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Kumemura M, Pekin D, Menon VA, Van Seuningen I, Collard D, Tarhan MC. Fabricating Silicon Resonators for Analysing Biological Samples. MICROMACHINES 2021; 12:1546. [PMID: 34945396 PMCID: PMC8708134 DOI: 10.3390/mi12121546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 11/17/2022]
Abstract
The adaptability of microscale devices allows microtechnologies to be used for a wide range of applications. Biology and medicine are among those fields that, in recent decades, have applied microtechnologies to achieve new and improved functionality. However, despite their ability to achieve assay sensitivities that rival or exceed conventional standards, silicon-based microelectromechanical systems remain underutilised for biological and biomedical applications. Although microelectromechanical resonators and actuators do not always exhibit optimal performance in liquid due to electrical double layer formation and high damping, these issues have been solved with some innovative fabrication processes or alternative experimental approaches. This paper focuses on several examples of silicon-based resonating devices with a brief look at their fundamental sensing elements and key fabrication steps, as well as current and potential biological/biomedical applications.
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Affiliation(s)
- Momoko Kumemura
- Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, 2-4 Hibikino, Wakamatsu-ku, Kitakyushu-shi, Fukuoka 808-0196, Japan;
- LIMMS/CNRS-IIS, Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan; (D.P.); (D.C.)
| | - Deniz Pekin
- LIMMS/CNRS-IIS, Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan; (D.P.); (D.C.)
- CNRS/IIS/COL/Lille University, SMMiL-E Project, CNRS Délégation Nord-Pas de Calais et Picardie, 2 rue de Canonniers, CEDEX, 59046 Lille, France
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277—CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France;
| | - Vivek Anand Menon
- Division of Mechanical Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu-shi, Gunma 376-8515, Japan;
| | - Isabelle Van Seuningen
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277—CANTHER—Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France;
| | - Dominique Collard
- LIMMS/CNRS-IIS, Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan; (D.P.); (D.C.)
- CNRS/IIS/COL/Lille University, SMMiL-E Project, CNRS Délégation Nord-Pas de Calais et Picardie, 2 rue de Canonniers, CEDEX, 59046 Lille, France
| | - Mehmet Cagatay Tarhan
- LIMMS/CNRS-IIS, Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan; (D.P.); (D.C.)
- CNRS/IIS/COL/Lille University, SMMiL-E Project, CNRS Délégation Nord-Pas de Calais et Picardie, 2 rue de Canonniers, CEDEX, 59046 Lille, France
- Univ. Lille, CNRS, Centrale Lille, Junia, University Polytechnique Hauts-de-France, UMR 8520—IEMN, Institut
d’Electronique de Microélectronique et de Nanotechnologie, F-59000 Lille, France
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Fabregat G, Lanzalaco S, Aït Saïd J, Muñoz-Pascual X, Llorca J, Alemán C. Immobilization of glucose oxidase on plasma-treated polyethylene for non-invasive glucose detection. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115509] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Zanuy D, Puiggalí-Jou A, Conflitti P, Bocchinfuso G, Palleschi A, Alemán C. Aggregation propensity of therapeutic fibrin-homing pentapeptides: insights from experiments and molecular dynamics simulations. SOFT MATTER 2020; 16:10169-10179. [PMID: 33165494 DOI: 10.1039/d0sm00930j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
CREKA (Cys-Arg-Glu-Lys-Ala) and its engineered analogue CRMeEKA, in which Glu has been replaced by N-methyl-Glu to provide resistance against proteolysis, are emerging pentapeptides that were specifically designed to bind fibrin-fibronectin complexes accumulated in the walls of tumour vessels. However, many of the intrinsic properties of CREKA and CRMeEKA, which are probably responsible for their different behaviour when combined with other materials (such as polymers) for diagnosis and therapeutics, remain unknown yet. The intrinsic tendency of these pentapeptides to form aggregates has been analysed by combining experimental techniques and atomistic Molecular Dynamics (MD) simulations. Dynamic light scattering assays show the formation of nanoaggregates that increase in size with the peptide concentration, even though aggregation occurs sooner for CRMeEKA, independently of the peptide concentration. FTIR and circular dichroism spectroscopy studies suggest that aggregated pentapeptides do not adopt any secondary structure. Atomistic MD trajectories show that CREKA aggregates faster and forms bigger molecular clusters than CRMeEKA. This behaviour has been explained by stability of the conformations adopted by un-associated peptide strands. While CREKA molecules organize by forming intramolecular backbone - side chain hydrogen bonds, CRMeEKA peptides display main chain - main chain hydrogen bonds closing very stable γ- or β-turns. Besides, energetic analyses reveal that CRMeEKA strands are better solvated in water than CREKA ones, independent of whether they are assembled or un-associated.
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Affiliation(s)
- David Zanuy
- Department of Chemical Engineering and Barcelona Research Center in Multiscale Science and Engineering, Universitat Polytècnica de Catalunya, 08019 Barcelona, Spain.
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Martí D, Ainsley J, Ahumada O, Alemán C, Torras J. Tethering of the IgG1 Antibody to Amorphous Silica for Immunosensor Development: A Molecular Dynamics Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:12658-12667. [PMID: 33058684 DOI: 10.1021/acs.langmuir.0c02203] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A key factor for improving the sensitivity and performance of immunosensors based on mechanical-plasmonic methods is the orientation of the antibody proteins immobilized on the inorganic surface. Although experimental techniques fail to determine surface phenomena at the molecular level, modern simulations open the possibility for improving our understanding of protein-surface interactions. In this work, replica exchange molecular dynamics (REMD) simulations have been used to model the IgG1 protein tethered onto the amorphous silica surface by considering a united-atom model and a relatively large system (2500 nm2 surface). Additional molecular dynamics (MD) simulations have been conducted to derive an atomistic model for the amorphous silica surface using the cristobalite crystal structure as a starting point and to examine the structure of the free IgG1 antibody in the solution for comparison when immobilized. Analyses of the trajectories obtained for the tethered IgG1, which was sampled considering 32 different temperatures, have been used to define the geometry of the protein with respect to the inorganic surface. The tilt angle of the protein with respect to the surface plane increases with temperature, the most populated values being 24, 66, and 87° at the lowest (250 K), room (298 K), and the highest (380 K) temperatures. This variation indicates that the importance of protein-surface interactions decreases with increasing temperature. The influence of the surface on the structure of the antibody is very significant in the constant region, which is directly involved in the tethering process, while it is relatively unimportant for the antigen-binding fragments, which are farthest from the surface. These results are expected to contribute to the development of improved mechanical-plasmonic sensor microarrays in the near future.
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Affiliation(s)
- Didac Martí
- Department of Chemical Engineering (EEBE), Universitat Politècnica de Catalunya, C/Eduard Maristany 10-14, Ed I2, 08019 Barcelona, Spain
- Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany 10-14, 08019 Barcelona, Spain
| | - Jon Ainsley
- Department of Chemical Engineering (EEBE), Universitat Politècnica de Catalunya, C/Eduard Maristany 10-14, Ed I2, 08019 Barcelona, Spain
- Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG U.K
| | - Oscar Ahumada
- Mecwins S.A., Ronda de Poniente 15, Tres Cantos, Madrid, 28760, Spain
| | - Carlos Alemán
- Department of Chemical Engineering (EEBE), Universitat Politècnica de Catalunya, C/Eduard Maristany 10-14, Ed I2, 08019 Barcelona, Spain
- Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany 10-14, 08019 Barcelona, Spain
| | - Juan Torras
- Department of Chemical Engineering (EEBE), Universitat Politècnica de Catalunya, C/Eduard Maristany 10-14, Ed I2, 08019 Barcelona, Spain
- Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany 10-14, 08019 Barcelona, Spain
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Lopes-Rodrigues M, Puiggalí-Jou A, Martí-Balleste D, del Valle LJ, Michaux C, Perpète EA, Alemán C. Thermomechanical Response of a Representative Porin for Biomimetics. ACS OMEGA 2018; 3:7856-7867. [PMID: 31458928 PMCID: PMC6644815 DOI: 10.1021/acsomega.8b00463] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 07/02/2018] [Indexed: 06/09/2023]
Abstract
The thermomechanical response of Omp2a, a representative porin used for the fabrication of smart biomimetic nanomembranes, has been characterized using microcantilever technology and compared with standard proteins. For this purpose, thermally induced transitions involving the conversion of stable trimers to bigger aggregates, local reorganizations based on the strengthening or weakening of intermolecular interactions, and protein denaturation have been detected by the microcantilever resonance frequency and deflection as a function of the temperature. Measurements have been carried out on arrays of 8-microcantilevers functionalized with proteins (Omp2a, lysozyme and bovine serum albumin). To interpret the measured nanofeatures, the response of proteins to temperature has been also examined using other characterization techniques, including real time wide angle X-ray diffraction. Results not only demonstrate the complex behavior of porins, which exhibit multiple local thermal transitions before undergoing denaturation at temperatures higher than 105 °C, but also suggest a posttreatment to control the orientation of immobilized Omp2a molecules in functionalized biomimetic nanomembranes and, thus, increase their efficacy in ion transport.
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Affiliation(s)
- Maximilien Lopes-Rodrigues
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, Ed.
I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, 10-14, 08019 Barcelona, Spain
- Laboratoire
de Chimie Physique des Biomolécules, Unité de Chimie
Physique Théorique et Structurale (UCPTS), University of Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
| | - Anna Puiggalí-Jou
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, Ed.
I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, 10-14, 08019 Barcelona, Spain
| | - Didac Martí-Balleste
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, Ed.
I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, 10-14, 08019 Barcelona, Spain
| | - Luis J. del Valle
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, Ed.
I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, 10-14, 08019 Barcelona, Spain
| | - Catherine Michaux
- Laboratoire
de Chimie Physique des Biomolécules, Unité de Chimie
Physique Théorique et Structurale (UCPTS), University of Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
| | - Eric A. Perpète
- Laboratoire
de Chimie Physique des Biomolécules, Unité de Chimie
Physique Théorique et Structurale (UCPTS), University of Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
| | - Carlos Alemán
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, Ed.
I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, 10-14, 08019 Barcelona, Spain
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Li M, Guo X, Li H, Zuo X, Hao R, Song H, Aldalbahi A, Ge Z, Li J, Li Q, Song S, Li S, Shao N, Fan C, Wang L. Epitope Binning Assay Using an Electron Transfer-Modulated Aptamer Sensor. ACS APPLIED MATERIALS & INTERFACES 2018; 10:341-349. [PMID: 29241329 DOI: 10.1021/acsami.7b17324] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Surface plasmon resonance and quartz crystal microbalance are workhorses of protein-DNA interaction research for over 20 years, providing ways to quantitatively determine the protein-DNA binding. However, the cost, necessary technical expertise, and severe nonspecific adsorption poses barriers to their use. Convenient and effective techniques for the measurement of protein-DNA binding affinity and the epitope binning between DNA and proteins for developing highly sensitive detection platform remain challenging. Here, we develop a binding-induced alteration in electron transfer kinetics of the redox reporter labeled (methylene blue) on DNA aptamer to measure the binding affinity between prostate-specific antigen (PSA) and aptamer. We demonstrate that the binding of PSA to aptamer decreases the electron transfer rate of methylene blue for ∼45%. Further, we identify the best pairwise selection of aptamers for developing sandwich assay by sorting from 10 pairwise modes with the PSA detection limit of 500 ng/mL. Our study provides promising ways to analyze the binding affinity between ligand and receptor and to sort pairwise between aptamers or antibodies for the development of highly sensitive sandwich immunoassays.
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Affiliation(s)
- Min Li
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Xudong Guo
- Institute of Disease Control and Prevention, AMMS , Beijing 100071, China
| | - Hui Li
- Beijing Institute of Basic Medical Sciences , Beijing 100850, China
| | - Xiaolei Zuo
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
- Institute of Molecular Medicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Rongzhang Hao
- Institute of Disease Control and Prevention, AMMS , Beijing 100071, China
| | - Hongbin Song
- Institute of Disease Control and Prevention, AMMS , Beijing 100071, China
| | - Ali Aldalbahi
- Chemistry Department, King Saud University , Riyadh 11451, Saudi Arabia
| | - Zhilei Ge
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Jiang Li
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Qian Li
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Shiping Song
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Shaohua Li
- Beijing Institute of Basic Medical Sciences , Beijing 100850, China
| | - Ningsheng Shao
- Beijing Institute of Basic Medical Sciences , Beijing 100850, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
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