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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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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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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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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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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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Sohna Sohna JE, Cooper MA. Does the Sauerbrey equation hold true for binding of peptides and globular proteins to a QCM? SENSING AND BIO-SENSING RESEARCH 2016. [DOI: 10.1016/j.sbsr.2016.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Tenenbaum E, Segal E. Optical biosensors for bacteria detection by a peptidomimetic antimicrobial compound. Analyst 2016; 140:7726-33. [PMID: 26456237 DOI: 10.1039/c5an01717c] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In this work we present a label-free optical biosensor for rapid bacteria detection using a novel peptide-mimetic compound, as the recognition element. The biosensor design is based on an oxidized porous silicon (PSiO2) nanostructure used as the optical transducer, functionalized with the sequence K-[C12K]7 (referred to as K-7α12), which is a synthetic antimicrobial peptide. This compound is a member of a family of oligomers of acylated lysines (OAKs), mimicking the hydrophobicity and charge of natural antimicrobial peptides. The OAK is tethered to the PSiO2 film and the changes in the reflectivity spectrum are monitored upon exposure to Escherichia coli (E. coli) bacterial suspensions and their lysates. We show that capture of bacterial cell fragments induces predictable changes in the reflectivity spectrum, proportional to E. coli concentrations, thereby enabling rapid, sensitive and reproducible detection of E. coli at concentrations as low as 10(3) cells per mL. While for intact bacterial cells, the K-7α12-tethered PSiO2 shows a poor capturing ability, resulting in an insignificant optical response. The biosensor performance is also studied upon exposure to model Gram positive and negative bacterial lysates, suggesting preferential capture of E. coli cell fragments in the presented scheme. These OAK-based biosensors offer significant advantages in comparison with conventional antibody-based assays, in terms of their simple and cost-effective production, while providing numerous possible sequence combinations for designing new detection schemes.
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Affiliation(s)
- Elena Tenenbaum
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel.
| | - Ester Segal
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel. and Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa, Israel
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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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