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Naoumi N, Araya-Farias M, Megariti M, Alexandre L, Papadakis G, Descroix S, Gizeli E. Acoustic detection of a mutation-specific Ligase Chain Reaction based on liposome amplification. Analyst 2024; 149:3537-3546. [PMID: 38758167 DOI: 10.1039/d3an02142d] [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: 05/18/2024]
Abstract
Single nucleotide variants (SNVs) play a crucial role in understanding genetic diseases, cancer development, and personalized medicine. However, existing ligase-based amplification and detection techniques, such as Rolling Circle Amplification and Ligase Detection Reaction, suffer from low efficiency and difficulties in product detection. To address these limitations, we propose a novel approach that combines Ligase Chain Reaction (LCR) with acoustic detection using highly dissipative liposomes. In our study, we are using LCR combined with biotin- and cholesterol-tagged primers to produce amplicons also modified at each end with a biotin and cholesterol molecule. We then apply the LCR mix without any purification directly on a neutravidin modified QCM device Au-surface, where the produced amplicons can bind specifically through the biotin end. To improve sensitivity, we finally introduce liposomes as signal enhancers. For demonstration, we used the detection of the BRAF V600E point mutation versus the wild-type allele, achieving an impressive detection limit of 220 aM of the mutant target in the presence of the same amount of the wild type. Finally, we combined the assay with a microfluidic fluidized bed DNA extraction technology, offering the potential for semi-automated detection of SNVs in patients' crude samples. Overall, our LCR/acoustic method outperforms other LCR-based approaches and surface ligation biosensing techniques in terms of detection efficiency and time. It effectively overcomes challenges related to DNA detection, making it applicable in diverse fields, including genetic disease and pathogen detection.
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Affiliation(s)
- Nikoletta Naoumi
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion, 70013, Greece
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece.
| | - Monica Araya-Farias
- Laboratoire Physico-Chimie Curie, CNRS UMR 168, Institut Curie, PSL Research University, Paris, France
- Institut Pierre-Gilles de Gennes for Microfluidic (IPGG), Paris, France
| | - Maria Megariti
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece.
| | - Lucile Alexandre
- Laboratoire Physico-Chimie Curie, CNRS UMR 168, Institut Curie, PSL Research University, Paris, France
- Institut Pierre-Gilles de Gennes for Microfluidic (IPGG), Paris, France
| | - George Papadakis
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece.
| | - Stephanie Descroix
- Laboratoire Physico-Chimie Curie, CNRS UMR 168, Institut Curie, PSL Research University, Paris, France
- Institut Pierre-Gilles de Gennes for Microfluidic (IPGG), Paris, France
| | - Electra Gizeli
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion, 70013, Greece
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece.
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2
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Reviakine I. Quartz crystal microbalance in soft and biological interfaces. Biointerphases 2024; 19:010801. [PMID: 38416603 DOI: 10.1116/6.0003312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 02/05/2024] [Indexed: 03/01/2024] Open
Abstract
Applications of quartz crystal microbalance with dissipation to studying soft and biological interfaces are reviewed. The focus is primarily on data analysis through viscoelastic modeling and a model-free approach focusing on the acoustic ratio. Current challenges and future research and development directions are discussed.
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3
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Bonet NF, Cava DG, Vélez M. Quartz crystal microbalance and atomic force microscopy to characterize mimetic systems based on supported lipids bilayer. Front Mol Biosci 2022; 9:935376. [PMID: 35992275 PMCID: PMC9382308 DOI: 10.3389/fmolb.2022.935376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/05/2022] [Indexed: 11/23/2022] Open
Abstract
Quartz Crystal Microbalance (QCM) with dissipation and Atomic Force Microscopy (AFM) are two characterization techniques that allow describing processes taking place at solid-liquid interfaces. Both are label-free and, when used in combination, provide kinetic, thermodynamic and structural information at the nanometer scale of events taking place at surfaces. Here we describe the basic operation principles of both techniques, addressing a non-specialized audience, and provide some examples of their use for describing biological events taking place at supported lipid bilayers (SLBs). The aim is to illustrate current strengths and limitations of the techniques and to show their potential as biophysical characterization techniques.
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Naoumi N, Michaelidou K, Papadakis G, Simaiaki AE, Fernández R, Calero M, Arnau A, Tsortos A, Agelaki S, Gizeli E. Acoustic Array Biochip Combined with Allele-Specific PCR for Multiple Cancer Mutation Analysis in Tissue and Liquid Biopsy. ACS Sens 2022; 7:495-503. [PMID: 35073481 DOI: 10.1021/acssensors.1c02245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Regular screening of point mutations is of importance to cancer management and treatment selection. Although techniques like next-generation sequencing and digital polymerase chain reaction (PCR) are available, these are lacking in speed, simplicity, and cost-effectiveness. The development of alternative methods that can detect the extremely low concentrations of the target mutation in a fast and cost-effective way presents an analytical and technological challenge. Here, an approach is presented where for the first time an allele-specific PCR (AS-PCR) is combined with a newly developed high fundamental frequency quartz crystal microbalance array as biosensor for the amplification and detection, respectively, of cancer point mutations. Increased sensitivity, compared to fluorescence detection of the AS-PCR amplicons, is achieved through energy dissipation measurement of acoustically "lossy" liposomes binding to surface-anchored dsDNA targets. The method, applied to the screening of BRAF V600E and KRAS G12D mutations in spiked-in samples, was shown to be able to detect 1 mutant copy of genomic DNA in an excess of 104 wild-type molecules, that is, with a mutant allele frequency (MAF) of 0.01%. Moreover, validation of tissue and plasma samples obtained from melanoma, colorectal, and lung cancer patients showed excellent agreement with Sanger sequencing and ddPCR; remarkably, the efficiency of this AS-PCR/acoustic methodology to detect mutations in real samples was demonstrated to be below 1% MAF. The combined high sensitivity and technology-readiness level of the methodology, together with the ability for multiple sample analysis (24 array biochip), cost-effectiveness, and compatibility with routine workflow, make this approach a promising tool for implementation in clinical oncology labs for tissue and liquid biopsy.
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Affiliation(s)
- Nikoletta Naoumi
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
| | - Kleita Michaelidou
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Vassilika Vouton, Heraklion 70013, Crete, Greece
| | - George Papadakis
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
| | - Agapi E. Simaiaki
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
| | - Román Fernández
- Advanced Wave Sensors S. L., Algepser 24, Paterna 46988, Spain
- Centro de Investigación e Innovación en Bioingeniería, Universitat Politècnica de València, Valencia 46022, Spain
| | - Maria Calero
- Centro de Investigación e Innovación en Bioingeniería, Universitat Politècnica de València, Valencia 46022, Spain
| | - Antonio Arnau
- Advanced Wave Sensors S. L., Algepser 24, Paterna 46988, Spain
- Centro de Investigación e Innovación en Bioingeniería, Universitat Politècnica de València, Valencia 46022, Spain
| | - Achilleas Tsortos
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
| | - Sofia Agelaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Vassilika Vouton, Heraklion 70013, Crete, Greece
- Department of Medical Oncology, University General Hospital of Heraklion, Vassilika Vouton, Crete 71500, Greece
| | - Electra Gizeli
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
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Abstract
The present work deals with the development of a Love-wave biosensor for the diagnosis of the modification of cell viscosity. The relevant device performance such as insertion loss, attenuation, phase velocity, and sensitivity needs to be analysed as a function of the device structure and also regarding the effect of the liquid loading. In this study, we used an analytical model based on the equation of motions for a Love wave propagating in a three-layer structure. We show that the effect of the viscous coupling leads to insertion losses and a phase shift that impact the acoustic ratio. A comparison between experimental and theoretical results showed a good agreement between the behaviours as it was observed for the phase shift vs. the insertion loss with a limited difference in values (3.11/3.09—experimental/simulation for the sensitivity to the viscosity for different insertion losses) due to the assumptions made on the model used.
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Lee J, Kim SH, Se T, Kim D. Characterization of Noise in a Single-Molecule Fluorescence Signal. J Phys Chem B 2022; 126:1160-1167. [PMID: 35129336 DOI: 10.1021/acs.jpcb.1c08621] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Single-molecule fluorescence experiments allow monitoring of the structural change and dynamics of a single biomolecule in real time using dye molecules attached to the molecule. Often, the molecules are immobilized on the surface to observe a longer molecular dynamics, yet the finite photon budget available from an individual dye molecule before photobleaching sets the limit to the relatively poor signal-to-noise level. To increase the accuracy of these single-molecule experiments, it is necessary to study the cause of noise in the fluorescence signal from the single molecules. To find the origin of this noise, the lifetime of the fluorescent dye molecules labeled on surface-immobilized DNA was measured by using time-correlation single photon counting. The standard deviation of the fluorescence lifetimes obtained from repeated measurements of a single dye molecule with the total photon number N decreased as 1/N, thus following a shot noise of the Poisson statistics. On the other hand, an additional constant noise source, which is independent of the photon number, was observed from the lifetime uncertainties from many molecules and became more dominant after a certain photon number N. This trend was also followed in the uncertainties of the single-molecule FRET signals obtained from single and many molecules. This additional noise is considered to come from the inhomogeneous environment of each DNA immobilized on the surface.
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Affiliation(s)
- Jaejin Lee
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107 Korea
| | - Sung Hyun Kim
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2629 JB, Netherlands
| | - Tola Se
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107 Korea
| | - Doseok Kim
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107 Korea
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Rabus D, Lotthammer F, Degret J, Arapan L, Palmino F, Friedt JM, Cherioux F. Degradation of Sub-Micrometer Sensitive Polymer Layers of Acoustic Sensors Exposed to Chlorpyrifos Water-Solution. SENSORS (BASEL, SWITZERLAND) 2022; 22:1203. [PMID: 35161948 PMCID: PMC8840410 DOI: 10.3390/s22031203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/28/2022] [Accepted: 02/02/2022] [Indexed: 11/20/2022]
Abstract
The detection of organophosphates, a wide class of pesticides, in water-solution has a huge impact in environmental monitoring. Acoustic transducers are used to design passive wireless sensors for the direct detection of pesticides in water-solution by using tailored polymers as sensitive layers. We demonstrate by combining analytical chemistry tools that organophosphate molecules strongly alter polymer layers widely used in acoustic sensors in the presence of water. This chemical degradation can limit the use of these polymers in detection of organophosphates in water-solution.
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Affiliation(s)
| | | | | | | | | | - Jean-Michel Friedt
- Franche-Comté Électronique Mécanique Thermique et Optique-Sciences et Technologies, Université de Franche-Comté, CNRS, 15B Avenue des Montboucons, CEDEX, F-25030 Besancon, France; (D.R.); (F.L.); (J.D.); (L.A.); (F.P.)
| | - Frédéric Cherioux
- Franche-Comté Électronique Mécanique Thermique et Optique-Sciences et Technologies, Université de Franche-Comté, CNRS, 15B Avenue des Montboucons, CEDEX, F-25030 Besancon, France; (D.R.); (F.L.); (J.D.); (L.A.); (F.P.)
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8
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Nair MP, Teo AJT, Li KHH. Acoustic Biosensors and Microfluidic Devices in the Decennium: Principles and Applications. MICROMACHINES 2021; 13:24. [PMID: 35056189 PMCID: PMC8779171 DOI: 10.3390/mi13010024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/11/2021] [Accepted: 12/20/2021] [Indexed: 12/27/2022]
Abstract
Lab-on-a-chip (LOC) technology has gained primary attention in the past decade, where label-free biosensors and microfluidic actuation platforms are integrated to realize such LOC devices. Among the multitude of technologies that enables the successful integration of these two features, the piezoelectric acoustic wave method is best suited for handling biological samples due to biocompatibility, label-free and non-invasive properties. In this review paper, we present a study on the use of acoustic waves generated by piezoelectric materials in the area of label-free biosensors and microfluidic actuation towards the realization of LOC and POC devices. The categorization of acoustic wave technology into the bulk acoustic wave and surface acoustic wave has been considered with the inclusion of biological sample sensing and manipulation applications. This paper presents an approach with a comprehensive study on the fundamental operating principles of acoustic waves in biosensing and microfluidic actuation, acoustic wave modes suitable for sensing and actuation, piezoelectric materials used for acoustic wave generation, fabrication methods, and challenges in the use of acoustic wave modes in biosensing. Recent developments in the past decade, in various sensing potentialities of acoustic waves in a myriad of applications, including sensing of proteins, disease biomarkers, DNA, pathogenic microorganisms, acoustofluidic manipulation, and the sorting of biological samples such as cells, have been given primary focus. An insight into the future perspectives of real-time, label-free, and portable LOC devices utilizing acoustic waves is also presented. The developments in the field of thin-film piezoelectric materials, with the possibility of integrating sensing and actuation on a single platform utilizing the reversible property of smart piezoelectric materials, provide a step forward in the realization of monolithic integrated LOC and POC devices. Finally, the present paper highlights the key benefits and challenges in terms of commercialization, in the field of acoustic wave-based biosensors and actuation platforms.
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Affiliation(s)
| | | | - King Ho Holden Li
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Singapore; (M.P.N.); (A.J.T.T.)
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Schofield MM, Delgado-Buscalioni R. Quantitative description of the response of finite size adsorbates on a quartz crystal microbalance in liquids using analytical hydrodynamics. SOFT MATTER 2021; 17:8160-8174. [PMID: 34525162 DOI: 10.1039/d1sm00492a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Despite being a fundamental tool in soft matter research and biosensing, quartz crystal microbalance (QCM) analyses of discrete macromolecules in liquids so far lack a firm theoretical basis. Quite often, acoustic signals of discrete particles are qualitatively interpreted using ad hoc frameworks based on effective electrical circuits, effective springs and trapped-solvent models with many fitting parameters. Nevertheless, due to its extreme sensitivity, the QCM technique pledges to become an accurate predictive tool. Using unsteady low Reynolds hydrodynamics we derive analytical expressions for the acoustic impedance of adsorbed discrete spheres. The present approach is successfully validated against 3D simulations and a plethora of experimental results covering more than a decade of research on proteins, viruses, liposomes, and massive nanoparticles, with sizes ranging from a few to hundreds of nanometers. The agreement without fitting parameters indicates that the acoustic response is dominated by the hydrodynamic propagation of the particle surface stress over the resonator. Understanding this leading contribution is a prerequisite for deciphering the secondary contributions arising from the relevant specific molecular and physico-chemical forces.
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Affiliation(s)
- Marc Meléndez Schofield
- Departmento de Fisica de la Materia Condensada, Universidad Autonoma de Madrid, and Institute for Condensed Matter Physics, IFIMAC, Campus de Cantoblanco, Madrid 28049, Spain.
| | - Rafael Delgado-Buscalioni
- Departmento de Fisica de la Materia Condensada, Universidad Autonoma de Madrid, and Institute for Condensed Matter Physics, IFIMAC, Campus de Cantoblanco, Madrid 28049, Spain.
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Gopalakrishna S, Langhoff A, Brenner G, Johannsmann D. Soft Viscoelastic Particles in Contact with a Quartz Crystal Microbalance (QCM): A Frequency-Domain Lattice Boltzmann Simulation. Anal Chem 2021; 93:10229-10235. [PMID: 34270892 DOI: 10.1021/acs.analchem.1c01612] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Shifts of frequency and bandwidth of a quartz crystal microbalance (QCM) in contact with a structured, viscoelastic sample have been computed with a linearized version of the lattice Boltzmann method (LBM). The algorithm operates in the frequency domain and covers viscoelasticity. The different domains are characterized by different values of the complex viscosity, η, equivalent to different values of the shear modulus, G. Stiff particles are given large |ηSph|, where |ηSph| must be less than ∼100 ηbulk with ηbulk the viscosity of the ambient liquid. Critical to the computational efficiency is a match of the LBM populations at the upper boundary of the simulation box to an analytical solution of the Stokes equation in the bulk above the box. The application example is a test of the ΔΓ/(-Δf)-extrapolation scheme, where Δf and ΔΓ are the shifts in resonance frequency and half bandwidth, respectively. For adsorbed particles, plots of ΔΓ/(-Δf) versus - Δf/n (with n the overtone order) show almost straight lines. The extrapolation of these lines to zero yields a frequency shift, which, after conversion to a thickness with the Sauerbrey equation, closely agrees with the height of the particles. Plots of Δf/n and ΔΓ/n versus n look similar to the corresponding plots obtained for viscoelastic films, where the parameters, which would usually be extracted from those plots (apparent mass and apparent compliance), depend on the geometry and the sample's viscoelasticity in a nontrivial way.
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Affiliation(s)
- Sunil Gopalakrishna
- Institute of Physical Chemistry, Clausthal University of Technology, D-38678 Clausthal-Zellerfeld, Germany
| | - Arne Langhoff
- Institute of Physical Chemistry, Clausthal University of Technology, D-38678 Clausthal-Zellerfeld, Germany
| | - Gunther Brenner
- Institute of Applied Mechanics, Clausthal University of Technology, D-38678 Clausthal-Zellerfeld, Germany
| | - Diethelm Johannsmann
- Institute of Physical Chemistry, Clausthal University of Technology, D-38678 Clausthal-Zellerfeld, Germany
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11
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Lechner B, Hageneder S, Schmidt K, Kreuzer MP, Conzemius R, Reimhult E, Barišić I, Dostalek J. In Situ Monitoring of Rolling Circle Amplification on a Solid Support by Surface Plasmon Resonance and Optical Waveguide Spectroscopy. ACS APPLIED MATERIALS & INTERFACES 2021; 13:32352-32362. [PMID: 34212712 DOI: 10.1021/acsami.1c03715] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The growth of surface-attached single-stranded deoxyribonucleic acid (ssDNA) chains is monitored in situ using an evanescent wave optical biosensor that combines surface plasmon resonance (SPR) and optical waveguide spectroscopy (OWS). The "grafting-from" growth of ssDNA chains is facilitated by rolling circle amplification (RCA), and the gradual prolongation of ssDNA chains anchored to a gold sensor surface is optically tracked in time. At a sufficient density of the polymer chains, the ssDNA takes on a brush architecture with a thickness exceeding 10 μm, supporting a spectrum of guided optical waves traveling along the metallic sensor surface. The simultaneous probing of this interface with the confined optical field of surface plasmons and additional more delocalized dielectric optical waveguide modes enables accurate in situ measurement of the ssDNA brush thickness, polymer volume content, and density gradients. We report for the first time on the utilization of the SPR/OWS technique for the measurement of the RCA speed on a solid surface that can be compared to that in bulk solutions. In addition, the control of ssDNA brush properties by changing the grafting density and ionic strength and post-modification via affinity reaction with complementary short ssDNA staples is discussed. These observations may provide important leads for tailoring RCA toward sensitive and rapid assays in affinity-based biosensors.
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Affiliation(s)
- Bernadette Lechner
- Biosensor Technologies, AIT-Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
- CEST Competence Center for Electrochemical Surface Technologies, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Simone Hageneder
- Biosensor Technologies, AIT-Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Katharina Schmidt
- Biosensor Technologies, AIT-Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Mark P Kreuzer
- Biosensor Technologies, AIT-Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
- Instituto de Nanosistemas, Universidad Nacional de San Martín, Campus Miguelete, 25 de Mayo 1021, San Martín, CP 1650 Provincia de Buenos Aires, Argentina
| | - Rick Conzemius
- Molecular Diagnostics, Health & Environment, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Erik Reimhult
- Institute for Biologically Inspired Materials, Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 11, Vienna 1190, Austria
| | - Ivan Barišić
- Molecular Diagnostics, Health & Environment, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Jakub Dostalek
- Biosensor Technologies, AIT-Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
- FZU-Institute of Physics, Czech Academy of Sciences, Na Slovance 2, Prague 182 21, Czech Republic
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12
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Samarentsis AG, Pantazis AK, Tsortos A, Friedt JM, Gizeli E. Hybrid Sensor Device for Simultaneous Surface Plasmon Resonance and Surface Acoustic Wave Measurements. SENSORS 2020; 20:s20216177. [PMID: 33138312 PMCID: PMC7662402 DOI: 10.3390/s20216177] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 11/19/2022]
Abstract
Surface plasmon resonance (SPR) and Love wave (LW) surface acoustic wave (SAW) sensors have been established as reliable biosensing technologies for label-free, real-time monitoring of biomolecular interactions. This work reports the development of a combined SPR/LW-SAW platform to facilitate simultaneous optical and acoustic measurements for the investigation of biomolecules binding on a single surface. The system’s output provides recordings of two acoustic parameters, phase and amplitude of a Love wave, synchronized with SPR readings. We present the design and manufacturing of a novel experimental set-up employing, in addition to the SPR/LW-SAW device, a 3D-printed plastic holder combined with a PDMS microfluidic cell so that the platform can be used in a flow-through mode. The system was evaluated in a systematic study of the optical and acoustic responses for different surface perturbations, i.e., rigid mass loading (Au deposition), pure viscous loading (glycerol and sucrose solutions) and protein adsorption (BSA). Our results provide the theoretical and experimental basis for future application of the combined system to other biochemical and biophysical studies.
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Affiliation(s)
- Anastasios G. Samarentsis
- Institute of Molecular Biology & Biotechnology, FO.R.T.H, Vassilika Vouton, 70013 Heraklion, Greece; (A.G.S.); (A.T.)
- Department of Biology, University of Crete, Vassilika Vouton, 71409 Heraklion, Greece;
| | - Alexandros K. Pantazis
- Department of Biology, University of Crete, Vassilika Vouton, 71409 Heraklion, Greece;
- Institute of Electronic Structure & Laser, FO.R.T.H, Vassilika Vouton, 71409 Heraklion, Greece
| | - Achilleas Tsortos
- Institute of Molecular Biology & Biotechnology, FO.R.T.H, Vassilika Vouton, 70013 Heraklion, Greece; (A.G.S.); (A.T.)
| | - Jean-Michel Friedt
- SENSeOR SAS, Time and Frequency Department, FEMTO-ST Institute, 15B Avenue des Montboucons, 25030 Besançon, France;
| | - Electra Gizeli
- Institute of Molecular Biology & Biotechnology, FO.R.T.H, Vassilika Vouton, 70013 Heraklion, Greece; (A.G.S.); (A.T.)
- Department of Biology, University of Crete, Vassilika Vouton, 71409 Heraklion, Greece;
- Correspondence: ; Tel.: +30-2810-394373
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13
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Kim J, Park J, Park S, Seo J, Kwon J, Lee H, Kim S, Yang H. Surface‐Plasmonic‐Field‐Induced Photoredox Catalysis and Mediated Electron Transfer for Washing‐Free DNA Detection. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jihyeon Kim
- Department of Chemistry Pusan National University Busan 46241 Korea
| | - Jongkyoon Park
- Department of Cogno-Mechatronics Engineering Pusan National University Busan 46241 Korea
| | - Seonhwa Park
- Department of Chemistry Pusan National University Busan 46241 Korea
| | - Jeongwook Seo
- Department of Chemistry Pusan National University Busan 46241 Korea
| | - Jeongwook Kwon
- Department of Chemistry Pusan National University Busan 46241 Korea
| | - Hyunsoo Lee
- Department of Cogno-Mechatronics Engineering Pusan National University Busan 46241 Korea
| | - Seungchul Kim
- Department of Cogno-Mechatronics Engineering Pusan National University Busan 46241 Korea
- Department of Optics and Mechatronics Engineering Pusan National University Busan 46241 Korea
| | - Haesik Yang
- Department of Chemistry Pusan National University Busan 46241 Korea
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14
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Kim J, Park J, Park S, Seo J, Kwon J, Lee H, Kim S, Yang H. Surface-Plasmonic-Field-Induced Photoredox Catalysis and Mediated Electron Transfer for Washing-Free DNA Detection. Angew Chem Int Ed Engl 2020; 59:19202-19208. [PMID: 32618117 DOI: 10.1002/anie.202007318] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Indexed: 11/08/2022]
Abstract
Distance-dependent electromagnetic radiation and electron transfer have been commonly employed in washing-free fluorescence and electrochemical bioassays, respectively. In this study, we combined the two distance-dependent phenomena for sensitive washing-free DNA detection. A distance-dependent surface plasmonic field induces rapid photoredox catalysis of surface-bound catalytic labels, and distance-dependent mediated electron transfer allows for rapid electron transfer from the surface-bound labels to the electrode. An optimal system consists of a chemically reversible acceptor (Ru(NH3 )6 3+ ), a chemically reversible photoredox catalyst (eosin Y), and a chemically irreversible donor (triethanolamine). Side reactions with O2 do not significantly decrease the efficiency of photoredox catalysis. Energy transfer quenching between the electrode and the label can be lowered by increasing the distance between them. Washing-free DNA detection had a detection limit of approximately 0.3 nm in buffer and 0.4 nm in serum without a washing step.
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Affiliation(s)
- Jihyeon Kim
- Department of Chemistry, Pusan National University, Busan, 46241, Korea
| | - Jongkyoon Park
- Department of Cogno-Mechatronics Engineering, Pusan National University, Busan, 46241, Korea
| | - Seonhwa Park
- Department of Chemistry, Pusan National University, Busan, 46241, Korea
| | - Jeongwook Seo
- Department of Chemistry, Pusan National University, Busan, 46241, Korea
| | - Jeongwook Kwon
- Department of Chemistry, Pusan National University, Busan, 46241, Korea
| | - Hyunsoo Lee
- Department of Cogno-Mechatronics Engineering, Pusan National University, Busan, 46241, Korea
| | - Seungchul Kim
- Department of Cogno-Mechatronics Engineering, Pusan National University, Busan, 46241, Korea.,Department of Optics and Mechatronics Engineering, Pusan National University, Busan, 46241, Korea
| | - Haesik Yang
- Department of Chemistry, Pusan National University, Busan, 46241, Korea
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15
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Meléndez M, Vázquez-Quesada A, Delgado-Buscalioni R. Load Impedance of Immersed Layers on the Quartz Crystal Microbalance: A Comparison with Colloidal Suspensions of Spheres. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:9225-9234. [PMID: 32660251 DOI: 10.1021/acs.langmuir.0c01429] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The analytical theories derived here for the acoustic load impedance measured by a quartz crystal microbalance (QCM), due to the presence of layers of different types (rigid, elastic, and viscous) immersed in a fluid, display generic properties, such as "vanishing mass" and positive frequency shifts, which have been observed in QCM experiments with soft-matter systems. These phenomena seem to contradict the well-known Sauerbrey relation at the heart of many QCM measurements, but here, we show that they arise as a natural consequence of hydrodynamics. We compare our one-dimensional immersed plate theory with three-dimensional simulations of rigid and flexible submicron-sized suspended spheres and with experimental results for adsorbed micron-sized colloids, which yield a "negative acoustic mass". The parallel behavior unveiled indicates that the QCM response is highly sensitive to hydrodynamics, even for adsorbed colloids. Our conclusions call for a revision of existing theories based on adhesion forces and elastic stiffness at contact, which should, in most cases, include hydrodynamics.
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Affiliation(s)
- Marc Meléndez
- Department of Theoretical Condensed Matter Physics, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
| | | | - Rafael Delgado-Buscalioni
- Department of Theoretical Condensed Matter Physics, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
- Institute for Condensed Matter Physics, IFIMAC, Campus de Cantoblanco, 28049 Madrid, Spain
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16
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Mataji-Kojouri A, Ozen MO, Shahabadi M, Inci F, Demirci U. Entangled Nanoplasmonic Cavities for Estimating Thickness of Surface-Adsorbed Layers. ACS NANO 2020; 14:8518-8527. [PMID: 32639713 DOI: 10.1021/acsnano.0c02797] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Plasmonic sensors provide real-time and label-free detection of biotargets with unprecedented sensitivity and detection limit. However, they usually lack the ability to estimate the thickness of the target layer formed on top of the sensing surface. Here, we report a sensing modality based on reflection spectroscopy of a nanoplasmonic Fabry-Perot cavity array, which exhibits characteristics of both surface plasmon polaritons and localized plasmon resonances and outperforms its conventional counterparts by providing the thickness of the surface-adsorbed layers. Through numerical simulations, we demonstrate that the designed plasmonic surface resembles two entangled Fabry-Perot cavities excited from both ends. Performance of the device is evaluated by studying sensor response in the refractive index (RI) measurement of aqueous glycerol solutions and during formation of a surface-adsorbed layer consisting of protein (i.e., NeutrAvidin) molecules. By tracking the resonance wavelengths of the two modes of the nanoplasmonic surface, it is therefore possible to measure the thickness of a homogeneous adsorbed layer and RI of the background solution with precisions better than 4 nm and 0.0001 RI units. Using numerical simulations, we show that the thickness estimation algorithm can be extended for layers consisting of nanometric analytes adsorbed on an antibody-coated sensor surface. Furthermore, performance of the device has been evaluated to detect exosomes. By providing a thickness estimation for adsorbed layers and differentiating binding events from background RI variations, this device can potentially supersede conventional plasmonic sensors.
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Affiliation(s)
- Amideddin Mataji-Kojouri
- Photonics Research Laboratory, Center of Excellence on Applied Electromagnetic Systems, School of Electrical and Computer Engineering, College of Engineering, University of Tehran, Tehran 1439957131, Iran
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Department of Radiology, Stanford School of Medicine, Stanford University, Palo Alto, California 94304, United States
| | - Mehmet Ozgun Ozen
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Department of Radiology, Stanford School of Medicine, Stanford University, Palo Alto, California 94304, United States
| | - Mahmoud Shahabadi
- Photonics Research Laboratory, Center of Excellence on Applied Electromagnetic Systems, School of Electrical and Computer Engineering, College of Engineering, University of Tehran, Tehran 1439957131, Iran
| | - Fatih Inci
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Department of Radiology, Stanford School of Medicine, Stanford University, Palo Alto, California 94304, United States
| | - Utkan Demirci
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Department of Radiology, Stanford School of Medicine, Stanford University, Palo Alto, California 94304, United States
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17
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Milioni D, Mateos-Gil P, Papadakis G, Tsortos A, Sarlidou O, Gizeli E. Acoustic Methodology for Selecting Highly Dissipative Probes for Ultrasensitive DNA Detection. Anal Chem 2020; 92:8186-8193. [PMID: 32449355 DOI: 10.1021/acs.analchem.0c00366] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The objective of this work is to present a methodology for the selection of nanoparticles such as liposomes to be used as acoustic probes for the detection of very low concentrations of DNA. Liposomes, applied in the past as mass amplifiers and detected through frequency measurement, are employed in the current work as probes for energy-dissipation enhancement. Because the dissipation signal is related to the structure of the sensed nanoentity, a systematic investigation of the geometrical features of the liposome/DNA complex was carried out. We introduce the parameter of dissipation capacity by which several sizes of liposome and DNA structures were compared with respect to their ability to dissipate acoustic energy at the level of a single molecule/particle. Optimized 200 nm liposomes anchored to a dsDNA chain led to an improvement of the limit of detection (LoD) by 3 orders of magnitude when compared to direct DNA detection, with the new LoD being 1.2 fmol (or 26 fg/μL or 2 pM). Dissipation monitoring was also shown to be 8 times more sensitive than the corresponding frequency response. The high versatility of this new methodology is demonstrated in the detection of genetic biomarkers down to 1-2 target copies in real samples such as blood. This study offers new prospects in acoustic detection with potential use in real-world diagnostics.
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Affiliation(s)
- Dimitra Milioni
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Pablo Mateos-Gil
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - George Papadakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Achilleas Tsortos
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Olga Sarlidou
- Department of Biology, University of Crete, Heraklion, Crete 71110, Greece
| | - Electra Gizeli
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece.,Department of Biology, University of Crete, Heraklion, Crete 71110, Greece
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18
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Papadakis G, Pantazis AK, Ntogka M, Parasyris K, Theodosi GI, Kaprou G, Gizeli E. 3D-printed Point-of-Care Platform for Genetic Testing of Infectious Diseases Directly in Human Samples Using Acoustic Sensors and a Smartphone. ACS Sens 2019; 4:1329-1336. [PMID: 30964650 DOI: 10.1021/acssensors.9b00264] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The objective of this work is to develop a methodology and associated platform for nucleic acid detection at the point-of-care (POC) that is sensitive, user-friendly, affordable, rapid, and robust. The heart of this system is an acoustic wave sensor, based on a Surface Acoustic Wave (SAW) or Quartz Crystal Microbalance (QCM) device, which is employed for the label-free detection of isothermally amplified target DNA. Nucleic acids amplification and detection is demonstrated inside three crude human samples, i.e., whole blood, saliva, and nasal swab, spiked in with 10-100 Salmonella cells. To qualify for POC applications, a portable platform was developed based on 3D printing, integrating inside a single box: (i) simple fluidics based on plastic tubing and a mini peristaltic pump, (ii) a heating plate combined with disposable reaction tubes for isothermal amplification; (iii) a mini antenna analyzer operated through a tablet; and (iv) an acoustic wave device housing unit. The simplicity of the method combined with smartphone operation and detection, rapid sample-to-answer analysis time (30 min), and high performance (detection limit 4 × 103 CFU/ml) in three of the most important human samples in diagnostics suggest that the methodology could become a tool of choice for nucleic acid detection at the POC. In addition, the low cost of the platform and assay holds promise for its adoption in resource limited areas. The acoustic detection method is shown to give similar results with a standard colorimetric assay carried out in saliva and nasal swab but can also be used to detect nucleic acids inside whole blood, where a colorimetric assay failed to perform.
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Affiliation(s)
- George Papadakis
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
| | - Alexandros K. Pantazis
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
| | - Maria Ntogka
- Department of Biology, University of Crete, Voutes, Heraklion 70013, Greece
| | | | - Gesthimani-Ioanna Theodosi
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
- Department of Biology, University of Crete, Voutes, Heraklion 70013, Greece
| | - Georgia Kaprou
- Department of Biology, University of Crete, Voutes, Heraklion 70013, Greece
- Institute of Nanoscience and Nanotechnology, NCSR-Demokritos, Patr. Gregoriou E’ and 27 Neapoleos Str., 15341 Aghia Paraskevi, Attiki, Greece
| | - Electra Gizeli
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
- Department of Biology, University of Crete, Voutes, Heraklion 70013, Greece
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19
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Mustafa G, Chuang CY, Roy WA, Farhath MM, Pokhrel N, Ma Y, Nagasawa K, Antony E, Comstock MJ, Basu S, Balci H. A force sensor that converts fluorescence signal into force measurement utilizing short looped DNA. Biosens Bioelectron 2018; 121:34-40. [PMID: 30195120 DOI: 10.1016/j.bios.2018.08.073] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/13/2018] [Accepted: 08/30/2018] [Indexed: 01/27/2023]
Abstract
A force sensor concept is presented where fluorescence signal is converted into force information via single-molecule Förster resonance energy transfer (smFRET). The basic design of the sensor is a ~100 base pair (bp) long double stranded DNA (dsDNA) that is restricted to a looped conformation by a nucleic acid secondary structure (NAS) that bridges its ends. The looped dsDNA generates a tension across the NAS and unfolds it when the tension is high enough. The FRET efficiency between donor and acceptor (D&A) fluorophores placed across the NAS reports on its folding state. Three dsDNA constructs with different lengths were bridged by a DNA hairpin and KCl was titrated to change the applied force. After these proof-of-principle measurements, one of the dsDNA constructs was used to maintain the G-quadruplex (GQ) construct formed by thrombin binding aptamer (TBA) under tension while it interacted with a destabilizing protein and stabilizing small molecule. The force required to unfold TBA-GQ was independently investigated with high-resolution optical tweezers (OT) measurements that established the relevant force to be a few pN, which is consistent with the force generated by the looped dsDNA. The proposed method is particularly promising as it enables studying NAS, protein, and small molecule interactions using a highly-parallel FRET-based assay while the NAS is kept under an approximately constant force.
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Affiliation(s)
- Golam Mustafa
- Department of Physics, Kent State University, Kent, OH 44242, United States
| | - Cho-Ying Chuang
- Department of Physics, Michigan State University, East Lansing, MI 48824, United States
| | - William A Roy
- Department of Physics, Kent State University, Kent, OH 44242, United States
| | - Mohamed M Farhath
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, United States
| | - Nilisha Pokhrel
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, United States
| | - Yue Ma
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Edwin Antony
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, United States
| | - Matthew J Comstock
- Department of Physics, Michigan State University, East Lansing, MI 48824, United States
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, United States
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, United States.
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20
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Papadakis G, Murasova P, Hamiot A, Tsougeni K, Kaprou G, Eck M, Rabus D, Bilkova Z, Dupuy B, Jobst G, Tserepi A, Gogolides E, Gizeli E. Micro-nano-bio acoustic system for the detection of foodborne pathogens in real samples. Biosens Bioelectron 2018; 111:52-58. [DOI: 10.1016/j.bios.2018.03.056] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 02/21/2018] [Accepted: 03/26/2018] [Indexed: 01/30/2023]
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21
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Kapuscinski M, Agthe M, Bergström L. Time-resolved viscoelastic properties of self-assembling iron oxide nanocube superlattices probed by quartz crystal microbalance with dissipation monitoring. J Colloid Interface Sci 2018; 522:104-110. [DOI: 10.1016/j.jcis.2018.03.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/09/2018] [Accepted: 03/12/2018] [Indexed: 11/28/2022]
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22
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Du X, Fang J, Zhu DM. Modified Sauerbrey equation: a facile method to quantitatively probe the conformation of isolated molecules at solid–liquid interfaces. Analyst 2018; 143:3209-3216. [DOI: 10.1039/c8an00487k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It is found that a quartz crystal microbalance signal is proportional to the product of mass and intrinsic viscosity of molecules at solid–liquid interfaces, with a constant coefficient. This relationship provides a convenient way to semi-quantitatively probe the conformation of a discrete polymer at solid–liquid interfaces.
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Affiliation(s)
- Xianbin Du
- State Key Laboratory of Particle Detection and Electronics
- University of Science and Technology of China
- Hefei 230026
- China
- Department of Modern Physics
| | - Jiajie Fang
- State Key Laboratory of Particle Detection and Electronics
- University of Science and Technology of China
- Hefei 230026
- China
- Department of Modern Physics
| | - Da-Ming Zhu
- Department of Physics and Astronomy
- University of Missouri-Kansas City
- Kansas City
- USA
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23
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Highly sensitive Escherichia coli shear horizontal surface acoustic wave biosensor with silicon dioxide nanostructures. Biosens Bioelectron 2017; 93:146-154. [DOI: 10.1016/j.bios.2016.09.035] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 08/25/2016] [Accepted: 09/10/2016] [Indexed: 11/20/2022]
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24
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Giamblanco N, Petralia S, Conoci S, Messineo C, Marletta G. Ionic strength-controlled hybridization and stability of hybrids of KRAS DNA single-nucleotides: A surface plasmon resonance study. Colloids Surf B Biointerfaces 2017; 158:41-46. [PMID: 28662393 DOI: 10.1016/j.colsurfb.2017.06.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 06/17/2017] [Accepted: 06/19/2017] [Indexed: 11/25/2022]
Abstract
The discrimination of a fully matched, unlabeled KRAS wild-type (WT) (C-G) target sample with respect to three of the most frequent KRAS codon mutations (G12 S (C-A), G12 R (C-C), G12C (C-T)) was investigated using an optimized detection strategy involving surface plasmon resonance (SPR), based on optimized probe-surface density and ionic strength control. The changes observed in the SPR signal were always larger for WT compared with the single-mismatch target DNA oligonucleotides, and were aligned with the theoretical energy differences between the base pair C-G, C-T, C-A, C-C. Hybridization rates of ∼106M-1s-1 were detected without the introduction of high temperature and labels, usually needed in conventional hybridization methods. One hundred percent mutation discrimination of the matched KRAS wild-type (C-G) sequence with respect to three mismatched G12C (C-T), G12 S (C-A), G12 R (C-C) target sequences was achieved.
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Affiliation(s)
- N Giamblanco
- Dept. of Chemical Sciences, University of Catania, Viale A. Doria 6 - 95129 Catania, Italy.
| | - S Petralia
- STMicroelectronics, Stradale Primosole 50, 95121 Catania, Italy
| | - S Conoci
- STMicroelectronics, Stradale Primosole 50, 95121 Catania, Italy.
| | - C Messineo
- Dept. of Chemical Sciences, University of Catania, Viale A. Doria 6 - 95129 Catania, Italy
| | - G Marletta
- Dept. of Chemical Sciences, University of Catania, Viale A. Doria 6 - 95129 Catania, Italy
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25
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Márquez IF, Mateos-Gil P, Shin JY, Lagos R, Monasterio O, Vélez M. Mutations on FtsZ lateral helix H3 that disrupt cell viability hamper reorganization of polymers on lipid surfaces. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017. [PMID: 28642045 DOI: 10.1016/j.bbamem.2017.06.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
FtsZ filaments localize at the middle of the bacterial cell and participate in the formation of a contractile ring responsible for cell division. Previous studies demonstrated that the highly conserved negative charge of glutamate 83 and the positive charge of arginine 85 located in the lateral helix H3 bend of Escherichia coli FtsZ are required for in vivo cell division. In order to understand how these lateral mutations impair the formation of a contractile ring,we extend previous in vitro characterization of these mutants in solution to study their behavior on lipid modified surfaces. We study their interaction with ZipAand look at their reorganization on the surface. We found that the dynamic bundling capacity of the mutant proteins is deficient, and this impairment increases the more the composition and spatial arrangement of the reconstituted system resembles the situation inside the cell: mutant proteins completely fail to reorganize to form higher order aggregates when bound to an E.coli lipid surface through oriented ZipA.We conclude that these surface lateral point mutations affect the dynamic reorganization of FtsZ filaments into bundles on the cell membrane, suggesting that this event is relevant for generating force and completing bacterial division.
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Affiliation(s)
- Ileana F Márquez
- Instituto de Catálisis y Petroleoquímica, c/Marie Curie 2, Cantoblanco, Madrid 28049, Spain
| | - Pablo Mateos-Gil
- Instituto de Catálisis y Petroleoquímica, c/Marie Curie 2, Cantoblanco, Madrid 28049, Spain
| | - Jae Yen Shin
- Departamento de Biología, Facultad de Ciencias, Casilla 653, Santiago 1, Chile
| | - Rosalba Lagos
- Departamento de Biología, Facultad de Ciencias, Casilla 653, Santiago 1, Chile
| | - Octavio Monasterio
- Departamento de Biología, Facultad de Ciencias, Casilla 653, Santiago 1, Chile
| | - Marisela Vélez
- Instituto de Catálisis y Petroleoquímica, c/Marie Curie 2, Cantoblanco, Madrid 28049, Spain.
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26
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Papadakis G, Friedt JM, Eck M, Rabus D, Jobst G, Gizeli E. Optimized acoustic biochip integrated with microfluidics for biomarkers detection in molecular diagnostics. Biomed Microdevices 2017; 19:16. [DOI: 10.1007/s10544-017-0159-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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27
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Milioni D, Tsortos A, Velez M, Gizeli E. Extracting the Shape and Size of Biomolecules Attached to a Surface as Suspended Discrete Nanoparticles. Anal Chem 2017; 89:4198-4203. [DOI: 10.1021/acs.analchem.7b00206] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Dimitra Milioni
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Achilleas Tsortos
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Marisela Velez
- Instituto de Catálisis y Petroleoquímica, CSIC, C/Marie Curie 2, 28049 Madrid, Spain
| | - Electra Gizeli
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
- Department
of Biology, University of Crete, Heraklion 71110, Greece
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28
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Agthe M, Wetterskog E, Bergström L. Following the Assembly of Iron Oxide Nanocubes by Video Microscopy and Quartz Crystal Microbalance with Dissipation Monitoring. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:303-310. [PMID: 27991791 DOI: 10.1021/acs.langmuir.6b03570] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We have studied the growth of ordered arrays by evaporation-induced self-assembly of iron oxide nanocubes with edge lengths of 6.8 and 10.1 nm using video microscopy (VM) and quartz crystal microbalance with dissipation monitoring (QCM-D). Ex situ electron diffraction of the ordered arrays demonstrates that the crystal axes of the nanocubes are coaligned and confirms that the ordered arrays are mesocrystals. Time-resolved video microscopy shows that growth of the highly ordered arrays at slow solvent evaporation is controlled by particle diffusion and can be described by a simple growth model. The growth of each mesocrystal depends only on the number of nanoparticles within the accessible region irrespective of the relative time of formation. The mass of the dried mesocrystals estimated from the analysis of the bandwidth-shift-to-frequency-shift ratio correlates well with the total mass of the oleate-coated nanoparticles in the deposited dispersion drop.
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Affiliation(s)
- Michael Agthe
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University , SE-10691 Stockholm, Sweden
| | - Erik Wetterskog
- Department of Engineering Sciences, Ångström Laboratory, Uppsala University , SE-75121 Uppsala, Sweden
| | - Lennart Bergström
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University , SE-10691 Stockholm, Sweden
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29
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Papadakis G, Palladino P, Chronaki D, Tsortos A, Gizeli E. Sample-to-answer acoustic detection of DNA in complex samples. Chem Commun (Camb) 2017; 53:8058-8061. [DOI: 10.1039/c6cc10175e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The present study demonstrates the sensitive and label-free acoustic detection of dsDNA amplicons produced from whole Salmonella Thyphimurium cells without employing any DNA extraction and/or purification step, in the presence of the lysed bacterial cells and in a hybridization-free assay.
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Affiliation(s)
- George Papadakis
- Institute of Molecular Biology and Biotechnology-FORTH
- Heraklion
- Greece
| | | | - Dimitra Chronaki
- Institute of Molecular Biology and Biotechnology-FORTH
- Heraklion
- Greece
- Dept. of Biology
- Univ. of Crete
| | - Achilleas Tsortos
- Institute of Molecular Biology and Biotechnology-FORTH
- Heraklion
- Greece
| | - Electra Gizeli
- Institute of Molecular Biology and Biotechnology-FORTH
- Heraklion
- Greece
- Dept. of Biology
- Univ. of Crete
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30
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Chronaki D, Stratiotis DI, Tsortos A, Anastasiadou E, Gizeli E. Screening between normal and cancer human thyroid cells through comparative adhesion studies using the Quartz Crystal Microbalance. SENSING AND BIO-SENSING RESEARCH 2016. [DOI: 10.1016/j.sbsr.2016.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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31
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Rapid Salmonella detection using an acoustic wave device combined with the RCA isothermal DNA amplification method. SENSING AND BIO-SENSING RESEARCH 2016. [DOI: 10.1016/j.sbsr.2016.10.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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32
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Chen Q, Xu S, Liu Q, Masliyah J, Xu Z. QCM-D study of nanoparticle interactions. Adv Colloid Interface Sci 2016; 233:94-114. [PMID: 26546115 DOI: 10.1016/j.cis.2015.10.004] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 10/04/2015] [Accepted: 10/05/2015] [Indexed: 12/25/2022]
Abstract
Quartz crystal microbalance with dissipation monitoring (QCM-D) has been proven to be a powerful research tool to investigate in situ interactions between nanoparticles and different functionalized surfaces in liquids. QCM-D can also be used to quantitatively determine adsorption kinetics of polymers, DNA and proteins from solutions on various substrate surfaces while providing insights into conformations of adsorbed molecules. This review aims to provide a comprehensive overview on various important applications of QCM-D, focusing on deposition of nanoparticles and attachment-detachment of nanoparticles on model membranes in complex fluid systems. We will first describe the working principle of QCM-D and DLVO theory pertinent to understanding nanoparticle deposition phenomena. The interactions between different nanoparticles and functionalized surfaces for different application areas are then critically reviewed. Finally, the potential applications of QCM-D in other important fields are proposed and knowledge gaps are identified.
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33
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Affiliation(s)
- Achilleas Tsortos
- Institute of Molecular Biology & Biotechnology, FO.R.T.H, Vassilika Vouton, 70013, Heraklion, Greece
| | - George Papadakis
- Institute of Molecular Biology & Biotechnology, FO.R.T.H, Vassilika Vouton, 70013, Heraklion, Greece
| | - Electra Gizeli
- Institute of Molecular Biology & Biotechnology, FO.R.T.H, Vassilika Vouton, 70013, Heraklion, Greece
- Department
of Biology, University of Crete, Vassilika Vouton, 71409, Heraklion, Greece
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34
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Chen CK, Lin DT, Juang YD, Hu YC, Kuo YT, Chen CY. The Innovated Flexible Surface Acoustic Wave Devices on Fully InkJet Printing Technology. SMART SCIENCE 2016. [DOI: 10.1080/23080477.2013.11665581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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35
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Mateos-Gil P, Tsortos A, Vélez M, Gizeli E. Monitoring structural changes in intrinsically disordered proteins using QCM-D: application to the bacterial cell division protein ZipA. Chem Commun (Camb) 2016; 52:6541-4. [DOI: 10.1039/c6cc02127a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Characterization of structural changes in an intrinsically disordered protein attached on a QCM-D, with a sensitivity of 1.8 nm or better.
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Affiliation(s)
- Pablo Mateos-Gil
- Instituto de Catálisis y Petroleoquímica (ICP-CSIC)
- 28049 Madrid
- Spain
| | | | - Marisela Vélez
- Instituto de Catálisis y Petroleoquímica (ICP-CSIC)
- 28049 Madrid
- Spain
| | - Electra Gizeli
- Institute of Molecular Biology & Biotechnology
- Heraklion
- Greece
- Department of Biology
- University of Crete
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36
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Zhang X, Daaboul GG, Spuhler PS, Freedman DS, Yurt A, Ahn S, Avci O, Ünlü MS. Nanoscale characterization of DNA conformation using dual-color fluorescence axial localization and label-free biosensing. Analyst 2015; 139:6440-9. [PMID: 25340741 DOI: 10.1039/c4an01425a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantitative determination of the density and conformation of DNA molecules tethered to the surface can help optimize and understand DNA nanosensors and nanodevices, which use conformational or motional changes of surface-immobilized DNA for detection or actuation. We present an interferometric sensing platform that combines (i) dual-color fluorescence spectroscopy for precise axial co-localization of two fluorophores attached at different nucleotides of surface-immobilized DNA molecules and (ii) independent label-free quantification of biomolecule surface density at the same site. Using this platform, we examined the conformation of DNA molecules immobilized on a three-dimensional polymeric surface and demonstrated simultaneous detection of DNA conformational change and binding in real-time. These results demonstrate that independent quantification of both surface density and molecular nanoscale conformation constitutes a versatile approach for nanoscale solid-biochemical interface investigations and molecular binding assays.
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Affiliation(s)
- Xirui Zhang
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA.
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37
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Wong YR. Micro- and nano-force evaluation of bioengineered muscle cells: a non-contact two-dimensional biosensing using surface acoustic wave devices. NANOTECHNOLOGY 2015; 26:312501. [PMID: 26183643 DOI: 10.1088/0957-4484/26/31/312501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A high degree of cell-generated force measurement is required to evaluate the biomechanical performance of bioengineered muscle tissues. However, the conventional cantilever types of direct force measurement methods have limitations in developing a non-contact two-dimensional force sensing device for a single muscle cell. In this paper, a method is proposed and discussed by using focused surface acoustic wave and magneto-optic Kerr measurements. To depict the capability of the proposed method, a conceptual design of such a sensory device is demonstrated for non-contact two-dimensional force measurement of a single muscle cell.
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Affiliation(s)
- Yoke-Rung Wong
- Biomechanics Laboratory Singapore General Hospital, 20 College Road, Academia, Level 1, 169856 Singapore
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38
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Papadakis G, Skandalis N, Dimopoulou A, Glynos P, Gizeli E. Bacteria Murmur: Application of an Acoustic Biosensor for Plant Pathogen Detection. PLoS One 2015; 10:e0132773. [PMID: 26177507 PMCID: PMC4503732 DOI: 10.1371/journal.pone.0132773] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 06/19/2015] [Indexed: 12/13/2022] Open
Abstract
A multi-targeting protocol for the detection of three of the most important bacterial phytopathogens, based on their scientific and economic importance, was developed using an acoustic biosensor (the Quartz Crystal Microbalance) for DNA detection. Acoustic detection was based on a novel approach where DNA amplicons were monitored and discriminated based on their length rather than mass. Experiments were performed during real time monitoring of analyte binding and in a direct manner, i.e. without the use of labels for enhancing signal transduction. The proposed protocol improves time processing by circumventing gel electrophoresis and can be incorporated as a routine detection method in a diagnostic lab or an automated lab-on-a-chip system for plant pathogen diagnostics.
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Affiliation(s)
- George Papadakis
- Institute of Molecular Biology and Biotechnology, Heraklion Crete, Greece
| | - Nicholas Skandalis
- Benaki Phytopathological Institute, 8 St. Delta, Kifissia, Athens, Greece
| | | | - Paraskevas Glynos
- Benaki Phytopathological Institute, 8 St. Delta, Kifissia, Athens, Greece
| | - Electra Gizeli
- Institute of Molecular Biology and Biotechnology, Heraklion Crete, Greece
- Dept. of Biology, University of Crete, Vassilika Vouton, Heraklion Crete, Greece
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39
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Lane S, West P, François A, Meldrum A. Protein biosensing with fluorescent microcapillaries. OPTICS EXPRESS 2015; 23:2577-90. [PMID: 25836122 DOI: 10.1364/oe.23.002577] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Capillaries with a high-index fluorescent coating represent a new type of whispering-gallery-mode (WGM) microcavity sensor. By coating silicon quantum dots (Si-QDs) onto the channel wall of a microcapillary, a cylindrical microcavity forms in which the optical confinement arises from the index contrast at the interface between the QD layer and the glass capillary wall. However, the ability to functionalize the QD layer for biosensing applications is an open question, since the layer consists of a mixture of Si-QDs embedded in a glassy SiOx matrix. Here, we employ a polyelectrolyte (PE) multilayer approach to functionalize the microcapillary inner surface and demonstrate the potential of this refractive index sensing platform for label-free biosensing applications, using biotin-neutravidin as a specific interaction model.
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40
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Fang J, Ren C, Zhu T, Wang K, Jiang Z, Ma Y. Comparison of the different responses of surface plasmon resonance and quartz crystal microbalance techniques at solid–liquid interfaces under various experimental conditions. Analyst 2015; 140:1323-36. [DOI: 10.1039/c4an01756k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The different characteristics of surface plasmon resonance and quartz crystal microbalance techniques under different experimental scenarios are discussed.
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Affiliation(s)
- Jiajie Fang
- Collaborative Innovation Center of Advanced Microstructures and Department of Physics
- Nanjing University
- Nanjing 210093
- China
| | - Chunlai Ren
- Collaborative Innovation Center of Advanced Microstructures and Department of Physics
- Nanjing University
- Nanjing 210093
- China
| | - Tao Zhu
- Collaborative Innovation Center of Advanced Microstructures and Department of Physics
- Nanjing University
- Nanjing 210093
- China
| | - Kaiyu Wang
- Collaborative Innovation Center of Advanced Microstructures and Department of Physics
- Nanjing University
- Nanjing 210093
- China
| | - Zhongying Jiang
- Collaborative Innovation Center of Advanced Microstructures and Department of Physics
- Nanjing University
- Nanjing 210093
- China
- School of Electronics and Information and College of Chemistry and Biological Science
| | - Yuqiang Ma
- Collaborative Innovation Center of Advanced Microstructures and Department of Physics
- Nanjing University
- Nanjing 210093
- China
- Laboratory of Soft Condensed Matter Physics and Interdisciplinary Research
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41
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Tsortos A, Grammoustianou A, Lymbouridou R, Papadakis G, Gizeli E. The detection of multiple DNA targets with a single probe using a conformation-sensitive acoustic sensor. Chem Commun (Camb) 2015; 51:11504-7. [DOI: 10.1039/c5cc03436a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Acoustic sensing of DNA targets using a single probe that produces hybridization products of different conformations.
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42
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March C, García JV, Sánchez Á, Arnau A, Jiménez Y, García P, Manclús JJ, Montoya Á. High-frequency phase shift measurement greatly enhances the sensitivity of QCM immunosensors. Biosens Bioelectron 2014; 65:1-8. [PMID: 25461131 DOI: 10.1016/j.bios.2014.10.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 09/10/2014] [Accepted: 10/01/2014] [Indexed: 10/24/2022]
Abstract
In spite of being widely used for in liquid biosensing applications, sensitivity improvement of conventional (5-20MHz) quartz crystal microbalance (QCM) sensors remains an unsolved challenging task. With the help of a new electronic characterization approach based on phase change measurements at a constant fixed frequency, a highly sensitive and versatile high fundamental frequency (HFF) QCM immunosensor has successfully been developed and tested for its use in pesticide (carbaryl and thiabendazole) analysis. The analytical performance of several immunosensors was compared in competitive immunoassays taking carbaryl insecticide as the model analyte. The highest sensitivity was exhibited by the 100MHz HFF-QCM carbaryl immunosensor. When results were compared with those reported for 9MHz QCM, analytical parameters clearly showed an improvement of one order of magnitude for sensitivity (estimated as the I50 value) and two orders of magnitude for the limit of detection (LOD): 30μgl(-1) vs 0.66μgL(-1)I50 value and 11μgL(-1) vs 0.14μgL(-1) LOD, for 9 and 100MHz, respectively. For the fungicide thiabendazole, I50 value was roughly the same as that previously reported for SPR under the same biochemical conditions, whereas LOD improved by a factor of 2. The analytical performance achieved by high frequency QCM immunosensors surpassed those of conventional QCM and SPR, closely approaching the most sensitive ELISAs. The developed 100MHz QCM immunosensor strongly improves sensitivity in biosensing, and therefore can be considered as a very promising new analytical tool for in liquid applications where highly sensitive detection is required.
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Affiliation(s)
- Carmen March
- Instituto Interuniversitario de Investigación en Bioingeniería y Tecnología Orientada al Ser Humano (I3BH), Universitat Politècnica de València, Camino de Vera s/n, Edificio 8B-N, 46022 Valencia, Spain; Advanced Wave Sensors S.L. Valencia, Spain.
| | - José V García
- Advanced Wave Sensors S.L. Valencia, Spain; Grupo de Fenómenos Ondulatorios (GFO), Universitat Politècnica de València, Camino de Vera s/n, Edificio 7F, 46022 Valencia, Spain
| | - Ángel Sánchez
- Instituto Interuniversitario de Investigación en Bioingeniería y Tecnología Orientada al Ser Humano (I3BH), Universitat Politècnica de València, Camino de Vera s/n, Edificio 8B-N, 46022 Valencia, Spain
| | - Antonio Arnau
- Advanced Wave Sensors S.L. Valencia, Spain; Grupo de Fenómenos Ondulatorios (GFO), Universitat Politècnica de València, Camino de Vera s/n, Edificio 7F, 46022 Valencia, Spain
| | - Yolanda Jiménez
- Advanced Wave Sensors S.L. Valencia, Spain; Grupo de Fenómenos Ondulatorios (GFO), Universitat Politècnica de València, Camino de Vera s/n, Edificio 7F, 46022 Valencia, Spain
| | | | - Juan J Manclús
- Instituto Interuniversitario de Investigación en Bioingeniería y Tecnología Orientada al Ser Humano (I3BH), Universitat Politècnica de València, Camino de Vera s/n, Edificio 8B-N, 46022 Valencia, Spain
| | - Ángel Montoya
- Instituto Interuniversitario de Investigación en Bioingeniería y Tecnología Orientada al Ser Humano (I3BH), Universitat Politècnica de València, Camino de Vera s/n, Edificio 8B-N, 46022 Valencia, Spain
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43
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Rodrigues RMM, de-Carvalho J, Ferreira GNM. Kinetic characterization of the retinoic X receptor binding to specific and unspecific DNA oligoduplexes with a quartz crystal microbalance. Analyst 2014; 139:3434-40. [PMID: 24824382 DOI: 10.1039/c4an00286e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quartz Crystal Microbalance (QCM) biosensor technology was used to study the interaction of the DNA-binding domain (DBD) of the transcription factor RXRα with immobilized specific (DR1) and unspecific (DR1neg) DNA oligoduplexes. We identify the QCM sensor frequency at the susceptance minimum (fBmin) as a better measuring parameter, and we show that fBmin is proportional to the mass adsorbed at the sensor surface and is not influenced by interferences coming from viscoelastic variations of the adsorbed layers or buffers. This parameter was used to study the binding of RXRα to DNA and to calculate the association and dissociation kinetic constants of RXRαDBD-DR1 interaction. We show that RXRαDBD binds to DNA both as a monomer and as a homodimer, and that the mechanism of binding is salt dependent and occurs in two steps. The QCM biosensor data reveal that a high ionic strength buffer prevents the unspecific interactions and at a lower ionic strength the dissociation of RXRαDBD-DR1 occurs in two phases.
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Affiliation(s)
- Rogério M M Rodrigues
- IBB-Institute for Biotechnology and Bioengineering, Centro de Biomedicina Molecular e Estrutural, Universidade do Algarve, 8005-139 Faro, Portugal.
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44
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Papadakis G, Tsortos A, Kordas A, Tiniakou I, Morou E, Vontas J, Kardassis D, Gizeli E. Acoustic detection of DNA conformation in genetic assays combined with PCR. Sci Rep 2014; 3:2033. [PMID: 23778520 PMCID: PMC3686166 DOI: 10.1038/srep02033] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 06/03/2013] [Indexed: 11/09/2022] Open
Abstract
Application of PCR to multiplexing assays is not trivial; it requires multiple fluorescent labels for amplicon detection and sophisticated software for data interpretation. Alternative PCR-free methods exploiting new concepts in nanotechnology exhibit high sensitivities but require multiple labeling and/or amplification steps. Here, we propose to simplify the problem of simultaneous analysis of multiple targets in genetic assays by detecting directly the conformation, rather than mass, of target amplicons produced in the same PCR reaction. The new methodology exploits acoustic wave devices which are shown to be able to characterize in a fully quantitative manner multiple double stranded DNAs of various lengths. The generic nature of the combined acoustic/PCR platform is shown using real samples and, specifically, during the detection of SNP genotyping in Anopheles gambiae and gene expression quantification in treated mice. The method possesses significant advantages to TaqMan assay and real-time PCR regarding multiplexing capability, speed, simplicity and cost.
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Affiliation(s)
- G Papadakis
- Institute of Molecular Biology & Biotechnology, FORTH, Vassilika Vouton, 70013 Heraklion, Greece.
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45
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Mitsakakis K, Tsortos A, Gizeli E. Quantitative determination of protein molecular weight with an acoustic sensor; significance of specific versus non-specific binding. Analyst 2014; 139:3918-25. [DOI: 10.1039/c4an00616j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A multi-analyte acoustic biosensor determines the molecular weight of proteinsviathe phase change of the acoustic signal.
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Affiliation(s)
- Konstantinos Mitsakakis
- Institute of Molecular Biology & Biotechnology
- Foundation for Research & Technology Hellas
- GR-70013 Heraklion, Greece
- Department of Materials Science & Technology
- University of Crete
| | - Achilleas Tsortos
- Institute of Molecular Biology & Biotechnology
- Foundation for Research & Technology Hellas
- GR-70013 Heraklion, Greece
| | - Electra Gizeli
- Institute of Molecular Biology & Biotechnology
- Foundation for Research & Technology Hellas
- GR-70013 Heraklion, Greece
- Department of Biology
- University of Crete
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46
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Ivanov IE, Morrison AE, Cobb JE, Fahey CA, Camesano TA. Creating antibacterial surfaces with the peptide chrysophsin-1. ACS APPLIED MATERIALS & INTERFACES 2012; 4:5891-5897. [PMID: 23043421 DOI: 10.1021/am301530a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Immobilization of antimicrobial peptides (AMPs) holds potential for creating surfaces with bactericidal properties. In order to successfully incorporate AMPs into desired materials, increased fundamental understanding of the relationship between AMP immobilization and the efficacy of bound peptides as antibacterial agents is required. In this study, we characterize the relationship between surface binding of the AMP and subsequent ability of the peptide to kill bacteria. Surface immobilization of the AMP chrysophsin-1 (CHY1) via a flexible linker is studied in real-time, using a quartz crystal microbalance with dissipation monitoring (QCM-D). Depending on whether the AMP is physically adsorbed to the surface or attached covalently via a zero-length or flexible cross-linker, changes could be observed in AMP orientation, surface density, flexibility, and activity against bacteria. Covalent surface binding of CHY1 led to the formation of solvated monolayers of vertically positioned peptide molecules, while the physical adsorption of CHY1 led to the deposition of rigid monolayers of horizontally positioned peptide molecules on the sensor surface. Covalently bound peptides were not removed by extensive washing and did not leach from the surface. Zero-length immobilization of the peptide decreased its ability to kill E. coli to 34% ± 7% of added bacteria, while binding via a flexible linker resulted in 82% ± 11% of bacteria being killed by the AMP.
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Affiliation(s)
- Ivan E Ivanov
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, USA
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47
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Eisele NB, Andersson FI, Frey S, Richter RP. Viscoelasticity of Thin Biomolecular Films: A Case Study on Nucleoporin Phenylalanine-Glycine Repeats Grafted to a Histidine-Tag Capturing QCM-D Sensor. Biomacromolecules 2012; 13:2322-32. [DOI: 10.1021/bm300577s] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nico B. Eisele
- Biosurfaces Unit, CIC biomaGUNE, Paseo Miramon 182, 20009
Donostia - San Sebastian, Spain
- Department of Cellular
Logistics, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen,
Germany
| | | | - Steffen Frey
- Department of Cellular
Logistics, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen,
Germany
| | - Ralf P. Richter
- Biosurfaces Unit, CIC biomaGUNE, Paseo Miramon 182, 20009
Donostia - San Sebastian, Spain
- Max Planck Institute for Intelligent Systems, Heisenbergstraße 3, 70569
Stuttgart, Germany
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48
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Papadakis G, Tsortos A, Bender F, Ferapontova EE, Gizeli E. Direct Detection of DNA Conformation in Hybridization Processes. Anal Chem 2012; 84:1854-61. [DOI: 10.1021/ac202515p] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- George Papadakis
- Institute of Molecular Biology
and Biotechnology, Foundation for Research and Technology Hellas, 100 N. Plastira, Vassilika Vouton, 70013 Heraklion,
Greece
| | - Achilleas Tsortos
- Institute of Molecular Biology
and Biotechnology, Foundation for Research and Technology Hellas, 100 N. Plastira, Vassilika Vouton, 70013 Heraklion,
Greece
| | - Florian Bender
- Institute of Molecular Biology
and Biotechnology, Foundation for Research and Technology Hellas, 100 N. Plastira, Vassilika Vouton, 70013 Heraklion,
Greece
- Department of
Electrical and
Computer Engineering, Marquette University, 1515 West Wisconsin Avenue, Milwaukee, Wisconsin 53233, United
States
| | - Elena E. Ferapontova
- Danish National Research
Foundation:
Center for DNA Nanotechnology, and Department of Chemistry and iNANO, Aarhus University, Ny Munkegade 1521, DK-8000 Aarhus
C, Denmark
| | - Electra Gizeli
- Institute of Molecular Biology
and Biotechnology, Foundation for Research and Technology Hellas, 100 N. Plastira, Vassilika Vouton, 70013 Heraklion,
Greece
- Department of Biology, University of Crete, Vassilika Vouton, 71409, Heraklion,
Greece
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49
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Pang W, Zhao H, Kim ES, Zhang H, Yu H, Hu X. Piezoelectric microelectromechanical resonant sensors for chemical and biological detection. LAB ON A CHIP 2012; 12:29-44. [PMID: 22045252 DOI: 10.1039/c1lc20492k] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Piezoelectric microelectromechanical systems (MEMS) resonant sensors, known for their excellent mass resolution, have been studied for many applications, including DNA hybridization, protein-ligand interactions, and immunosensor development. They have also been explored for detecting antigens, organic gas, toxic ions, and explosives. Most piezoelectric MEMS resonant sensors are acoustic sensors (with specific coating layers) that enable selective and label-free detection of biological events in real time. These label-free technologies have recently garnered significant attention for their sensitive and quantitative multi-parameter analysis of biological systems. Since piezoelectric MEMS resonant sensors do more than transform analyte mass or thickness into an electrical signal (e.g., frequency and impedance), special attention must be paid to their potential beyond microweighing, such as measuring elastic and viscous properties, and several types of sensors currently under development operate at different resonant modes (i.e., thickness extensional mode, thickness shear mode, lateral extensional mode, flexural mode, etc.). In this review, we provide an overview of recent developments in micromachined resonant sensors and activities relating to biochemical interfaces for acoustic sensors.
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Affiliation(s)
- Wei Pang
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin, China 300072
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50
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Reviakine I, Johannsmann D, Richter RP. Hearing what you cannot see and visualizing what you hear: interpreting quartz crystal microbalance data from solvated interfaces. Anal Chem 2011; 83:8838-48. [PMID: 21939220 DOI: 10.1021/ac201778h] [Citation(s) in RCA: 523] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Over the last 2 decades, the quartz crystal microbalance (QCM or QCM-D) has emerged as a versatile tool for investigating soft and solvated interfaces between solid surfaces and bulk liquids because it can provide a wealth of information about key structural and functional parameters of these interfaces. In this Feature, we offer QCM users a set of guidelines for interpretation and quantitative analysis of QCM data based on a synthesis of well-established concepts rooted in rheological research of the last century and of new results obtained in the last several years.
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Affiliation(s)
- Ilya Reviakine
- Biosurfaces Unit, CIC biomaGUNE, Paseo Miramon 182, 20009 Donostia-San Sebastian, Spain.
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