, Physical Chemistry Department), Universidade Estadual Paulista (São Paulo State University, UNESP), CP 355, 14800-900, Araraquara, São Paulo, Brazil
| | - Jason J. Davis
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1
3TA, United Kingdom
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18
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Steinkuehler J, Charwat V, Richter L, Ertl P. Characterization of double layer alterations induced by charged particles and protein-membrane interactions using contactless impedance spectroscopy. J Phys Chem B 2012; 116:10461-9. [PMID: 22594659 DOI: 10.1021/jp3008392] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Double layer interactions between charged particles and surfaces play a vital role in a variety of technical and biological systems because they determine the stability of, e.g., protein-membrane biointerfaces. The underlying theoretical principle is based on the overlap of two different double layers that induce surface charges to be shifted to a new equilibrium distribution, which can be approximated by the Poisson-Boltzmann equation. In the present work we show theoretical and experimental results involving double layer capacitance of surfaces that exhibit charge regulation behavior. Charge regulation is an important parameter to consider when investigating protein-membrane interactions because it defines surface properties between ideal constant charge and constant potential behavior. In this work we introduce a novel theoretical model that also includes charge regulation behavior and can assess changes of double layer disruptions at TiO(2) and supported lipid-bilayers (SLB). The selected surfaces represent important biointerfaces that can be found on implants or cell membranes. We also demonstrate that contactless impedance spectroscopy is well suited to measure double layer capacitance interactions using differently charged silica beads. The combination of a theoretical model with experimental data allowed us further to identify charge regulation effects during protein adsorption (BSA and Annexin V) events at supported lipid-bilayers (SLB) used as a simple cell membrane model. Finally, the first indications of changed charge regulation behavior during protein surface crystallization events were also documented.
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Affiliation(s)
- Jan Steinkuehler
- AIT Austrian Institute of Technology GmbH, Muthgasse 11/2, 1190 Vienna, Austria
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19
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Mascini M, Palchetti I, Tombelli S. Nucleic acid and peptide aptamers: fundamentals and bioanalytical aspects. Angew Chem Int Ed Engl 2011; 51:1316-32. [PMID: 22213382 DOI: 10.1002/anie.201006630] [Citation(s) in RCA: 244] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Indexed: 12/11/2022]
Abstract
In recent years new nucleic acid and protein-based combinatorial molecules have attracted the attention of researchers working in various areas of science, ranging from medicine to analytical chemistry. These molecules, called aptamers, have been proposed as alternatives to antibodies in many different applications. The aim of this Review is to illustrate the peculiarities of these combinatorial molecules which have initially been explored for their importance in molecular medicine, but have enormous potential in other biotechnological fields historically dominated by antibodies, such as bioassays. A description of these molecules is given, and the methods for their selection and production are also summarized. Moreover, critical aspects related to these molecules are discussed.
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Affiliation(s)
- Marco Mascini
- Dipartimento di Chimica Ugo Schiff, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
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20
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Mascini M, Palchetti I, Tombelli S. Nucleinsäure- und Peptidaptamere: Grundlagen und bioanalytische Aspekte. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006630] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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21
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Thibaut J, Mérieux Y, Rigal D, Gillet G. A novel assay for the detection of anti-human platelet antigen antibodies (HPA-1a) based on peptide aptamer technology. Haematologica 2011; 97:696-704. [PMID: 22133781 DOI: 10.3324/haematol.2011.051276] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Neonatal alloimmune thrombocytopenia is mostly due to the presence of maternal antibodies against the fetal platelet antigen HPA-1a on the platelet integrin GPIIb-IIIa. Accurate detection of anti-HPA-1a antibodies in the mother is, therefore, critical. Current diagnostic assays rely on the availability of pools of human platelets that vary according to donors and blood centers. There is still no satisfactory standardization of these assays. DESIGN AND METHODS Peptide aptamer was used to detect and identify HPA-1a-specific antibodies in human serum that do not require human platelets. A peptide aptamer library was screened using an anti-HPA-1a human monoclonal antibody as a bait to isolate an aptamer that mimics the human platelet antigen HPA-1a. RESULTS This is the first report in platelet immunology of the use of a peptide aptamer for diagnostic purposes. This assay gives better results than the MAIPA currently in use, detecting around 90% of the expected alloantibodies. CONCLUSIONS This assay could help define a standard for the quantitation of anti-HPA antibodies. This report also demonstrates that peptide aptamers can potentially detect a variety of biomarkers in body fluids; this is of particular interest for diagnostic purposes.
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Affiliation(s)
- Julien Thibaut
- Université de Lyon, IBCP, UMR 5086 CNRS-Université Lyon, Lyon, France
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22
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Electrochemical plasmonic sensors. Anal Bioanal Chem 2011; 402:1773-84. [DOI: 10.1007/s00216-011-5404-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2011] [Revised: 08/17/2011] [Accepted: 09/06/2011] [Indexed: 10/17/2022]
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23
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Stadler LKJ, Hoffmann T, Tomlinson DC, Song Q, Lee T, Busby M, Nyathi Y, Gendra E, Tiede C, Flanagan K, Cockell SJ, Wipat A, Harwood C, Wagner SD, Knowles MA, Davis JJ, Keegan N, Ferrigno PK. Structure-function studies of an engineered scaffold protein derived from Stefin A. II: Development and applications of the SQT variant. Protein Eng Des Sel 2011; 24:751-63. [PMID: 21616931 DOI: 10.1093/protein/gzr019] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Constrained binding peptides (peptide aptamers) may serve as tools to explore protein conformations and disrupt protein-protein interactions. The quality of the protein scaffold, by which the binding peptide is constrained and presented, is of crucial importance. SQT (Stefin A Quadruple Mutant-Tracy) is our most recent development in the Stefin A-derived scaffold series. Stefin A naturally uses three surfaces to interact with its targets. SQT tolerates peptide insertions at all three positions. Peptide aptamers in the SQT scaffold can be expressed in bacterial, yeast and human cells, and displayed as a fusion to truncated pIII on phage. Peptides that bind to CDK2 can show improved binding in protein microarrays when presented by the SQT scaffold. Yeast two-hybrid libraries have been screened for binders to the POZ domain of BCL-6 and to a peptide derived from PBP2', specific to methicillin-resistant Staphylococcus aureus. Presentation of the Noxa BH3 helix by SQT allows specific interaction with Mcl-1 in human cells. Together, our results show that Stefin A-derived scaffolds, including SQT, can be used for a variety of applications in cellular and molecular biology. We will henceforth refer to Stefin A-derived engineered proteins as Scannins.
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Affiliation(s)
- Lukas Kurt Josef Stadler
- Section of Experimental Therapeutics, Leeds Institute of Molecular Medicine, St James's University Hospital, Leeds, UK
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24
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Song Q, Stadler LKJ, Peng J, Ko Ferrigno P. Peptide aptamer microarrays: bridging the bio-detector interface. Faraday Discuss 2011; 149:79-92; discussion 137-57. [PMID: 21413175 DOI: 10.1039/c005376g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the near future, personalised medicine and phase-0 trials will require that clinical practitioners move from the "one biomarker per disease" paradigm to the use of molecular signatures of disease for diagnosis and the prediction of a patient's response to treatment. These signatures will be composed of biomarkers specific to the disease, and will include over-expression of normal protein from a gene that does not carry a mutation; loss of expression of an essential protein; expression of a protein from a mutant gene; and metabolites whose levels are altered in disease. Surrogates for protein expression, such as alterations in the messenger RNA that encode for them, have already proved their value. The next challenge, then, in clinical biosensing is to enable the multiplexed detection of protein biomarkers, and perhaps the multiplexed detection of mixed biomarkers (metabolites, RNA and proteins) all in a single test. Given the plethora of available antibodies specific for biomarkers, why is this not already happening? We believe that the limitation lies in the nature of the antibody molecule itself, and especially the fact that antibodies have evolved to function in solution, while most diagnostic tests take place at a surface. We have accordingly turned to the design of alternative antibodies, and have identified a protein that appears to be unusually stable on surfaces. The new, non-antibody, scaffold protein is derived from human Stefin A, a natural inhibitor of the cathepsin family of proteases. We have engineered this protein so that it lacks natural binding partners, and introduced a series of new binding surfaces through randomisation or directed replacement of the surfaces used by Stefin A to bind to cathepsins. Our new probes show exquisite specificity and binding affinities comparable to antibodies, and can be used to probe biology in intact cells. More importantly, together and in collaboration with other groups in Chemistry or Engineering Departments, we have shown that these designer proteins can be used in optical detection of labelled target proteins from whole cell lysates in a highly multiplexed microarray format, as well as in label-free detection of unlabelled proteins using surface plasmon resonance, QCM, microcantilevers and using electrochemical assays on gold electrodes. We believe that the combination of optimised surface chemistry, robust and combinatorial designer biological probes and novel, robust and sensitive detection technologies will enable, in the near future, the introduction of multiplexed biomarker detection in the clinical setting, most likely in cancer where multiple biomarkers are known, but probes are still lacking.
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Affiliation(s)
- Qifeng Song
- Section of Experimental Therapeutics, Wellcome Trust Brenner Building, St James's University Hospital, Beckett Street, Leeds, LS9 7TF
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25
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Johnson S, Chan J, Evans D, Davies AG, Wälti C. Effect of chain length on the assembly of mercaptoalkanoic acid multilayer films ligated through divalent Cu ions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:1033-1037. [PMID: 21214203 DOI: 10.1021/la103733j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The structural stability of alkenthiolate monolayers assembled on gold surfaces is a result of the well-defined organization of the individual molecules within the film. The formation of three-dimensional films assembled by stacking multiple molecular monolayers is substantially more challenging because the correct organization of the molecular components is required not only within the individual monolayers but also between the monolayers of the film. In this paper we examine the structure of multilayer films based on mercaptoalkanoic acid monolayers in which ligation between adjacent monolayers is achieved using the interaction of carboxylic acid and thiol groups with a divalent Cu ion. Using contact angle analysis and atomic force microscopy, we show that the use of Cu(2+) has profound implications on the properties and structure of the multilayer film. In particular, the divalent ions effectively prohibit the complete assembly of the next monolayer. For multilayer SAMs assembled from short alkane chains with six methylene groups, we find that molecules in the incomplete adlayer organize themselves randomly over the underlying monolayer. However, as the number of methylene groups increases (11 and 16 methylene groups), the upper layer tends to fracture into discrete islands which cover around 50% of the surface. The height of these islands is found to be equal to that expected for a complete, well-ordered monolayer assembled from the equivalent mercaptoalkanoic acid molecules. This relationship between chain length and island growth results from the migration of molecules into ordered aggregates driven by the reduction of free energy associated with maximizing intermolecular interactions.
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Affiliation(s)
- Steven Johnson
- School of Electronic and Electrical Engineering, University of Leeds, Leeds LS2 9JT, UK.
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26
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Ray S, Mehta G, Srivastava S. Label-free detection techniques for protein microarrays: prospects, merits and challenges. Proteomics 2010; 10:731-48. [PMID: 19953541 PMCID: PMC7167936 DOI: 10.1002/pmic.200900458] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein microarrays, on which thousands of discrete proteins are printed, provide a valuable platform for functional analysis of the proteome. They have been widely used for biomarker discovery and to study protein–protein interactions. The accomplishments of DNA microarray technology, which had enabled massive parallel studies of gene expression, sparked great interest for the development of protein microarrays to achieve similar success at the protein level. Protein microarray detection techniques are often classified as being label‐based and label‐free. Most of the microarray applications have employed labelled detection such as fluorescent, chemiluminescent and radioactive labelling. These labelling strategies have synthetic challenges, multiple label issues and may exhibit interference with the binding site. Therefore, development of sensitive, reliable, high‐throughput, label‐free detection techniques are now attracting significant attention. Label‐free detection techniques monitor biomolecular interactions and simplify the bioassays by eliminating the need for secondary reactants. Moreover, they provide quantitative information for the binding kinetics. In this article, we will review several label‐free techniques, which offer promising applications for the protein microarrays, and discuss their prospects, merits and challenges.
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Affiliation(s)
- Sandipan Ray
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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27
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Estrela P, Paul D, Song Q, Stadler LKJ, Wang L, Huq E, Davis JJ, Ferrigno PK, Migliorato P. Label-Free Sub-picomolar Protein Detection with Field-Effect Transistors. Anal Chem 2010; 82:3531-6. [DOI: 10.1021/ac902554v] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pedro Estrela
- Electrical Engineering Division, Department of Engineering, University of Cambridge, 9 J. J. Thomson Avenue, Cambridge CB3 0FA, U.K., Leeds Institute of Molecular Medicine, St. James’s University Hospital, Leeds LS9 7TF, U.K., Central Microstructure Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, U.K., and Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Debjani Paul
- Electrical Engineering Division, Department of Engineering, University of Cambridge, 9 J. J. Thomson Avenue, Cambridge CB3 0FA, U.K., Leeds Institute of Molecular Medicine, St. James’s University Hospital, Leeds LS9 7TF, U.K., Central Microstructure Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, U.K., and Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Qifeng Song
- Electrical Engineering Division, Department of Engineering, University of Cambridge, 9 J. J. Thomson Avenue, Cambridge CB3 0FA, U.K., Leeds Institute of Molecular Medicine, St. James’s University Hospital, Leeds LS9 7TF, U.K., Central Microstructure Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, U.K., and Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Lukas K. J. Stadler
- Electrical Engineering Division, Department of Engineering, University of Cambridge, 9 J. J. Thomson Avenue, Cambridge CB3 0FA, U.K., Leeds Institute of Molecular Medicine, St. James’s University Hospital, Leeds LS9 7TF, U.K., Central Microstructure Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, U.K., and Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Ling Wang
- Electrical Engineering Division, Department of Engineering, University of Cambridge, 9 J. J. Thomson Avenue, Cambridge CB3 0FA, U.K., Leeds Institute of Molecular Medicine, St. James’s University Hospital, Leeds LS9 7TF, U.K., Central Microstructure Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, U.K., and Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Ejaz Huq
- Electrical Engineering Division, Department of Engineering, University of Cambridge, 9 J. J. Thomson Avenue, Cambridge CB3 0FA, U.K., Leeds Institute of Molecular Medicine, St. James’s University Hospital, Leeds LS9 7TF, U.K., Central Microstructure Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, U.K., and Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Jason J. Davis
- Electrical Engineering Division, Department of Engineering, University of Cambridge, 9 J. J. Thomson Avenue, Cambridge CB3 0FA, U.K., Leeds Institute of Molecular Medicine, St. James’s University Hospital, Leeds LS9 7TF, U.K., Central Microstructure Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, U.K., and Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Paul Ko Ferrigno
- Electrical Engineering Division, Department of Engineering, University of Cambridge, 9 J. J. Thomson Avenue, Cambridge CB3 0FA, U.K., Leeds Institute of Molecular Medicine, St. James’s University Hospital, Leeds LS9 7TF, U.K., Central Microstructure Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, U.K., and Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Piero Migliorato
- Electrical Engineering Division, Department of Engineering, University of Cambridge, 9 J. J. Thomson Avenue, Cambridge CB3 0FA, U.K., Leeds Institute of Molecular Medicine, St. James’s University Hospital, Leeds LS9 7TF, U.K., Central Microstructure Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, U.K., and Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
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Rousserie G, Sukhanova A, Even-Desrumeaux K, Fleury F, Chames P, Baty D, Oleinikov V, Pluot M, Cohen JH, Nabiev I. Semiconductor quantum dots for multiplexed bio-detection on solid-state microarrays. Crit Rev Oncol Hematol 2010; 74:1-15. [DOI: 10.1016/j.critrevonc.2009.04.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2008] [Revised: 04/09/2009] [Accepted: 04/17/2009] [Indexed: 10/20/2022] Open
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29
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Hoffmann T, Stadler LKJ, Busby M, Song Q, Buxton AT, Wagner SD, Davis JJ, Ko Ferrigno P. Structure-function studies of an engineered scaffold protein derived from stefin A. I: Development of the SQM variant. Protein Eng Des Sel 2010; 23:403-13. [PMID: 20179045 PMCID: PMC2851446 DOI: 10.1093/protein/gzq012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Non-antibody scaffold proteins are used for a range of applications, especially the assessment of protein-protein interactions within human cells. The search for a versatile, robust and biologically neutral scaffold previously led us to design STM (stefin A triple mutant), a scaffold derived from the intracellular protease inhibitor stefin A. Here, we describe five new STM-based scaffold proteins that contain modifications designed to further improve the versatility of our scaffold. In a step-by-step approach, we introduced restriction sites in the STM open reading frame that generated new peptide insertion sites in loop 1, loop 2 and the N-terminus of the scaffold protein. A second restriction site in 'loop 2' allows substitution of the native loop 2 sequence with alternative oligopeptides. None of the amino acid changes interfered significantly with the folding of the STM variants as assessed by circular dichroism spectroscopy. Of the five scaffold variants tested, one (stefin A quadruple mutant, SQM) was chosen as a versatile, stable scaffold. The insertion of epitope tags at varying positions showed that inserts into loop 1, attempted here for the first time, were generally well tolerated. However, N-terminal insertions of epitope tags in SQM had a detrimental effect on protein expression.
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Affiliation(s)
- Toni Hoffmann
- Section of Experimental Therapeutics, Leeds Institute of Molecular Medicine, St James's University Hospital, Beckett St, Leeds LS97TF, UK.
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30
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Abstract
Speed and throughput are vital ingredients for discovery-driven, "-omics" research. The small molecule microarray is one such platform, which delivers phenomenal screening throughput and capabilities. The concept at the heart of the technology is elegant, yet simple: by presenting large collections of molecules at a high density on a flat surface, one is able to interrogate them quickly and conveniently, evaluating all possible interactions in a single step. SMMs have, over the last decade, been established as a robust platform for screening, lead discovery, and molecular characterization. In this chapter, we describe the ways in which microarrays have been constructed and applied, focusing on the practical challenges faced when designing and performing SMM experiments. This is written as an introduction for new readers to the field, explaining the key principles and laying the foundation for the chapters that follow.
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Affiliation(s)
- Mahesh Uttamchandani
- DSO National Laboratories, Defence Medical and Environmental Research Institute, Singapore, Singapore
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31
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Qavi AJ, Washburn AL, Byeon JY, Bailey RC. Label-free technologies for quantitative multiparameter biological analysis. Anal Bioanal Chem 2009; 394:121-35. [PMID: 19221722 PMCID: PMC2667559 DOI: 10.1007/s00216-009-2637-8] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 01/12/2009] [Accepted: 01/20/2009] [Indexed: 11/26/2022]
Abstract
In the postgenomic era, information is king and information-rich technologies are critically important drivers in both fundamental biology and medicine. It is now known that single-parameter measurements provide only limited detail and that quantitation of multiple biomolecular signatures can more fully illuminate complex biological function. Label-free technologies have recently attracted significant interest for sensitive and quantitative multiparameter analysis of biological systems. There are several different classes of label-free sensors that are currently being developed both in academia and in industry. In this critical review, we highlight, compare, and contrast some of the more promising approaches. We describe the fundamental principles of these different methods and discuss advantages and disadvantages that might potentially help one in selecting the appropriate technology for a given bioanalytical application.
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Affiliation(s)
- Abraham J. Qavi
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801
| | - Adam L. Washburn
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801
| | - Ji-Yeon Byeon
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801
| | - Ryan C. Bailey
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801
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Davis JJ, Tkac J, Humphreys R, Buxton AT, Lee TA, Ko Ferrigno P. Peptide Aptamers in Label-Free Protein Detection: 2. Chemical Optimization and Detection of Distinct Protein Isoforms. Anal Chem 2009; 81:3314-20. [DOI: 10.1021/ac802513n] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jason J. Davis
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, and Section of Experimental Therapeutics, Leeds Institute of Molecular Medicine, St. James’s University Hospital, Beckett Street, Leeds LS9 7TF
| | - Jan Tkac
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, and Section of Experimental Therapeutics, Leeds Institute of Molecular Medicine, St. James’s University Hospital, Beckett Street, Leeds LS9 7TF
| | - Rachel Humphreys
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, and Section of Experimental Therapeutics, Leeds Institute of Molecular Medicine, St. James’s University Hospital, Beckett Street, Leeds LS9 7TF
| | - Anthony T. Buxton
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, and Section of Experimental Therapeutics, Leeds Institute of Molecular Medicine, St. James’s University Hospital, Beckett Street, Leeds LS9 7TF
| | - Tracy A. Lee
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, and Section of Experimental Therapeutics, Leeds Institute of Molecular Medicine, St. James’s University Hospital, Beckett Street, Leeds LS9 7TF
| | - Paul Ko Ferrigno
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, and Section of Experimental Therapeutics, Leeds Institute of Molecular Medicine, St. James’s University Hospital, Beckett Street, Leeds LS9 7TF
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Sadik OA, Aluoch AO, Zhou A. Status of biomolecular recognition using electrochemical techniques. Biosens Bioelectron 2008; 24:2749-65. [PMID: 19054662 DOI: 10.1016/j.bios.2008.10.003] [Citation(s) in RCA: 190] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Revised: 10/01/2008] [Accepted: 10/03/2008] [Indexed: 11/16/2022]
Abstract
The use of nanoscale materials (e.g., nanoparticles, nanowires, and nanorods) for electrochemical biosensing has seen explosive growth in recent years following the discovery of carbon nanotubes by Sumio Ijima in 1991. Although the resulting label-free sensors could potentially simplify the molecular recognition process, there are several important hurdles to be overcome. These include issues of validating the biosensor on statistically large population of real samples rather than the commonly reported relatively short synthetic oligonucleotides, pristine laboratory standards or bioreagents; multiplexing the sensors to accommodate high-throughput, multianalyte detection as well as application in complex clinical and environmental samples. This article reviews the status of biomolecular recognition using electrochemical detection by analyzing the trends, limitations, challenges and commercial devices in the field of electrochemical biosensors. It provides a survey of recent advances in electrochemical biosensors including integrated microelectrode arrays with microfluidic technologies, commercial multiplex electrochemical biosensors, aptamer-based sensors, and metal-enhanced electrochemical detection (MED), with limits of detection in the attomole range. Novel applications are also reviewed for cancer monitoring, detection of food pathogens, as well as recent advances in electrochemical glucose biosensors.
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Affiliation(s)
- Omowunmi A Sadik
- Department of Chemistry, Center for Advanced Sensors & Environmental Monitoring, State University of New York-Binghamton, P.O. Box 6000, Binghamton, NY 13902, United States.
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Highly specific label-free protein detection from lysed cells using internally referenced microcantilever sensors. Biosens Bioelectron 2008; 24:233-7. [DOI: 10.1016/j.bios.2008.03.036] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 03/24/2008] [Accepted: 03/25/2008] [Indexed: 11/21/2022]
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Label-Free Detection of Protein interactions with peptide aptamers by open circuit potential measurement. Electrochim Acta 2008. [DOI: 10.1016/j.electacta.2008.04.036] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Abstract
Peptide aptamers are combinatorial recognition proteins that were introduced more than ten years ago. They have since found many applications in fundamental and therapeutic research, including their recent use in microarrays to detect individual proteins from complex mixtures.
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Affiliation(s)
- Pierre Colas
- Station Biologique, CNRS, UPS 2682, Place Georges Teissier, 29280 Roscoff, France.
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